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Package drat (in drat.i) - 2D transport equation solver
Index of documented functions or symbols:
DOCUMENT adjust_ireg(ireg) returns the input IREG with the regions specified in drat_ireg_adj zeroed. Beware-- the ireg array is actually modified.
SEE ALSO: drat_ireg_adj
DOCUMENT apply_funcs(streak_result)
or apply_funcs(transp, selfem)
or apply_funcs(transp, selfem, time)
or apply_funcs(transp, selfem, times)
applies the drat_backlight and drat_channel options (if any)
to the input streak_result. This destroys the separate
transparency and self-emission information returned by streak.
transp= streak_result(,1,..) and selfem= streak_result(,2,..).
If time is not given, time=0.0 is passed to the functions.
If times is a vector, it must match the final dimension of
transp and selfem.
DOCUMENT B_nu(hnu, kt) returns the specific intensity emitted by a black surface at photon energy HNU and temperature KT. The units of HNU and KT must be the same. The units of the result are determined by the variable B_nu_scale, which must be consistent with the units of HNU and KT. B_nu_scale is the Stefan-Boltzmann constant (sigma in sigma*T^4) times 15/pi^5. By default, B_nu_scale is set to 0.05040366 ((jrk/sh)/(cm^2 ster))/keV^4. (1 jrk/sh = 10^17 W) HNU and KT may be arrays, provided they are conformable.
SEE ALSO: B_nu_bar
DOCUMENT B_nu_bar(hnub, kt) returns the specific intensity emitted by a black surface at temperature KT in the energy bins whose boundary energies are HNUB. HNUB must be a 1-D array of bin boundary energies; the units of KT must match the units of KT. Both are in keV, by default; see B_nu for a discussion of units. The result will have dimensions (numberof(HNUB)-1)-by-dimsof(KT). The algorithm has an accuracy of 0.2 percent. The idea is to difference an analytic approximation to the integral of B_nu.
SEE ALSO: B_nu
DOCUMENT default_gate(times) initial value of drat_gate. Refer to the source code to learn how to write your own gate function, making proper use of drat_start and drat_stop options in addition to the input times.
SEE ALSO: gauss_gate, drat_gate
DOCUMENT atten_emit= default_integrate(f, mesh, time, irays, slimits)
is the default drat_integrate routine.
On entry, file F is positioned at TIME, from which MESH has already
been read. IRAYS and SLIMITS are the rays coordinates (in internal
format) and integration limits.
The result should be ngroup-by-2-by-raydims, where the second index
is 1 for the attenuation factor, 2 for the self-emission (specific
intensity due to emission along the ray).
OPTIONS: drat_linear, drat_ocompute, drat_oadjust,
drat_emult, drat_amult, drat_omult, drat_nomilne,
drat_ekap, drat_akap, drat_glist
SEE ALSO: streak
DOCUMENT default_ocompute(f, time) initial value of drat_ocompute. Extracts drat_akap and drat_ekap from file F, possibly using the subset drat_glist. TIME is unused.
SEE: drat_rt
DOCUMENT drat_amult, drat_emult, drat_omult
are optional opacity multipliers used by the streak, snap, and
streak_save functions. The multipliers are applied to the
opacity and source functions before the transport equation is
integrated. Setting them to [] is the same as setting them
to 1.0.
DRAT_EMULT - multiply the emissivity by this factor,
without affecting the absorption
opac <- opac
source <- source*DRAT_EMULT
DRAT_AMULT - multiply the absorption opacity by this
factor, without affecting the emissivity
opac <- opac*(DRAT_AMULT+1.e-20)
source <- source/(DRAT_AMULT+1.e-20)
DRAT_OMULT - multiply BOTH the absorption opacity and the
emissivity by this factor
opac <- opac*DRAT_OMULT
source <- source
DRAT_IREG_ADJ - list of region numbers to be zeroed. This
has the same effect as a zero DRAT_OMULT in
the corresponding zones, but is more efficient.
Since opac and source are mesh-by-ngroup (where mesh is usually
kmax-by-lmax), DRAT_EMULT, DRAT_AMULT, DRAT_OMULT can
be scalars, mesh arrays, 1-by-1-by-ngroup arrays, or
kmax-by-lmax-by-ngroup arrays. If DRAT_GLIST is non-nil, ngroup
should be numberof(DRAT_GLIST), not the total number of groups.
SEE ALSO: drat_glist, adjust_ireg
DOCUMENT func drat_backlight(time) { extern gb, gav; ... }
or drat_backlight=
or drat_backlight=
supplies a backlighter for the snap function.
Given ngroup-by-nrays transparency fraction transp and self-emission
selfem (in specific intensity units), snap applies the backlighter
using:
result= backlighter*transp + selfem;
where backlighter is drat_backlight(time), if drat_backlight is
a function, or drat_backlight itself, if drat_backlight is an
array.
