1) Add Projections directory from amrex - we will deprecate the one i…

…n amrex soon.

2) Remove trailing white spaces and tabs.

.github/workflows/docs.yml

@@ -15,7 +15,7 @@ jobs:
           echo "Installing python packages for docs..."
           pip3 install sphinx sphinx_rtd_theme breathe
 
-      - name: Build Doxygen Docs 
+      - name: Build Doxygen Docs
         run: |
           ./build_doxygen_docs.sh
 

.github/workflows/style/check_tabs.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.md" -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.cpp" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.cpp" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/\t/\ \ \ \ /g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTabs are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

.github/workflows/style/check_trailing_whitespaces.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.cpp" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.cpp" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/[[:blank:]]\+$//g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTrailing whitespaces at the end of a line are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

CMakeLists.txt

@@ -86,6 +86,7 @@ add_subdirectory(Slopes)
 add_subdirectory(Utils)
 add_subdirectory(MOL)
 add_subdirectory(Godunov)
+add_subdirectory(Projections)
 
 if (HYDRO_EB)
    add_subdirectory(EBMOL)

Docs/source/EBGodunov.rst

@@ -43,8 +43,8 @@ extrapolated from :math:`(i,j,k)`, where
 .. math::
    :label: eq1-ebg2
 
-   \hat{u}_{i+\frac{1}{2},j,k}^{L} = u_{i,j,k}^n + 
-   \left( \delta x - \frac{dt}{2} u_{i,j,k}^n \right) 
+   \hat{u}_{i+\frac{1}{2},j,k}^{L} = u_{i,j,k}^n +
+   \left( \delta x - \frac{dt}{2} u_{i,j,k}^n \right)
    \; {u^x}_{i,j,k} +  \delta y \; {u^y}_{i,j,k} + \delta z \; {u^z}_{i,j,k}
 
 and
@@ -55,23 +55,23 @@ and
    \tilde{u}_{i+\frac{1}{2},j,k}^{R,\frac{1}{2}} = \hat{u}_{i+\frac{1}{2},j,k}^{R} +
    \frac{dt}{2} (-(\widehat{v u_y})_{i+1,j,k} - (\widehat{w u_z})_{i+1,j,k} + f_{x,i+1,j,k}^n)
 
-extrapolated from :math:`(i+1,j,k),` where 
+extrapolated from :math:`(i+1,j,k),` where
 
 .. math::
    :label: eq2-ebg2
 
-   \hat{u}_{i+\frac{1}{2},j,k}^{R} = u_{i+1,j,k}^n + 
-   \left(\delta_x  - \frac{dt}{2} u_{i,j,k}^n \right) 
+   \hat{u}_{i+\frac{1}{2},j,k}^{R} = u_{i+1,j,k}^n +
+   \left(\delta_x  - \frac{dt}{2} u_{i,j,k}^n \right)
    \; {u^x}_{i+1,j,k} +  \delta y \; {u^y}_{i+1,j,k} + \delta z \; {u^z}_{i+1,j,k}
 
 Here, :math:`f` is the sum of external forces, discussed later.
 
-Here the slopes :math:`(u^x,u^y,u^z)` are calculated using a least-squares fit to available data and 
-:math:`\delta_x,` :math:`\delta_y` and :math:`\delta_z` are the components of the distance vector 
-from the cell centroid to the face centroid of the :math:`x`-face at :math:`(i-\frac{1}{2},j,k)`. 
-These slopes are limited with a Barth-Jesperson type of limiter that enforces no new maxima or minima 
-when the state is predicted to the face centroids. (If sufficient data is available for cells 
-with unit volume fraction, this computation instead uses a standard second- or fourth-order 
+Here the slopes :math:`(u^x,u^y,u^z)` are calculated using a least-squares fit to available data and
+:math:`\delta_x,` :math:`\delta_y` and :math:`\delta_z` are the components of the distance vector
+from the cell centroid to the face centroid of the :math:`x`-face at :math:`(i-\frac{1}{2},j,k)`.
+These slopes are limited with a Barth-Jesperson type of limiter that enforces no new maxima or minima
+when the state is predicted to the face centroids. (If sufficient data is available for cells
+with unit volume fraction, this computation instead uses a standard second- or fourth-order
 slope calculation with limiting as described in Colella (1985).)
 
