STYLE: DMD: simplify various parts of the class

src/functionObjects/field/DMD/DMD.C

@@ -114,7 +114,7 @@ void Foam::functionObjects::DMD::initialise()
     if (nSnapTotal <= 0)
     {
         FatalErrorInFunction
-            << "  # Zero-size input field = " << fieldName_ << " #"
+            << "Zero-size input field = " << fieldName_
             << exit(FatalError);
     }
 
@@ -150,7 +150,7 @@ Foam::functionObjects::DMD::DMD
     if (runTime.isAdjustTimeStep())
     {
         WarningInFunction
-            << "  # DMD: Available only for fixed time-step computations. #"
+            << "DMD is available only for fixed time-step computations."
             << endl;
     }
 
@@ -158,7 +158,7 @@ Foam::functionObjects::DMD::DMD
     if (mesh_.topoChanging())
     {
         FatalErrorInFunction
-            << "  # DMD: Available only for non-changing mesh topology. #"
+            << "DMD is available only for non-changing mesh topology."
             << exit(FatalError);
     }
 
@@ -230,11 +230,9 @@ bool Foam::functionObjects::DMD::end()
     if (step_ < 2)
     {
         WarningInFunction
-            << "  # DMD needs at least three snapshots to produce output #"
+            << "DMD needs at least three snapshots to produce output" << nl
-            << nl
+            << "    Only " << step_ + 1 << " snapshots are available" << nl
-            << "  # Only " << step_ + 1 << " snapshots are available #"
+            << "    Skipping DMD output calculation and write"
-            << nl
-            << "  # Skipping DMD output calculation and write #"
             << endl;
 
         return false;

src/functionObjects/field/DMD/DMD.H

@@ -69,7 +69,7 @@ Description
     Output files:
     \verbatim
       dynamics_<field>.dat            | Dynamics data for each mode
-      filteredDynamics_<field>.dat    | Filtered dynamics data for each mode
+      filtered_dynamics_<field>.dat   | Filtered dynamics data for each mode
     \endverbatim
 
     wherein for each mode, the following quantities are output into files:
@@ -173,10 +173,12 @@ class DMD
         //- Dynamic mode decomposition model
         autoPtr<DMDModel> DMDModelPtr_;
 
-        //- Snapshot matrix (effectively a column vector)
+        //- Augmented snapshot matrix (effectively a column vector)
         //  Upper half = current-time snapshot slot
         //  Lower half = previous-time snapshot slot
         //  A snapshot is an input dataset to be processed per execution step
+        //  A single snapshot is usually referred to as the snapshot of a single
+        //  time step, an augmented snapshot is constructed of two snapshots
         RMatrix z_;
 
         //- Name of operand field
@@ -195,7 +197,7 @@ class DMD
 
     // Private Member Functions
 
-        // Process
+        // Evaluation
 
             //- Initialise snapshot at the first-execution step
             //  Initialisation at the ctor or read level is not possible
@@ -210,11 +212,12 @@ class DMD
             template<class Type>
             bool getSnapshot();
 
-            //- Get operand field based on its geometric field type
+            //- Store operand field based on its geometric
+            //- field type after few manipulations
             //  Move previous-time field into previous-time slot in snapshot
             //  copy new current-time field into current-time slot in snapshot
             template<class GeoFieldType>
-            bool getSnapshotField();
+            bool storeSnapshot();
 
 
         // Access

src/functionObjects/field/DMD/DMDModels/DMDModel/DMDModel.H

@@ -149,7 +149,7 @@ public:
 
     // Member Functions
 
-        // Process
+        // Evaluation
 
             //- Initialise model data members with a given snapshot
             virtual bool initialise(const RMatrix& snapshot) = 0;
@@ -169,7 +169,7 @@ public:
             }
 
 
-        // IO
+        // I-O
 
             //- Read model settings
             virtual bool read(const dictionary& dict) = 0;

src/functionObjects/field/DMD/DMDModels/derived/STDMD/STDMD.C

@@ -64,7 +64,7 @@ Foam::scalar Foam::DMDModels::STDMD::L2norm(const RMatrix& z) const
     if (z.n() != 1)
     {
         FatalErrorInFunction
-            << "  # Input matrix is not a column vector. #"
+            << "Input matrix is not a column vector."
             << exit(FatalError);
     }
     #endif
@@ -609,7 +609,7 @@ void Foam::DMDModels::STDMD::magnitudes()
                 std::iota(w.begin(), w.end(), 1);
                 w = sin(twoPi/step_*(w - 1 - 0.25*step_))*pr + pr;
 
