Merge branch 'master' into fix/cf

.github/workflows/CI_sequential 1.yml

@@ -34,24 +34,8 @@ jobs:
         mkl: ['YES','NO']
         exclude:
         - compiler: gfortran
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'YES'
-        - compiler: gfortran
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'YES'          
         - compiler: ifort
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'NO'
-        - compiler: ifort
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'NO'          
     # Steps represent a sequence of tasks that will be executed as part of the job
 

.github/workflows/CI_sequential 3.yml

@@ -34,24 +34,8 @@ jobs:
         mkl: ['YES','NO']
         exclude:
         - compiler: gfortran
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'YES'
-        - compiler: gfortran
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'YES'          
         - compiler: ifort
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'NO'
-        - compiler: ifort
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'NO'          
     # Steps represent a sequence of tasks that will be executed as part of the job
 

.github/workflows/CI_sequential 4.yml

@@ -34,24 +34,8 @@ jobs:
         mkl: ['YES','NO']
         exclude:
         - compiler: gfortran
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'YES'
-        - compiler: gfortran
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'YES'          
         - compiler: ifort
-          mode: RELEASE
-          comm: SEQUENTIAL
-          enable_threads: YES
-          mkl: 'NO'
-        - compiler: ifort
-          mode: DEBUG
-          comm: SEQUENTIAL
-          enable_threads: YES
           mkl: 'NO'          
     # Steps represent a sequence of tasks that will be executed as part of the job
 

CITATION.cff

@@ -0,0 +1,47 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+preferred-citation:
+  authors:
+    - family-names: Ferrer
+      given-names: Esteban
+    - family-names: Rubio
+      given-names: Gonzalo
+    - family-names: Ntoukas
+      given-names: Gerasimos
+    - family-names: Laskowski
+      given-names: Wojciech
+    - family-names: Mariño
+      given-names: Óscar A.
+    - family-names: Colombo
+      given-names: Stefano
+    - family-names: Mateo-Gabín
+      given-names: Andrés
+    - family-names: Marbona
+      given-names: Himpu
+    - family-names: Manrique de Lara
+      given-names: Fernando
+    - family-names: Huergo
+      given-names: David
+    - family-names: Manzanero
+      given-names: Juan
+    - family-names: Rueda-Ramírez
+      given-names: Andrés M.
+    - family-names: Kopriva
+      given-names: David A.
+    - family-names: Valero
+      given-names: Eusebio
+  doi: 10.1016/j.cpc.2023.108700
+  journal: "Computer Physics Communications"
+  keywords:
+    - Navier-Stokes
+    - Discontinuous Galerkin
+    - High-order method
+    - Multiphase
+    - Aeroacoustics
+    - Immersed boundary method
+  month: 6
+  start: 108700
+  title: "HORSES3D: A high-order discontinuous Galerkin solver for flow simulations and multi-physics applications"
+  type: article
+  volume: 287
+  year: 2023

CONTRIBUTORS.md

@@ -1,6 +1,4 @@
-################################################################################ 
-#                          **List of Contributors**                            #
-################################################################################ 
+# List of Contributors
 
 This is a (possibly incomplete) list of the people who has contributed to HORSES3D (or older versions).  
 
@@ -18,4 +16,4 @@ This is a (possibly incomplete) list of the people who has contributed to HORSES
 - Fernando Manrique de Lara  
 - David Huergo  
 - Oliver Browne  
-- Moritz Kompenhans  
+- Moritz Kompenhans

LICENSE.md

@@ -1,8 +1,5 @@
-################################################################################ 
-#            HORSES3D High-Order (DG) Spectral Element Solver                  #
-#                             **MIT License**                                  #
-################################################################################ 
 MIT License  
+
 Copyright (c) 2021 NUMATH https://numath.dmae.upm.es  
 
 Permission is hereby granted, free of charge, to any person obtaining a copy

README.md

@@ -1,6 +1,7 @@
 # HORSES3D High-Order (DG) Spectral Element Solver
 
 MIT License
+
 Copyright (c) 2021 NUMATH https://numath.dmae.upm.es
 
 
@@ -55,9 +56,15 @@ The following external routines/libraries can be used with **HORSES3D**, but are
 
     - COMM=PARALLEL/**SEQUENTIAL**
 
-    - ENABLE THREADS=NO/**YES**
+    - ENABLE_THREADS=NO/**YES**
+
+    - WITH_PETSC=y/**n**
+
+    - WITH_METIS=y/**n**
+
+    - WITH_HDF5=y/**n**
 
-    - WITH MKL=y/**n**
+    - WITH_MKL=y/**n**
 
     For example:
 
@@ -76,21 +83,24 @@ The following external routines/libraries can be used with **HORSES3D**, but are
 