 We note that if any of the four faces that contribute to the transverse derivatives for a particular cell have zero area, all of the transverse *and* forcing terms are identically set to 0.  For example, when constructing :math:`\tilde{u}_{i+\half,j,k}^{L,\nph}`, if any of the areas :math:`a_{i,\jph,k}, a_{i,\jmh,k}, a_{i,j,\kmh}` or :math:`a_{i,j,\kph}` are zero, then we simply define
@@ -82,19 +82,19 @@ We note that if any of the four faces that contribute to the transverse derivati
    \tilde{u}_{i+\half,j,k}^{L,\nph} = \hat{u}_{i+\half,j,k}^{L}
 
 The transverse derivative terms ( :math:`\widehat{v u_y}` and :math:`\widehat{w u_z}` in this case)
-are evaluated by first extrapolating all velocity components 
-to the face centroids of the transverse faces from the cell centers on either side, 
+are evaluated by first extrapolating all velocity components
+to the face centroids of the transverse faces from the cell centers on either side,
 then choosing between these states using the upwinding procedure
 defined below.  In particular, in the :math:`y` direction we define
-:math:`\widehat{\boldsymbol{U}}^F_{i,j+\frac{1}{2},k}` and 
+:math:`\widehat{\boldsymbol{U}}^F_{i,j+\frac{1}{2},k}` and
 :math:`\widehat{\boldsymbol{U}}^T_{i,j+\frac{1}{2},k}`
-analogously to how we defined 
-:math:`\hat{u}_{i+\frac{1}{2},j,k}^{R}` and :math:`\hat{u}_{i+\frac{1}{2},j,k}^{L}`, 
+analogously to how we defined
+:math:`\hat{u}_{i+\frac{1}{2},j,k}^{R}` and :math:`\hat{u}_{i+\frac{1}{2},j,k}^{L}`,
 but here on the y-faces and including all three velocity components.
 Values are similarly traced from :math:`(i,j,k)` and :math:`(i,j,k+1)`
 to the :math:`(i,j,k+\frac{1}{2})` faces to define
-:math:`\widehat{\boldsymbol{U}}^D_{i,j,k+\frac{1}{2}}` and 
-:math:`\widehat{\boldsymbol{U}}^{U}_{i,j,k+\frac{1}{2}}`, respectively. 
+:math:`\widehat{\boldsymbol{U}}^D_{i,j,k+\frac{1}{2}}` and
+:math:`\widehat{\boldsymbol{U}}^{U}_{i,j,k+\frac{1}{2}}`, respectively.
 
 In this upwinding procedure we first define a normal advective
 velocity on the face
@@ -203,8 +203,8 @@ extrapolated from :math:`(i,j,k)`, where
 .. math::
    :label: postebg-eq2
 
-   \hat{s}_{i+\half,j,k}^{L} = s_{i,j,k}^n + 
-    \left( \delta_x - \frac{dt}{2} u_{i,j,k}^n \right) 
+   \hat{s}_{i+\half,j,k}^{L} = s_{i,j,k}^n +
+    \left( \delta_x - \frac{dt}{2} u_{i,j,k}^n \right)
     \; {s^x}_{i,j,k} +  \delta_y \; {s^y}_{i,j,k} + \delta_z \; {s^z}_{i,j,k}
 
 and
@@ -218,11 +218,11 @@ extrapolated from :math:`(i+1,j,k),` where
 .. math::
    :label: postebg-eq3
 
-   \hat{u}_{i+\half,j,k}^{R} = u_{i+1,j,k}^n + 
-        \left(\delta_x  - \frac{dt}{2} u_{i,j,k}^n \right) 
+   \hat{u}_{i+\half,j,k}^{R} = u_{i+1,j,k}^n +
+        \left(\delta_x  - \frac{dt}{2} u_{i,j,k}^n \right)
      \; {s^x}_{i+1,j,k} +  \delta_y \; {s^y}_{i+1,j,k} + \delta_z \; {s^z}_{i+1,j,k}
 
-Here again the slopes :math:`(s^x,s^y,s^z)` are calculated using a least-squares fit to available data and 
+Here again the slopes :math:`(s^x,s^y,s^z)` are calculated using a least-squares fit to available data and
 :math:`\delta_x,` :math:`\delta_y` and :math:`\delta_z` are the components of the distance vector from the cell centroid to the face centroid of the :math:`x`-face at :math:`(i-\half,j,k).`  The transverse terms are computed exactly as described earlier except for the upwinding process; where we previously used the predicted states themselves to upwind, we now use the component of :math:`\U^{MAC}` normal to the face in question.
 
