updates version number to 4.1.0

VERSION

@@ -1 +1 @@
-4.0.0
+4.1.0

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for Specfem3D 4.0.0.
+# Generated by GNU Autoconf 2.71 for Specfem3D 4.1.0.
 #
 # Report bugs to <see the wiki>.
 #
@@ -609,8 +609,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='Specfem3D'
 PACKAGE_TARNAME='Specfem3D'
-PACKAGE_VERSION='4.0.0'
-PACKAGE_STRING='Specfem3D 4.0.0'
+PACKAGE_VERSION='4.1.0'
+PACKAGE_STRING='Specfem3D 4.1.0'
 PACKAGE_BUGREPORT='see the wiki'
 PACKAGE_URL=''
 
@@ -1473,7 +1473,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures Specfem3D 4.0.0 to adapt to many kinds of systems.
+\`configure' configures Specfem3D 4.1.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1539,7 +1539,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of Specfem3D 4.0.0:";;
+     short | recursive ) echo "Configuration of Specfem3D 4.1.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1703,7 +1703,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-Specfem3D configure 4.0.0
+Specfem3D configure 4.1.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -2093,7 +2093,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by Specfem3D $as_me 4.0.0, which was
+It was created by Specfem3D $as_me 4.1.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -12530,7 +12530,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Specfem3D $as_me 4.0.0, which was
+This file was extended by Specfem3D $as_me 4.1.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -12598,7 +12598,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-Specfem3D config.status 4.0.0
+Specfem3D config.status 4.1.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

doc/USER_MANUAL/02_getting_started.tex

@@ -201,6 +201,26 @@ \section{Using the ADIOS library for I/O}
 ADIOS is currently only usable for meshfem3D generated mesh (i.e. not for meshes generated
 with CUBIT). Additional control parameters are discussed in section~\ref{cha:Main-Parameter}.
 
+%-----------------------------------------------------------------------------------------------------------------------------------%
+\section{Using HDF5 for file I/O}
+%-----------------------------------------------------------------------------------------------------------------------------------%
+
+As file I/O can be a bottleneck in large-scale simulations, SPECFEM3D supports file I/O using the HDF5 format
+for movie snapshots and database files. To support this feature, you will need to compile the code with corresponding HDF5 flags.
+The configuration of the package could look for example like:
+{\small
+\begin{verbatim}
+  ./configure --with-hdf5 HDF5_INC="/opt/homebrew/include" HDF5_LIBS="-L/opt/homebrew/lib" \
+      ..
+\end{verbatim}
+}
+In the main \texttt{Par\_file}, you will then have to turn on the HDF5 flag \texttt{HDF5\_ENABLED}.
+Note that additional MPI processes can be launched specifically to handle the file I/O in an asynchronous way.
+The number of these additional MPI processes is specified by the parameter \texttt{HDF5\_IO\_NODES}, such that
+the total number of MPI processes to launch the executables becomes \texttt{NPROC + HDF5\_IO\_NODES}.
+
+
+
 %-----------------------------------------------------------------------------------------------------------------------------------%
 \section{Adding OpenMP support in addition to MPI}
 %-----------------------------------------------------------------------------------------------------------------------------------%

doc/USER_MANUAL/04_creating_databases.tex

@@ -65,6 +65,11 @@ \section{Main parameter file \texttt{Par\_file}}\label{cha:Main-Parameter}
 is not used at the time of generating the distributed databases but
 is required for the solver. Please see also Section~\ref{sec:Choosing-the-Time-Step}
 for further details.
+\item [{\texttt{LTS\_MODE}}] Turning this flag on will use a local-time stepping scheme for the Newmark time scheme.
+It will re-distribute the mesh partitioning to balance out elements with similar local-time step sizes.
+This feature can help improve the time-to-solution when the mesh contains elements of various sizes,
+in particular when the mesh contains only a few very small elements that would limit the global time step size.
+
 \end{description}
 
 \vspace{1cm}
@@ -409,17 +414,27 @@ \section{Main parameter file \texttt{Par\_file}}\label{cha:Main-Parameter}
 
 \item [{\texttt{GPU\_MODE}}] Turn this flag on to use GPUs.
 
