Merge remote-tracking branch 'upstream/master' into bugFixes

Author: wilfonba

.github/workflows/cleanliness.yml

@@ -34,42 +34,48 @@ jobs:
                 sed -i '/\/master\//d' master.txt
             
             - name: Unused Variables Diff
+              continue-on-error: true
               run: |
                 grep -F 'Wunused-variable' master.txt > mUnused.txt
                 grep -F 'Wunused-variable' pr.txt > prUnused.txt
-                diff prUnused.txt mUnused.txt || true
+                diff prUnused.txt mUnused.txt
             
             - name: Unused Dummy Arguments Diff
+              continue-on-error: true
               run: |
-                grep -F 'Wunused-dummy-argument' pr.txt > prDummy.txt
+                grep -F 'Wunused-dummy-argument' pr.txt > prDummy.txt 
                 grep -F 'Wunused-dummy-argument' master.txt > mDummy.txt
-                diff prDummy.txt mDummy.txt || true
+                diff prDummy.txt mDummy.txt
 
             - name: Unused Value Diff
+              continue-on-error: true
               run: |
                 grep -F 'Wunused-value' pr.txt > prUnused_val.txt
                 grep -F 'Wunused-value' master.txt > mUnused_val.txt
-                diff prUnused_val.txt mUnused_val.txt || true
+                diff prUnused_val.txt mUnused_val.txt
 
             - name: Maybe Uninitialized Variables Diff
+              continue-on-error: true
               run: |
                 grep -F 'Wmaybe-uninitialized' pr.txt > prMaybe.txt
                 grep -F 'Wmaybe-uninitialized' master.txt > mMaybe.txt
-                diff prMaybe.txt mMaybe.txt || true
+                diff prMaybe.txt mMaybe.txt
 
 
             - name: Everything Diff
+              continue-on-error: true
               run: |
-                grep '\-W' pr.txt > pr_every.txt 
+                grep '\-W' pr.txt > pr_every.txt
                 grep '\-W' master.txt > m_every.txt
-                diff pr_every.txt m_every.txt || true
+                diff pr_every.txt m_every.txt
 
             - name: List of Warnings
               run: |
                 cat pr_every.txt
                 
 
             - name: Summary
+              continue-on-error: true
               run: |  
                 pr_variable=$(grep -c -F 'Wunused-variable' pr.txt)
                 pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt)
@@ -100,6 +106,5 @@ jobs:
               if: env.pr_everything > env.master_everything 
               run: |
                 echo "Difference between warning count in PR is greater than in master."
-                exit 1
 
 

CMakeLists.txt

@@ -69,8 +69,8 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
         message(FATAL_ERROR "ERROR: When using NVHPC, v21.7 or newer is required to build MFC.\n${__err_msg}")
     endif()
 
-    if ((CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.11) AND (CMAKE_BUILD_TYPE STREQUAL "Debug") AND MFC_OpenACC)
-        message(FATAL_ERROR "ERROR: When using NVHPC, MFC with Debug and GPU options requires NVHPC v23.11 or newer.\n${__err_msg}")
+    if ((CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 24.5) AND (CMAKE_BUILD_TYPE STREQUAL "Debug") AND MFC_OpenACC)
+        message(FATAL_ERROR "ERROR: When using NVHPC, MFC with Debug and GPU options requires NVHPC v24.5 or newer.\n${__err_msg}")
     endif()
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_C_COMPILER_ID STREQUAL "AppleClang")
     message(FATAL_ERROR "ERROR: MFC does not support the Apple Clang compilers. Please consult the documentation.\n${__err_msg}")
@@ -216,7 +216,9 @@ if (CMAKE_BUILD_TYPE STREQUAL "Release")
     # Enable LTO/IPO if supported
     if (CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC")
         if (MFC_Unified)
-            message(STATUS "IPO is not available with NVHPC using Unified Memory")
+            message(STATUS "LTO/IPO is not available with NVHPC using Unified Memory")
+        elseif(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS "23.11")
+            message(STATUS "LTO/IPO is not supported in NVHPC Version < 23.11. Use a newer version of NVHPC for best performance.")
         else()
             message(STATUS "Performing IPO using -Mextract followed by -Minline")
             set(NVHPC_USE_TWO_PASS_IPO TRUE)

docs/documentation/case.md

@@ -536,7 +536,6 @@ If `file_per_process` is true, then pre_process, simulation, and post_process mu
 
 - `probe_wrt` activates the output of state variables at coordinates specified by `probe(i)%[x;y,z]`.
 
