From 6a541ccc92468758ca0a4787ef0f7f4c2fcd4081 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Thu, 15 Mar 2018 15:20:00 +0100
Subject: [PATCH] COMP: avoid attempted auto-vivify with PackedBoolList []

- also ensure fewer side-effects from inplaceReorder

- provide ListOps::reorder especially for PackedList and PackedBoolList
  since they behave differently from regular lists.
---
 applications/test/ListOps/Test-ListOps.C      | 40 ++++++++-
 .../containers/Lists/ListOps/ListOps.C        | 57 +++++++++++++
 .../containers/Lists/ListOps/ListOps.H        | 56 ++++++++++--
 .../Lists/ListOps/ListOpsTemplates.C          | 85 +++++++++++++++++--
 .../polyTopoChange/polyTopoChange.C           | 16 +---
 5 files changed, 226 insertions(+), 28 deletions(-)

diff --git a/applications/test/ListOps/Test-ListOps.C b/applications/test/ListOps/Test-ListOps.C
index e722ced197..c4fb44a0f5 100644
--- a/applications/test/ListOps/Test-ListOps.C
+++ b/applications/test/ListOps/Test-ListOps.C
@@ -125,7 +125,6 @@ int main(int argc, char *argv[])
            ) << nl
         << endl;
 
-
     test6.append(identity(13));
 
     // Randomize the list
@@ -135,6 +134,45 @@ int main(int argc, char *argv[])
     inplaceUniqueSort(test6);
     Info<< "Unique    : " << flatOutput(test6) << endl;
 
+
+    // List reorder
+    labelList oldToNew(identity(40));
+    std::random_shuffle(oldToNew.begin(), oldToNew.end());
+
+    // Force a few -1:
+    oldToNew[4] = oldToNew[8] = -1;
+
+    Info<<"Test reorder - oldToNew:" << nl
+        << flatOutput(oldToNew) << nl << nl;
+
+    PackedBoolList bitset
+    (
+        ListOps::createWithValue<bool>
+        (
+            25,
+            labelList({8, 12, 15, 22, 4}),
+            true
+        )
+    );
+
+    Info<<"bitset input: " << flatOutput(bitset) << nl;
+    inplaceReorder(oldToNew, bitset);
+    Info<<"     reorder: " << flatOutput(bitset) << nl << nl;
+
+    PackedList<2> packed
+    (
+        ListOps::createWithValue<label>
+        (
+            25,
+            labelList({8, 12, 15, 22, 4}),
+            2
+        )
+    );
+
+    Info<<"packed input: " << flatOutput(packed) << nl;
+    inplaceReorder(oldToNew, packed);
+    Info<<"     reorder: " << flatOutput(packed) << nl << nl;
+
     Info<< "\nEnd\n" << endl;
 
     return 0;
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOps.C b/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
index 96e2afe42c..72b34de0ca 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
@@ -105,6 +105,7 @@ Foam::labelList Foam::identity(const label len, const label start)
 {
     labelList map(len);
 
+    // Same as std::iota(map.begin(), map.end(), start);
     for (label i = 0; i < len; ++i)
     {
         map[i] = i + start;
@@ -114,4 +115,60 @@ Foam::labelList Foam::identity(const label len, const label start)
 }
 
 
+Foam::PackedBoolList Foam::reorder
+(
+    const labelUList& oldToNew,
+    const PackedBoolList& input,
+    const bool prune
+)
+{
+    const label len = input.size();
+
+    PackedBoolList output(len);
+    output.reserve(len);
+
+    for (label i=0; i < len; ++i)
+    {
+        if (input.test(i))
+        {
+            const label newIdx = oldToNew[i];
+
+            if (newIdx >= 0)
+            {
+                output.set(newIdx);
+            }
+            else if (!prune)
+            {
+                output.set(i);
+            }
+        }
+    }
+
+    if (prune)
+    {
+        output.trim();
+    }
+
+    // Verify addresses (for movable refs)
+    // Info<< "reordered in " << long(input.storage().cdata()) << nl
+    //     << "reordered out " << long(output.storage().cdata()) << nl;
+
+    return output;
+}
+
+
+void Foam::inplaceReorder
+(
+    const labelUList& oldToNew,
+    PackedBoolList& input,
+    const bool prune
+)
+{
+    input = reorder(oldToNew, input, prune);
+
+    // Verify address (for movable refs)
+    // Info<< "now have " << long(input.storage().cdata()) << nl;
+}
+
+
 // ************************************************************************* //
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
index 54033086d2..9f9511601d 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
@@ -65,14 +65,14 @@ static const List<Type>& emptyList()
 
 
 //- Renumber the values (not the indices) of a list.
-//  Negative ListType elements are left untouched.
-template<class ListType>
-ListType renumber(const labelUList& oldToNew, const ListType& input);
+//  Negative IntListType elements are left untouched.
+template<class IntListType>
+IntListType renumber(const labelUList& oldToNew, const IntListType& input);
 
 //- Inplace renumber the values (not the indices) of a list.
-//  Negative ListType elements are left untouched.
-template<class ListType>
-void inplaceRenumber(const labelUList& oldToNew, ListType& input);
+//  Negative IntListType elements are left untouched.
+template<class IntListType>
+void inplaceRenumber(const labelUList& oldToNew, IntListType& input);
 
 
 //- Reorder the elements of a list.
@@ -102,6 +102,50 @@ void inplaceReorder
 );
 
