From 4b933332924e29ca2f8914ff7bc0a46d6096e15a Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 7 Mar 2017 10:53:40 +0100
Subject: [PATCH 1/6] ENH: improve handling of noFunctionObjects /
 withFunctionObjects (issue #352)

- do not enable function objects by default if there is no means of
  disabling them.
---
 src/OpenFOAM/db/Time/Time.C | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/OpenFOAM/db/Time/Time.C b/src/OpenFOAM/db/Time/Time.C
index 12e62219c0..6aabf93eab 100644
--- a/src/OpenFOAM/db/Time/Time.C
+++ b/src/OpenFOAM/db/Time/Time.C
@@ -515,7 +515,9 @@ Foam::Time::Time
         *this,
         argList::validOptions.found("withFunctionObjects")
       ? args.optionFound("withFunctionObjects")
-      : !args.optionFound("noFunctionObjects")
+      : argList::validOptions.found("noFunctionObjects")
+      ? !args.optionFound("noFunctionObjects")
+      : false
     )
 {
     libs_.open(controlDict_, "libs");
@@ -590,7 +592,6 @@ Foam::Time::Time
 {
     libs_.open(controlDict_, "libs");
 
-
     // Explicitly set read flags on objectRegistry so anything constructed
     // from it reads as well (e.g. fvSolution).
     readOpt() = IOobject::MUST_READ_IF_MODIFIED;

From 865f09e6239b2f4b87e2596b7db71616f677659c Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 7 Mar 2017 18:48:57 +0100
Subject: [PATCH 2/6] STYLE: comments in codedFvOptionTemplate

---
 etc/codeTemplates/dynamicCode/codedFvOptionTemplate.H | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/etc/codeTemplates/dynamicCode/codedFvOptionTemplate.H b/etc/codeTemplates/dynamicCode/codedFvOptionTemplate.H
index c276419362..a30727ccb6 100644
--- a/etc/codeTemplates/dynamicCode/codedFvOptionTemplate.H
+++ b/etc/codeTemplates/dynamicCode/codedFvOptionTemplate.H
@@ -39,11 +39,11 @@ Description
     setValue
     (
          fvMatrix<Type}>& eqn,
-        const label fieldi
+         const label fieldi
     )
 
     where :
-        fld is the field in fieldNames
+        fieldi is the index in the fields entry
         eqn is the fvMatrix
 
     energySource
@@ -55,7 +55,7 @@ Description
 
         scalarCodedSourceCoeffs
         {
-            fieldNames      (h);
+            fields  (h);
             name    sourceTime;
 
             codeInclude

From b7dc6d04418f3a11b4917ad0694b2fb34caf5c13 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 7 Mar 2017 17:00:30 +0100
Subject: [PATCH 3/6] ENH: add subsetList/inplaceSubsetList functions with
 unary predicate

- these are suitable for use with lambda functions.

- Deprecate the unused 3-parameter version of subset/inplaceSubset.

- Deprecate initList and initListList in favour of initializer_list

STYLE: adjust some comments, remove dead code in regionSizeDistribution.C
---
 applications/test/ListOps/Test-ListOps.C      | 16 +++-
 .../containers/Lists/ListOps/ListOps.C        |  9 +-
 .../containers/Lists/ListOps/ListOps.H        | 91 ++++++++++++-------
 .../Lists/ListOps/ListOpsTemplates.C          | 73 +++++++++++----
 .../primitives/strings/lists/stringListOps.H  | 10 +-
 .../regionSizeDistribution.C                  | 18 ----
 6 files changed, 135 insertions(+), 82 deletions(-)

diff --git a/applications/test/ListOps/Test-ListOps.C b/applications/test/ListOps/Test-ListOps.C
index fbbe90deb9..2efba98c7f 100644
--- a/applications/test/ListOps/Test-ListOps.C
+++ b/applications/test/ListOps/Test-ListOps.C
@@ -109,7 +109,21 @@ int main(int argc, char *argv[])
     SubList<label> test5SubList(test5, 4, 3);
     Info<< "List                            : " << test5 << endl;
     inplaceReverseList(test5SubList);
-    Info<< "Reverse Sublist between 3 and 6 : " << test5 << endl;
+    Info<< "Reverse Sublist between 3 and 6 : " << test5 << nl << endl;
+
+    Info<< nl << "Test lambda predicates:" << nl << endl;
+
+    List<label> test6(identity(19));
+    // shift range for general testing
+    std::for_each(test6.begin(), test6.end(), [](label& x){ x -= 10; });
+
+    Info<< "Subset of non-zero, even values: "
+        << subsetList
+           (
+               test6,
+               [](const label& x){ return x && !(x % 2); }
+           ) << nl
+        << endl;
 
