[cig-commits] [commit] devel: changed 'examples' to 'EXAMPLES' in the users manual, and removed the obsolete file README_SPECFEM3D_FAULT (cbc549f)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:55:29 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branch : devel
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit cbc549f10dbc1a5bc18e512f70924927feb94330
Author: Dimitri Komatitsch <komatitsch at lma.cnrs-mrs.fr>
Date: Thu Jun 19 01:44:37 2014 +0200
changed 'examples' to 'EXAMPLES' in the users manual, and removed the obsolete file README_SPECFEM3D_FAULT
>---------------------------------------------------------------
cbc549f10dbc1a5bc18e512f70924927feb94330
README_SPECFEM3D_FAULT | 472 -------------------------
doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf | Bin 12651446 -> 12651502 bytes
doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex | 34 +-
3 files changed, 17 insertions(+), 489 deletions(-)
diff --git a/README_SPECFEM3D_FAULT b/README_SPECFEM3D_FAULT
deleted file mode 100644
index ac0cb12..0000000
--- a/README_SPECFEM3D_FAULT
+++ /dev/null
@@ -1,472 +0,0 @@
-
-********************************************************************************
- PLEASE IGNORE THIS FILE IF YOU DO NOT PLAN TO USE THE DYNAMIC FAULT RUPTURE
- CAPABILITIES OF SPECFEM; in that case, just refer to the regular users manual
- in the "doc" directory. If you plan to model dynamic rupture capabilities,
- please refer to the file below but read the users manual first,
- since some of the installation instructions below are probably obsolete.
-********************************************************************************
-
-This file documents modifications done by
-J.-P. Ampuero (Caltech Seismolab), P. Galvez (ETH Zurich) and S. N. Somala (Caltech)
-to model dynamic and kinematic earthquake rupture on non-planar faults.
-
-The main modifications are encapsulated in the following modules:
- decompose_mesh_SCOTCH/fault_scotch.f90
- generate_databases/fault_generate_databases.f90
- specfem3d/fault_solver_dynamic.f90
- specfem3d/fault_solver_kinematic.f90
- specfem3d/fault_solver_common.f90
-We also include examples and Matlab functions for post-processing and visualization.
-
-This is a preliminary version, still under development and testing.
-The features and the format of inputs and outputs are subject to change.
-
-Details about the original package are described in its manual (manual_SPECFEM3D.pdf).
-The current README file describes how to install and run our modified version of the code.
-It is not a replacement for the original manual, which you should read first.
-
-Contents:
-
- Download and updates
- Installation
- Mesh generation with split nodes
- Cubit-python scripts for fault
- Running a simulation
- Examples
- Sign convention for fault quantities
- Input files
- Output files
- Post-processing and visualization
-
-
-
-DOWNLOAD AND UPDATES
----------------------
-
-Please refer to the users manual in the "doc" directory.
-
-
-INSTALLATION
--------------
-
-Please refer to the users manual in the "doc" directory.
-
-
-MESH GENERATION WITH SPLIT NODES
----------------------------------
-
-Faults need to be handled in a special way during mesh generation.
-A fault surface must lie at the interface between elements (the mesh
-must honor the fault surfaces). Moreover, a fault is made of two surfaces
-in contact. Each of these two surfaces needs a separate set of nodes.
-This approach is known as "split nodes".
-To facilitate the mesh generation with split nodes in Cubit, we need to
-separate the two fault surfaces by a small distance, effectively
-creating a tiny opening of the fault. Note that only the interior of
-the fault must be opened, its edges must remain closed (except the edge
-on the free surface). The fault is automatically closed later by SPECFEM3D.
-
-Here is an example Cubit script to generate a mesh with split nodes
-for a buried vertical strike-slip fault:
-
- reset
- brick x 10 y 10 z 10
- webcut volume all with plane xplane
- webcut volume all with plane yplane
- webcut volume all with plane xplane offset 3
- webcut volume all with plane zplane offset 3
- webcut volume all with plane zplane offset -3
- imprint all
- merge all
- unmerge surf 160
- mesh vol all
- set node constraint off
- node in surf 168 move X 0 Y 0.01 Z 0
- node in surf 160 move X 0 Y -0.01 Z 0
-
-The Cubit scripts (*.jou and *.py) in the directory EXAMPLES generate more complicated meshes.
