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Commit 50586504 authored by Stéphane Del Pino's avatar Stéphane Del Pino
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Fix the set of typos reported by Alexiane

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...@@ -56,7 +56,7 @@ of some [[https:github.com/kokkos/kokkos][Kokkos]] mechanisms. ...@@ -56,7 +56,7 @@ of some [[https:github.com/kokkos/kokkos][Kokkos]] mechanisms.
The philosophy of ~pugs~ is to provide "simple" numerical tools that are The philosophy of ~pugs~ is to provide "simple" numerical tools that are
assembled together through a high-level language (a DSL[fn:DSL-def] assembled together through a high-level language (a DSL[fn:DSL-def]
close to the mathematics) to build more complex solvers. This approach close to the mathematics) to build more complex solvers. This approach
is inspired by the success of [[http://freefem.org][FreeFEM]], which use a similar approach. is inspired by the success of [[http://freefem.org][FreeFEM]], which uses a similar approach.
Before detailing the leading concepts and choices that we have made to Before detailing the leading concepts and choices that we have made to
develop ~pugs~, we give a simple example. develop ~pugs~, we give a simple example.
...@@ -118,7 +118,7 @@ The example is quite easy to read. ...@@ -118,7 +118,7 @@ The example is quite easy to read.
allow* the modifications of values of variables of *non-basic* allow* the modifications of values of variables of *non-basic*
types. This is discussed in the section [[high-level-types]]. types. This is discussed in the section [[high-level-types]].
- Finally, the last block consists in saving the obtained mesh in a - Finally, the last block consists in saving the obtained mesh in a
~gnuplot~ file. The result is shown on Figure [[fig:intro-example]]. ~gnuplot~ file. The result is shown in Figure [[fig:intro-example]].
#+NAME: intro-transform-mesh-img #+NAME: intro-transform-mesh-img
#+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/intro-transform-mesh.png") #+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/intro-transform-mesh.png")
...@@ -144,10 +144,10 @@ already be discussed. ...@@ -144,10 +144,10 @@ already be discussed.
- There is no predefined constant in ~pugs~. Here a value is provided - There is no predefined constant in ~pugs~. Here a value is provided
for ~pi~. for ~pi~.
- There are two kinds of variable in ~pugs~: variables of basic types - There are two kinds of variable in ~pugs~: variables of basic types
and variable of high-level types. This two kinds of variable behave and variables of high-level types. This two kinds of variable behave
almost the same but one must know their differences to understand almost the same but one must know their differences to understand
better the underlying mechanisms and choices that we made. See better the underlying mechanisms and choices that we made. See
section [[basic-types]] and [[high-level-types]] for details. sections [[basic-types]] and [[high-level-types]] for details.
- Also, there are two types of functions: *user-defined* functions and - Also, there are two types of functions: *user-defined* functions and
*builtin* functions. In this example, ~theta~, ~M~ and ~T~ are user-defined *builtin* functions. In this example, ~theta~, ~M~ and ~T~ are user-defined
functions. All other functions (~cos~, ~cartesianMesh~,...) are functions. All other functions (~cos~, ~cartesianMesh~,...) are
...@@ -168,9 +168,9 @@ calculations,... ...@@ -168,9 +168,9 @@ calculations,...
*** A C++ toolbox driven by a user friendly language *** A C++ toolbox driven by a user friendly language
Numerical simulation packages are software of a particular Numerical simulation packages are softwares of a particular
kind. Generally, in order to run a calculation, one has to define a kind. Generally, in order to run a calculation, one has to define a
set of data and parameters. This can simply be definition of a set of data and parameters. This can simply be the definition of a
discretization parameter such as the mesh size. One can also specify discretization parameter such as the mesh size. One can also specify
boundary conditions, equations of state, source terms for a specific boundary conditions, equations of state, source terms for a specific
model. Choosing a numerical method or even more, setting the model model. Choosing a numerical method or even more, setting the model
...@@ -195,11 +195,11 @@ There are lots of reasons not to use data files. By data file, we ...@@ -195,11 +195,11 @@ There are lots of reasons not to use data files. By data file, we
refer to a set of options that describe physical models, numerical refer to a set of options that describe physical models, numerical
methods or their settings. methods or their settings.