-
 ### 8. Acoustic Source {#acoustic-source}
 
 | Parameter                             | Type    | Description |
@@ -744,7 +743,7 @@ $$ u = patch\_icpp(1)\%vel(1) * tanh(y\_cc * mixlayer\_vel\_profile) $$
 | `pi_fac`               | Real    | Ratio of artificial and true `pi_\infty` values|
 
 - `pi_fac` specifies the ratio of artificial and true `pi_\infty` values (`=` artificial `pi_\infty` / true `pi_\infty`).
-This parameter enables the use of true `pi_\infty` in bubble dynamics models, when the `pi_\infty` given in the `case.py` file is an artificial value.
+This parameter enables the use of true `pi_\infty` in bubble dynamics models when the `pi_\infty` given in the `case.py` file is an artificial value.
 
 ### 13. Body Forces
 
@@ -760,7 +759,23 @@ This parameter enables the use of true `pi_\infty` in bubble dynamics models, wh
 
 $$ a_{x[y,z]} = g_{x[y,z]} + k_{x[y,z]}\sin\left(w_{x[y,z]}t + p_{x[y,z]}\right). $$
 
-Positive accelerations are in the `x[y,z]` direction are in the positive `x[y,z]` direction by convention.
+By convention, positive accelerations in the `x[y,z]` direction are in the positive `x[y,z]` direction.
+
+### 14. Cylindrical Coordinates
+
+When ``cyl_coord = 'T'`` is set in 3D the following constraints must be met:
+
+- `bc_y%beg = -14`  enables the axis boundary condition
+
+- `bc_z%beg = bc_z%end = -1`  enables periodic boundary conditions in the azimuthal direction
+
+- `z_domain%beg = 0`  sets the azimuthal starting point to 0
+
+- `z_comain%end = 2*math.pi` to set the azimuthal ending point to $2\pi$ (note, requires `import math` in the case file)
+
+When ``cyl_coord = 'T'`` is set in 2D the following constraints must be met:
+
+- `bc_y%beg = -2` to enable reflective boundary conditions
 
 ## Enumerations
 

docs/documentation/expectedPerformance.md

@@ -30,7 +30,7 @@ Note:
 | NVIDIA V100               |                           | GPU           | 1 GPU        | 0.99             | NVHPC 22.11          | GT Phoenix  |
 | NVIDIA A30                |                           | GPU           | 1 GPU        | 1.1              | NVHPC 24.1           | GT Rogues Gallery  |
 | AMD MI250X                |                           | GPU           | 1 _GCD_*     | 1.1              | CCE 16.0.1           | OLCF Frontier  |
-| AMD EPYC 9965             | Turin                     | CPU           | 192 cores    | 1.3              | GNU 13.2.0           | AMD Volcano    |
+| AMD EPYC 9965             | Turin                     | CPU           | 192 cores    | 1.2              | AOCC 5.0.0           | AMD Volcano    |
 | AMD MI100                 |                           | GPU           | 1 GPU        | 1.4              | CCE 16.0.1           | Cray internal system |
 | Intel Xeon 6980P          | Granite Rapids            | CPU           | 128 cores    | 1.4              | Intel 2024.2         | Intel Endeavour   |
 | NVIDIA L40S               | FP32-only GPU             | GPU           | 1 GPU        | 1.7              | NVHPC 24.5           | GT ICE  |