 ## Additional libraries
 
-- HDF5:
+- PETSc:
 
     ```shell
-    export HDF5_ROOT=path_to_hdf5
-    export HDF5_DIR=$HDF5_ROOT
+    export PETSC_DIR=path_to_petsc
     ```
 
-- PETSc:
+- METIS:
 
     ```shell
-    export PETSC_DIR=path_to_petsc
+    export METIS_DIR=path_to_metis
     ```
 
-- METIS:
+- HDF5:
 
     ```shell
-    export METIS_HOME=path_to_metis
+    export HDF5_DIR=path_to_hdf5
     ```
+
+
+
+

Solver/Makefile.in

@@ -15,6 +15,9 @@ MODE?=RELEASE
 COMM?=SEQUENTIAL
 ENABLE_THREADS?=YES
 WITH_PETSC?=NO
+WITH_METIS?=NO
+WITH_HDF5?=NO
+WITH_MKL?=NO
 
 MAKE=make
 AR=ar
@@ -117,19 +120,6 @@ else ifeq ($(MODE),DEBUG)
      endif
 endif
 
-##########################
-## 	Link MKL 	##
-##########################
-ifeq '$(WITH_MKL)''YES'
-	ifeq '$(FC)''gfortran'
-		MACROS+= -DHAS_MKL -DHAS_LAPACK
-  	LIBS += $(LIB_BLAS) $(LIB_LAPACK)
-  else #ifort
-  	MACROS+= -DHAS_MKL -DHAS_LAPACK
-  	FFLAGS+= -mkl
-  endif
-endif
-
 ##########################
 ## 	MPI      	##
 ##########################
@@ -150,42 +140,73 @@ ifeq ($(ENABLE_THREADS),YES)
     FFLAGS+=-fopenmp
 endif
 
+##########################
+## 	Link MKL 	##
+##########################
+ifeq '$(WITH_MKL)''YES'
+  ifeq '$(FC)''gfortran'
+    ifeq '$(strip $(LIB_BLAS)$(LIB_LAPACK))'''
+      $(error option WITH_MKL = YES with gfortran requires defining path to blas and lapack with LIB_BLAS and LIB_LAPACK)
+    endif
+	LIB_BLAS := $(strip $(LIB_BLAS))
+	LIB_LAPACK := $(strip $(LIB_LAPACK))
+	MACROS+= -DHAS_MKL -DHAS_LAPACK
+  	LIBS += $(LIB_BLAS) $(LIB_LAPACK)
+  else #ifort
+  	MACROS+= -DHAS_MKL -DHAS_LAPACK
+  	FFLAGS+= -qmkl
+  endif
+endif
+
 ################
 ## Link METIS ##
 ################
-ifeq ($(COMM),PARALLEL)
-   ifdef METIS_HOME
+ifeq ($(WITH_METIS),YES)
+   METIS_DIR ?= $(METIS_HOME)  	#keep this for retrocompatibility
+   METIS_DIR := $(strip $(METIS_DIR))
+   ifdef METIS_DIR
       MACROS+= -D_HAS_METIS_
-      LIBS+=-L$(METIS_HOME)/lib -lmetis
-   endif
+      LIBS+=-L$(METIS_DIR)/lib -lmetis
+   else 
+    $(error option WITH_METIS = YES requires defining path to METIS with METIS_DIR)
+  endif
 endif
 
 ##########################
 ## 	Link PETSc 	##
 ##########################
 ifeq ($(WITH_PETSC),YES)
   ifdef PETSC_DIR
+	PETSC_DIR := $(strip $(PETSC_DIR))
     MACROS+= -DHAS_PETSC
     LIBS += -L$(PETSC_DIR)/lib -lpetsc
     EXTLIB_INC+= -I$(PETSC_DIR)/include
-  endif
+  else 
+    $(error option WITH_PETSC = YES requires defining path to PETSC with PETSC_DIR)
+  endif 
 endif
 
