Commit 2f167825 authored by laura.gassner's avatar laura.gassner

update of the manual, chapters 5, 6 and 7

parent b7000a3b
......@@ -38,6 +38,8 @@ Tilman Metz
Niklas Thiel
Florian Wittkamp
\end{minipage}
\hfill
\begin{minipage}[h]{0.65\textwidth}
......
......@@ -27,13 +27,13 @@ This directory contains documentation on the software (this users guide) as well
Contains the model and benchmark files for DENISE.
\textbf{mfiles}\\
Here some Matlab routines (m-files) are stored. These Matlab programs can be used to find optimal relaxation frequencies to approximate a constant Q (qapprox.m) or to plot Q as a function of frequency for certain relaxation frequencies and value of tau (qplot.m). It is necessary to have the Matlab Optimization Toolbox installed. For further details on the theory behind these algorithms we refer to the Phd thesis of T. Bohlen \cite{bohlen:98} and to the paper in which the so-called tau-method is described \cite{blanch:95}. The parameter tau is used in this software to define the level of attenuation.
Here some Matlab routines (m-files) are stored. These Matlab programs can be used to find optimal relaxation frequencies to approximate a constant Q (qapprox.m) or to plot Q as a function of frequency for certain relaxation frequencies and value of tau (qplot.m). It is necessary to have the Matlab Optimization Toolbox installed. For further details we refer to \cite{bohlen:98} and to the paper in which the so-called tau-method is described \cite{blanch:95}.
\textbf{par}\\
Parameter files for DENISE modeling.
\textbf{scripts}\\
Here, you will find examples of script-files used to submit modeling jobs on cluster-computers.
% \textbf{scripts}\\
% Here, you will find examples of script-files used to submit modeling jobs on cluster-computers.
\textbf{src}\\
This directory contains the complete source codes. The following programs are available and may be compiled using make $<$program$>$.
......@@ -46,11 +46,7 @@ Before compiling the main program DENISE you have to compile the required additi
\textit{make}
\newline
% {\color{blue}{\begin{verbatim}
% -bash-2.05b$:~/DENISE/par> make
% \end{verbatim}}}
which should install the following libraries:
which will install the following libraries:
{\color{blue}{\begin{verbatim}
lib cseife
......@@ -71,44 +67,33 @@ The source code of DENISE is located in the directory DENISE/src. To compile DEN
# source code for model generation
MODEL_EL = half_space.c
#MODEL = hh.c
MODEL = ../genmod/1D_linear_gradient_visc.c
MODEL_AC = ../genmod/1D_linear_gradient_ac.c
MODEL_EL = ../genmod/1D_linear_gradient_el.c
MODEL_VAC = ../genmod/1D_linear_gradient_viscac.c
EXEC= ../bin
# Description:
# CC = Compiler
# LFLAGS = Linker flag
# CFLAGS = Compiler flag
# Compiler (LAM: CC=hcc, CRAY T3E: CC=cc)
# ON Linux cluster running LAM (options for DENISE)
#CC=hcc
#LFLAGS=-lm -lmpi -lcseife
#CFLAGS=-O3
#SFLAGS=-L./../libcseife
#IFLAGS=-I./../libcseife
# On CRAY T3E
# CC=cc
# On MARWIN
CC=mpicc
LFLAGS=-lm -lcseife
# LINUX with OpenMPI / IntelMPI and INTEL Compiler
# Use icc whenever possible, this will be much faster than gcc
CC=mpiicc
LFLAGS=-lm -lcseife -lstfinv -laff -lfourierxx -lfftw3 -lstdc++
CFLAGS=-O3
SFLAGS=-L./../libcseife
IFLAGS=-I./../libcseife
# On HLRN system
#CC=mpcc
#LFLAGS=-lm
SFLAGS=-L./../contrib/libcseife -L./../contrib/bin
IFLAGS=-I./../contrib/libcseife -I./../contrib/header -I.
# ALTIX
#CC=icc
#CFLAGS=-mp -O3 -ipo
#LFLAGS=-lmpi -lm -i-static
# LINUX with OpenMPI / IntelMPI and GCC Compiler
#CC=mpicc
#LFLAGS=-lm -lcseife -lstfinv -laff -lfourierxx -lfftw3 -lstdc++
#CFLAGS=-O3
#SFLAGS=-L./../contrib/libcseife -L./../contrib/bin
#IFLAGS=-I./../contrib/libcseife -I./../contrib/header -I.
