ran the code beautifier, which now removes accented letters and clean…

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Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt

@@ -10,19 +10,19 @@ Hi Ryan and all,
 I met with Ebru, Emanuele, Frederica, Elliott, and Lion on Thursday
 night at AGU. (We scheduled at the last minute and missed Min and
 Hejun, unfortunately.) Below are some discussion points and questions.
-You already have plenty to discuss anyway, so you don’t have to
+You already have plenty to discuss anyway, so you don't have to
 consider any of these, of course. I cced Emanuele and Frederica,
-though I don’t think they’ll be back by Monday.
+though I don't think they'll be back by Monday.
 
 + It seems like those in our discussion were supportive of the move
-from “legacy” utilities (perl, sac, flexwin, measure_adj) to
+from "legacy" utilities (perl, sac, flexwin, measure_adj) to
 python-based utilities (obspy, pyflex, pyadj). Lion seemed quite
-willing to rewrite measure_adj into python (pyadj) – the multitaper
+willing to rewrite measure_adj into python (pyadj) - the multitaper
 measurement is the key piece, and there are Slepian tapers within
 python libraries, apparently.
 
 + Lion suggested that, in his opinion, the hdf5 file format would be
-optimal for seismograms and adjoint sources. I don’t know the details
+optimal for seismograms and adjoint sources. I don't know the details
 about this. But clearly this is an important decision, since it
 impacts the processing scripts, adjoint sources, the moment tensor
 inversion codes, etc.
@@ -63,10 +63,10 @@ little regarding the adjoint tomography workflow since 2009. But I
 have several projects that will move forward in 2015, lead by me
 (southern California), my student Vipul Silwal (Alaska), my postdoc
 Amir Allam (fault zones up to 5-10 Hz), and Yoshihiro Kaneko (New
-Zealand). I’d like to get these folks on the right track and am open
+Zealand). I'd like to get these folks on the right track and am open
 to trying out new things. Hopefully we can help in this effort.
 
-I’ll talk to you soon. Thanks for including me in the call.
+I'll talk to you soon. Thanks for including me in the call.
 
 Carl
 

Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt

@@ -11,27 +11,27 @@ for 1.
 i kept the routines very similar, some differences occur when reading in mesh files and e.g. where the maximum of the gradient is taken for the update step length. in future, i want to have them also merged into the same set of SPECFEM function library.
 
 for 2.
-good point, the jacobian is used for smoothing of the kernels in the global code, but isn’t currently used for the cartesian code. that is one of the differences that has to be checked again (thus smoothing in the cartesian is based solely on point distance, not volume)
+good point, the jacobian is used for smoothing of the kernels in the global code, but isn't currently used for the cartesian code. that is one of the differences that has to be checked again (thus smoothing in the cartesian is based solely on point distance, not volume)
 
 best wishes,
 daniel
 
 
 > > On 22 Dec 2014, at 5:50 pm, Carl Tape wrote:
-> > 
+> >
 > > Hi all,
-> > 
+> >
 > > Thanks for the call. I wanted to ask two questions.
-> > 
+> >
 > > 1. Daniel, can you briefly describe the differences between the
 > > src/tomograhy/ files in SPECFEM3D and SPECFEM3D_GLOBE? Would it be
 > > simpler to have only one set of files?
-> > 
+> >
 > > 2. Isn't the jacobian of the mesh needed for many of the optimization
 > > operations (dot product, integration, etc)? So my impression is that
 > > you need more than just the kernel name to do something like smoothing
 > > -- you also need the jacobian. Probably this is already in the
 > > scripts, but the discussion in the call did not mention it.
-> > 
+> >
 > > Carl
-> > 
+> >

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_6sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_5sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_elastic_absorbing_CPML_6sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_6sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/DSM_FOR_SPECFEM3D/example_simple_small/station_for_simulation.txt