-The *.py files are Python scripts that execute Cubit commands and use the Cubit-python interface
-for SPECFEM3D (see next section). The Python language allows to define and manipulate variables
-to parameterize the mesh. Alternatively, the Python script can call a Cubit journal file (*.jou),
-which looks like the example above. Variables can be defined and manipulated there using the
-APREPRO language built in Cubit.
-
-Note: you should avoid gaps in the list of indices of mesh objects
-with the following Cubit command:
- compress ids hex face edge node')
-(otherwise you will get a segmentation fault during domain decomposition)
-
-
-
-CUBIT-PYTHON SCRIPTS FOR FAULTS
--------------------------------
-
-The mesh generated in Cubit needs to be processed and exported in a format compatible with SPECFEM3D.
-This is achieved in the Python scripts by calling the Python-Cubit interface functions
-defined in the CUBIT directory:
-1. Function "define_bc" (or similar ones) must be called to set up the absorbing boundaries database
-2. Function "fault_input" must be called once for each fault to set up the fault database
-3. Function "cubit2specfem3d.export2SESAME" must be called at the very end of the script to export the
- mesh in a SPECFEM3D format.
-The functions in #1 and #3 are part of the main SPECFEM3D-SESAME distribution and are not documented here.
-We focus here on #2:
-
- Function: fault_input
- Purpose: export a fault mesh database from Cubit to a SPECFEM3D-compliant file
- Syntax: fault_input(id_fault, ids_surf_1, ids_surf_2)
-
- Inputs: id_fault integer index assigned to the fault.
- The user must number all the faults, starting at 1, with unit increments.
- ids_surf_1 list of Cubit ids of all surfaces that form side 1 of the fault
- ids_surf_2 list of Cubit ids of all surfaces that form side 2 of the fault
- The user must decide which side of the fault is side 1.
- This choice affects the sign conventions of fault quantities
- as explained in a later section.
-
- Outputs: file "fault_file_X.dat", where X is the fault id (id_fault).
-
- Example: For the example in the previous section:
-
- A1 = [168]
- A2 = [160]
- faultA = fault_input(1,A1,A2)
-
-
-
-RUNNING A SIMULATION
----------------------
-
-1. Copy the input files to the work directory:
-
- >> cd ~/SPECFEM3D
- >> cp -r EXAMPLES/splay_faults/DATA ./
-
-
-2. Create a mesh with CUBIT:
- (If you have not installed CUBIT yet skip this step and use the mesh files included
- with the examples.)
-
- See the previous section "MESH GENERATION WITH SPLIT NODES" or
- move to the directory CUBIT, open the cubit GUI, run a CUBIT script:
- >> cd ~/SPECFEM3D/CUBIT
- >> cubit
- In CUBIT's menu "Tools", select "Play Journal File" and select a script file,
- for instance:
- EXAMPLES/splay_faults/splay_faults.py
-
- This creates several mesh files in directory CUBIT/MESH/:
- absorbing_surface_file_* (5 files)
- free_surface_file
- materials_file
- mesh_file
- nodes_coords_file
- nummaterial_velocity_file
-
- The CUBIT graphics window should show the mesh (e.g. EXAMPLES/splay_faults/splay_faults.jpg)
- You can zoom, pan or rotate using mouse gestures. To look at the block of your interest,
- set "visibility off" in the other blocks.
-
- To run CUBIT from different working directories it is convenient to
- include the path to SPECFEM3D/CUBIT in an environment variable PYTHONPATH
-
-
-3. Partition the mesh with the domain decomposition software SCOTCH.
-
- >> cd ~/SPECFEM3D/decompose_mesh_SCOTH
- >> ./xdecompose_mesh_SCOTCH 'nproc' ../CUBIT/MESH/ ../DATABASES_MPI/
-
- where 'nproc' is the number of processors that you will use in the simulation.
- The second argument (../CUBIT/MESH/ in this example) is the path to the directory
- containing the mesh files that were generated by CUBIT.
