Fix the access to layers in a nc cube file that has more that one variable.

doc/rst/source/modules-classic.rst

@@ -145,6 +145,7 @@ All modules are requested via a call to the :doc:`gmt` program.
     supplements/mgd77/mgd77path
     supplements/mgd77/mgd77sniffer
     supplements/mgd77/mgd77track-classic
+    supplements/nswing/nswing
     supplements/potential/gmtflexure
     supplements/potential/gmtgravmag3d
     supplements/potential/gravfft
@@ -315,6 +316,7 @@ Supplemental Modules
     - :doc:`/supplements/mgd77/mgd77path`
     - :doc:`/supplements/mgd77/mgd77sniffer`
     - :doc:`/supplements/mgd77/mgd77track-classic`
+    - :doc:`nswing </supplements/nswing/nswing>`
     - :doc:`gmtflexure </supplements/potential/gmtflexure>`
     - :doc:`gmtgravmag3d </supplements/potential/gmtgravmag3d>`
     - :doc:`/supplements/potential/gravfft`
@@ -675,6 +677,13 @@ MGD77
 | :doc:`/supplements/mgd77/mgd77track-classic`  | |mgd77track_purpose|   |
 +-----------------------------------------------+------------------------+
 
+nswing
+------
+
++-----------------------------------------------+------------------------+
+| :doc:`nswing </supplements/nswing/nswing>`    | |nswing_purpose|       |
++-----------------------------------------------+------------------------+
+
 potential
 ---------
 

doc/rst/source/modules.rst

@@ -143,6 +143,7 @@ All modules are requested via a call to the :doc:`gmt` program.
    supplements/mgd77/mgd77path
    supplements/mgd77/mgd77sniffer
    supplements/mgd77/mgd77track
+   supplements/nswing/nswing
    supplements/potential/gmtflexure
    supplements/potential/gmtgravmag3d
    supplements/potential/gravfft
@@ -323,6 +324,7 @@ Supplemental Modules
     - :doc:`/supplements/mgd77/mgd77path`
     - :doc:`/supplements/mgd77/mgd77sniffer`
     - :doc:`/supplements/mgd77/mgd77track`
+    - :doc:`/supplements/nswing/nswing`
     - :doc:`/supplements/potential/gmtflexure`
     - :doc:`/supplements/potential/gravfft`
     - :doc:`/supplements/potential/gmtgravmag3d`
@@ -703,6 +705,13 @@ MGD77
 | :doc:`/supplements/mgd77/mgd77track`     | |mgd77track_purpose|   |
 +------------------------------------------+------------------------+
 
+nswing
+------
+
++------------------------------------------+------------------------+
+| :doc:`/supplements/nswing/nswing`        | |nswing_purpose|       |
++------------------------------------------+------------------------+
+
 potential
 ---------
 

doc/rst/source/supplements/module_supplements_purpose.rst_

@@ -106,6 +106,8 @@
 
 .. |rotsmoother_purpose| replace:: Get mean rotations and covariance matrices from set of finite rotations
 
+.. |nswing_purpose| replace:: A tsunami maker
+
 .. |grdbarb_purpose| replace:: Plot wind barb field from two component grids
 