@@ -0,0 +1,47 @@
+PREFIX=velocity_Z_it
+OUT=./movie
+
+
+declare -i it itmax istep
+
+
+istep=25
+itmax=3500 #30000
+
+
+it=0
+
+while [ "$it" -le "$itmax" ] ; do
+
+   if [ "$it" -lt 1000000 ]; then
+     FICHIER=$PREFIX${it}
+   fi;
+
+   if [ "$it" -lt 100000 ]; then
+    FICHIER=$PREFIX"0"${it}
+   fi;
+
+   if [ "$it" -lt 10000 ]; then
+      FICHIER=$PREFIX"00"${it}
+   fi;
+
+   if [ "$it" -lt 1000 ]; then
+     FICHIER=$PREFIX"000"${it}
+   fi;
+
+   if [ "$it" -lt 100 ]; then
+      FICHIER=$PREFIX"0000"${it}
+   fi;
+
+
+   echo $FICHIER.mesh
+   ./mesh2vtu.pl -i $OUT/$FICHIER.mesh -o $FICHIER.vtu
+   it="$it+$istep"
+
+done;
+
+echo $PREFIX
+
+mv $PREFIX* ./movie_vtu/
+
+

EXAMPLES/Mount_StHelens/convert_lonlat2utm.pl

@@ -93,9 +93,9 @@ sub geo2utm {
 
 #! some extracts about UTM:
 #!
-#! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180°W.
+#! There are 60 longitudinal projection zones numbered 1 to 60 starting at 180 degrees W.
 #! Each of these zones is 6 degrees wide, apart from a few exceptions around Norway and Svalbard.
-#! There are 20 latitudinal zones spanning the latitudes 80°S to 84°N and denoted
+#! There are 20 latitudinal zones spanning the latitudes 80 degrees S to 84 degrees N and denoted
 #! by the letters C to X, ommitting the letter O.
 #! Each of these is 8 degrees south-north, apart from zone X which is 12 degrees south-north.
 #!

EXAMPLES/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/slices.txt

@@ -1,4 +1,4 @@
 0
 1
 2
-3
+3

doc/GJI_2011_paper_about_the_code/paper_GJI_2011_about_the_code.tex

@@ -378,7 +378,7 @@ \subsection{Acoustic domain}\label{subsec:acoustic}
  \bv   =   \rho^{-1}\,\bnabla \partial_t \phi\, ,
  \eequ
 \bequ
-  p  =   \mbox{} - \kappa\, (\bnabla \cdot \bs ) =  \mbox{}- \partial_t^2 \phi\, .	\label{equ:pressure}
+  p  =   \mbox{} - \kappa\, (\bnabla \cdot \bs ) =  \mbox{}- \partial_t^2 \phi\, .  \label{equ:pressure}
 \eequ
 The resulting formulation for pressure $p$ is the reason why we choose to define the potential $\phi$ as in equation (\ref{equ:acousticdisplacement}).
 Since pressure is continuous across first-order discontinuities,
@@ -899,7 +899,7 @@ \section{Conclusions and future work}\label{sec:Conclusions}
 The goal is to harness the power of forward and adjoint modeling tools,
 such as \href{http://www.geodynamics.org/cig/software/specfem3d}{SPECFEM3D},
 together with modern computers to enhance
-the quality of images of EarthÕs interior and the earthquake rupture process.
+the quality of images of Earth's interior and the earthquake rupture process.
 Most traditional tomographic methods utilize traveltime or phase information measured by comparing data with simulations,
 and interpret such measurements based on ray theory or other approximate methods.
 Because of the limitations of these approximate theories, only parts of seismograms can be used,
@@ -963,7 +963,7 @@ \subsection{Pressure waveform misfit kernels}\label{appendix:acoustickernels1}
 The corresponding action in the acoustic case is given by
 \bequ
 \chi = \frac{1}{2} \sum_i \int || p_i^{\mathrm{syn}} - p_i^{\mathrm{obs}} ||^2 \, \mathrm{d}t
-						- \int \int_{\Omega} \lambda\, \left[ \kappa^{-1}\, \partial_t^2 \phi - \bnabla \cdot \left( \rho^{-1} \,\bnabla \phi \right) - f  \right] \,\mathrm{d}^3\bx \, \mathrm{d}t\,,
+            - \int \int_{\Omega} \lambda\, \left[ \kappa^{-1}\, \partial_t^2 \phi - \bnabla \cdot \left( \rho^{-1} \,\bnabla \phi \right) - f  \right] \,\mathrm{d}^3\bx \, \mathrm{d}t\,,
 \eequ
 where $\lambda$ denotes a scalar Lagrange multiplier.
 Setting $ \Delta p_i = p_i^{\mathrm{syn}}  - p_i^{\mathrm{obs}}$