     Info<< "\nEnd\n" << endl;
 
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOps.C b/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
index 78c9cbbf3e..762b7fe8d6 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOps.C
@@ -28,7 +28,7 @@ License
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
-const Foam::labelList Foam::emptyLabelList = Foam::labelList(0);
+const Foam::labelList Foam::emptyLabelList;
 
 
 // * * * * * * * * * * * * * * * Global Functions  * * * * * * * * * * * * * //
@@ -43,7 +43,7 @@ Foam::labelList Foam::invert
 
     forAll(map, i)
     {
-        label newPos = map[i];
+        const label newPos = map[i];
 
         if (newPos >= 0)
         {
@@ -89,7 +89,7 @@ Foam::labelListList Foam::invertOneToMany
 
     forAll(map, i)
     {
-        label newI = map[i];
+        const label newI = map[i];
 
         if (newI >= 0)
         {
@@ -105,10 +105,11 @@ Foam::labelList Foam::identity(const label len)
 {
     labelList map(len);
 
-    forAll(map, i)
+    for (label i = 0; i < len; ++i)
     {
         map[i] = i;
     }
+
     return map;
 }
 
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
index faacc501b4..0c56f43cf5 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
@@ -55,26 +55,27 @@ static const List<Type>& emptyList()
     return *reinterpret_cast<const List<Type>*>(&emptyLabelList);
 }
 
+
 //- Renumber the values (not the indices) of a list.
 //  Negative ListType elements are left as is.
 template<class ListType>
-ListType renumber(const labelUList& oldToNew, const ListType&);
+ListType renumber(const labelUList& oldToNew, const ListType& lst);
 
 //- Inplace renumber the values of a list.
 //  Negative ListType elements are left as is.
 template<class ListType>
-void inplaceRenumber(const labelUList& oldToNew, ListType&);
+void inplaceRenumber(const labelUList& oldToNew, ListType& lst);
 
 
 //- Reorder the elements (indices, not values) of a list.
 //  Negative ListType elements are left as is.
 template<class ListType>
-ListType reorder(const labelUList& oldToNew, const ListType&);
+ListType reorder(const labelUList& oldToNew, const ListType& lst);
 
 //- Inplace reorder the elements of a list.
 //  Negative ListType elements are left as is.
 template<class ListType>
-void inplaceReorder(const labelUList& oldToNew, ListType&);
+void inplaceReorder(const labelUList& oldToNew, ListType& lst);
 
 
 // Variants to work with iterators and sparse tables.
@@ -82,65 +83,81 @@ void inplaceReorder(const labelUList& oldToNew, ListType&);
 
 //- Map values. Do not map negative values.
 template<class Container>
-void inplaceMapValue(const labelUList& oldToNew, Container&);
+void inplaceMapValue(const labelUList& oldToNew, Container& lst);
 
 //- Recreate with mapped keys. Do not map elements with negative key.
 template<class Container>
-void inplaceMapKey(const labelUList& oldToNew, Container&);
+void inplaceMapKey(const labelUList& oldToNew, Container& lst);
 
 
 //- Generate the (stable) sort order for the list
 template<class T>
-void sortedOrder(const UList<T>&, labelList& order);
+void sortedOrder(const UList<T>& lst, labelList& order);
 
 template<class T, class Cmp>
-void sortedOrder(const UList<T>&, labelList& order, const Cmp& cmp);
+void sortedOrder(const UList<T>& lst, labelList& order, const Cmp& cmp);
+
 
 //- Generate (sorted) indices corresponding to duplicate list values
 template<class T>
-void duplicateOrder(const UList<T>&, labelList& order);
+void duplicateOrder(const UList<T>& lst, labelList& order);
 
 template<class T, class Cmp>
-void duplicateOrder(const UList<T>&, labelList& order, const Cmp& cmp);
+void duplicateOrder(const UList<T>& lst, labelList& order, const Cmp& cmp);
+
 