Note that the result (or value) of backlighter_func must be
conformable with transp and selfem. Most commonly, drat_backlight
will be a vector of length ngroup -- a Planckian backlighter at
temperature Tr would be
drat_backlight= B_nu(gav, Tr);
-- but that a scalar, 1-by-nrays, or ngroup-by-nrays are all
possible.
Note also that if drat_backlight is a function, the gb and gav
arrays read from the history file are available as external
variables.
SEE ALSO: snap, drat_channel, drat_gate, apply_funcs
DOCUMENT func drat_channel(time) { extern gb, gav; ... }
or drat_channel=
or drat_channel=
supplies a channel response for the snap function.
Use the drat_glist option to select a subset of the groups;
drat_channel can be used in addition to drat_glist.
Given ngroup-by-nrays specific intensity, snap applies the
channel response using:
result= drat_channel(..,+)*specific_intensity(+,..);
if drat_channel is an array, or
result= drat_channel(specific_intensity, time);
if drat_channel is a function.
Note that if drat_channel is an array, its final dimension must
be of length ngroup. A multidimensional drat_channel represents
more than one channel response function. Most drat_channel
arrays will be proportional to the bin widths gb(dif). The
correct way to interpolate a filter function transmission
fraction known at photon enrgies efa is:
drat_channel= integ(ffa, efa, f.gb)(dif)
If you have more than one channel, the first dimension of
drat_channel should be the channel number.
The best way to generate a filter response function is to
use Yorick's cold opacity library. To do this:
#include "coldopac/xray.i"
This will define the functions cold_opacity and cold_reflect,
which you can use to build up channel response functions from
filter materials and thicknesses and mirror compositions.
Note also that if drat_channel is a function, the gb and gav
arrays read from the history file are available as external
variables.
SEE ALSO: drat_glist, snap, drat_backlight, drat_gate, apply_funcs
DOCUMENT func drat_compress(transp, selfem, time)
or drat_compress=
supplies a compression algorithm to the streak function.
The drat_compress can return anything, as long as it returns the
same shape array (or nil) at each time. The snap_worker and
streak_saver routines are examples of compression algorithms.
SEE: drat_rt
SEE: drat_amult
DOCUMENT func drat_gate(times) { extern gb, gav; ... }
or drat_gate=
supplies a gate (to make gated images) for the snap function.
For a simple gate, the drat_start and drat_stop options will
be more efficient than drat_gate.
The input to drat_gate is the list of dump times; the output
should be the "effective dt" for each of these dumps. This is
the product of the actual time interval and the gate transparency;
the sum of the return vector is the gate time. See the default_gate
and gaussian_gate functions for examples.
Note that the gb and gav arrays read from the history file are
available as external variables, in case the gate transparency is
frequency dependent.
SEE ALSO: snap, drat_backlight, drat_channel, apply_funcs, drat_start, drat_stop, gaussian_gate, default_gate
SEE: drat_rt
SEE: drat_rt
DOCUMENT drat_glist if non-nil, an index list into the final dimension of akap and ekap. Only these groups will be read from disk and used in the transport calculation. All other options which depend on "ngroup" or "gav" should use numberof(DRAT_GLIST) or gav(DRAT_GLIST) instead. The "gb" group boundary array is not well-defined in this case, since the group boundaries need not be contiguous. The best strategy is to save drat_glist and the original gb array. DRAT_GLIST must be a 1-D, 1-origin index list. (1-origin even if gav and gb are not 1-origin, since use_origins(0) will be in effect when DRAT_GLIST is used.) The streak function will be most efficient if DRAT_GLIST is strictly increasing.
SEE ALSO: drat_channel
DOCUMENT func drat_integrate(file, mesh, time, irays, slimits) { ... }
or drat_integrate=
integrate the transport equation. FILE is positioned to TIME, and
MESH has already been read. IRAYS are the rays in internal format
and SLIMITS is the integration limits. The return value should be
ngroup-by-2-by-raydims (where irays is 6-by-raydims). The default
integrator is default_integrate, which handles the drat_ocompute,
drat_oadjust, drat_amult, drat_emult, drat_omult, drat_akap,
drat_ekap, drat_glist, drat_linear, and drat_nomilne options.
Reasons to replace the default routine include: (1) Some or all of
the opacities come from a source other than the FILE, e.g.- a second
post processing file. (2) The total number of zones times number of
groups is debilitatingly large, even though the number of rays times
the number of groups is not.
SEE: drat_rt
SEE: drat_amult
SEE: drat_rt
SEE: drat_rt
SEE: drat_rt
DOCUMENT drat_linear, drat_nomilne
Set DRAT_LINEAR to 1 in order to use integ_linear to perform the
transport integration instead of the default integ_flat.
The DRAT_NOMILNE option, if non-nil, is a list of "norad"
edges in the (rt,zt) mesh (other than the khold and lhold lines),
which is required for the source function point centering operation.