# On the workstations in Karlsruhe (GPI)
CC=mpicc
LFLAGS=-lm -lcseife -lstfinv -laff -lfourierxx -lfftw3 -lstdc++
CFLAGS=-O3
SFLAGS=-L./../libcseife -L./../contrib/bin
IFLAGS=-I./../libcseife -I./../contrib/header
# after this line, no further editing should be necessary
# --------------------------------------------------------
......@@ -124,89 +109,67 @@ The command to start a simulation on 8 processor with the lowest priority of -19
\textit{mpirun -np 8 nice -19 ../bin/denise DENISE.json }
\newline
% {\color{blue}{\begin{verbatim}
% mpirun -np 8 nice -19 ../bin/denise DENISE.json
% \end{verbatim}}}
It is often useful to save the standard output of the program for later reference. The screen output may be saved to DENISE.out using
\newline
\textit{mpirun -np 8 nice -19 ../bin/denise DENISE.json > DENISE.out}
\newline
% {\color{blue}{\begin{verbatim}
% mpirun -np 8 nice -19 ../bin/denise DENISE.json > DENISE.out
% \end{verbatim}}}
% \newpage
\newpage
After the output of geometry and model parameters the code starts the time stepping and displaying timing information:
After the output of geometry and model parameters the code starts the time stepping and displaying information:
{\color{blue}{\begin{verbatim}
===============================================================================
MYID=0 ***** Starting simulation (forward model) for shot 1 of 1 **********
===============================================================================
Number of samples (nts) in source file: 3462
Number of samples (nts) in source file: 3462
Message from function wavelet written by PE 0
1 source positions located in subdomain of PE 0
have been assigned with a source signal.
PE 0 outputs source time function in SU format to start/source_signal.0.su.shot1
Computing timestep 1000 of 3462
**Message from update_v (printed by PE 0):
Updating particle velocities ... finished (real time: 0.00 s).
particle velocity exchange between PEs ... finished (real time: 0.00 s).
**Message from update_s (printed by PE 0):
Updating stress components ... finished (real time: 0.00 s).
stress exchange between PEs ... finished (real time: 0.00 s).
total real time for timestep 1000 : 0.01 s.
Computing timestep 2000 of 3462
**Message from update_v (printed by PE 0):
Updating particle velocities ... finished (real time: 0.00 s).
particle velocity exchange between PEs ... finished (real time: 0.00 s).
**Message from update_s (printed by PE 0):
Updating stress components ... finished (real time: 0.00 s).
stress exchange between PEs ... finished (real time: 0.00 s).
total real time for timestep 2000 : 0.01 s.
Computing timestep 3000 of 3462
**Message from update_v (printed by PE 0):
Updating particle velocities ... finished (real time: 0.00 s).
particle velocity exchange between PEs ... finished (real time: 0.00 s).
**Message from update_s (printed by PE 0):
Updating stress components ... finished (real time: 0.00 s).
stress exchange between PEs ... finished (real time: 0.00 s).
total real time for timestep 3000 : 0.01 s.
PE 0 is writing 11 seismograms (vx) to
su/DENISE_US_x.su.shot1.it1
PE 0 is writing 11 seismograms (vy) to
su/DENISE_US_y.su.shot1.it1
**Info from main (written by PE 0):
CPU time of program per PE: 17 seconds.
Total real time of program: 18.08 seconds.
Average times for
velocity update: 0.003 seconds
stress update: 0.002 seconds
velocity exchange: 0.000 seconds
stress exchange: 0.000 seconds
timestep: 0.005 seconds
==============================================================================
MYID=0 * Starting simulation (forward model) for shot 1 of 5. Iteration 1 **
==============================================================================
****************************************
****************************************
==============================================================================
MYID=0 * Starting simulation (forward model) for shot 2 of 5. Iteration 1 **
==============================================================================
****************************************
****************************************
==============================================================================
MYID=0 * Starting simulation (forward model) for shot 3 of 5. Iteration 1 **
==============================================================================
****************************************
****************************************
==============================================================================
MYID=0 * Starting simulation (forward model) for shot 4 of 5. Iteration 1 **
==============================================================================
****************************************
****************************************
==============================================================================
MYID=0 * Starting simulation (forward model) for shot 5 of 5. Iteration 1 **
==============================================================================
****************************************
****************************************
Forward calculation finished.
\end{verbatim}}}
\section{Postprocessing}
The wavefield snapshots can be merged using the program \textit{snapmerge}. The program snapmerge is not a MPI program. Therefore, it can be executed without MPI and the mpirun command. You can run snapmerge on any PC since a MPI environment (e.g. LAM) is not required. You may therefore copy the snapshot outputs of the different nodes to another non-MPI computer to merge the files together. \textit{snapmerge} reads the required information from the DENISE parameter file. Simply type
The wavefield snapshots can be merged using the program \textit{snapmerge}. The program snapmerge is not a MPI program. Therefore, it can be executed without MPI and the mpirun command. You can run snapmerge on any PC since a MPI environment is not required. You may therefore copy the snapshot outputs of the different nodes to another non-MPI computer to merge the files together. \textit{snapmerge} reads the required information from the DENISE parameter file. Simply type
\newline
\textit{../bin/snapmerge DENISE.json }
......