- This creates one mesh file proc000***_Database per processor in directory DATABASES_MPI.
- These files can be large, so you might want to place DATABASES_MPI in a scratch disk
- and specify the path accordingly when executing xdecompose_mesh_SCOTCH.
-
-
-4. Edit the file DATA/Par_file: (copy an example here, see III.2)
-
- LOCAL_PATH = should be the path to DATABASES_MPI
- NPROC = number of processors. The same as the number of partitions in SCOTCH (step 3).
-
-
-5. Generate databases:
-
- >> cd ~/SPECFEM3D
- >> mpirun -np nproc ./xgenerate_databases
- or
- >> ./run/run.xdatabases
- or
- >> qsub -l nodes=... -l walltime=... go_mesher
- (the script go_mesher is in utils/)
-
- This creates several binary mesh files for each processor (proc000***.bin)
- in directory DATABASES_MPI.
-
-
-6. If this is the first time you run a simulation with this mesh, set the parameter
- DT (the time step) DATA/Par_file to a value smaller than the
- "Maximum suggested time step" in OUTPUT_FILES/output_mesher.txt.
- Consider the note in section IV about the effect of Kelvin-Voigt damping on the critical timestep.
- Edit the variables NSTEP and NTSTEP_* in DATA/Par_file accordingly.
-
-
-7. Run the solver:
-
- >> mpirun -np nproc ./xspecfem3D
- or
- >>./run/run.xspecfem3d
- or
- >> qsub -l nodes=... -l walltime=... go_solver
- (the script go_solver is in utils/)
-
-
-
-EXAMPLES
----------
-
-The package includes examples, the SCEC benchmark problems:
- + TPV5, a planar vertical strike-slip fault
- + TPV14 and TPV15, vertical strike-slip fault system with a fault branch
- + Splay fault models from Wendt et al. (2009)
-
-To run the examples:
-
-1. Read the documents in the directory EXAMPLES/*/description. They contain a description of the example
- and additional instructions to run it.
-
-2. replace the contents of directory DATA/* by one of the EXAMPLES/tpv*/DATA,
- for instance:
-
- >> cp -r EXAMPLES/tpv5/DATA ./
-
-3. follow all the steps in section II above.
-
-4. Visualize the results with the matlab scripts in the directory EXAMPLES/*/post
-
-
-
-SIGN CONVENTION FOR FAULT QUANTITIES
--------------------------------------
-
-During mesh generation, the fault is defined by two surfaces in contact.
-Let's denote as "side 1" the SECOND surface declared by the user in the call
-to the python function "fault_input", and the FIRST surface as "side 2".
-The local coordinate system on the fault is defined as the right-handed coordinate system
-defined by (strike, dip, normal), where "normal" is the normal vector outgoing
-from side 1, "dip" is parallel to the along-dip direction pointing downwards,
-and "strike" is the horizontal along-strike vector such that the system is right-handed.
-
-Slip is defined as displacement on side 2 minus displacement on side 1.
-In the local coordinate system on the fault,
-positive along-strike slip is right-lateral
-and positive along-dip slip is thrust if side 1 is on the hanging wall
-(normal faulting if side 1 is on the foot wall).
-
-Traction is defined as the stress induced on side 1 by side 2,
-which is the stress tensor times the normal vector outgoing from side 1.
-In the local coordinate system on the fault,
-the normal traction is negative in compression,
-positive along-strike traction generates right-lateral slip
-and positive along-dip traction generates thrust slip if side 1 is on the hanging wall
-(normal faulting if side 1 is on the foot wall).
-
-
-
-INPUT FILES
-------------
-
-DATA/Par_file See SPECFEM3D manual page 17.
- A first version of this file is generated by ./configure.
-
-DATA/STATIONS List of stations outside the fault (see manual page 23).
-
-DATA/Par_file_faults contains parameters of the fault. The first part of this file
- has a strict format:
-
- Line 1: Number of faults (NF)
- Lines 2 to NF+1: Kelvin Voigt damping (in seconds) for each fault. (See below how to set this parameter)
- Line NF+2: Type of simulation (1=dynamic , 2 = kinematic)
- Line NF+3: Number of time steps between updates of the time series outputs at selected
- fault points (see DATA/FAULT_STATIONS), usually a large number (100s or 1000s).