 We note again that if any of the four faces that contribute to the transverse derivatives for a particular cell have zero area, all of the transverse *and* forcing terms are identically set to 0.  For example, when constructing :math:`\tilde{s}_{i+\half,j,k}^{L,\nph}`, if any of the areas :math:`a_{i,\jph,k}, a_{i,\jmh,k}, a_{i,j,\kmh}` or :math:`a_{i,j,\kph}` are zero, then we simply define
@@ -232,15 +232,15 @@ We note again that if any of the four faces that contribute to the transverse de
 
    \tilde{s}_{i+\half,j,k}^{L,\nph} = \hat{s}_{i+\half,j,k}^{L}
 
-We upwind :math:`\tilde{s}_{i+\half,j,k}^{L,\nph}` and :math:`\tilde{s}_{i+\half,j,k}^{L,\nph}` using the normal component of :math:`\U^{MAC}` to define :math:`\tilde{s}_{i+\half,j,k}^{\nph}.`  Again, suppressing the subscripts, we define 
+We upwind :math:`\tilde{s}_{i+\half,j,k}^{L,\nph}` and :math:`\tilde{s}_{i+\half,j,k}^{L,\nph}` using the normal component of :math:`\U^{MAC}` to define :math:`\tilde{s}_{i+\half,j,k}^{\nph}.`  Again, suppressing the subscripts, we define
 
 .. math::
    :label: postebg-eq5
 
    \tilde{s}^{\nph} = \left\{\begin{array}{lll}
      \tilde{s}^{L,\nph}              & \mbox{if $u^{MAC} > 0$}  \\
    \frac{1}{2} (\tilde{s}^{L,\nph} + \tilde{s}^{R,\nph}) & \mbox{if $u^{MAC} = 0$}  \\
-     \tilde{s}^{R,\nph}  & \mbox{if $u^{MAC} < 0$} 
+     \tilde{s}^{R,\nph}  & \mbox{if $u^{MAC} < 0$}
    \end{array} \right.
 
 Computing the Fluxes (`ComputeFluxes`_)

Docs/source/EBMOL.rst

@@ -1,16 +1,16 @@
 EBMOL
 =====
 
-The procedure for computing MAC velocities and edge states with EB-aware MOL 
+The procedure for computing MAC velocities and edge states with EB-aware MOL
 does not involve any time derivatives. All slope computations use
 second-order limited slopes as described in
 `Slopes`_.
 
 .. _`Slopes`: https://amrex-codes.github.io/amrex/hydro_html/Slopes.html
 
 .. note::
-   
-   Note: if a cell and all of its immediate neighbors have volume fraction of 1 (i.e. they 
+
+   Note: if a cell and all of its immediate neighbors have volume fraction of 1 (i.e. they
    are not cut cells), the EBMOL methodology will return exactly the same answer (to machine
    precision) as the MOL methodology.
 
@@ -19,8 +19,8 @@ We define :math:`\varepsilon = 1.e-8` in **Utils / hydro_constants.H**
 Notation
 --------
 
-For every cut cell we define :math:`a_x`, :math:`a_y,` and :math:`a_z` to be the area fractions of the faces 
-and :math:`V` is the volume fraction of the cell.  All area and volume fractions are greater than or equal to zero 
+For every cut cell we define :math:`a_x`, :math:`a_y,` and :math:`a_z` to be the area fractions of the faces
+and :math:`V` is the volume fraction of the cell.  All area and volume fractions are greater than or equal to zero
 and less than or equal to 1.
 