 //- Generate (sorted) indices corresponding to unique list values
 template<class T>
-void uniqueOrder(const UList<T>&, labelList& order);
+void uniqueOrder(const UList<T>& lst, labelList& order);
 
 template<class T, class Cmp>
-void uniqueOrder(const UList<T>&, labelList& order, const Cmp& cmp);
+void uniqueOrder(const UList<T>& lst, labelList& order, const Cmp& cmp);
+
 
 //- Extract elements of List when select is a certain value.
-//  eg, to extract all selected elements:
-//    subset<bool, labelList>(selectedElems, true, lst);
+//  \deprecated use subsetList instead (deprecated Mar 2017)
 template<class T, class ListType>
 ListType subset(const UList<T>& select, const T& value, const ListType&);
 
 //- Inplace extract elements of List when select is a certain value.
-//  eg, to extract all selected elements:
-//    inplaceSubset<bool, labelList>(selectedElems, true, lst);
+//  \deprecated use inplaceSubsetList instead (deprecated Mar 2017)
 template<class T, class ListType>
 void inplaceSubset(const UList<T>& select, const T& value, ListType&);
 
+
 //- Extract elements of List when select is true
 //  eg, to extract all selected elements:
 //    subset<boolList, labelList>(selectedElems, lst);
-//  Note a labelHashSet could also be used for the bool-list
+//  Note a labelHashSet can also be used as the bool-list.
+//  Do not use FixedList for the input list, since it doesn't resize.
 template<class BoolListType, class ListType>
-ListType subset(const BoolListType& select, const ListType&);
+ListType subset(const BoolListType& select, const ListType& lst);
 
 //- Inplace extract elements of List when select is true
 //  eg, to extract all selected elements:
 //    inplaceSubset<boolList, labelList>(selectedElems, lst);
-//  Note a labelHashSet could also be used for the bool-list
+//  Note a labelHashSet can also be used as the bool-list.
+//  Do not use FixedList for the input list, since it doesn't resize.
 template<class BoolListType, class ListType>
-void inplaceSubset(const BoolListType& select, ListType&);
+void inplaceSubset(const BoolListType& select, ListType& lst);
+
+
+//- Copy a subset of the input list when predicate is true.
+//  Do not use FixedList for the input list, since it doesn't resize.
+template<class ListType, class UnaryPredicate>
+ListType subsetList(const ListType& input, UnaryPredicate pred);
+
+//- Inplace subset of the list when predicate is true.
+//  Do not use FixedList for the input list, since it doesn't resize.
+template<class ListType, class UnaryPredicate>
+void inplaceSubsetList(ListType& input, UnaryPredicate pred);
+
 
 //- Invert one-to-one map. Unmapped elements will be -1.
-labelList invert(const label len, const labelUList&);
+labelList invert(const label len, const labelUList& map);
 
 //- Invert one-to-many map. Unmapped elements will be size 0.
-labelListList invertOneToMany(const label len, const labelUList&);
+labelListList invertOneToMany(const label len, const labelUList& map);
 
 //- Invert many-to-many.
 //  Input and output types need to be inherited from List.
@@ -156,7 +173,7 @@ List<OutList> invertManyToMany(const label len, const UList<InList>& in)
     return out;
 }
 
-//- Create identity map (map[i] == i) of given length
+//- Create identity map of the given length with (map[i] == i)
 labelList identity(const label len);
 
 //- Find first occurence of given element and return index,
@@ -173,8 +190,8 @@ label findIndex
 template<class ListType>
 labelList findIndices
 (
-    const ListType&,
-    typename ListType::const_reference,
+    const ListType& l,
+    typename ListType::const_reference t,
     const label start=0
 );
 
@@ -182,9 +199,9 @@ labelList findIndices
 template<class ListType>
 void setValues
 (
-    ListType&,
+    ListType& l,
     const labelUList& indices,
-    typename ListType::const_reference
+    typename ListType::const_reference t
 );
 
 //- Opposite of findIndices: set values at indices to given value
@@ -200,13 +217,13 @@ ListType createWithValues
 //- Find index of max element (and larger than given element).
 //  return -1 if not found. Linear search.
 template<class ListType>
-label findMax(const ListType&, const label start=0);
+label findMax(const ListType& l, const label start=0);
 