- Note that the sampling rate of the time series is usually much higher.
- Line NF+4: Number of time steps between fault snapshot outputs (quantities at every fault
- point exported at regular times), usually a large number (100s or 1000s).
- Line NF+5: Slip velocity threshold below which frictional healing is set (friction coefficient
- is reset to its static value). If this value is negative healing is disabled.
- Line NF+6: Slip velocity threshold to define the rupture front. Only used for outputs.
-
- The rest of this file is made of namelist input blocks (see "namelist" in a Fortran 9x manual).
- The input for each fault has the following sequence (arguments in [brackets] are optional):
-
- &BEGIN_FAULT /
- &INIT_STRESS S1, S2, S3 [,n1, n2, n3] /
- followed by (n1+n2+n3) &DIST2D blocks
- &SWF mus, mud, dc [, nmus, nmud, ndc] /
- followed by (nmus+nmud+ndc) &DIST2D blocks
-
- The &INIT_STRESS input block sets the initial fault stresses relative to the foot-wall side of
- the fault. Initial stresses are composed of a constant background value possibly overwritten
- in prescribed regions by heterogeneous distributions (see &DIST2D blocks below):
- S1 = constant background value of along-strike shear stress
- (positive in the usual strike direction)
- S2 = constant background value of along-dip shear
- (positive is down-dip, normal faulting)
- S3 = constant background value of normal stress (negative in compresion)
- n1 = number of heterogeneous items for along-strike shear stress [default is 0]
- n2 = number of heterogeneous items for along-dip shear stress [default is 0]
- n3 = number of heterogeneous items for normal stress [default is 0]
-
- The &SWF input block sets the slip-weakening friction parameters of the fault:
- mus = constant background value of static friction coefficient
- mud = constant background value of dynamic friction coefficient
- dc = constant background value of critical slip-weakening distance
- nmus = number of heterogeneous items for static friction coefficient [default is 0]
- nmud = number of heterogeneous items for dynamic friction coefficient [default is 0]
- ndc = number of heterogeneous items for critical slip-weakening distance [default is 0]
-
- The &DIST2D input blocks modify (overwrite) the value of a fault parameter by a heterogeneous
- spatial distribution:
-
- &DIST2D shape='square', val, xc, yc, zc, l /
- sets a constant value (val) within a cube with center (xc,yc,zc) and edge size l.
-
- &DIST2D shape='rectangle', val, xc, yc, zc, lx, ly, lz /
- sets a constant value (val) within a rectangular prism with center (xc,yc,zc)
- and edge sizes (lx,ly,lz).
-
- &DIST2D shape='rectangle-taper', val, valh, xc, yc, zc, lx, ly, lz /
- sets a vertical linear gradient
- within a rectangular prism with center (xc,yc,zc) and edge sizes (lx,ly,lz).
- Values vary linearly as a function of vertical position z
- between value val at z = zc-lz/2 and value valh at z = zc+lz/2 .
-
- &DIST2D shape='circular', val, xc, yc, zc, r /
- sets a constant value (val) within a sphere with center (xc,yc,zc) and radius r.
-
-
-DATA/FAULT_STATIONS Stations in the fault plane.
- Line 1: number of stations.
- Line 2 to end: 5 columns: X, Y, Z (-depth), station name, fault-id
- The fault-id identifies the fault that contains the station.
- It is the index of appearance in the faults list after line 2 of Par_file_faults
-
-
-DATA/input_file.txt Heterogeneous stresses and friction parameters
- Documented in page 10 of EXAMPLES/tpv16.crack/description/TPV16_17_Description_v03.pdf
- To activate this feature, in fault_solver.f90 set
- TPV16 = .true.
- then re-compile the code:
- cd SPECFEM3D
- make
-
-
-Heterogeneous velocity models can be given in a regular grid.
- In the mesh generation Python file (.py) or in the CUBIT journal file (.jou),
- set the material 1st attribute to -1:
- block * attribute index 1 -1
- In module model_tomography.f90:
- Set the parameter TOMO_FILENAME to the name of the file containing the velocity model.