 .. |barb_purpose| replace:: Plot wind barbs in 2-D and 3-D

doc/rst/source/supplements/nswing/nswing.rst

@@ -0,0 +1,303 @@
+.. index:: ! nswing
+.. include:: ../module_supplements_purpose.rst_
+
+******
+nswing
+******
+
+.. only:: not man
+
+    |nswing_purpose|
+
+Synopsis
+--------
+
+.. include:: ../../common_SYN_OPTs.rst_
+
+**nswing**
+*bathy.grd* *initial.grd*
+**-t**\ *dt*
+[ **-1**\ *bat_lev1* ] [ **-2**\ *bat_lev2* ] [ **-3**\ *...* ]
+[ |-A|\ *fname.sww* ]
+[ |-C| ]
+[ |-D| ]
+[ |-E|\ [**p**][**m**][**+a**][,\ *decim*] ]
+[ |-F|\ *x_epic/y_epic/dip/strike/rake/slip/length/width/topDepth* ]
+[ |-F|\ **k**\ [**c**]\ *w/e/s/n* ]
+[ |-G|\ *name*\ [**+m**],\ *int* ]
+[ |-H|\ [*momentM,momentN*\ [,\ *t*]] ]
+[ |-P|\ *time_jump*\ [**+t**\ *run_time_jump*] ]
+[ |-L|\ [*name1,name2*] ]
+[ |-M|\ [**-**\|\ **+**\ [*maskname*]] ]
+[ |-N|\ *n_cycles* ]
+[ |-O|\ *BCfile* ]
+[ |-Q|\ *z_offset* ]
+[ |SYN_OPT-R| ]
+[ |-S|\ [**x**\|\ **y**\|\ **n**][**+m**][**+s**][**+a**] ]
+[ |-T|\ *mareg*\|\ *x/y*\ [**+o**\ *outmaregs*][**+t**\ *int*] ]
+[ |-X|\ *manning0*\ [,\ *...*] ]
+[ |SYN_OPT-V| ]
+[ |SYN_OPT-f| ]
+[ **-x**\ *n* ]
+[ |SYN_OPT--| ]
+
+|No-spaces|
+
+Description
+-----------
+
+**nswing** is a Non-linear Shallow Water model that propagates a tsunami over a
+bathymetry grid. Starting from a base level bathymetry and an initial-condition
+(source) grid it integrates the shallow water equations in time and writes the
+resulting wave field (water level, velocity, momentum, energy, ...) either as a
+series of GMT grids, a 3D netCDF file, or as time series sampled at virtual
+maregraph (tide-gauge) locations. Nested grids of increasing resolution may be
+used to refine the solution near the coast, and a tsunami source can be generated
+on the fly from Okada fault parameters.
+
+Required Arguments
+------------------
+
+*bathy.grd*
+    The base level bathymetry grid (positive up; negative = below sea level).
+    (See :ref:`Grid File Formats <grd_inout_full>`).
+*initial.grd*
+    The initial-condition (source) grid holding the sea surface displacement at
+    time zero. (See :ref:`Grid File Formats <grd_inout_full>`).
+
+.. _-t:
+
+**-t**\ *dt*
+    Time step (in seconds) for the simulation.
+
+Optional Arguments
+------------------
+
+**-1**\ *bat_lev1* **-2**\ *bat_lev2* ... **-9**\ *bat_lev9*
+    Nested bathymetry grids, one per nesting level. Each level refines the solution inside
+    the area covered by its grid. Warning, the grids must be aligned and have a cell size
+    that is an integer fraction of the previous level. The number of levels is determined
+    by the number of **-1** ... **-9** options given. These grids are not trivial to create,
+    the best way is to use the Mirone TINTOL tool.
+
+.. _-A:
+
+**-A**\ *fname.sww*
+    Save the result as a *.sww* ANUGA-format file.
+
+**-n**\ *base*
+    Basename for MOST triplet files (no extension).
+
+.. _-C:
+
+**-C**
+    Add the Coriolis effect.
+
+.. _-D:
+
+**-D**
+    Write grids with the total water depth. These grids will have wave height
+    on the ocean and water thickness on land.
+
+.. _-E:
+
+**-E**\ [**p**][**m**][**+a**][,\ *decim*]
+    Write grids with energy, or with power if **p** is appended (**-Ep**).
+    Append **m** to save only a single grid holding the max values. This can
+    noticeably slow the run, so optionally append a *decim* decimator factor
+    after the comma (causes aliasing visible under shaded illumination). The
+    file name comes from *name* in **-G** complemented with a *_max*
+    prefix; saving of multiple grids is then disabled.
+
+    With **-G**'s 3D netCDF cube, Energy/Power replaces the sea-surface
+    (*z*) variable unless **+a** is appended, in which case Energy/Power is
+    written as an extra variable alongside *z* (same idea as **-S**'s
+    **+a**).
+
+.. _-F:
+
+**-F**\ *x_epic/y_epic/dip/strike/rake/slip/length/width/topDepth*
+    Okada fault parameters used to build the source. *x_epic*, *y_epic* are the
+    x and y coordinates of the beginning of the fault trace; *dip*, *strike*
+    (azimuth), *rake*, *slip* (m), *length*, *width* and *topDepth* (depth from
+    the sea-bottom) follow. All dimensions must be in km.
+
+    If no bathymetry grid is given, **-F** (or **-Fk**) together with **-R**
+    and **-G** computes the deformation over **-R**'s grid geometry (e.g.
+    **-R**\ *grid*) and writes it straight to **-G**'s name: no simulation is
+    run, so **-t** and **-G**'s saving interval are not needed.
+
+**-F**\ **k**\ *west/east/south/north*
+    Build a prism source with these limits and a height of 1 meter.
+
+    - **-Fkc**\ *x/y/nx/ny* - alternatively give the prism size as centre *x/y*
+      and *nx/ny* half-width cell numbers.
+    - **-Fk**\ *...*\ **/**\ *RxC* - loop over a matrix of size *R* by *C*
+      starting at the Lower Left Corner given by *w/e/s/n*.
+    - **-Fk**\ *...*\ **/**\ *dx*\ [/*dy*] - given the *w/e/s/n* region (pixel
+      registration) loop over the prisms obtained by dividing the region in
+      increments of *dx/dy* (if *dy* is not given, *dy* = *dx*).
+
+    Using **-Fk** sets the output maregraph file to netCDF, unless rows = cols = 1.
+
+.. _-G:
+
+**-G**\ *name*\ [**+m**],\ *int*
+    Save the water level every *int* time steps in a single 3D netCDF file
+    called *name*\ **.nc** (the extension is appended when *name* has none).
+    Append **+m** to instead write each saved step as a separate grid; files
+    are then named *name#*\ **.grd**. When doing nested grids the finest level
+    is the one saved.
+
+.. _-H:
+
+**-H**
+    Write grids with the momentum (velocity times water depth).
+
+    - **-H**\ *fname_momentM,fname_momentN*\ [,\ *t*] - hot start using these
