release version: v0.3

seismology-RUB · Dec 13, 2019 · 37ee265 · 37ee265
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diff --git a/Makefile b/Makefile
@@ -1,6 +1,6 @@
 #-----------------------------------------------------------------------
 #   Copyright 2011-2016 Lasse Lambrecht (Ruhr-Universität Bochum, GER)
-#   Copyright 2014-2018 Marc S. Boxberg (Ruhr-Universität Bochum, GER)
+#   Copyright 2014-2019 Marc S. Boxberg (Ruhr-Universität Bochum, GER)
 #
 #   This file is part of NEXD 2D.
 #
@@ -74,6 +74,8 @@ else ifeq ($(F95),mpif90)
 	#                        problem to correctly work with constants.h.
 	# recommended flags for developers:
 #	FFLAGS = -Og -J$(moduledir) -fimplicit-none -ffixed-line-length-none -ffree-line-length-none -fbounds-check -fbacktrace -Wall -Wpedantic -Wextra
+	# recommended flags for profiling (CP CP):
+#	FFLAGS = -O3 -J$(moduledir) -fimplicit-none -ffixed-line-length-none -ffree-line-length-none -funroll-all-loops -pg -g -no-pie
 	# recommended flags for users:
 	FFLAGS = -O3 -J$(moduledir) -fimplicit-none -ffixed-line-length-none -ffree-line-length-none -funroll-all-loops
 else ifeq ($(F95),mpiifort)
@@ -276,7 +278,7 @@ DEPDIRS = $(srcdir)
 	$(F95) -c $(FFLAGS) $< -o $(obsdir)/$@
 %.o: %.f
 	$(F95) -c $(FFLAGS) -fimplicit-none -ffixed-line-length-132 $< -o $(obsdir)/$@
-%.o: %.c    
+%.o: %.c
 	gcc -c $(CFLAGS) $< -o $(obsdir)/$@
 #--------------------------------------------------------------
 #  Object string for linking:

diff --git a/doc/manual.pdf b/doc/manual.pdf
diff --git a/doc/tex/1_Introduction.tex b/doc/tex/1_Introduction.tex
@@ -3,7 +3,7 @@ \chapter{Introduction}
 % use \chaptermark{}
 % to alter or adjust the chapter heading in the running head
 
-This manual describes NEXD 2D (\textbf{N}odal \textbf{D}iscontinuous \textbf{G}alerkin Finite \textbf{E}lement in \textbf{X} \textbf{D}imensions) version 0.2. NEXD is a Fortran based implementation of the nodal version of the discontinuous Galerkin approach. It is designed to simulate seismic wave propagation in complex geological structures with general physical properties and is not restricted with regard to the size of the model. The programs are currently designed to work on CPUs, only. GPUs are not supported. To run the code, no programming knowledge is required.     
+This manual describes NEXD 2D (\textbf{N}odal \textbf{D}iscontinuous \textbf{G}alerkin Finite \textbf{E}lement in \textbf{X} \textbf{D}imensions) version 0.3. NEXD is a Fortran based implementation of the nodal version of the discontinuous Galerkin approach. It is designed to simulate seismic wave propagation in complex geological structures with general physical properties and is not restricted with regard to the size of the model. The programs are currently designed to work on CPUs, only. GPUs are not supported. To run the code, no programming knowledge is required.     
 \section{Supplied programs}
 	The following programs are part of the software package NEXD 2D:
 	\begin{itemize}
@@ -14,9 +14,9 @@ \section{Supplied programs}
 \section{Functionality}
 \label{functions and applications}
 	\subsection{General features}    
-    As of release version v0.2 the following features are included:
+    As of release version v0.3 the following features are included:
     \begin{itemize}
-        \item Forward simulation of wave-propagation in elastic and anelastic media
+        \item Forward simulation of wave-propagation in elastic, anelastic and poroelastic media
         \item Wave-propagation across fractures (elastic media only)
     \end{itemize}
     Since no restrictions are imposed on size and shape of the media of interest, NEXD can be used in any situation, where the propagation of elastic waves is the key information. It is able to yield the wave field at every time step of propagating waves and the output of simulated receivers. Free surface and absorbing boundary conditions (BC) are implemented. In addition, Perfectly Matched Layers (PML) \citep{Lambrecht.2017} are available to enhance the absorbing BC.
@@ -37,4 +37,4 @@ \section{License}
 NEXD is designed and developed by Lasse Lambrecht, Andre Lamert, Wolfgang Friederich, Thomas M{\"o}ller and Marc S. Boxberg. NEXD 2D and its components, as well as documentation and some examples, are available under terms of the GNU General Public License (version 3 or higher).
 