+%% ADIOS
 \item [\texttt{ADIOS\_ENABLED}] Turn this flag on to enable ADIOS. If set to \texttt{.false.}, subsequent ADIOS
 parameters will not be considered.
 \item [\texttt{ADIOS\_FOR\_DATABASES}] Turn this flag on to use ADIOS for xmeshfem3D output and
 xgenerate\_database input.
 \item [\texttt{ADIOS\_FOR\_MESH}]  Turn this flag on to use ADIOS for generated databases.
 \item [\texttt{ADIOS\_FOR\_FORWARD\_ARRAYS}] Turn this flag on to read and write forward arrays using ADIOS.
 \item [\texttt{ADIOS\_FOR\_KERNELS}] Turn this flag on to produce ADIOS kernels that can later be visualized with the ADIOS version of combine\_vol\_data.
+
+%% HDF5
+\item [\texttt{HDF5\_ENABLED}] Turn this flag on to enable HDF5 file I/O. If set to \texttt{.false.}, subsequent HDF5
+parameters will not be considered.
+\item [\texttt{HDF5\_FOR\_MOVIES}] Turn this flag on to use HDF5 format for movie outputs.
+\item [\texttt{HDF5\_IO\_NODES}] Setting this number >0 will allocate additional MPI processes specifically to handle
+the HDF5 file I/O in an asynchronous way.
+
 \end{description}
 There are quite a few more parameters to change the default setup of your runs. Please check the comments in the \texttt{DATA/Par\_file} directly for further explanations.\newline
 
 
+
 \subsection{PML absorbing boundary layers}
 
 If you use PML, the mesh elements that belong to the PML layers can

doc/USER_MANUAL/authors.tex

@@ -33,6 +33,7 @@ \section*{Authors}
 Paul Cristini,
 Cl\'ement Durochat,
 Percy Galvez,
+Rahul Garg,
 Rene Gassmoeller,
 Hom Nath Gharti,
 Dominik G\"oddeke,

doc/USER_MANUAL/copyright_and_version.tex

@@ -20,6 +20,12 @@ \chapter*{Copyright}
 \noindent
 \textbf{\underline{Evolution of the code:}}\newline
 
+version 4.1, November 2023:
+Rahul Garg, Hom Nath Gharti, Masaru Nagaso, Elif Oral, Daniel Peter.
+HDF5 file IO support; local time stepping; strain seismograms; movie output for stresses; 
+reuse feature for external STF; various updates and improvements.\newline
+
+
 version 4.0, March 2023:
 Rafael Almada, Jean-Paul Ampuero, Etienne Bachmann, Kangchen Bai, Stephen Beller, Jordan Bishop, Alexis Bottero,
 Emanuele Casarotti, Clement Durochat, Rene Gassmoeller, Hom Nath Gharti, Leopold Grinberg, Aakash Gupta,

doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex

@@ -172,7 +172,7 @@
 
 \author{\copyright \, CNRS (France), Princeton University (USA),\\
 and ETH Z\"urich (Switzerland)\\
-Version 4.0}
+Version 4.1}
 
 % date of last edit
 \date{\today}

src/specfem3D/specfem3D.F90

@@ -269,6 +269,11 @@
 ! Evolution of the code:
 ! ---------------------
 !
+! version 4.1, November 2023:
+!   Rahul Garg, Hom Nath Gharti, Masaru Nagaso, Elif Oral, Daniel Peter.
+!     HDF5 file IO support; local time stepping; strain seismograms; movie output for stresses; 
+!     reuse feature for external STF; various updates and improvements.
+!
 ! version 4.0, March 2023:
 !   Rafael Almada, Jean-Paul Ampuero, Etienne Bachmann, Kangchen Bai, Stephen Beller, Jordan Bishop,
 !   Alexis Bottero, Emanuele Casarotti, Clement Durochat, Rene Gassmoeller, Hom Nath Gharti, Leopold Grinberg,