From 0c1d0884ffa19d2c9f2bde13e47195efbd6aa879 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Mon, 23 Jun 2008 18:06:06 +0100
Subject: [PATCH] small updates and removing X permissions
---
applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C | 0
.../mdEquilibrationFoam/mdEquilibrationFoam.C | 0
.../mdEquilibrationFoam/readmdEquilibrationDict.H | 0
src/lagrangian/Allwmake | 4 +++-
.../bufferedAccumulator/bufferedAccumulator.C | 0
.../bufferedAccumulator/bufferedAccumulator.H | 0
.../bufferedAccumulator/bufferedAccumulatorI.H | 0
.../bufferedAccumulator/bufferedAccumulatorIO.C | 0
.../molecularDynamics/molecule/distribution/distribution.C | 0
.../molecularDynamics/molecule/distribution/distribution.H | 0
.../molecularDynamics/molecule/distribution/distributionI.H | 0
.../molecularDynamics/molecule/distribution/distributionIO.C | 0
.../molecularDynamics/molecule/mdTools/averageMDFields.H | 0
.../molecularDynamics/molecule/mdTools/calculateMDFields.H | 0
.../molecularDynamics/molecule/mdTools/createMDFields.H | 0
src/lagrangian/molecularDynamics/molecule/mdTools/md.H | 0
.../molecule/mdTools/meanMomentumEnergyAndNMols.H | 0
.../molecularDynamics/molecule/mdTools/resetMDFields.H | 0
.../molecule/mdTools/temperatureAndPressure.H | 0
.../molecule/mdTools/temperatureAndPressureVariables.H | 0
.../molecule/mdTools/temperatureEquilibration.H | 0
src/lagrangian/molecularDynamics/molecule/molecule/molecule.C | 0
src/lagrangian/molecularDynamics/molecule/molecule/molecule.H | 0
.../molecularDynamics/molecule/molecule/moleculeI.H | 0
.../molecularDynamics/molecule/molecule/moleculeIO.C | 0
.../molecularDynamics/molecule/moleculeCloud/moleculeCloud.C | 0
.../molecularDynamics/molecule/moleculeCloud/moleculeCloud.H | 0
.../moleculeCloudApplyConstraintsAndThermostats.C | 0
.../moleculeCloud/moleculeCloudBuildCellInteractionLists.C | 0
.../molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C | 0
.../moleculeCloud/moleculeCloudBuildCellReferralLists.C | 0
.../moleculeCloud/moleculeCloudBuildDirectInteractionList.H | 0
.../moleculeCloud/moleculeCloudBuildReferredInteractionList.H | 0
.../moleculeCloud/moleculeCloudCalculateExternalForce.C | 0
.../molecule/moleculeCloud/moleculeCloudCalculateForce.C | 0
.../molecule/moleculeCloud/moleculeCloudCalculatePairForce.C | 0
.../moleculeCloud/moleculeCloudCalculatePairForceRealCells.H | 0
.../moleculeCloudCalculatePairForceRealCellsCalculationStep.H | 0
.../moleculeCloudCalculatePairForceReferredCells.H | 0
.../moleculeCloud/moleculeCloudCalculateTetherForce.C | 0
.../molecule/moleculeCloud/moleculeCloudCodeSnippets.H | 0
.../molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H | 0
.../moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C | 0
.../molecule/moleculeCloud/moleculeCloudReadMDParameters.H | 0
.../moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C | 0
.../moleculeCloudReferredCellsInRangeOfSegment.C | 0
.../moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C | 0
.../moleculeCloudRemoveHighEnergyOverlapsRealCells.H | 0
...uleCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H | 0
.../moleculeCloudRemoveHighEnergyOverlapsReferredCells.H | 0
.../moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C | 0
.../moleculeCloud/moleculeCloudTestPointFaceDistance.C | 0
.../molecule/referralLists/receivingReferralList.C | 0
.../molecule/referralLists/receivingReferralList.H | 0
.../molecule/referralLists/receivingReferralListI.H | 0
.../molecule/referralLists/sendingReferralList.C | 0
.../molecule/referralLists/sendingReferralList.H | 0
.../molecule/referralLists/sendingReferralListI.H | 0
.../molecularDynamics/molecule/referredCell/referredCell.C | 0
.../molecularDynamics/molecule/referredCell/referredCell.H | 0
.../molecularDynamics/molecule/referredCell/referredCellI.H | 0
.../molecule/referredCellList/referredCellList.C | 0
.../molecule/referredCellList/referredCellList.H | 0
.../molecule/referredCellList/referredCellListI.H | 0
.../molecule/referredMolecule/referredMolecule.C | 0
.../molecule/referredMolecule/referredMolecule.H | 0
.../molecule/referredMolecule/referredMoleculeI.H | 0
.../potential/pairPotential/basic/pairPotentialI.H | 0
.../pairPotential/pairPotentialList/pairPotentialList.C | 0
.../pairPotential/pairPotentialList/pairPotentialList.H | 0
.../pairPotential/pairPotentialList/pairPotentialListI.H | 4 ++--
.../tetherPotential/tetherPotentialList/tetherPotentialList.C | 0
.../tetherPotential/tetherPotentialList/tetherPotentialList.H | 0
.../tetherPotentialList/tetherPotentialListI.H | 0
.../constrictedChannel/constant/polyMesh/blockMeshDict | 0
tutorials/gnemdFoam/constrictedChannel/system/controlDict | 0
tutorials/gnemdFoam/constrictedChannel/system/fvSchemes | 0
tutorials/gnemdFoam/constrictedChannel/system/fvSolution | 0
tutorials/gnemdFoam/constrictedChannel/system/mdSolution | 0
tutorials/gnemdFoam/constrictedChannel/system/molConfigDict | 0
tutorials/gnemdFoam/constrictedChannel/system/potentialDict | 0
.../gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict | 0
tutorials/gnemdFoam/nanoNozzle/system/controlDict | 0
tutorials/gnemdFoam/nanoNozzle/system/decomposeParDict | 0
tutorials/gnemdFoam/nanoNozzle/system/fvSchemes | 0
tutorials/gnemdFoam/nanoNozzle/system/fvSolution | 0
tutorials/gnemdFoam/nanoNozzle/system/mdSolution | 0
tutorials/gnemdFoam/nanoNozzle/system/molConfigDict | 0
88 files changed, 5 insertions(+), 3 deletions(-)
mode change 100755 => 100644 applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C
mode change 100755 => 100644 applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