 \section{Citation}
-Please cite \cite{Lambrecht.2017} if you use NEXD. If you use the feature to simulate the effect of fractures please cite \cite{moeller.2018}.
+Please cite \cite{Lambrecht.2017} if you use NEXD. If you use poroelasticity please cite \cite{Boxberg.2017} or \cite{Boxberg.2019} and if you use the feature to simulate the effect of fractures please cite \cite{Moeller.2019}.
diff --git a/doc/tex/2_Installation.tex b/doc/tex/2_Installation.tex
@@ -21,11 +21,16 @@ \section{Software requirements}
 To install NEXD the user needs the following software installed on his system:
 \begin{itemize}
     \item GNU Make (\url{https://www.gnu.org/software/make/}),
-    \item Fortran compiler (GNU Fortran or Intel Fortran). The software has been tested using the following compiler versions:
+    \item Fortran compiler (GNU Fortran or Intel Fortran). The version 0.3 of this software has been tested using the following compiler versions:
 		\begin{itemize}
-			\item Intel Fortran version 17.0.4 and 19.0.0
-			\item GNU Fortran version 4.9.2, 5.4.0, 6.3.0 and 7.3.0
+			\item Intel Fortran version 19.0.0
+			\item GNU Fortran version 4.9.2, 6.3.0 and 7.4.0
 		\end{itemize}
+	Version 0.2 of NEXD 2D also worked with:
+		\begin{itemize}
+			\item Intel Fortran version 17.0.4
+			\item GNU Fortran version 5.4.0 and 7.3.0
+		\end{itemize}	
     \item LAPACK libraries (\url{http://www.netlib.org/lapack/},
     \item MPI libraries, e.g. OpenMPI, 
     \item METIS (\url{http://glaros.dtc.umn.edu/gkhome/metis/metis/overview}, tested with version 4.0.3) for parallel applications,
@@ -66,9 +71,9 @@ \section{Changing the Makefile}
         captionpos=b, 
         label=lis:make2, 
         caption=Exemplary content of the Makefile.,
-        firstnumber = 292, 
-        firstline=292, 
-        lastline=296,
+        firstnumber = 294, 
+        firstline=294, 
+        lastline=298,
         breaklines=true,
         postbreak=\mbox{\textcolor{red}{$\hookrightarrow$}\space}
     ]{source_files/Makefile.txt}
@@ -86,23 +91,29 @@ \section{Clean installation directory}
 	[doc, label=right:{Contains all files related to the documentation, including the Latex source files}] 
     [simulations
         [2layer\_pml\_att
-            [cubit, label=right:{Contains the files: 2layer\_pml\_att.jou, cubit2dg.py and runcubit.py}]
+            [cubit, label=right:{Contains the files: 2layer\_pml\_att.jou, cubit2dg.py and run\_cubit.py}]
             [data, label=right:{Contains the files: parfile, source and stations}]
             [ref
                [att, label=right:{Contains reference seismograms with attenuation (66 files)}]
                [no\_att, label=right:{Contains reference seismograms without attenuation (66 files)}]
             ]
         ]
         [example\_linearSlipInterface
-            [cubit, label=right:{Contains the files: lsi.jou, cubit2dg.py and runcubit.py}]
-            [data, label=right:{Contains the files: parfile, source, stations interfaces and fracs}]
+            [cubit, label=right:{Contains the files: lsi.jou, cubit2dg.py and run\_cubit.py}]
+            [data, label=right:{Contains the files: parfile, source, stations, interfaces and fracs}]
             [ref
                 [noPML, label=right:{Contains reference seismograms with PML (60 files)}]
                 [withPML, label=right:{Contains reference seismograms without PML (60 files)}]
             ]
         ]
+        [example\_poro
+            [cubit, label=right:{Contains the files: example\_poro.jou, matpropporo, cubit2dg.py and run\_cubit.py}]
+            [data, label=right:{Contains the files: parfile, source and stations}]
+            [ref, label=right:{Contains reference seismograms (178 Files)}]
+            [tools, label=right:{Contains Matlab Code to calculate velocities and required element size.}]
+        ]
         [lambs
-            [cubit, label=right:{Contains the files: lambs.jou, cubit2dg.py and runcubit.py}]
+            [cubit, label=right:{Contains the files: lambs.jou, cubit2dg.py and run\_cubit.py}]
             [data, label=right:{Contains the files: parfile, source and stations}]
             [ref, label=right:{Contains reference seismograms and a README (13 Files)}]    
         ]