- Re-compile the code:
- cd SPECFEM3D
- make
- The format of the velocity file is:
- Line 1: ORIG_X, ORIG_Y, ORIG_Z, END_X, END_Y, END_Z
- (coordinates of the two extreme corners of the box)
- Line 2: SPACING_X, SPACING_Y, SPACING_Z
- (regular grid spacing in each direction)
- Line 3: NX, NY, NZ
- (number of grid point in each direction)
- Line 4: VP_MIN, VP_MAX, VS_MIN, VS_MAX, RHO_MIN, RHO_MAX
- (min and max values of P wave speed, S wave speed and density)
- Line 5 to 4+NX*NY*NZ:
- x_tomo,y_tomo,z_tomo,vp_tomo,vs_tomo,rho_tomo
- (position, P wave speed, S wave speed, density)
-
-
-Several files are generated automatically by xgenerate_databases in directory DATABASES_MPI
-and do not need to be modified by the user.
-
-
-
-HOW TO SET THE KELVIN-VOIGT DAMPING PARAMETER
-----------------------------------------------
-
-The purpose of the Kelvin-Voigt viscosity in the dynamic fault solver is to damp spurious oscillations
-generated by the fault slip at frequencies that are too high to be resolved by the mesh.
-The viscosity "eta" (in seconds) depends on the size of the elements on the fault.
-Here is how to set it:
-
-1. Determine the average linear size of the elements on the fault plane, "h_fault".
- Usually this value is prescribed by the user during mesh generation.
- Otherwise it can be found by inspection of the mesh inside the Cubit GUI.
-2. Use the matlab function utils/critical_timestep.m to compute
- dtc_fault = critical_timestep(cp,h_fault,ngll)
- This is the critical time step in an elastic medium for a hypothetical element of cubic shape
- with size equal to h_fault.
-3. Set eta in Par_file_faults to (0.1 to 0.3)*dtc_fault.
- A larger eta damps high-frequencies more aggresively but it might also affect lower frequencies
- and rupture speed.
-
-Viscosity reduces numerical stability: the critical timestep in a simulation with Kelvin-Voigt damping
-needs to be smaller than that in a purely elastic simulation. Here is how to set the time step accordingly:
-4. Run a test simulation without viscosity (eta=0 and only a few time steps)
-5. Look for the "maximum suggested time step" in OUTPUT_FILES/output_mesher.txt
- This is the critical timestep of a purely elastic simulation, "dtc_bulk".
-6. Reset the timestep of the simulation with a Kelvin-Voigt material to a value smaller than
- dtc_kv = eta*( sqrt(1+dtc_bulk^2/eta^2)-1 )
-
-Note that in general dtc_bulk is smaller than dtc_fault,
-because elements off the fault might be smaller or more distorted than element faces on the fault.
-
-
-
-OUTPUT FILES
--------------
-
-Several output files are saved in ~/SPECFEM3D/OUTPUT_FILES:
-
-1. Seismograms for each station on the fault plane given in DATA/FAULT_STATIONS.
- One output file is generated for each station, named after the station. The files
- are ascii and start with a header (22 lines long) followed by a data block with the
- following format, one line per time sample:
-
- # Column #1 = Time (s)
- # Column #2 = horizontal right-lateral slip (m)
- # Column #3 = horizontal right-lateral slip rate (m/s)
- # Column #4 = horizontal right-lateral shear stress (MPa)
- # Column #5 = vertical up-dip slip (m)
- # Column #6 = vertical up-dip slip rate (m/s)
- # Column #7 = vertical up-dip shear stress (MPa)
- # Column #8 = normal stress (MPa)
-
- The stresses are relative to the footwall side of the fault (this convention controls
- their sign, but not their amplitude). Slip is defined as displacement of the hanging
- wall relative to the footwall.
-
-2. Seismograms at stations in the bulk (out of the fault plane) given in DATA/STATIONS.
- The name and format of these output files is described in page 51 of the manual.
-
-3. Rupture time files are named Rupture_time_FAULT-id. One file is generated for each fault.