 Pre-MAC (`ExtrapVelToFaces`_)
@@ -38,14 +38,14 @@ For computing the pre-MAC edge states to be MAC-projected, we define on every x-
 
 where we calculate :math:`u^x`, :math:`u^y` and :math:`u^z` simultaneously using a least squares approach,
 as described in `Slopes`_,
-and :math:`\delta_x`, :math:`\delta_y`, and :math:`\delta_z` are the components of the distance vector from 
+and :math:`\delta_x`, :math:`\delta_y`, and :math:`\delta_z` are the components of the distance vector from
 the cell centroid to the face centroid of the face at :math:`(i-\frac{1}{2},j,k).`
 
 At each face we then upwind based on :math:`u_L` and :math:`u_R`
 
 .. math::
 
-   u_{i-\frac{1}{2},j,k} = 
+   u_{i-\frac{1}{2},j,k} =
    \begin{cases}
    0, & \mathrm{if} \; u_L < 0 \;\; \mathrm{and} \;\; u_R > 0 \; \mathrm{else} \\
    u_L, & \mathrm{if} \; u_L + u_R \ge  \varepsilon  \; \mathrm{else} \\
@@ -56,7 +56,7 @@ At each face we then upwind based on :math:`u_L` and :math:`u_R`
 We similarly compute :math:`v_{i,j-\frac{1}{2},k}` on y-faces and
 :math:`w_{i,j,k-\frac{1}{2}}` on z-faces.
 
-Boundary conditions (`SetXEdgeBCs`_, `SetYEdgeBCs`_, `SetZEdgeBCs`_) 
+Boundary conditions (`SetXEdgeBCs`_, `SetYEdgeBCs`_, `SetZEdgeBCs`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. _`SetXEdgeBCs`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroBC.html#ab90f8ce229a7ebbc521dc27d65f2db9a
@@ -70,8 +70,8 @@ adjacent to the domain boundary (see `Slopes`_).
 
 (2) Second, if the face is on a domain boundary and the boundary
 condition type is extdir, we set both :math:`u_L` and :math:`u_R` to the
-boundary value. If the boundary condition type is foextrap, hoextrap, or 
-reflecteven on the low side of the domain, 
+boundary value. If the boundary condition type is foextrap, hoextrap, or
+reflecteven on the low side of the domain,
 we set :math:`u_L = u_R.` (If on the high side then we
 set :math:`u_R = u_L.`) If the boundary condition type is reflectodd , we set
 :math:`u_L = u_R = 0.`
@@ -100,7 +100,7 @@ Once we have the MAC-projected velocities, we predict all quantities to faces wi
 
 where we calculate :math:`s^x`, :math:`s^y` and :math:`s^z` simultaneously using a least squares approach,
 as described in `Slopes`_,
-and :math:`\delta_x`, :math:`\delta_y`, and :math:`\delta_z` are the components of the distance vector from 
+and :math:`\delta_x`, :math:`\delta_y`, and :math:`\delta_z` are the components of the distance vector from
 the cell centroid to the face centroid of the face at :math:`(i-\frac{1}{2},j,k).`
 
 The domain boundary conditions affect the solution as described above in
@@ -118,11 +118,11 @@ At each face we then upwind based on :math:`u^{MAC}_{i-\frac{1}{2},j,k}`
 
 .. math::
 
-   s_{i-\frac{1}{2},j,k} = 
+   s_{i-\frac{1}{2},j,k} =
    \begin{cases}
    s_L, & \mathrm{if} \; u^{MAC}_{i-\frac{1}{2},j,k}\; \ge  \; \varepsilon  \; \mathrm{else} \\
    s_R, & \mathrm{if} \; u^{MAC}_{i-\frac{1}{2},j,k}\; \le  \; -\varepsilon  \; \mathrm{else} \\
-   \frac{1}{2}(s_L + s_R), 
+   \frac{1}{2}(s_L + s_R),
    \end{cases}
 
 Computing the Fluxes (`ComputeFluxes`_)

Docs/source/FluxRedistribution.rst

@@ -15,11 +15,11 @@ of the convective fluxes, :math:`F`
 
 .. math:: (\nabla \cdot {F})^c_i = \dfrac{1}{\mathcal{V}_i} \sum_{f=1}^{N_f} ({F}_f\cdot{n}_f) A_f
 
-Here :math:`N_f` is the number of faces of cell :math:`i`, :math:`\vec{n}_f` and :math:`A_f` 
+Here :math:`N_f` is the number of faces of cell :math:`i`, :math:`\vec{n}_f` and :math:`A_f`
 are the unit normal and area of the :math:`f` -th face respectively,
 and :math:`\mathcal{V}_i` is the volume of cell :math:`i` given by
 
-.. math:: \mathcal{V}_i = (\Delta x \Delta y \Delta z)\cdot \mathcal{K}_i 
+.. math:: \mathcal{V}_i = (\Delta x \Delta y \Delta z)\cdot \mathcal{K}_i
 
 where :math:`\mathcal{K}_i` is the volume fraction of cell :math:`i` .
 