 
 //- Find index of min element (and less than given element).
 //  return -1 if not found. Linear search.
 template<class ListType>
-label findMin(const ListType&, const label start=0);
+label findMin(const ListType& l, const label start=0);
 
 
 //- Find first occurrence of given element in sorted list and return index,
@@ -214,8 +231,8 @@ label findMin(const ListType&, const label start=0);
 template<class ListType>
 label findSortedIndex
 (
-    const ListType&,
-    typename ListType::const_reference,
+    const ListType& l,
+    typename ListType::const_reference t,
     const label start=0
 );
 
@@ -225,8 +242,8 @@ label findSortedIndex
 template<class ListType, class BinaryOp>
 label findLower
 (
-    const ListType&,
-    typename ListType::const_reference,
+    const ListType& l,
+    typename ListType::const_reference t,
     const label start,
     const BinaryOp& bop
 );
@@ -237,20 +254,24 @@ label findLower
 template<class ListType>
 label findLower
 (
-    const ListType&,
-    typename ListType::const_reference,
+    const ListType& l,
+    typename ListType::const_reference t,
     const label start=0
 );
 
 
 //- To construct a List from a C array. Has extra Container type
 //  to initialise e.g. wordList from arrays of char*.
+//
+//  \deprecated can often use initializer_list instead (deprecated Mar 2017)
 template<class Container, class T, int mRows>
 List<Container> initList(const T[mRows]);
 
 
 //- To construct a (square) ListList from a C array. Has extra Container type
 //  to initialise e.g. faceList from arrays of labels.
+//
+//  \deprecated can often use initializer_list instead (deprecated Mar 2017)
 template<class Container, class T, int mRows, int nColumns>
 List<Container> initListList(const T[mRows][nColumns]);
 
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
index c0e055a271..69dbca60ec 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2017 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -34,11 +34,8 @@ ListType Foam::renumber
     const ListType& lst
 )
 {
-    // Create copy
     ListType newLst(lst.size());
-
-    // ensure consistent addressable size (eg, DynamicList)
-    newLst.setSize(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizing (eg, DynamicList)
 
     forAll(lst, elemI)
     {
@@ -76,11 +73,8 @@ ListType Foam::reorder
     const ListType& lst
 )
 {
-    // Create copy
     ListType newLst(lst.size());
-
-    // ensure consistent addressable size (eg, DynamicList)
-    newLst.setSize(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizes (eg, DynamicList)
 
     forAll(lst, elemI)
     {
@@ -104,11 +98,8 @@ void Foam::inplaceReorder
     ListType& lst
 )
 {
-    // Create copy
     ListType newLst(lst.size());
-
-    // ensure consistent addressable size (eg, DynamicList)
-    newLst.setSize(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizing (eg, DynamicList)
 
     forAll(lst, elemI)
     {
@@ -303,9 +294,7 @@ ListType Foam::subset
     }
 
     ListType newLst(lst.size());
-
-    // ensure consistent addressable size (eg, DynamicList)
-    newLst.setSize(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizing (eg, DynamicList)
 
     label nElem = 0;
     forAll(lst, elemI)
@@ -366,9 +355,7 @@ ListType Foam::subset
     // eg, when it is a PackedBoolList or a labelHashSet
 
     ListType newLst(lst.size());
-
-    // ensure consistent addressable size (eg, DynamicList)
-    newLst.setSize(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizing (eg, DynamicList)
 
     label nElem = 0;
     forAll(lst, elemI)
@@ -411,6 +398,54 @@ void Foam::inplaceSubset
 }
 