- Data files are not flexible. This implies in then one hand that - Data files are not flexible. This implies in the one hand that
application scenarios must be known somehow precisely to reflect application scenarios must be known somehow precisely to reflect
possible option combinations and in the other hand even defining a possible option combinations and in the other hand even defining a
specific initial data may require the creation of a new option and specific initial data may require the creation of a new option and
the associated code (in ~C++~ for instance). \\ its associated code (in ~C++~ for instance). \\
Usually, the last point is addressed by adding a local interpreter Usually, the last point is addressed by adding a local interpreter
to evaluate user functions. to evaluate user functions.
- Data files may contain irrelevant information. Actually, it is quite - Data files may contain irrelevant information. Actually, it is quite
...@@ -226,7 +226,7 @@ to write the code can be tempting. It has the advantage that no ...@@ -226,7 +226,7 @@ to write the code can be tempting. It has the advantage that no
particular treatment is necessary to build a parser (to read data particular treatment is necessary to build a parser (to read data
files or a script), but it presents several drawbacks. files or a script), but it presents several drawbacks.
- The first one is probably that it allows to much freedom. While - The first one is probably that it allows too much freedom. While
defining the model and numerical options, the user has generally defining the model and numerical options, the user has generally
access to the whole code and can change almost everything, even access to the whole code and can change almost everything, even
things that should not be changed. things that should not be changed.
...@@ -238,7 +238,7 @@ files or a script), but it presents several drawbacks. ...@@ -238,7 +238,7 @@ files or a script), but it presents several drawbacks.
coupled physics. coupled physics.
- Another difficulty is related to the fact that code's internal API - Another difficulty is related to the fact that code's internal API
is likely to change permanently in a research code. Thus valid is likely to change permanently in a research code. Thus valid
constructions or setting may become rapidly obsolete. In other constructions or settings may become rapidly obsolete. In other
words keeping up to date embedded "data file" might be difficult. words keeping up to date embedded "data file" might be difficult.
- Finally it requires recompilation of pieces of code (which can be - Finally it requires recompilation of pieces of code (which can be
large in some cases) even if one is just changing a simple large in some cases) even if one is just changing a simple
...@@ -294,7 +294,7 @@ writing of new methods. ...@@ -294,7 +294,7 @@ writing of new methods.
*new functions in the language*. Moreover, if a new method is close to *new functions in the language*. Moreover, if a new method is close to
an existing one, it is generally *better* to use completely new an existing one, it is generally *better* to use completely new
underlying ~C++~ code than to patch existing methods. Starting from a underlying ~C++~ code than to patch existing methods. Starting from a
*copy* of the existing code ~C++~ is *encouraged* for developments. This *copy* of the existing ~C++~ code is *encouraged* for developments. This
may sound weird since classical development guidelines encourage may sound weird since classical development guidelines encourage
inheritance or early redesign. Actually, this policy is the result inheritance or early redesign. Actually, this policy is the result
of the following discussion. of the following discussion.
...@@ -306,7 +306,7 @@ writing of new methods. ...@@ -306,7 +306,7 @@ writing of new methods.
corrections. corrections.
- It is much more difficult to introduce bugs in existing methods, - It is much more difficult to introduce bugs in existing methods,
since previously validated methods are unchanged! since previously validated methods are unchanged!
- For the same reason, existing methods performances are naturally - For the same reason, existing method performances are naturally
unchanged by new developments. unchanged by new developments.
- Also, when comparing methods, it is better to compare to the - Also, when comparing methods, it is better to compare to the
original existing code. original existing code.
...@@ -338,7 +338,7 @@ writing of new methods. ...@@ -338,7 +338,7 @@ writing of new methods.