 
+//- Reorder the elements of a packed list.
+//  Similar to the general templated form, but with auto-vivify
+//  for PackedList.
+template<unsigned Width>
+PackedList<Width> reorder
+(
+    const labelUList& oldToNew,
+    const PackedList<Width>& input,
+    const bool prune = false
+);
+
+//- Inplace reorder the elements of a packed list.
+//  Similar to the general templated form, but with auto-vivify
+//  for PackedList.
+template<unsigned Width>
+void inplaceReorder
+(
+    const labelUList& oldToNew,
+    PackedList<Width>& input,
+    const bool prune = false
+);
+
+
+//- Reorder the elements of a list.
+//  Similar to the general templated form, but with auto-vivify
+//  for PackedBoolList.
+PackedBoolList reorder
+(
+    const labelUList& oldToNew,
+    const PackedBoolList& input,
+    const bool prune = false
+);
+
+//- Inplace reorder the elements of a list.
+//  Similar to the general templated form, but with auto-vivify
+//  for PackedBoolList.
+void inplaceReorder
+(
+    const labelUList& oldToNew,
+    PackedBoolList& input,
+    const bool prune = false
+);
+
+
 // Variants to work with iterators and sparse tables.
 // Need to have iterators and insert()
 
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
index 0ac119e1b2..068d4187bd 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
@@ -29,16 +29,16 @@ License
 
 // * * * * * * * * * * * * * * * Global Functions  * * * * * * * * * * * * * //
 
-template<class ListType>
-ListType Foam::renumber
+template<class IntListType>
+IntListType Foam::renumber
 (
     const labelUList& oldToNew,
-    const ListType& input
+    const IntListType& input
 )
 {
     const label len = input.size();
 
-    ListType output(len);
+    IntListType output(len);
     output.resize(len);     // Consistent sizing (eg, DynamicList)
 
     for (label i=0; i < len; ++i)
@@ -53,11 +53,11 @@ ListType Foam::renumber
 }
 
 
-template<class ListType>
+template<class IntListType>
 void Foam::inplaceRenumber
 (
     const labelUList& oldToNew,
-    ListType& input
+    IntListType& input
 )
 {
     const label len = input.size();
@@ -120,13 +120,17 @@ template<class ListType>
 void Foam::inplaceReorder
 (
     const labelUList& oldToNew,
-    ListType& input,
+    ListType& inputOutput,
     const bool prune
 )
 {
     // NOTE: cannot use std::move() since we have no guarantee that
     // the oldToNew map is unique (ie, shuffle)
 
+    // Use const reference to ensure we obtain the proper operator[]
+    // on lazy lists (eg, List<bool>, PackedBoolList)
+
+    const ListType& input = inputOutput;
     const label len = input.size();
 
     ListType output(len);
@@ -159,7 +163,72 @@ void Foam::inplaceReorder
         output.resize(maxIdx+1);
     }
 
-    input.transfer(output);
+    inputOutput.transfer(output);
+}
+
+
+template<unsigned Width>
+Foam::PackedList<Width> Foam::reorder
+(
+    const labelUList& oldToNew,
+    const PackedList<Width>& input,
+    const bool prune
+)
+{
+    const label len = input.size();
+
+    PackedList<Width> output(len);
+
+    label maxIdx = -1;      // For pruning: newSize = maxIdx+1
+    for (label i=0; i < len; ++i)
+    {
+        const auto& val = input.get(i);
+
+        const label newIdx = oldToNew[i];
+
+        if (newIdx >= 0)
+        {
+            // Could enforce (newIdx < len)
+            // ... or just rely on FULLDEBUG from UList
+
+            output.set(newIdx, val);
+
+            if (maxIdx < newIdx)
+            {
+                maxIdx = newIdx;
+            }
+        }
+        else if (!prune)
+        {
+            output.set(i, val);
+        }
+    }
+
+    if (prune)
+    {
+        output.resize(maxIdx+1);
+    }
+
+    // Verify addresses (for movable refs)
+    // Info<< "reordered in " << long(input.storage().cdata()) << nl
+    //     << "reordered out " << long(output.storage().cdata()) << nl;
+
+    return output;
+}
+
+
+template<unsigned Width>
+void Foam::inplaceReorder
+(
+    const labelUList& oldToNew,
+    PackedList<Width>& input,
+    const bool prune
+)
+{
+    input = reorder(oldToNew, input, prune);
+
+    // Verify address (for movable refs)
+    // Info<< "now have " << long(input.storage().cdata()) << nl;
 }
 
 
diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
index 6170cd2fce..38b7f23091 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
@@ -1222,18 +1222,8 @@ void Foam::polyTopoChange::compact
                         {
                             faces_[facei].flip();
                             Swap(faceOwner_[facei], faceNeighbour_[facei]);
-                            flipFaceFlux_[facei] =
-                            (
-                                flipFaceFlux_[facei]
-                              ? 0
-                              : 1
-                            );
-                            faceZoneFlip_[facei] =
-                            (
-                                faceZoneFlip_[facei]
-                              ? 0
-                              : 1
-                            );
+                            flipFaceFlux_.set(facei, !flipFaceFlux_.test(facei));
+                            faceZoneFlip_.set(facei, !faceZoneFlip_.test(facei));
                         }
                     }
                 }
@@ -2809,7 +2799,7 @@ Foam::label Foam::polyTopoChange::addFace
     }
     reverseFaceMap_.append(facei);
 
-    flipFaceFlux_[facei] = (flipFaceFlux ? 1 : 0);
+    flipFaceFlux_.set(facei, flipFaceFlux);
 
     if (zoneID >= 0)
     {