 
+template<class ListType, class UnaryPredicate>
+ListType Foam::subsetList
+(
+    const ListType& lst,
+    UnaryPredicate pred
+)
+{
+    ListType newLst(lst.size());
+    newLst.setSize(lst.size()); // Consistent sizing (eg, DynamicList)
+
+    label nElem = 0;
+    forAll(lst, elemI)
+    {
+        if (pred(lst[elemI]))
+        {
+            newLst[nElem++] = lst[elemI];
+        }
+    }
+    newLst.setSize(nElem);
+
+    return newLst;
+}
+
+
+template<class ListType, class UnaryPredicate>
+void Foam::inplaceSubsetList
+(
+    ListType& lst,
+    UnaryPredicate pred
+)
+{
+    label nElem = 0;
+    forAll(lst, elemI)
+    {
+        if (pred(lst[elemI]))
+        {
+            if (nElem != elemI)
+            {
+                lst[nElem] = lst[elemI];
+            }
+            ++nElem;
+        }
+    }
+
+    lst.setSize(nElem);
+}
+
+
 template<class InList, class OutList>
 void Foam::invertManyToMany
 (
diff --git a/src/OpenFOAM/primitives/strings/lists/stringListOps.H b/src/OpenFOAM/primitives/strings/lists/stringListOps.H
index 927118e87f..677d4e8a07 100644
--- a/src/OpenFOAM/primitives/strings/lists/stringListOps.H
+++ b/src/OpenFOAM/primitives/strings/lists/stringListOps.H
@@ -45,7 +45,7 @@ SourceFiles
 
 namespace Foam
 {
-    // single-string matches:
+    // Single-string matches:
 
     //- Return true if string matches one of the regular expressions
     inline bool findStrings
@@ -57,14 +57,14 @@ namespace Foam
         return matcher.match(str);
     }
 
-    // multi-string matches:
+    // Multi-string matches:
 
     //- Return list indices for matching strings
     template<class Matcher, class StringType>
     labelList findMatchingStrings
     (
-        const Matcher&,
-        const UList<StringType>&,
+        const Matcher& matcher,
+        const UList<StringType>& lst,
         const bool invert=false
     );
 
@@ -92,7 +92,7 @@ namespace Foam
     )
     {
         const regExp re(rePattern);
-        return findStrings(re, lst, invert);
+        return findMatchingStrings(re, lst, invert);
     }
 
     //- Return list indices for strings matching the regular expression
diff --git a/src/functionObjects/field/regionSizeDistribution/regionSizeDistribution.C b/src/functionObjects/field/regionSizeDistribution/regionSizeDistribution.C
index 48504de23d..8ae33b507f 100644
--- a/src/functionObjects/field/regionSizeDistribution/regionSizeDistribution.C
+++ b/src/functionObjects/field/regionSizeDistribution/regionSizeDistribution.C
@@ -42,24 +42,6 @@ namespace Foam
             dictionary
         );
     }
-
-    //- Plus op for FixedList<scalar>
-    template<class T, unsigned Size>
-    class ListPlusEqOp
-    {
-        public:
-        void operator()
-        (
-            FixedList<T, Size>& x,
-            const FixedList<T, Size>& y
-        ) const
-        {
-            forAll(x, i)
-            {
-                x[i] += y[i];
-            }
-        }
-    };
 }
 
 

From 3d3c14cbffbc5ddb9e1fad244b59123df10d4bfe Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Wed, 8 Mar 2017 11:10:16 +0100
Subject: [PATCH 4/6] ENH: add inplaceUniqueSort function

- determines a unique sort order (as per uniqueOrder) and uses that to
  reorder the list and possibly truncate it.
---
 applications/test/ListOps/Test-ListOps.C      | 14 ++++++-
 .../containers/Lists/ListOps/ListOps.H        | 11 ++++++
 .../Lists/ListOps/ListOpsTemplates.C          | 37 +++++++++++++++++--
 3 files changed, 57 insertions(+), 5 deletions(-)

diff --git a/applications/test/ListOps/Test-ListOps.C b/applications/test/ListOps/Test-ListOps.C
index 2efba98c7f..e722ced197 100644
--- a/applications/test/ListOps/Test-ListOps.C
+++ b/applications/test/ListOps/Test-ListOps.C
@@ -113,9 +113,9 @@ int main(int argc, char *argv[])
 
     Info<< nl << "Test lambda predicates:" << nl << endl;
 
-    List<label> test6(identity(19));
+    List<label> test6(identity(11));
     // shift range for general testing
-    std::for_each(test6.begin(), test6.end(), [](label& x){ x -= 10; });
+    std::for_each(test6.begin(), test6.end(), [](label& x){ x -= 4; });
 
     Info<< "Subset of non-zero, even values: "
         << subsetList
@@ -125,6 +125,16 @@ int main(int argc, char *argv[])
            ) << nl
         << endl;
 