-                forAll(amps_, i)
+                forAll(mags_, i)
                 {
                     mags_[i] = sorter(w, amps_[i], evals_[i], modeNorm);
                 }
@@ -622,9 +622,9 @@ void Foam::DMDModels::STDMD::magnitudes()
                 Info<< "weighted amplitude scaling method" << endl;
 
                 const scalar modeNorm = 1;
-                const List<scalar> w(step_, 1.0);
+                const List<scalar> w(step_, 1);
 
-                forAll(amps_, i)
+                forAll(mags_, i)
                 {
                     mags_[i] = sorter(w, amps_[i], evals_[i], modeNorm);
                 }
@@ -664,7 +664,7 @@ Foam::scalar Foam::DMDModels::STDMD::sorter
     // Omit eigenvalues with very large or very small mags
     if (!(mag(eigenvalue) < GREAT && mag(eigenvalue) > VSMALL))
     {
-        Info<< "  Returning zero magnitude for mag(eigenvalue) = "
+        Info<< "    Returning zero magnitude for mag(eigenvalue) = "
             << mag(eigenvalue) << endl;
 
         return 0;
@@ -673,7 +673,7 @@ Foam::scalar Foam::DMDModels::STDMD::sorter
     // Omit eigenvalue-STDMD step combinations that pose a risk of overflow
     if (mag(eigenvalue)*step_ > sortLimiter_)
     {
-        Info<< "  Returning zero magnitude for"
+        Info<< "    Returning zero magnitude for"
             << " mag(eigenvalue) = " << mag(eigenvalue)
             << " current index = " << step_
             << " sortLimiter = " << sortLimiter_
@@ -784,7 +784,7 @@ void Foam::DMDModels::STDMD::filter()
 {
     Info<< tab << "Filtering objects of dynamics" << endl;
 
-    // Filter objects according to iMags
+    // Filter objects according to magsi
     filterIndexed(evals_, magsi_);
     filterIndexed(evecs_, magsi_);
     filterIndexed(freqs_, magsi_);
@@ -924,17 +924,17 @@ bool Foam::DMDModels::STDMD::read(const dictionary& dict)
         );
 
     Info<< tab << "Settings are read for:" << nl
-        << "    field: " << fieldName_ << nl
+        << tab << "    field: " << fieldName_ << nl
-        << "    modeSorter: " << modeSorterTypeNames[modeSorter_] << nl
+        << tab << "    modeSorter: " << modeSorterTypeNames[modeSorter_] << nl
-        << "    nModes: " << nModes_ << nl
+        << tab << "    nModes: " << nModes_ << nl
-        << "    maxRank: " << maxRank_ << nl
+        << tab << "    maxRank: " << maxRank_ << nl
-        << "    nGramSchmidt: " << nGramSchmidt_ << nl
+        << tab << "    nGramSchmidt: " << nGramSchmidt_ << nl
-        << "    fMin: " << fMin_ << nl
+        << tab << "    fMin: " << fMin_ << nl
-        << "    fMax: " << fMax_ << nl
+        << tab << "    fMax: " << fMax_ << nl
-        << "    minBasis: " << minBasis_ << nl
+        << tab << "    minBasis: " << minBasis_ << nl
-        << "    minEVal: " << minEval_ << nl
+        << tab << "    minEVal: " << minEval_ << nl
-        << "    sortLimiter: " << sortLimiter_ << nl
+        << tab << "    sortLimiter: " << sortLimiter_ << nl
-        << "    nAgglomerationProcs: " << nAgglomerationProcs_ << nl
+        << tab << "    nAgglomerationProcs: " << nAgglomerationProcs_ << nl
         << endl;
 
     return true;
@@ -973,7 +973,12 @@ bool Foam::DMDModels::STDMD::initialise(const RMatrix& z)
                 nSnap
             );
 
-            std::copy(z.cbegin(), z.cbegin() + nSnap, snapshot0.begin());
+            std::copy
+            (
+                z.cbegin(),
+                z.cbegin() + nSnap,
+                snapshot0.begin()
+            );
 
             const IOstreamOption streamOpt
             (
@@ -1052,7 +1057,7 @@ bool Foam::DMDModels::STDMD::fit()
 
         filter();
 
-        writeToFile(word("filteredDynamics"));
+        writeToFile(word("filtered_dynamics"));
     }
 
     step_ = 0;

src/functionObjects/field/DMD/DMDModels/derived/STDMD/STDMD.H

@@ -92,13 +92,10 @@ Usage
     \verbatim
     DMD1
     {
-        // Mandatory/Optional entries
+        // Mandatory entries
-        ...
-
-        // Mandatory entries (unmodifiable)
         DMDModel            STDMD;
 