doc/README_gravityPerturbation_bis.txt

@@ -1,13 +1,13 @@
-SPECFEM3D has the capability to compute the perturbations of gravity 
-induced by seismic waves at arbitrary locations above the Earth's surface. 
-The current file documents the usage of this feature and the related code 
+SPECFEM3D has the capability to compute the perturbations of gravity
+induced by seismic waves at arbitrary locations above the Earth's surface.
+The current file documents the usage of this feature and the related code
 modifications.
 
 
 Theory
 ------
 
-The computation of gravity perturbations induced by deformation is based on 
+The computation of gravity perturbations induced by deformation is based on
 equation 4 of:
 J. Harms, R. DeSalvo, S. Dorsher and V. Mandic (2009), "Simulation of underground
 gravity gradients from stochastic seismic fields", Phys. Rev. D, 80, 122001
@@ -16,8 +16,8 @@ gravity gradients from stochastic seismic fields", Phys. Rev. D, 80, 122001
 Enabling gravity computations
 -----------------------------
 
-Gravity perturbation can be computed in any SPECFEM3D simulation by 
-placing a file called "gravity_stations" in the DATA directory, in 
+Gravity perturbation can be computed in any SPECFEM3D simulation by
+placing a file called "gravity_stations" in the DATA directory, in
 addition to the regular input files.
 
 
@@ -26,15 +26,15 @@ Input file format
 
 The format of the "gravity_stations" input file is:
 
-n	dt_gap
-x1	y1	z1
-x2	y2	z2
-...	...	...
-xn	yn 	zn
+n dt_gap
+x1  y1  z1
+x2  y2  z2
+... ... ...
+xn  yn  zn
 
 where
  n : number of stations where gravity time series are needed
- dt_gap : gravity time series are sampled every dt_gap time steps of the 
+ dt_gap : gravity time series are sampled every dt_gap time steps of the
           SPECFEM3D simulation
 
 
@@ -44,22 +44,22 @@ Output file format
 Time series of gravity are output in files named "OUTPUT_FILES/stat*.grav",
 where * is the station index (one file per station). Their format is four
 columns:
-  t  ax  ay  az 
+  t  ax  ay  az
 (time and acceleration along x, y and z, respectively).
 
 
 Code modifications
 ------------------
 
-All the routines related to the gravity perturbation computations are 
-placed in one module called specfem3d/gravity_perturbation.f90. The module 
-provides three public subroutines and a flag. Each subroutine is invoked 
+All the routines related to the gravity perturbation computations are
+placed in one module called specfem3d/gravity_perturbation.f90. The module
+provides three public subroutines and a flag. Each subroutine is invoked
 in one of the following stages:
- 1. during the initialization, 
- 2. during the iterative time stepping scheme and 
+ 1. during the initialization,
+ 2. during the iterative time stepping scheme and
  3. at the output stage.
-In #1 the code checks for the presence of the input file "gravity_stations". 
-If the file exists, the flag "GRAVITY_SIMULATION" is turned on and the 
+In #1 the code checks for the presence of the input file "gravity_stations".
+If the file exists, the flag "GRAVITY_SIMULATION" is turned on and the
 subroutines #2 and #3 are invoked.
 