+
+    test6.append(identity(13));
+
+    // Randomize the list
+    std::random_shuffle(test6.begin(), test6.end());
+
+    Info<< "Randomized: " << flatOutput(test6) << endl;
+    inplaceUniqueSort(test6);
+    Info<< "Unique    : " << flatOutput(test6) << endl;
+
     Info<< "\nEnd\n" << endl;
 
     return 0;
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
index 0c56f43cf5..441c785408 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOps.H
@@ -114,6 +114,17 @@ template<class T, class Cmp>
 void uniqueOrder(const UList<T>& lst, labelList& order, const Cmp& cmp);
 
 
+//- Inplace sorting and removal of duplicates.
+//  Do not use FixedList for the input list, since it doesn't resize.
+template<class ListType>
+void inplaceUniqueSort(ListType& lst);
+
+//- Inplace sorting and removal of duplicates.
+//  Do not use FixedList for the input list, since it doesn't resize.
+template<class ListType, class Cmp>
+void inplaceUniqueSort(ListType& lst, const Cmp& cmp);
+
+
 //- Extract elements of List when select is a certain value.
 //  \deprecated use subsetList instead (deprecated Mar 2017)
 template<class T, class ListType>
diff --git a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
index 69dbca60ec..9267221e99 100644
--- a/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
+++ b/src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C
@@ -227,8 +227,9 @@ void Foam::duplicateOrder
 
     sortedOrder(lst, order, cmp);
 
+    const label last = (order.size()-1);
     label n = 0;
-    for (label i = 0; i < order.size() - 1; ++i)
+    for (label i = 0; i < last; ++i)
     {
         if (lst[order[i]] == lst[order[i+1]])
         {
@@ -262,20 +263,50 @@ void Foam::uniqueOrder
 
     if (order.size() > 1)
     {
+        const label last = (order.size()-1);
         label n = 0;
-        for (label i = 0; i < order.size() - 1; ++i)
+        for (label i = 0; i < last; ++i)
         {
             if (lst[order[i]] != lst[order[i+1]])
             {
                 order[n++] = order[i];
             }
         }
-        order[n++] = order[order.size()-1];
+        order[n++] = order[last];
         order.setSize(n);
     }
 }
 
 
+template<class ListType>
+void Foam::inplaceUniqueSort(ListType& lst)
+{
+    inplaceUniqueSort
+    (
+        lst,
+        typename UList<typename ListType::value_type>::less(lst)
+    );
+}
+
+
+template<class ListType, class Cmp>
+void Foam::inplaceUniqueSort(ListType& lst, const Cmp& cmp)
+{
+    labelList order;
+    uniqueOrder(lst, order, cmp);
+
+    ListType newLst(order.size());
+    newLst.setSize(order.size()); // Consistent sizing (eg, DynamicList)
+
+    forAll(order, elemI)
+    {
+        newLst[elemI] = lst[order[elemI]];
+    }
+
+    lst.transfer(newLst);
+}
+
+
 template<class T, class ListType>
 ListType Foam::subset
 (

From 8060792b921bafaa94d21b869173998533cff3a6 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Wed, 8 Mar 2017 13:15:28 +0100
Subject: [PATCH 5/6] ENH: provide canRead, canWrite tests for triSurface

- for symmetry with MeshedSurface etc.
---
 src/triSurface/triSurface/triSurface.C | 64 ++++++++++++++++++++++++++
 src/triSurface/triSurface/triSurface.H | 15 ++++++
 2 files changed, 79 insertions(+)

diff --git a/src/triSurface/triSurface/triSurface.C b/src/triSurface/triSurface/triSurface.C
index 2ea0e6eea8..a95013c858 100644
--- a/src/triSurface/triSurface/triSurface.C
+++ b/src/triSurface/triSurface/triSurface.C
@@ -32,6 +32,7 @@ License
 #include "SortableList.H"
 #include "PackedBoolList.H"
 #include "surfZoneList.H"
+#include "surfaceFormatsCore.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
@@ -41,6 +42,69 @@ namespace Foam
 }
 