-        // Conditional mandatory entries (runtime modifiable)
+        // Conditional mandatory entries
 
             // Option-1
             interval            5.5;
@@ -106,7 +103,7 @@ Usage
             // Option-2
             executeInterval     10;
 
-        // Optional entries (runtime modifiable)
+        // Optional entries
         modeSorter          kiewat;
         nGramSchmidt        5;
         maxRank             50;
@@ -115,12 +112,12 @@ Usage
         fMax                1000000000;
         nAgglomerationProcs 20;
 
-        // Optional entries (runtime modifiable, yet not recommended)
+        // Optional entries (not recommended to change)
         minBasis            0.00000001;
         minEVal             0.00000001;
         sortLimiter         500.0;
 
-        // Mandatory/Optional (inherited) entries
+        // Inherited entries
         ...
     }
     \endverbatim
@@ -335,7 +332,7 @@ class STDMD
 
     // Private Member Functions
 
-        // Process
+        // Evaluation
 
             //- Return (parallel) L2-norm of a given column vector
             scalar L2norm(const RMatrix& z) const;
@@ -355,9 +352,6 @@ class STDMD
             //- Compress orthonormal basis for 'Q' and 'G' if '(Q.n()>maxRank)'
             void compress();
 
-
-        // Evaluation
-
             //- Return reduced Koopman operator 'Atilde' (K:Eq. 78)
             //  Also fills 'RxInv'.
             //  The function was not divided into subsections to ensure
@@ -435,7 +429,7 @@ class STDMD
             );
 
 
-        // IO
+        // I-O
 
             //- Write objects of dynamics
             void writeToFile(const word& fileName) const;

src/functionObjects/field/DMD/DMDModels/derived/STDMD/STDMDTemplates.C

@@ -43,7 +43,7 @@ void Foam::DMDModels::STDMD::filterIndexed
 
     // Copy if frequency of element is within [a, b]
     label j = 0;
-    for (const auto& i : indices)
+    for (const label i : indices)
     {
         lstWithin[j] = lst[i];
         ++j;
@@ -64,7 +64,7 @@ void Foam::DMDModels::STDMD::filterIndexed
 
     // Copy if frequency of element is within [a, b]
     label j = 0;
-    for (const auto& i : indices)
+    for (const label i : indices)
     {
         matWithin.subColumn(j) = mat.subColumn(i);
         ++j;
@@ -149,19 +149,19 @@ bool Foam::DMDModels::STDMD::calcModes()
         {
             if (patch_.empty())
             {
-                auto& inModeRe = modeRe.primitiveFieldRef();
+                auto& re = modeRe.primitiveFieldRef();
-                auto& inModeIm = modeIm.primitiveFieldRef();
+                auto& im = modeIm.primitiveFieldRef();
 
-                calcMode(inModeRe, inModeIm, primitiveMode, i);
+                calcMode(re, im, primitiveMode, i);
             }
             else
             {
                 const label patchi = mesh_.boundaryMesh().findPatchID(patch_);
 
-                auto& bfModeRe = modeRe.boundaryFieldRef()[patchi];
+                auto& re = modeRe.boundaryFieldRef()[patchi];
-                auto& bfModeIm = modeIm.boundaryFieldRef()[patchi];
+                auto& im = modeIm.boundaryFieldRef()[patchi];
 
-                calcMode(bfModeRe, bfModeIm, primitiveMode, i);
+                calcMode(re, im, primitiveMode, i);
             }
         }
 

src/functionObjects/field/DMD/DMDTemplates.C

@@ -38,11 +38,11 @@ bool Foam::functionObjects::DMD::getSnapshot()
 
     if (foundObject<VolFieldType>(fieldName_))
     {
-        return getSnapshotField<VolFieldType>();
+        return storeSnapshot<VolFieldType>();
     }
     else if (foundObject<SurfaceFieldType>(fieldName_))
     {
-        return getSnapshotField<SurfaceFieldType>();
+        return storeSnapshot<SurfaceFieldType>();
     }
 
     return false;
@@ -50,7 +50,7 @@ bool Foam::functionObjects::DMD::getSnapshot()
 
 
 template<class GeoFieldType>
-bool Foam::functionObjects::DMD::getSnapshotField()
+bool Foam::functionObjects::DMD::storeSnapshot()
 {
     if (step_ == 0)
     {