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anuga_core/documentation/user_manual/anuga_user_manual.tex
r7134 r7135 216 216 regions using symbolic tags. These tags may then be used to set the 217 217 actual boundary conditions and attributes for different regions 218 (e.g. the Manning friction coefficient) for each simulation.218 (e.g.\ the Manning friction coefficient) for each simulation. 219 219 220 220 Most \anuga components are written in the objectoriented programming … … 237 237 \item The mathematical model is the 2D shallow water wave equation. 238 238 As such it cannot resolve vertical convection and consequently not breaking 239 waves or 3D turbulence (e.g. vorticity).240 %\item The surface is assumed to be open, e.g. \anuga cannot model239 waves or 3D turbulence (e.g.\ vorticity). 240 %\item The surface is assumed to be open, e.g.\ \anuga cannot model 241 241 %flow under ceilings or in pipes 242 242 \item All spatial coordinates are assumed to be UTM (meters). As such, … … 467 467 468 468 which specifies that the surface level is set to a height of $0.4$, 469 i.e. 0.4 units (metres) below the zero level.469 i.e.\ 0.4 units (metres) below the zero level. 470 470 471 471 Although it is not necessary for this example, it may be useful to … … 524 524 may cause numerical instabilities propagating into the domain and 525 525 eventually causing \anuga to crash. If this occurs, 526 consider using e.g. a Dirichlet boundary condition with a stage value526 consider using e.g.\ a Dirichlet boundary condition with a stage value 527 527 less than the elevation at the boundary. 528 528 \item \textbf{Dirichlet boundary}\label{def:dirichlet boundary} Specifies … … 1079 1079 \subsubsection{Stage} 1080 1080 1081 The stage is initially set to 0.0 (i.e. Mean Sea Level) by the following statements:1081 The stage is initially set to 0.0 (i.e.\ Mean Sea Level) by the following statements: 1082 1082 1083 1083 \begin{verbatim} … … 1660 1660 1661 1661 \code{segments} is a list of segments. Each segment is defined by the start and end 1662 of the line by its point index, e.g. use \code{segments = [[0,1],[1,2]]} to make a1662 of the line by its point index, e.g.\ use \code{segments = [[0,1],[1,2]]} to make a 1663 1663 polyline between points 0, 1 and 2. 1664 1664 … … 1726 1726 1727 1727 \code{raw_boundary}, if \code{True} instructs the function to return the raw 1728 boundary, i.e. the regular edges of the alpha shape.1728 boundary, i.e.\ the regular edges of the alpha shape. 1729 1729 1730 1730 \code{remove_holes}, if \code{True} enables a filter to remove small holes … … 1735 1735 1736 1736 \code{expand_pinch}, if \code{True} tests for pinchoff and corrects 1737 (i.e. a boundary vertex with more than two edges).1737 (i.e.\ a boundary vertex with more than two edges). 1738 1738 \end{methoddesc} 1739 1739 … … 1874 1874 1875 1875 Default value is $10^{3}$ metre, but by setting this to a greater value, 1876 e.g. for large scale simulations, the computation time can be1876 e.g.\ for large scale simulations, the computation time can be 1877 1877 significantly reduced. 1878 1878 \end{methoddesc} … … 1946 1946 \end{itemize} 1947 1947 1948 Note that when model data in the SWW file are averaged (i.e. not stored uniquely),1948 Note that when model data in the SWW file are averaged (i.e.\ not stored uniquely), 1949 1949 then there will most likely be a small discrepancy between values extracted from the SWW 1950 1950 file and the same data stored in the model domain. This must be borne in mind when comparing … … 1958 1958 Return x,y coordinates of all nodes in the domain mesh. The nodes are ordered 1959 1959 in an \code{Nx2} array where N is the number of nodes. This is the same format 1960 they were provided in the constructor i.e. without any duplication.1960 they were provided in the constructor i.e.\ without any duplication. 1961 1961 1962 1962 \code{absolute} is a boolean which determines whether coordinates … … 2014 2014 2015 2015 This version of the mesh is useful for storing meshes with 2016 discontinuities at each node and is e.g. used for storing2016 discontinuities at each node and is e.g.\ used for storing 2017 2017 data in SWW files. 2018 2018 … … 2068 2068 the quantity in question 2069 2069 \item a list of numbers or a numeric array ordered the same way as the mesh vertices 2070 \item a function (e.g. see the samples introduced in Chapter 2)2070 \item a function (e.g.\ see the samples introduced in Chapter 2) 2071 2071 \item an expression composed of other quantities and numbers, arrays, lists (for 2072 2072 example, a linear combination of quantities, such as … … 2219 2219 2220 2220 The underlying algorithm used is as follows:\\ 2221 Given a time series (i.e. a series of values associated with2221 Given a time series (i.e.\ a series of values associated with 2222 2222 different times), whose values are either just numbers, a set of 2223 2223 numbers defined at the vertices of a triangular mesh (such as those … … 2257 2257 Module: \module{fit_interpolate.interpolate} 2258 2258 2259 Given a time series (i.e. a series of values associated with2259 Given a time series (i.e.