 
+// Note that these lists are a stop-gap measure until the read/write handling
+// gets properly updated
+const Foam::wordHashSet Foam::triSurface::readTypes_
+{
+    "ftr", "stl", "stlb", "gts", "obj", "off", "tri", "ac", "nas", "vtk"
+};
+
+
+const Foam::wordHashSet Foam::triSurface::writeTypes_
+{
+    "ftr", "stl", "stlb", "gts", "obj", "off", "tri", "ac", "smesh", "vtk"
+};
+
+
+// * * * * * * * * * * * * * Static Member Functions * * * * * * * * * * * * //
+
+bool Foam::triSurface::canReadType(const word& ext, const bool verbose)
+{
+    return fileFormats::surfaceFormatsCore::checkSupport
+    (
+        readTypes(),
+        ext,
+        verbose,
+        "reading"
+   );
+}
+
+
+bool Foam::triSurface::canWriteType(const word& ext, const bool verbose)
+{
+    return fileFormats::surfaceFormatsCore::checkSupport
+    (
+        writeTypes(),
+        ext,
+        verbose,
+        "writing"
+    );
+}
+
+
+bool Foam::triSurface::canRead(const fileName& name, const bool verbose)
+{
+    word ext = name.ext();
+    if (ext == "gz")
+    {
+        ext = name.lessExt().ext();
+    }
+    return canReadType(ext, verbose);
+}
+
+
+const Foam::wordHashSet& Foam::triSurface::readTypes()
+{
+    return readTypes_;
+}
+
+
+const Foam::wordHashSet& Foam::triSurface::writeTypes()
+{
+    return writeTypes_;
+}
+
+
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
 Foam::fileName Foam::triSurface::triSurfInstance(const Time& d)
diff --git a/src/triSurface/triSurface/triSurface.H b/src/triSurface/triSurface/triSurface.H
index e320bbfdfd..33265d95d3 100644
--- a/src/triSurface/triSurface/triSurface.H
+++ b/src/triSurface/triSurface/triSurface.H
@@ -90,6 +90,9 @@ class triSurface
         //  during reading and writing)
         geometricSurfacePatchList patches_;
 
+        static const wordHashSet readTypes_;
+        static const wordHashSet writeTypes_;
+
 
     // Demand driven private data.
 
@@ -240,6 +243,18 @@ public:
         //- Name of triSurface directory to use.
         static fileName triSurfInstance(const Time&);
 
+        //- Can we read this file format?
+        static bool canRead(const fileName& name, const bool verbose=false);
+
+        //- Can we read this file format?
+        static bool canReadType(const word& ext, const bool verbose=false);
+
+        //- Can we write this file format?
+        static bool canWriteType(const word& ext, const bool verbose=false);
+
+        static const wordHashSet& readTypes();
+        static const wordHashSet& writeTypes();
+
 
     // Constructors
 

From 37e7fca9dcb7129fc78511b3e9aa9f02e264a1ed Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Wed, 8 Mar 2017 13:30:43 +0100
Subject: [PATCH 6/6] BUG: STL ASCII being incorrectly detected as BINARY
 (fixes #422)

- now explicitly check for "SOLID" or "solid" in the header

- does not affect triSurface in the master branch, since that used a
  different parser.
---
 src/fileFormats/stl/STLCore.C | 56 +++++++++++++++++++++++------------
 src/fileFormats/stl/STLCore.H |  4 +--
 2 files changed, 39 insertions(+), 21 deletions(-)

diff --git a/src/fileFormats/stl/STLCore.C b/src/fileFormats/stl/STLCore.C
index 9b7c0c2e1c..bdfae0c025 100644
--- a/src/fileFormats/stl/STLCore.C
+++ b/src/fileFormats/stl/STLCore.C
@@ -32,9 +32,30 @@ License
 
 //! \cond fileScope
 
-//  The number of bytes in the STL binary header
+// The number of bytes in the STL binary header
 static const unsigned STLHeaderSize = 80;
 
+// Check if "SOLID" or "solid" appears as the first non-space content.
+// Assume that any leading space is less than 75 chars or so, otherwise
+// it is really bad input.
+static bool startsWithSolid(const char header[STLHeaderSize])
+{
+    unsigned pos = 0;
+    while (std::isspace(header[pos]) && pos < STLHeaderSize)
+    {
+        ++pos;
+    }
+
+    return
+    (
+        pos < (STLHeaderSize-5)  // At least 5 chars remaining
+     && std::toupper(header[pos+0]) == 'S'
+     && std::toupper(header[pos+1]) == 'O'
+     && std::toupper(header[pos+2]) == 'L'
+     && std::toupper(header[pos+3]) == 'I'
+     && std::toupper(header[pos+4]) == 'D'
+    );
+}
 //! \endcond
 