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......@@ -75,17 +75,6 @@
% biblio GJI
\bibliographystyle{abbrvnat}
% \newcommand{\toall}[1]{\textbf{*** All: #1 ***}}
% \newcommand{\tojeroen}[1]{\textbf{*** Jeroen: #1 ***}}
% \newcommand{\tobrian}[1]{\textbf{*** Brian: #1 ***}}
% \newcommand{\tovala}[1]{\textbf{*** Vala: #1 ***}}
% \newcommand{\tovalabrian}[1]{\textbf{*** Vala \& Brian: #1 ***}}
% \newcommand{\tovalaqinya}[1]{\textbf{*** Vala \& Qinya: #1 ***}}
% \newcommand{\toqinya}[1]{\textbf{*** Qinya: #1 ***}}
% \newcommand{\tomin}[1]{\textbf{*** Min: #1 ***}}
% \newcommand{\toalessia}[1]{\textbf{*** Alessia: #1 ***}}
% \newcommand{\todimitri}[1]{\textbf{*** Dimitri: #1 ***}}
\newcommand{\nexxi}{\mbox{\texttt{NEX\_XI\/}}}
\newcommand{\nexeta}{\mbox{\texttt{NEX\_ETA\/}}}
\newcommand{\nprocxi}{\mbox{\texttt{NPROC\_XI\/}}}
......@@ -112,14 +101,6 @@
\input{0_Title.tex}
% \begin{center}
% \thispagestyle{empty}%
% \vspace*{-1.8truecm}
% \noindent\makebox[\textwidth]{%
% \noindent\includegraphics[width=0.83\paperwidth]{figures/DENISE-cover.png}
% }
% \end{center}
\title{\textbf{DENISE}\\
\textbf{User Manual}}
......@@ -165,7 +146,8 @@ Martin Sch\"afer,\\
(since 2014) \\
Laura Ga\ss ner,\\
Tilman Metz,\\
Niklas Thiel.\\
Niklas Thiel,\\
Florian Wittkamp.\\
% (add other developers here in the future).
\newline
......@@ -197,29 +179,8 @@ If you use this code for your own research, please cite at least one article
written by the developers of the package, for instance:\\
\newline
\bibentry{koehn:11}\\
% \cite{koehn:11}\\
% \newline
% or\\
% \newline
% (XX add more references here)\\
% \newline
% and/or other articles from \urlwithparentheses{http://www.geophysik.uni-kiel.de/~dkoehn/publications.htm}
% \newline
%
% \noindent
% The corresponding Bib\TeX{} entries may be found
% in file \texttt{doc/USER\_MANUAL/thesis.bib}.
% %------------------------------------------------------------------------------------------------%
%
% \chapter*{Contact}
%
% %------------------------------------------------------------------------------------------------%
%
% Please e-mail your feedback, questions, comments, and suggestions
% to\\ Daniel K\"ohn \urlwithparentheses{dkoehn-AT-geophysik.uni-kiel.de}.
\noindent\bibentry{kohn2012influence}\\
\newpage{}
......
......@@ -35,26 +35,26 @@
@string{SEG02 = {73rd Ann. Internat. Mtg., Soc. Expl. Geophys., Expanded Abstracts}}
@string{SEG03 = {74th Ann. Internat. Mtg., Soc. Expl. Geophys., Expanded Abstracts}}
@article{shin2001efficient,
title={Efficient calculation of a partial-derivative wavefield using reciprocity for seismic imaging and inversion},
author={Shin, Changsoo and Yoon, Kwangjin and Marfurt, Kurt J and Park, Keunpil and Yang, Dongwoo and Lim, Harry Y and Chung, Seunghwan and Shin, Sungryul},
journal={Geophysics},
volume={66},
number={6},
pages={1856--1863},
year={2001},
publisher={Society of Exploration Geophysicists}
}
@article{plessix2004frequency,
title={Frequency-domain finite-difference amplitude-preserving migration},
author={Plessix, R-E and Mulder, WA},
journal={Geophysical Journal International},
volume={157},
number={3},
pages={975--987},
year={2004},
publisher={Oxford University Press}
}
@article{shin2001efficient,
title={Efficient calculation of a partial-derivative wavefield using reciprocity for seismic imaging and inversion},
author={Shin, Changsoo and Yoon, Kwangjin and Marfurt, Kurt J and Park, Keunpil and Yang, Dongwoo and Lim, Harry Y and Chung, Seunghwan and Shin, Sungryul},
journal={Geophysics},
volume={66},
number={6},
pages={1856--1863},
year={2001},
publisher={Society of Exploration Geophysicists}
}
@article{plessix2004frequency,
title={Frequency-domain finite-difference amplitude-preserving migration},
author={Plessix, R-E and Mulder, WA},
journal={Geophysical Journal International},
volume={157},
number={3},
pages={975--987},
year={2004},
publisher={Oxford University Press}
}
@book{aki:80,
AUTHOR = {Aki, K. and Richards, P.G. },
......@@ -1384,6 +1384,17 @@ author = {Inazaki, T. and Isahai, H. and Kawamura, S. and Kuruhashi, T. and Haya
SCHOOL = {{K}iel {U}niversity},
YEAR = {2011} }
@article{kohn2012influence,
title={On the influence of model parametrization in elastic full waveform tomography},
author={K{\"o}hn, D and De Nil, D and Kurzmann, A and Przebindowska, A and Bohlen, T},
journal={Geophysical Journal International},
volume={191},
number={1},
pages={325--345},
year={2012},
publisher={Oxford University Press}
}
@article{kolsky:56,
AUTHOR = {Kolsky, H.},
TITLE = {The propagation of stress pulses in viscoelastic solids},
......
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