\ a series of values associated with 2260 2260 different times) whose values are either just numbers or a set of 2261 2261 numbers defined at the vertices of a triangular mesh (such as those … … 2495 2495 2496 2496 This is a general class to modify any quantity according to a given rate of change. 2497 Other specific forcing terms are based on this class but it can be used by itself as well (e.g. to modify momentum).2497 Other specific forcing terms are based on this class but it can be used by itself as well (e.g.\ to modify momentum). 2498 2498 2499 2499 \code{domain} is the domain being evolved. … … 2504 2504 function of time. Positive values indicate increases, negative values indicate decreases. 2505 2505 The parameter \code{rate} can be \code{None} at initialisation but must be specified 2506 before a forcing term is applied (i.e. simulation has started).2507 The default value is 0.0  i.e. no forcing.2506 before a forcing term is applied (i.e.\ simulation has started). 2507 The default value is 0.0  i.e.\ no forcing. 2508 2508 2509 2509 \code{center} and \code{ radius} optionally restrict forcing to a circle with given center and radius. … … 3191 3191 \begin{tabular}{ll} 3192 3192 ASC, PRJ & Digital elevation models (gridded)\\ 3193 NC & Model outputs for use as boundary conditions (e.g. from MOST)3193 NC & Model outputs for use as boundary conditions (e.g.\ from MOST) 3194 3194 \end{tabular} 3195 3195 … … 3284 3284 3285 3285 A mesh file can also contain a georeference, which describes an 3286 offset to be applied to $x$ and $y$ values  e.g. to the vertices.3286 offset to be applied to $x$ and $y$ values  e.g.\ to the vertices. 3287 3287 3288 3288 \subsection{Formats for Storing Arbitrary Points and Attributes} … … 3372 3372 The $easting$ and $northing$ values are used if the user wishes to determine the output 3373 3373 within a specified rectangular area. The \code{reduction} input refers to a function 3374 to reduce the quantities over all time step of the SWW file, e.g. maximum.3374 to reduce the quantities over all time step of the SWW file, e.g.\ maximum. 3375 3375 \end{funcdesc} 3376 3376 … … 3395 3395 of points to select along with their longitudes and latitudes. This permutation will also be 3396 3396 stored in the STS file. If absent, all points are taken and the permutation will be trivial, 3397 i.e. $0, 1, \ldots, N1$, where $N$ is the total number of points stored.3397 i.e.\ $0, 1, \ldots, N1$, where $N$ is the total number of points stored. 3398 3398 \end{funcdesc} 3399 3399 … … 3423 3423 Optional parameter \code{floor_height} is the height of each building story. 3424 3424 3425 These can e.g. be converted to a \code{Polygon_function} for use with \code{add_quantity}3425 These can e.g.\ be converted to a \code{Polygon_function} for use with \code{add_quantity} 3426 3426 as shown on page \pageref{add quantity}. 3427 3427 \end{funcdesc} … … 3787 3787 Physical model time cannot be earlier than 1 Jan 1970 00:00:00. 3788 3788 If one wished to recreate scenarios prior to that date it must be done 3789 using some relative time (e.g. 0).3789 using some relative time (e.g.\ 0). 3790 3790 3791 3791 The \anuga domain has an attribute \code{starttime} which is used in cases where the … … 3817 3817 Throughout the \anuga interface, functions have optional boolean arguments \code{absolute} which controls 3818 3818 whether spatial data received is using the internal representation (\code{absolute=False}) or the 3819 user coordinate set (\code{absolute=True}). See e.g. \code{get_vertex_coordinates()} on \pageref{pg:get vertex coordinates}.3819 user coordinate set (\code{absolute=True}). See e.g.\ \code{get_vertex_coordinates()} on \pageref{pg:get vertex coordinates}. 3820 3820 3821 3821 DEMs, meshes and boundary conditions can have different origins. However, the internal representation in \anuga … … 4228 4228 4229 4229 The function returns a list containing the minimum and maximum of the points in all the 4230 input polygons, i.e. \code{[$x_{min}$, $x_{max}$, $y_{min}$, $y_{max}$]}.4230 input polygons, i.e.\ \code{[$x_{min}$, $x_{max}$, $y_{min}$, $y_{max}$]}. 4231 4231 \end{funcdesc} 4232 4232 … … 4285 4285 4286 4286 Note that the \code{Geospatial_data} object currently reads entire datasets 4287 into memory i.e. no memomry blocking takes place.4287 into memory i.e.\ no memomry blocking takes place. 4288 4288 For this we refer to the \code{set_quantity()} method which will read PTS and CSV 4289 4289 files into \anuga using memory blocking allowing large files to be used. … … 4519 4519 4520 4520 NOTE: The function will not work if the \code{data_file} extent is greater than the 4521 \code{boundary_poly} polygon or any of the boundaries, e.g. \code{north_boundary}, etc.4521 \code{boundary_poly} polygon or any of the boundaries, e.g.\ \code{north_boundary}, etc. 4522 4522 \end{methoddesc} 4523 4523 … … 4600 4600 4601 4601 \code{raw_boundary} sets the type to $raw$ if \code{True}, 4602 i.e. the regular edges of the alpha shape.4602 i.e.\ the regular edges of the alpha shape. 4603 4603 4604 4604 \code{remove_holes}, if \code{True} removes small holes ('small' is defined by
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