 
@@ -58,10 +79,10 @@ bool Foam::fileFormats::STLCore::isBinaryName
 
 // Check binary by getting the header and number of facets
 // this seems to work better than the old token-based method
-// - some programs (eg, pro-STAR) have 'solid' as the first word in
-//   the binary header.
 // - using wordToken can cause an abort if non-word (binary) content
 //   is detected ... this is not exactly what we want.
+// - some programs (eg, pro-STAR) have 'solid' as the first word in
+//   the binary header. This is just wrong and not our fault.
 int Foam::fileFormats::STLCore::detectBinaryHeader
 (
     const fileName& filename
@@ -93,27 +114,24 @@ int Foam::fileFormats::STLCore::detectBinaryHeader
     char header[STLHeaderSize];
     is.read(header, STLHeaderSize);
 
-    // Check that stream is OK, if not this may be an ASCII file
-    if (!is.good())
+    // If the stream is bad, it can't be a binary STL
+    if (!is.good() || startsWithSolid(header))
     {
         return 0;
     }
 
+
     // Read the number of triangles in the STL file
-    // (note: read as int so we can check whether >2^31)
-    int nTris;
-    is.read(reinterpret_cast<char*>(&nTris), sizeof(unsigned int));
+    // (note: read as signed so we can check whether >2^31)
+    int32_t nTris;
+    is.read(reinterpret_cast<char*>(&nTris), sizeof(int32_t));
 
     // Check that stream is OK and number of triangles is positive,
     // if not this may be an ASCII file
     //
     // Also compare the file size with that expected from the number of tris
-    // If the comparison is not sensible then it may be an ASCII file
-    if
-    (
-        !is
-     || nTris < 0
-    )
+    // If the comparison is still not sensible then it may be an ASCII file
+    if (!is || nTris < 0)
     {
         return 0;
     }
@@ -176,7 +194,7 @@ Foam::fileFormats::STLCore::readBinaryHeader
     is.read(header, STLHeaderSize);
 
     // Check that stream is OK, if not this may be an ASCII file
-    if (!is.good())
+    if (!is.good()) // could check again: startsWithSolid(header)
     {
         streamPtr.clear();
 
@@ -187,8 +205,8 @@ Foam::fileFormats::STLCore::readBinaryHeader
 
     // Read the number of triangles in the STl file
     // (note: read as int so we can check whether >2^31)
-    int nTris;
-    is.read(reinterpret_cast<char*>(&nTris), sizeof(unsigned int));
+    int32_t nTris;
+    is.read(reinterpret_cast<char*>(&nTris), sizeof(int32_t));
 
     // Check that stream is OK and number of triangles is positive,
     // if not this maybe an ASCII file
@@ -230,7 +248,7 @@ Foam::fileFormats::STLCore::readBinaryHeader
 void Foam::fileFormats::STLCore::writeBinaryHeader
 (
     ostream& os,
-    unsigned int nTris
+    uint32_t nTris
 )
 {
     // STL header with extra information about nTris
@@ -244,7 +262,7 @@ void Foam::fileFormats::STLCore::writeBinaryHeader
     }
 
     os.write(header, STLHeaderSize);
-    os.write(reinterpret_cast<char*>(&nTris), sizeof(unsigned int));
+    os.write(reinterpret_cast<char*>(&nTris), sizeof(uint32_t));
 }
 
 
diff --git a/src/fileFormats/stl/STLCore.H b/src/fileFormats/stl/STLCore.H
index fede83b850..6e8928d3c1 100644
--- a/src/fileFormats/stl/STLCore.H
+++ b/src/fileFormats/stl/STLCore.H
@@ -79,7 +79,7 @@ protected:
 
         //- Check contents to detect if the file is a binary STL.
         //  Return the estimated number of triangles or 0 on error.
-        static int detectBinaryHeader(const fileName&);
+        static int detectBinaryHeader(const fileName& filename);
 
 
         //- Read STL binary file header.
@@ -92,7 +92,7 @@ protected:
         );
 
         //- Write STL binary file and number of triangles to stream
-        static void writeBinaryHeader(ostream&, unsigned int);
+        static void writeBinaryHeader(ostream& os, uint32_t nTris);
 
 
     // Constructors