- The files are ascii and start with a header (12 lines long) followed by a data block
- with the following format, one line per fault node:
- # Column #1 = horizontal coordinate, distance along strike (m)
- # Column #2 = vertical coordinate, distance down-dip (m)
- # Column #3 = rupture time (s)
-
-4. Fault quantities (slip, slip rate, stresses, etc) at regular times are stored
- in binary data files called Snapshot#it#.bin, where #it# is the timestep number.
- These can be read in Matlab with the function Post-processing/FSEM3D_snapshot.m
-
-
-POST-PROCESSING AND VISUALIZATION
-----------------------------------
-
-Some Matlab functions for post-processing and visualization are included in directory
-Post-processing. The functions are internally documented (see their matlab help).
-
- FSEM3D_snapshot reads a fault data snapshot
-
-The directories EXAMPLES/*/post contain additional Matlab scripts to generate figures
-specific to each example.
-
diff --git a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf
index e8d270f..297dbfc 100644
Binary files a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf and b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf differ
diff --git a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
index ed116be..9e4ec5f 100644
--- a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
+++ b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.tex
@@ -764,7 +764,7 @@ and
number of cores.
\end{description}
Examples are provided in the SPECFEM3D Cartesian package in the subdirectory
-\texttt{examples/}. We strongly encourage you to contribute your own
+\texttt{EXAMPLES/}. We strongly encourage you to contribute your own
example to this package by contacting the CIG Computational Seismology
Mailing List \urlwithparentheses{cig-seismo at geodynamics.org}.
@@ -775,7 +775,7 @@ For the installation and handling of the CUBIT meshing tool suite,
please refer to the CUBIT user manual and documentation. In order
to give you a basic understanding of how to use CUBIT for our purposes,
examples are provided in the SPECFEM3D Cartesian package in the subdirectory
-\texttt{examples/}:
+\texttt{EXAMPLES/}:
\begin{description}
\item [{\texttt{homogeneous\_halfspace}}] Creates a single block model
and assigns elastic material parameters.
@@ -797,7 +797,7 @@ file during the databases creation by \texttt{xgenerate\_databases}.
\includegraphics[width=0.45\textwidth]{figures/example-water} \includegraphics[width=0.45\textwidth]{figures/example-tomo}
\par\end{centering}
-\caption{Screenshots of the CUBIT examples provided in subdirectory \texttt{examples/}:
+\caption{Screenshots of the CUBIT examples provided in subdirectory \texttt{EXAMPLES/}:
homogeneous halfspace (top-left), layered halfspace (top-right), water
layered halfspace (bottom-left) and tomographic model (bottom-right).}
@@ -814,7 +814,7 @@ contacting the CIG Computational Seismology Mailing List \urlwithparentheses{cig
In some cases, to re-create the meshes for the examples given, just type "claro ./create\_mesh.py" or similar
from the command line ("claro" is the command to run CUBIT from the command line).
-IMPORTANT note: in order to correctly set up GEOCUBIT and run the examples, please read the file called "examples/README";
+IMPORTANT note: in order to correctly set up GEOCUBIT and run the examples, please read the file called "EXAMPLES/README";
in particular, please make sure you correctly set up the Python paths as indicated in that file.
@@ -1386,7 +1386,7 @@ increasing order).
\end{itemize}
At the end of this file, you simply need to set the number of spectral
elements in the vertical direction for each layer. We provide a few
-models in the {\texttt{examples/}} directory. \\
+models in the {\texttt{EXAMPLES/}} directory. \\
Finally, depending on your system, you might need to provide a file
@@ -2218,7 +2218,7 @@ offset by a small distance on either side of the fault}
\end{figure}
-The CUBIT scripts ({*}.jou and {*}.py) in the directory $\mathtt{examples}$
+The CUBIT scripts ({*}.jou and {*}.py) in the directory $\mathtt{EXAMPLES}$
generate more complicated meshes. The {*}.py files are Python scripts
that execute CUBIT commands and use the CUBIT-python interface for
SPECFEM3D (see next section). The Python language allows to define
@@ -2294,10 +2294,10 @@ and
\item Splay fault models from Wendt et al. (2009)\\
\end{itemize}
-Read the documents in the directory $\mathtt{examples/*/description}$.