 

list_for_Zhinan_for_SPECFEM3D_PMLs.txt

@@ -5,7 +5,7 @@ Subject:  Re:Re: PML
 Date:   Wed, 17 Dec 2014 19:41:23 +0800 (CST)
 From:   xiezhinan
 To:   Dimitri Komatitsch
-CC:   Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clément Durochat , Yi Wang , Vadim Monteiller
+CC:   Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clement Durochat , Yi Wang , Vadim Monteiller
 
 Dear Dimitri, dear all,
 
@@ -53,16 +53,16 @@ Zhinan
 
 Subject: Re: PML
 Date: Thu, 22 Jan 2015 01:43:52 +0100
-From: Dimitri Komatitsch <[email protected]>
+From: Dimitri Komatitsch
 Organization: CNRS, Marseille, France
 To: xiezhinan
-CC:   Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clément Durochat , Yi Wang , Vadim Monteiller
+CC:   Jeroen Tromp , Matthieu Lefebvre , Ryan Modrak , Alexis Bottero , Daniel Peter , Mathilde Griveaux , Paul Cristini , Clement Durochat , Yi Wang , Vadim Monteiller
 
 Dear Zhinan, dear all,
 
-I would add one more thing to the list (we discussed it in the Skype 
-call of Dec 22):  committing the fluid-solid boundary kernels that are 
-currently implemented in a local version in your account of the 
+I would add one more thing to the list (we discussed it in the Skype
+call of Dec 22):  committing the fluid-solid boundary kernels that are
+currently implemented in a local version in your account of the
 Marseille supercomputer but not committed to Git yet.
 
 Thanks,
@@ -146,7 +146,7 @@ going on.
 
 Subject: Re: [specfem3d] Runing both PML and attenuation causes error results (#356)
 Date: Tue, 20 Jan 2015 23:58:21 +0100
-From: Dimitri Komatitsch <[email protected]>
+From: Dimitri Komatitsch
 Organization: CNRS, Marseille, France
 To: geodynamics/specfem3d , specfem3d-zhang-ksu
 CC: Zhinan Xie
@@ -239,7 +239,7 @@ Hi Zhinan,
 
 OK, thank you very much for your answer. I suggest we proceed as you
 plan below, i.e. in the next few days you can start cleaning the code
-(please do a git pull because Clément and Yi as well as Vadim have
+(please do a git pull because Clement and Yi as well as Vadim have
 changed many things in the code)  and you can start merging all your
 contributions from the last few months, which are not committed yet.
 Then, as soon as all of this is merged Vadim can have a look at how to
@@ -305,9 +305,9 @@ On 10/28/2014 01:52 PM, xiezhinan wrote:
 3/ add a more flexible function for scale factor and fix one error in create_mass_matrices.f90:
 
 Date:   Tue, 24 Jun 2014 07:15:03 +0800
-From:   谢志南 <xiezhinan1984
+From:   ??? <xiezhinan1984
 To:   Dimitri Komatitsch
-CC:   Clément Durochat, Paul Cristini, Elliott Sales de Andrade
+CC:   Clement Durochat, Paul Cristini, Elliott Sales de Andrade
 
 Dear Dimitri,
 
@@ -396,9 +396,9 @@ Subject: Bermudez (2007)
 Date: Sat, 29 Nov 2014 17:34:46 +0100
 From: Dimitri Komatitsch
 Organization: CNRS, Marseille, France
-To: Zhinan Xie 谢志南,  René Matzen, Paul Cristini
+To: Zhinan Xie ???,  Rene Matzen, Paul Cristini
 
-Hi Zhinan and René,
+Hi Zhinan and Rene,
 
 What do you think of the approach of Bermudez et al (2007) to make the
 damping profile linear and also reach zero on the outer edge of the

src/cuda/check_fields_cuda.cu

@@ -585,8 +585,8 @@ void FC_FUNC_(get_norm_acoustic_from_device,
    }
 
    // cublas function: cublasIsamax
-   //       finds the smallest index of the maximum magnitude element of single 
-   //      precision vector x
+   //       finds the smallest index of the maximum magnitude element of single
+   //      precision vector x
    int incr = 1;
    int imax = 0;
    imax = cublasIsamax(mp->NGLOB_AB,(realw*)mp->d_potential_dot_dot_acoustic, incr);