mode change 100755 => 100644 applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/md.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
mode change 100755 => 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/controlDict
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/fvSchemes
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/fvSolution
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/mdSolution
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/molConfigDict
mode change 100755 => 100644 tutorials/gnemdFoam/constrictedChannel/system/potentialDict
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/controlDict
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/decomposeParDict
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/fvSchemes
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/fvSolution
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/mdSolution
mode change 100755 => 100644 tutorials/gnemdFoam/nanoNozzle/system/molConfigDict
diff --git a/applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C b/applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C
old mode 100755
new mode 100644
diff --git a/applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C b/applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
old mode 100755
new mode 100644
diff --git a/applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H b/applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/Allwmake b/src/lagrangian/Allwmake
index 567f7a10def..0a5e86bdefa 100755
--- a/src/lagrangian/Allwmake
+++ b/src/lagrangian/Allwmake
@@ -5,4 +5,6 @@ wmake libso basic
wmake libso solidParticle
wmake libso intermediate
wmake libso dieselSpray
-wmake libso molecule
+(cd molecularDynamics && wmake libso potential)
+(cd molecularDynamics && wmake libso molecule)
+
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distribution.C b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distribution.H b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H b/src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C b/src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
old mode 100755
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diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
old mode 100755
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diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
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diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H
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diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
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diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
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diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
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diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
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index 32e01958c8b..1a9ff953b2d
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
@@ -36,12 +36,12 @@ inline Foam::label Foam::pairPotentialList::pairPotentialIndex
if (a < b)
{
- index = a*(2*nIds() - a - 1) / 2 + b;
+ index = a*(2*nIds() - a - 1)/2 + b;
}
else
{
- index = b*(2*nIds() - b - 1) / 2 + a;
+ index = b*(2*nIds() - b - 1)/2 + a;
}
if (index > size() - 1)
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
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diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
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diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
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diff --git a/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict b/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/controlDict b/tutorials/gnemdFoam/constrictedChannel/system/controlDict
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/fvSchemes b/tutorials/gnemdFoam/constrictedChannel/system/fvSchemes
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/fvSolution b/tutorials/gnemdFoam/constrictedChannel/system/fvSolution
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/mdSolution b/tutorials/gnemdFoam/constrictedChannel/system/mdSolution
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/molConfigDict b/tutorials/gnemdFoam/constrictedChannel/system/molConfigDict
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diff --git a/tutorials/gnemdFoam/constrictedChannel/system/potentialDict b/tutorials/gnemdFoam/constrictedChannel/system/potentialDict
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diff --git a/tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict b/tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/controlDict b/tutorials/gnemdFoam/nanoNozzle/system/controlDict
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/decomposeParDict b/tutorials/gnemdFoam/nanoNozzle/system/decomposeParDict
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/fvSchemes b/tutorials/gnemdFoam/nanoNozzle/system/fvSchemes
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/fvSolution b/tutorials/gnemdFoam/nanoNozzle/system/fvSolution
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/mdSolution b/tutorials/gnemdFoam/nanoNozzle/system/mdSolution
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diff --git a/tutorials/gnemdFoam/nanoNozzle/system/molConfigDict b/tutorials/gnemdFoam/nanoNozzle/system/molConfigDict
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--
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