+Read the documents in the directory $\mathtt{EXAMPLES/*/description}$.
They contain a description of the example and additional instructions
to run it. Visualize the results with the Matlab scripts in the directory
-$\mathtt{examples/*/post}$
+$\mathtt{EXAMPLES/*/post}$
\section{\label{sec:Sign-Convention-for}Sign Convention for Fault Quantities}
@@ -2475,7 +2475,7 @@ the index of appearance in the faults list after line 2 of Par\_file\_faults
parameters are documented in page 10 of
\begin{lyxlist}{00.00.0000}
-\item [{$\mathtt{examples/tpv16/description/TPV16\_17\_Description\_v03.pdf}$}]~
+\item [{$\mathtt{EXAMPLES/tpv16/description/TPV16\_17\_Description\_v03.pdf}$}]~
\end{lyxlist}
To activate this feature, in fault\_solver\_dynamic.f90 set \textbf{TPV16}
@@ -2597,7 +2597,7 @@ in directory $\mathtt{utils}$. The functions are internally documented
\texttt{FSEM3D\_snapshot} reads a fault data snapshot\\
-The directories $\mathtt{examples/*/post}$ contain additional Matlab
+The directories $\mathtt{EXAMPLES/*/post}$ contain additional Matlab
scripts to generate figures specific to each example.
@@ -2953,8 +2953,8 @@ statistics, e.g., the ensemble-averaged noise spectrum. Matlab scripts
are provided to help you to generate the necessary file.
-\texttt{examples/noise\_tomography/NOISE\_TOMOGRAPHY.m} (main program)\\
- \texttt{examples/noise\_tomography/PetersonNoiseModel.m}
+\texttt{EXAMPLES/noise\_tomography/NOISE\_TOMOGRAPHY.m} (main program)\\
+ \texttt{EXAMPLES/noise\_tomography/PetersonNoiseModel.m}
In Matlab, simply run:
@@ -3118,7 +3118,7 @@ given in \citet{trompetal2010}.
\section{Example}
In order to illustrate noise simulations in an easy way, one example
-is provided in \texttt{examples/noise\_tomography/}. See \texttt{examples/noise\_tomography/README}
+is provided in \texttt{EXAMPLES/noise\_tomography/}. See \texttt{EXAMPLES/noise\_tomography/README}
for explanations. \\
@@ -3126,7 +3126,7 @@ Note, however, that they are created for a specific workstation (CLOVER at PRINCETO
which has at least 4 cores with `mpif90' working properly. \\
-If your workstation is suitable, you can run the example in \texttt{examples/noise\_tomography/}
+If your workstation is suitable, you can run the example in \texttt{EXAMPLES/noise\_tomography/}
using:\\
@@ -4491,7 +4491,7 @@ fix: e.g. specify > ./configure FC=gfortran MPIF90=/usr/local/openmpi-gfortran/b
\item [{after executing \texttt{xmeshfem3D} I've got elements with skewness of 81\% percent, what does this mean:}] Look
at the skewness table printed in the \texttt{output\_mesher.txt} file
-after executing \texttt{xmeshfem3D} for the example given in \texttt{examples/meshfem3D\_examples/simple\_model/}:
+after executing \texttt{xmeshfem3D} for the example given in \texttt{EXAMPLES/meshfem3D\_examples/simple\_model/}:
\begin{lyxcode}
...~~\\
@@ -4539,14 +4539,14 @@ are tolerable, above that you should consider remeshing...
To give you an idea why some of the elements are distorted, see the
following figure \ref{fig:mesh.vp} of the mesh you obtain in the
-example \texttt{examples/meshfem3D\_examples/simple\_model/}.
+example \texttt{EXAMPLES/meshfem3D\_examples/simple\_model/}.
\begin{figure}[htbp]
\noindent \begin{centering}
\includegraphics[width=0.9\textwidth]{figures/mesh_vp}
\par\end{centering}
\caption{Paraview visualization using the mesh vtk-files for the example given
-in \texttt{examples/meshfem3D\_examples/simple\_model/}.}
+in \texttt{EXAMPLES/meshfem3D\_examples/simple\_model/}.}
\label{fig:mesh.vp}
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