docs/documentation/visualization.md

@@ -1,18 +1,47 @@
 # Flow visualization
 
-Post-processed database in Silo-HDF5 format can be visualized and analyzed using VisIt.
-VisIt is an open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
+A post-processed database in Silo-HDF5 format can be visualized and analyzed using Paraview and VisIt.
+After the post-processing of simulation data (see section [Running](running.md#running-1)), a directory named `silo_hdf5` contains a silo-HDF5 database.
+Here, `silo_hdf5/` includes a directory named `root/` that contains index files for flow field data at each saved time step.
+
+### Visualizing with Paraview
+
+Paraview is an open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
+Paraview 5.11.0 has been confirmed to work with the MFC databases for some parallel environments.
+Nevertheless, the installation and configuration of Paraview can be environment-dependent and are left to the user.
+
+The user can launch Paraview and open the index files under `/silo_hdf5/root`.
+Once the database is loaded, flow field variables contained in the database can be added to the render view.
+Further information on Paraview can be found in its [documentation](https://docs.paraview.org/en/latest/).
+The figure below shows the iso-contour of the liquid void fraction (`alpha1`) in the database generated by the example case `3D_sphbubcollapse`.
+
+![](../res/paraview.png)
+
+### Visualizing data in cylindrical coordinates
+
+Visualizing data in cylindrical coordinates requires a coordinate transformation of the raw data in the database file.
+In Paraview, this coordinate transformation can be accomplished with the following steps:
+
+1. Apply a `clean to grid` filter to the raw data
+
+2. Apply a `calculator` filter to the cleaned data
+    - Set the calculator `attribute type` to point data
+    - Check the box for `Coordinate Results`
+    - Enter the formula `coordsX*cos(coordsY)*iHat + coordsX*sin(coordsY)*jHat + coordsZ*kHat`
+    - click apply
+
+These steps will transform the raw data into cylindrical coordinates.
+For many cases, this step will require resizing the render view window.
+
+## Visualizing with VisIt
+
+VisIt is an alternative open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
 Versions of VisIt after 2.6.0 have been confirmed to work with the MFC databases for some parallel environments.
 Nevertheless, installation and configuration of VisIt can be environment-dependent and are left to the user.
 Further remarks on parallel flow visualization, analysis, and processing of the MFC database using VisIt can also be found in [Coralic (2015)](references.md#Coralic15) and [Meng (2016)](references.md#Meng16).
 
-## Procedure
-
-After the post-processing of simulation data (see section [Running](running.md#running-1)), a directory named `silo_hdf5` contains a silo-HDF5 database.
-Here, `silo_hdf5/` includes a directory named `root/` that contains index files for flow field data at each saved time step.
 The user can launch VisIt and open the index files under `/silo_hdf5/root`.
 Once the database is loaded, flow field variables contained in the database can be added to the plot.
-
 The figure below shows the iso-contour of the liquid void fraction (`alpha1`) in the database generated by the example case `3D_sphbubcollapse`.
 For analysis and processing of the database using VisIt's capability, the user is encouraged to address [VisIt user manual](https://wci.llnl.gov/simulation/computer-codes/visit/manuals).
 
@@ -22,9 +51,9 @@ For analysis and processing of the database using VisIt's capability, the user i
 
 ## Serial data output
 
-If `parallel_io = F` then MFC will output the conservative variables to a directory `D/`. 
+If ``parallel_io = 'F'``, MFC will output the conservative variables to a directory `D/`. 
 If multiple cores are used ($\mathtt{ppn > 1}$), then a separate file is created for each core.
-If there is only one coordinate dimension (`n = 0` and `p = 0`), the primitive variables will also be written to `D/`.
+If only one coordinate dimension (`n = 0` and `p = 0`) exists, the primitive variables will also be written to `D/`.
 The file names correspond to the variables associated with each equation solved by MFC.
 They are written at every `t_step_save` time step.
 The conservative variables are
@@ -39,7 +68,7 @@ where $N_c$ are the number of components `num_fluids` and $N_d$ is the number of
 There are exceptions: if `model_eqns = 3`, then the six-equation model appends these variables with the internal energies of each component.
 If there are sub-grid bubbles `bubbles = T`, then the bubble variables are also written. 
 These depend on the bubble dynamics model used.
-If `polytropic = T`, then the conservative variables are appended by 
+If ``polytropic = 'T'``, then the conservative variables are appended by 
 
 $$ n\_b R\_1, n\_b {\\dot R}\_1, \dots, n\_b R\_{N\_b}, n\_b {\\dot R}\_{N\_b} $$
 
@@ -62,11 +91,11 @@ Place the file `paceParview.zip` in your scratch direction on Phoenix and unzip
 Enter the new directory `paceParaview` and run `tar -xvf ParaView-5.11.0-egl-MPI-Linux-Python3.9-x86_64.tar.gz` to decompress the compiled binary.
 Now that you have the binary on Phoenix, you must download Paraview 5.11 on your local machine.
 Paraview binaries can be downloaded [here](https://www.paraview.org/download/).
-Be sure to select `v5.11` from the version drop-down bar and install a `5.11.0` version of Paraview.
+Select `v5.11` from the version drop-down bar and install a `5.11.0` version of Paraview.
 
 ### Step 2: Customizing the script
 
-While all of the options for the bash script could be passed as command-line arguments, hardcoding certain unlikely-to-change options saves time.
+While all of the bash script's options could be passed as command-line arguments, hardcoding certain unlikely-to-change options saves time.
 The following is a list of required and suggested updates to make to `pace-paraview-server`.
 