 ##########################
 ## 	Link HDF5 	##
 ##########################
-ifdef HDF5_ROOT
-	ifneq ("$(wildcard $(HDF5_ROOT)/lib/libhdf5_fortran-shared.so)","")
-		LIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran-shared
-		MACROS+= -DHAS_HDF5
-		EXTLIB_INC += -I$(HDF5_ROOT)/include/shared -I$(HDF5_ROOT)/include
-	else ifneq ("$(wildcard $(HDF5_ROOT)/lib/libhdf5_fortran.*)","")
-		LIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
-		MACROS+= -DHAS_HDF5
-		EXTLIB_INC += -I$(HDF5_ROOT)/include/shared -I$(HDF5_ROOT)/include
+ifeq ($(WITH_HDF5),YES)
+  HDF5_DIR ?= $(HDF5_ROOT)	#keep this for retrocompatibility
+  HDF5_DIR := $(strip $(HDF5_DIR))
+  ifdef HDF5_DIR
+    ifneq ("$(wildcard $(HDF5_DIR)/lib/libhdf5_fortran-shared.so)","")
+	  LIBS += -L$(HDF5_DIR)/lib -lhdf5_fortran-shared
+	  MACROS+= -DHAS_HDF5
+	  EXTLIB_INC += -I$(HDF5_DIR)/include/shared -I$(HDF5_DIR)/include
+	else ifneq ("$(wildcard $(HDF5_DIR)/lib/libhdf5_fortran.*)","")
+	  LIBS += -L$(HDF5_DIR)/lib -lhdf5_fortran
+	  MACROS+= -DHAS_HDF5
+	  EXTLIB_INC += -I$(HDF5_DIR)/include/shared -I$(HDF5_DIR)/include
 	endif
 ##  	FC = $(HDF5_EXE)
-endif
+  else 
+    $(error option WITH_HDF5 = YES requires defining path to HDF5 with HDF5_DIR)
+  endif 
+endif 
 
 ##########################################
 ##  	Select HORSES libraries 	##

Solver/src/libs/mesh/HexMesh.f90

@@ -70,8 +70,8 @@ MODULE HexMeshClass
          class(Zone_t), dimension(:), allocatable  :: zones
          logical                                   :: child       = .FALSE.         ! Is this a (multigrid) child mesh? default .FALSE.
          logical                                   :: meshIs2D    = .FALSE.         ! Is this a 2D mesh? default .FALSE.
-         integer                                   :: dir2D                         ! If it is in fact a 2D mesh, dir 2D stores the global direction IX, IY or IZ
-         integer                                   :: dir2D_ctrl                    ! dir2D as in the control file
+         integer                                   :: dir2D       = 0               ! If it is in fact a 2D mesh, dir 2D stores the global direction IX, IY or IZ
+         integer                                   :: dir2D_ctrl  = 0               ! dir2D as in the control file
          logical                                   :: anisotropic = .FALSE.         ! Is the mesh composed by elements with anisotropic polynomial orders? default false
          logical                                   :: ignoreBCnonConformities = .FALSE.
          contains

doc/UserManual.tex

@@ -72,6 +72,9 @@ \chapter{Compiling the code} \label{sect:compiling}
 \item COMPILER=ifort/\textbf{gfortran}
 \item COMM=PARALLEL/\textbf{SEQUENTIAL}
 \item ENABLE\_THREADS=NO/\textbf{YES}
+\item WITH\_PETSC=YES/\textbf{NO}
+\item WITH\_METIS=YES/\textbf{NO}
+\item WITH\_HDF5=YES/\textbf{NO}
 \item WITH\_MKL=YES/\textbf{NO}
 \end{itemize}
 
@@ -86,9 +89,11 @@ \chapter{Compiling the code} \label{sect:compiling}
 
 \item The COM=PARALLEL flag enables distributed memory simulations using MPI.
 
-\item To compile the code linking it with METIS (that is an option for creating the mesh partitions of MPI runs), it is needed that before compilation and running, an environment variable called METIS\_HOME is found. This variable must contain the path to the HDF5 installation folder (it must have been compiled with the same compiler as HORSES3D).
+\item The WITH\_METIS=YES flag activates METIS linking. To compile the code linking it with METIS (that is an option for creating the mesh partitions of MPI runs), it is needed that before compilation and running, an environment variable called METIS\_DIR is found. This variable must contain the path to the METIS installation folder (it must have been compiled with the same compiler as HORSES3D).
 
-\item To compile the code linking it with HDF5 (necessary for reading HOPR meshes), it is needed that before compilation and running, an environment variable called HDF5\_ROOT is found. This variable must contain the path to the METIS installation folder (it must have been compiled with the same compiler as HORSES3D). In addition, the lib folder must be added to the environment variable LD\_LIBRARY\_PATH.
+\item The WITH\_HDF5=YES flag activates HDF5 linking. To compile the code linking it with HDF5 (necessary for reading HOPR meshes), it is needed that before compilation and running, an environment variable called HDF5\_DIR is found. This variable must contain the path to the HDF5 installation folder (it must have been compiled with the same compiler as HORSES3D). In addition, the lib folder must be added to the environment variable LD\_LIBRARY\_PATH.
+
+\item The WITH\_PETSC=YES flag activates PETSC linking. To compile the code linking it with PETSC, it is needed that before compilation and running, an environment variable called PETSC\_DIR is found. This variable must contain the path to the PETSC installation folder.
 
 \item If you use \textit{environment modules}, it is advised to use the HORSES3D module file:\\
 \begin{lstlisting}[language=bash]