+      moment grids. The optional *t* is the hot-start time (also needs the
+      surface displacement corresponding to the time of these grids).
+
+.. _-P:
+
+**-P**\ *time_jump*\ [**+t**\ *run_time_jump*]
+    Do not write grids or maregraphs for times before *time_jump* (seconds).
+    When doing nested grids, append **+**\ *time* to NOT start nested-grid
+    computations before this time has elapsed. Allowed forms: **-P**\ *t1*,
+    **-P+**\ *t2*, **-P**\ *t1*\ **+**\ *t2* or **-P**\ *t1* **-P+**\ *t2*.
+
+.. _-L:
+
+**-L**
+    Use the linear approximation in the moment conservation equations (faster
+    but less accurate).
+
+    - **-L**\ *in_fname,out_fname* - do Lagrangian tracers, where *in_fname* is
+      the tracers initial-position file and *out_fname* the file to hold the
+      results.
+
+.. _-M:
+
+**-M**\ [**-**\|\ **+**\ [*maskname*]]
+    Write a grid with the max water level (name from *name* in **-G**, *_max*
+    prefix). Append **-** to instead compute the maximum water retreat, written
+    to a mask file (default *long_beach.grd*; append a name after **-** to
+    change it, e.g. **-M-**\ *beach_long.grd*). Append **+** for a mask with the
+    Run In extent (behaves like **-M-**). **-M** may be repeated, e.g.
+    **-M -M- -M+** computes all three. With **-G** the *long* and *short* beach
+    arrays are also saved in the *.nc* file.
+
+.. _-N:
+
+**-N**\ *n_cycles*
+    Number of cycles in the simulation [Default 1010]. Total simulation time is *n_cycles* times the time step *dt*.
+
+.. _-O:
+
+**-O**\ *BCfile*
+    Name of a Boundary Condition ASCII file (experimental).
+
+.. _-Q:
+
+**-Q**\ *z_offset*
+    Apply a vertical offset to ALL bathymetry grids (e.g. to simulate tide).
+
+.. _-R:
+
+.. |Add_-Rgeo| replace:: |Add_-R_auto_table|
+.. include:: ../../explain_-Rgeo.rst_
+
+Output grids only in the sub-region enclosed by *west/east/south/north*.
+
+.. _-S:
+
+**-S**\ [**x**\|\ **y**\|\ **n**][**+m**][**+s**][**+a**]
+    Write grids with the velocity (names get *_U* and *_V* suffixes). Use **x**
+    or **y** to save only one component, or **n** for no velocity grids
+    (maregraphs only). Append **+m** to also write velocity (vx,vy) at maregraph
+    locations (needs **-T**). Append **+s** to write the max speed
+    (|v|) (*_max_speed* suffix). Use the **n** flag to NOT output the U and V
+    components, e.g. **-Sn+s**.
+
+    With **-G**'s 3D netCDF cube, velocity is written as the only variable
+    unless **+a** is appended, in which case the sea-surface (*z*) variable
+    is also written (*z* + velocity).
+
+.. _-T:
+
+**-T**\ *mareg*\|\ *x/y*\ [**+o**\ *outmaregs*][**+t**\ *int*]
+    Save time series (maregraphs) at virtual tide-gauge locations. *mareg* is
+    the file with the (x y) locations of the virtual maregraphs. For a single
+    maregraph the location may be given directly as *x/y* instead of a file
+    name. Append **+o**\ *outmaregs* to set the output file name [Default is
+    *maregs_out.dat*]. A *.dat* extension is added when *outmaregs* has none;
+    use a *.nc* extension to write the maregraphs as a netCDF file instead.
+    Append **+t**\ *int* to save every *int* simulation time steps (set by
+    **-t**) [Default is every time step]. **-T** alone (without **-G**) is
+    allowed and runs a simulation that only outputs the maregraph series.
+
+.. _-X:
+
+**-X**\ *manning0*\ [,\ *manning1*\ [,\ *...*]][**+**\ *depth*]
+    Manning friction coefficients. If only one is provided, use it for all
+    nesting levels; otherwise specify one per level, comma separated. Append
+    **+**\ *depth* to apply Manning only at depths shallower than *depth*
+    (positive up).
+
+.. |Add_-V| replace:: |Add_-V_links|
+.. include:: ../../explain_-V.rst_
+    :start-after: **Syntax**
+    :end-before: **Description**
+
+.. |Add_-f| unicode:: 0x20 .. just an invisible code
+.. include:: ../../explain_-f.rst_
+
+    When **-fg** is not given, **nswing** first checks the grid's own metadata
+    (netCDF degree units) and, failing that, falls back to a coordinate-range
+    heuristic; if either indicates geographic coordinates a warning is issued
+    and **-fg** is set implicitly.
+
+**-x**\ *n*
+    Number of OpenMP threads to use [Default is all available cores]. Results
+    are identical for any number of threads.
+
+.. include:: ../../explain_core.rst_
+
+.. include:: ../../explain_help.rst_
+
+Examples
+--------
+
+To propagate a tsunami over the bathymetry *bathy.grd* given the source
+*source.grd*, using a 5 second time step and saving the water level every 10
+time steps to grids named *wave#.grd*, try::
+
+    gmt nswing bathy.grd source.grd -t5 -Gwave,10
+
+To run the same simulation but generate the source on the fly from Okada fault
+parameters and sample the wave field at the virtual maregraphs listed in
+*gauges.dat* every 5 time steps, try::
+
+    gmt nswing bathy.grd -t5 -F-8/37/12/90/90/3/100/50/10 -Tgauges.dat+t5
+
+To record only the time series at a single virtual tide gauge (no grids at
+all), give its location directly to **-T**::
+
+    gmt nswing bathy.grd source.grd -t5 -T-10.7/37.3
+
+To compute just the Okada co-seismic deformation over the geometry of the grid
+*bathy.grd* (no simulation), try::
+
+    gmt nswing -Rbathy.grd -F94.3/2.8/25/330/90/10/250/65/10 -Gdeform.grd
+
+A less hypothetical example that generates only a few layers in the tsu.nc cube::
+
+    gmt grdcut @earth_relief_02m_g -R-15/-7.5/34/39.5 -Gbat.grd
+    gmt nswing -Rbat.grd -F-12.49593345/35.93634937/25/58.2/90/10/215/53.75/10 -Ginit.grd
+    gmt nswing bat.grd init.grd -t3 -Gtsu,10 -N100 -V
+
+See Also
+--------
+
+:doc:`gmt </gmt>`,
+:doc:`grdinterpolate </grdinterpolate>`