 - (Optional) Update line 4 to customize the job name that will show up in the scheduler
@@ -80,7 +109,7 @@ Before running `pace-paraview-server` for the first time, you must update its pe
 Once this has been done, you can run `./pace-paraview-server` with the following options:
 
 - `--account` specifies the charge account for the job.
-If you updated line 51 of `pace-paraview-server` to reflect a default account, this option is optional, otherwise it is required.
+If you updated line 51 of `pace-paraview-server` to reflect a default account, this option is optional; otherwise, it is required.
 - `--nodes` specifies the number of nodes to request (default 1)
 - `--mem` specifies the memory per node to request (default is to request all memory)
 - `--gres` specifies the GPU resources to request.
@@ -96,7 +125,7 @@ Submitted batch job <job #>
 Waiting for ParaView server to start. This may take several minutes  ...
 ```
 
-When it's done initializing, you should see a dialogue with some recommended next steps numbered 1-4. 
+When initializing is done, you should see a dialogue with some recommended next steps, numbered 1-4. 
 Below is a slightly altered version of that dialogue:
 
 1) Create the appropriate port forwarding for your local ParaView session to connect with.
@@ -105,7 +134,7 @@ Below is a slightly altered version of that dialogue:
     * `ssh -L 8722:<nodeIdentifier>:53723 <paceSystemIdentifier>`
 
 2) Once you have `Paraview5.11.0` on your machine, select `File -> Connect..` to open the remote connection dialogue box.
-* If you've already set up the pace connection, simply double-click the existing configuration.
+* Double-click the existing configuration if you've already set up the PACE connection.
 * Click `Add Server` If you have not set up the PACE connection.
 This will create a new dialogue box where you can specify a configuration name and set the `Port` to `8722`.
 Once this is done, click `configure` and then `save` on the next dialogue box.

docs/index.html

@@ -273,15 +273,15 @@
                     <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="https://github.com/MFlowCode/MFC/releases/latest">
                         <i class="pr-4 fa-solid fa-download"></i>
                         <div class="flex-1">
-                            <span class="hidden sm:inline-block">Download </span>
+                            <span class="hidden sm:inline-block">Download</span>
                             <span id="release-ver"></span>
                         </div>
                     </a>
                     <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="documentation/md_getting-started.html">
                         <i class="pr-4 fa-solid fa-rocket"></i>
                         <span class="flex-1">Quick Start</span>
                     </a>
-                    <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="documentation/index.html">
+                    <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="documentation/md_readme.html">
                         <i class="pr-4 fa-solid fa-book"></i>
                         <span class="flex-1">Documentation</span>
                     </a>

docs/res/paraview.png

@@ -9,7 +9,8 @@
 module m_derived_types
 
     use m_constants  !< Constants
-    use m_thermochem !< Thermodynamic properties
+
+    use m_thermochem, only: num_species
 
     implicit none
 

src/common/m_derived_types.fpp

@@ -22,7 +22,9 @@ module m_variables_conversion
 
     use m_helper
 
-    use m_thermochem
+    use m_thermochem, only: &
+        num_species, get_temperature, get_pressure, &
+        get_mixture_molecular_weight, get_mixture_energy_mass
 
     ! ==========================================================================
 
@@ -1126,7 +1128,7 @@ contains
                                    q_prim_vf(i)%sf(j, k, l)/2d0
                     end do
 
-                    #:if chemistry
+                    if (chemistry) then
                         do i = chemxb, chemxe
                             Ys(i - chemxb + 1) = q_prim_vf(i)%sf(j, k, l)
                             q_cons_vf(i)%sf(j, k, l) = rho*q_prim_vf(i)%sf(j, k, l)
@@ -1140,7 +1142,7 @@ contains
                             dyn_pres + rho*e_mix
 
                         q_cons_vf(T_idx)%sf(j, k, l) = q_prim_vf(T_idx)%sf(j, k, l)
-                    #:else
+                    else
                         ! Computing the energy from the pressure
                         if ((model_eqns /= 4) .and. (bubbles .neqv. .true.)) then
                             ! E = Gamma*P + \rho u u /2 + \pi_inf + (\alpha\rho qv)
@@ -1156,7 +1158,7 @@ contains
                             !Tait EOS, no conserved energy variable
                             q_cons_vf(E_idx)%sf(j, k, l) = 0.
                         end if
-                    #:endif
+                    end if
 
                     ! Computing the internal energies from the pressure and continuities
                     if (model_eqns == 3) then