@@ -51,6 +51,6 @@ and the weights, :math:`w_{ij}` , are
 
 Note that :math:`\nabla \cdot{F}_i^{EB}` gives an update for :math:`\rho \phi` ; i.e.,
 
-.. math:: \frac{\phi_i^{n+1} - \phi_i^{n} }{\Delta t} = - \nabla \cdot{F}^{EB}_i 
+.. math:: \frac{\phi_i^{n+1} - \phi_i^{n} }{\Delta t} = - \nabla \cdot{F}^{EB}_i
 
 

Docs/source/MOL.rst

@@ -30,7 +30,7 @@ At each face we then upwind based on :math:`u_L` and :math:`u_R`
 
 .. math::
 
-   u_{i-\frac{1}{2},j,k} = 
+   u_{i-\frac{1}{2},j,k} =
    \begin{cases}
    0, & \mathrm{if} \; u_L < 0 \;\; \mathrm{and} \;\; u_R > 0 \; \mathrm{else} \\
    u_L, & \mathrm{if} \; u_L + u_R \ge  \varepsilon  \; \mathrm{else} \\
@@ -55,8 +55,8 @@ adjacent to the domain boundary (see `Slopes`_).
 
 (2) Second, if the face is on a domain boundary and the boundary
 condition type is extdir, we set both :math:`u_L` and :math:`u_R` to the
-boundary value. If the boundary condition type is foextrap, hoextrap, or 
-reflecteven on the low side of the domain, 
+boundary value. If the boundary condition type is foextrap, hoextrap, or
+reflecteven on the low side of the domain,
 we set :math:`u_L = u_R.` (If on the high side then we
 set :math:`u_R = u_L.`) If the boundary condition type is reflectodd , we set
 :math:`u_L = u_R = 0.`
@@ -101,25 +101,25 @@ At each face we then upwind based on :math:`u^{MAC}_{i-\frac{1}{2},j,k}`
 
 .. math::
 
-   s_{i-\frac{1}{2},j,k} = 
+   s_{i-\frac{1}{2},j,k} =
    \begin{cases}
    s_L, & \mathrm{if} \; u^{MAC}_{i-\frac{1}{2},j,k}\; \ge  \; \varepsilon  \; \mathrm{else} \\
    s_R, & \mathrm{if} \; u^{MAC}_{i-\frac{1}{2},j,k}\; \le  \; -\varepsilon  \; \mathrm{else} \\
-   \frac{1}{2}(s_L + s_R), 
+   \frac{1}{2}(s_L + s_R),
    \end{cases}
 
 Computing the Fluxes (`ComputeFluxes`_)
 ---------------------------------------
 
 .. _`ComputeFluxes`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceHydroUtils.html#ab70f040557a658e70ba076c9d105bab7
 
-The fluxes are computed from the edge states above by defining, e.g. 
+The fluxes are computed from the edge states above by defining, e.g.
 
 .. math::
 
    F_{i-\frac{1}{2},j,k}^{x,n} = u^{MAC}_{i-\frac{1}{2},j,k}\; s_{i-\frac{1}{2},j,k}^{n}
 
-on all x-faces, 
+on all x-faces,
 
 .. math::
 
@@ -164,7 +164,7 @@ where
 |
 |
 
-These alogrithms are applied in the MOL namespace. For API documentation, see 
+These alogrithms are applied in the MOL namespace. For API documentation, see
 `Doxygen: MOL Namespace`_.
 
 .. _`Doxygen: MOL Namespace`: https://amrex-codes.github.io/amrex-hydro/Doxygen/html/namespaceMOL.html

Docs/source/MOL_namespace.rst

@@ -1,8 +1,8 @@
 MOL Namespace
 =============
 
-Example Doxygen XML integration with Sphinx. 
+Example Doxygen XML integration with Sphinx.
 
 
-.. doxygennamespace:: MOL 
+.. doxygennamespace:: MOL
    :project: amrex-hydro