***** Why not python or any other scripting language? ***** Why not python or any other scripting language?
As it was already pointed out above, general purpose languages offer As it was already pointed out above, general purpose languages offer
to much freedom: it is not easy to protect data. For instance in the too much freedom: it is not easy to protect data. For instance in the
~pugs~ DSL, non basic variables are constant (see paragraph ~pugs~ DSL, non basic variables are constant (see paragraph
[[high-level-types]]). It is important since it prevents the user from [[high-level-types]]). It is important since it prevents the user from
modifying data in inconsistent ways. Also, one must keep in mind that modifying data in inconsistent ways. Also, one must keep in mind that
...@@ -2775,7 +2775,7 @@ gmsh -2 hybrid-2d.geo -format msh2 ...@@ -2775,7 +2775,7 @@ gmsh -2 hybrid-2d.geo -format msh2
write_mesh(gnuplot_writer("hybrid-2d"),m); write_mesh(gnuplot_writer("hybrid-2d"),m);
#+END_SRC #+END_SRC
The ~mesh~ is represented on Figure [[fig:gmsh-hybrid-2d]]. The ~mesh~ is represented in Figure [[fig:gmsh-hybrid-2d]].
#+NAME: gmsh-hybrid-2d-img #+NAME: gmsh-hybrid-2d-img
#+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/gmsh-hybrid-2d.png") #+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/gmsh-hybrid-2d.png")
...@@ -2810,7 +2810,7 @@ This function creates the diamond dual ~mesh~ of a primal ~mesh~. ...@@ -2810,7 +2810,7 @@ This function creates the diamond dual ~mesh~ of a primal ~mesh~.
The diamond dual mesh is defined by joining the nodes of the faces to The diamond dual mesh is defined by joining the nodes of the faces to
the center of the adjacent cells of the primal mesh. the center of the adjacent cells of the primal mesh.
The ~mesh~ is represented on Figure [[fig:gmsh-hybrid-2d]]. The ~mesh~ is represented in Figure [[fig:gmsh-hybrid-2d]].
#+NAME: diamond-dual-img #+NAME: diamond-dual-img
#+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/diamond-dual.png") #+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/diamond-dual.png")
...@@ -2863,7 +2863,7 @@ This function creates the median dual ~mesh~ of a primal ~mesh~. ...@@ -2863,7 +2863,7 @@ This function creates the median dual ~mesh~ of a primal ~mesh~.
The median dual mesh is defined by joining the centers of the faces to The median dual mesh is defined by joining the centers of the faces to
the centers of the adjacent cells of the primal mesh. the centers of the adjacent cells of the primal mesh.
The ~mesh~ is represented on Figure [[fig:gmsh-hybrid-2d]]. The ~mesh~ is represented in Figure [[fig:gmsh-hybrid-2d]].
#+NAME: median-dual-img #+NAME: median-dual-img
#+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/median-dual.png") #+BEGIN_SRC gnuplot :exports results :file (substitute-in-file-name "${PUGS_SOURCE_DIR}/doc/median-dual.png")
...@@ -2924,7 +2924,7 @@ that in ~pugs~ internals, there is only one connectivity object for ...@@ -2924,7 +2924,7 @@ that in ~pugs~ internals, there is only one connectivity object for
these two meshes. these two meshes.
#+END_note #+END_note
The result of the previous script is given on Figure The result of the previous script is given in Figure
[[fig:transformed]]. They all share the same connectivity in memory. [[fig:transformed]]. They all share the same connectivity in memory.
#+NAME: transformed-img #+NAME: transformed-img
...@@ -2990,7 +2990,7 @@ write_mesh(gnuplot_writer("relax_example_m2"), m2); ...@@ -2990,7 +2990,7 @@ write_mesh(gnuplot_writer("relax_example_m2"), m2);
#+END_SRC #+END_SRC
In this example, the relaxation parameter is set to $\theta=0.3$. The In this example, the relaxation parameter is set to $\theta=0.3$. The
different meshes produced in this example are displayed on Figure different meshes produced in this example are displayed in Figure
[[fig:relax]]. [[fig:relax]].
#+NAME: relax-img #+NAME: relax-img
...@@ -3538,7 +3538,7 @@ In this example, the ~mesh~ provided in the file ~zones-1d.msh~ is a 1d ...@@ -3538,7 +3538,7 @@ In this example, the ~mesh~ provided in the file ~zones-1d.msh~ is a 1d
~mesh~ of $]-1,1[$ made of $200$ cells that is partitioned into 3 ~mesh~ of $]-1,1[$ made of $200$ cells that is partitioned into 3
connected subdomains. The zones corresponding to these 3 subdomains connected subdomains. The zones corresponding to these 3 subdomains
are named ~LEFT~ for $]-1,-0.3[$, ~MIDDLE~ for $]-0.3, 0.3[$ and ~RIGHT~ for are named ~LEFT~ for $]-1,-0.3[$, ~MIDDLE~ for $]-0.3, 0.3[$ and ~RIGHT~ for
$]0.3,1[$. The result is displayed on Figure [[fig:zone-integrate-1d]]. In $]0.3,1[$. The result is displayed in Figure [[fig:zone-integrate-1d]]. In
the ~MIDDLE~ region, cell values are set to 0. the ~MIDDLE~ region, cell values are set to 0.