src/CMakeLists.txt

@@ -712,7 +712,7 @@ if (BUILD_SUPPLEMENTS)
 	# supplement directories to be built as supplement libraries
 	# SUPPL_EXTRA_DIRS are directories for custom supplements.
 	# See cmake/ConfigUserAdvancedTemplate.cmake for details.
-	set (GMT_SUPPL_DIRS geodesy gsfml gshhg img mgd77 potential segy seis spotter x2sys windbarbs ${SUPPL_EXTRA_DIRS})
+	set (GMT_SUPPL_DIRS geodesy gsfml gshhg img mgd77 potential segy seis spotter x2sys windbarbs nswing ${SUPPL_EXTRA_DIRS})
 
 	# process supplement directories and collect information for each supplement libraries
 	set (GMT_SUPPL_LIBRARIES) # empty the library list

src/gmt_api.c

@@ -1629,7 +1629,7 @@ GMT_LOCAL char ** gmtapi_process_keys (void *V_API, const char *string, char typ
 	size_t len, k, kk, n;
 	int o_id = GMT_NOTSET, family = GMT_NOTSET, geometry = GMT_NOTSET;
 	bool change_type = false;
-	char **s = NULL, *next = NULL, *tmp = NULL, magic = 0, revised[GMT_LEN64] = {""};
+	char **s = NULL, *next = NULL, *tmp = NULL, magic = 0, revised[GMT_LEN128] = {""};
 	struct GMT_OPTION *opt = NULL;
 	struct GMTAPI_CTRL *API = gmtapi_get_api_ptr (V_API);
 
@@ -1795,7 +1795,7 @@ GMT_LOCAL char ** gmtapi_process_keys (void *V_API, const char *string, char typ
 	n = kk;	/* May have lost some NULLs.  Make a revised string for debug output */
 	for (k = 0; k < n; k++) {
 		if (k) strcat (revised, ",");
-		strncat (revised, s[k], GMT_LEN64-1);
+		strncat (revised, s[k], GMT_LEN128-1);
 	}
 	if (revised[0]) GMT_Report (API, GMT_MSG_DEBUG, "gmtapi_process_keys: Revised keys string is %s\n", revised);
 	*n_items = (unsigned int)n;	/* Total number of remaining keys for this module */