#+NAME: zone-integrate-1d-img #+NAME: zone-integrate-1d-img
...@@ -3632,7 +3632,7 @@ Let us consider a simple example ...@@ -3632,7 +3632,7 @@ Let us consider a simple example
write_mesh(gnuplot_writer("random-mesh"), m); write_mesh(gnuplot_writer("random-mesh"), m);
#+END_SRC #+END_SRC
Running this script one gets the ~mesh~ displayed on Figure Running this script one gets the ~mesh~ displayed in Figure
[[fig:random-mesh]]. To reduce the vertices displacement, one can use the [[fig:random-mesh]]. To reduce the vertices displacement, one can use the
~relax~ function, see section [[relax-function]]. ~relax~ function, see section [[relax-function]].
...@@ -3692,7 +3692,7 @@ displacement is allowed for $x<2y$. ...@@ -3692,7 +3692,7 @@ displacement is allowed for $x<2y$.
write_mesh(gnuplot_writer("random-mesh-chi"), m); write_mesh(gnuplot_writer("random-mesh-chi"), m);
#+END_SRC #+END_SRC
Running this script one gets the ~mesh~ displayed on Figure Running this script one gets the ~mesh~ displayed in Figure
[[fig:random-mesh-chi]]. [[fig:random-mesh-chi]].
#+NAME: random-mesh-chi-img #+NAME: random-mesh-chi-img
...@@ -4228,10 +4228,10 @@ Let us illustrate it by an important second example. ...@@ -4228,10 +4228,10 @@ Let us illustrate it by an important second example.
write(gnuplot_writer("writer-example2-2"), output_list); write(gnuplot_writer("writer-example2-2"), output_list);
#+END_SRC #+END_SRC
Running this code produces the gnuplot file displayed on Figure Running this code produces the gnuplot file displayed in Figure
[[fig:writer-example2]]. One sees that ~f~ is the $\mathbb{P}_0(\mathbb{R})$ [[fig:writer-example2]]. One sees that ~f~ is the $\mathbb{P}_0(\mathbb{R})$
function corresponding to the function $x \to x$ and not to the function function corresponding to the function $x \to x$ and not to the function
$x -> |\cos(\pi x)|$. This later function is plotted on Figure $x -> |\cos(\pi x)|$. This later function is plotted in Figure
[[fig:writer-example2-2]] since ~output_list~ is set with the updated value [[fig:writer-example2-2]] since ~output_list~ is set with the updated value
of ~fh~. of ~fh~.
...@@ -4491,7 +4491,7 @@ Figure [[fig:writer-gp-sin]]. ...@@ -4491,7 +4491,7 @@ Figure [[fig:writer-gp-sin]].
plot '<(sed "" $PUGS_SOURCE_DIR/doc/gp_sin.gnu)' lw 2 w lp plot '<(sed "" $PUGS_SOURCE_DIR/doc/gp_sin.gnu)' lw 2 w lp
#+END_SRC #+END_SRC
#+CAPTION: Example of produced gnuplot results from the ~gnuplot_writer~. One can compare ths produced result to the one of the ~gnuplot_1d_writer~ given on Figure [[fig:writer-gp-1d-sin]] #+CAPTION: Example of produced gnuplot results from the ~gnuplot_writer~. One can compare ths produced result to the one of the ~gnuplot_1d_writer~ given in Figure [[fig:writer-gp-1d-sin]]
#+NAME: fig:writer-gp-sin #+NAME: fig:writer-gp-sin
#+ATTR_LATEX: :width 0.38\textwidth #+ATTR_LATEX: :width 0.38\textwidth
#+ATTR_HTML: :width 300px; #+ATTR_HTML: :width 300px;
......
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