DRAT_NOMILNE is a 2 or 3-D array with the format:
[[k1,l1], [k2,l2]]
or an array of elements of that form, where either k1==k2 or
l1==l2. (Where k is the first index of rt or zt and l is the second.)
DRAT_NOMILNE must always be a 1-origin index list into the (rt,zt)
mesh, independent of the index origins of rt and/or zt.
SEE ALSO: integ_linear, integ_flat
SEE: drat_linear
SEE: drat_ocompute
DOCUMENT func drat_ocompute(file, time) { extern opac, source; ...}
or drat_ocompute=
and func drat_oadjust(file, time) { extern opac, source; ...}
or drat_oadjust=
supply opacities from a source other than the file.drat_akap and
file.drat_ekap, or adjust these values. You need to be cognizant of
the drat_glist option (see get_kaps source code).
DRAT_OCOMPUTE must set opac and source entirely on its own;
DRAT_OADJUST will be called afterwards.
The default DRAT_OCOMPUTE (default_ocompute) reads drat_akap and
drat_ekap from FILE, optionally extracting drat_glist, and places
them in opac and source.
DRAT_OADJUST is free to modify opac and source them at will; the
default DRAT_OADJUST is nil, which means no adjustment.
Any opacity or emissivity multipliers will be applied after
DRAT_OADJUST, as will the point centering operation if necessary
(DRAT_OADJUST should return zone centered opacities).
SEE: drat_amult
DOCUMENT drat_quiet By default, Drat prints the total number of records it will process, and the number of the record it is currently processing. If drat_quiet is non-nil and non-zero, the printout is supressed.
DOCUMENT drat_rt, drat_zt, drat_ireg,
drat_akap, drat_ekap,
drat_isymz,
drat_khold, drat_lhold,
drat_gb, drat_gav
can be set to strings other than "rt", "zt", etc. (their default
values) to force the streak, snap, and streak_save routines to use
alternative names to look up these quantites in the history file.
The following 4 variables are NOT optional:
(rt, zt) must be a 2-D mesh in cylindrical coordinates
akap is a mesh-by-ngroup array of absorption opacities, in units
of reciprocal length (1/rt or 1/zt)
ekap is a mesh-by-ngroup array of source functions, in (arbitrary)
specific intensity units
The akap and ekap arrays must be zone centered; the first row and
column of akap and ekap will be ignored.
The remaining variables are all optional -- set the drat_.. variable
to [] to ignore them completely. Otherwise, they will be ignored if
they are not present in the history file, and used as follows
otherwise:
ireg is a mesh-size region number array (zone centered as akap and
ekap). Zones where ireg==0 do not exist.
isymz is non-zero if the problem has reflection symmetry about z=0,
zero otherwise. The drat_symmetry option overrides this value.
khold and lhold are mesh indices specifying "hold lines" --
khold is an index into the first dimension of (rt,zt), and
lhold is an index into the second dimension of (rt,zt).
These are used only if the drat_linear option is specified.
gb and gav are, respectively, the group boundary energies and group
center energies. These are used by the snap and streak_save
functions.
SEE ALSO: streak, snap, streak_save, drat_symmetry, drat_linear
DOCUMENT drat_start, drat_stop if non-nil, specify the minimum and maximum dump times which will be considered by the streak, snap, or streak_save functions.
DOCUMENT drat_static if non-nil, a list of strings representing variable names in the input file which the streak_save function should copy to the output file.
SEE ALSO: streak_save
SEE: drat_start
DOCUMENT drat_symmetry set to 2 to force spherical symmetry, 1 to force reflection symmetry about the z=0 plane, 0 to force no symmetry, [] (the default) to use the guess_symmetry function to compute problem symmetry. Special value drat_symmetry=2+khold where k=khold is a hold-line causes ray to reflect at the hold line. This doesn't mean anything physically (in fact, it is wrong), but may give qualitatively useful pictures in problems that are polar wedges.
SEE: drat_rt
DOCUMENT boundary= find_boundary(mesh)
or boundary= find_boundary(mesh, region, sense)
returns an array of 4 pointers representing the boundary of the
MESH, or of a particular REGION of the MESH, with a particular
SENSE -- 0 for counterclockwise in the (r,z)-plane, 1 for
clockwise. The returned arrays are:
*boundary(1) zone index list -- always 1-origin values
*boundary(2) side list 0, 1, 2, or 3
side 0 is from point zone to zone-1, side 1 is
from zone-1 to zone-imax-1
*boundary(3) z values of boundary points
*boundary(4) r values of boundary points
SEE ALSO: form_mesh, update_mesh
DOCUMENT form_mesh(zsym, khold, lhold)
returns an opaque "mesh" object, which will hold rt, zt, ireg,
and a boundary edge list. This opaque mesh object is required
as an input to the integ_flat and integ_linear routines.
ZSYM is 2 for spherical symmetry, 1 for z=0 reflection symmetry,
or 0 for no symmetry
KHOLD and LHOLD are the 1-origin indices of "hold" lines in the
mesh, or 0 if none. This information is used only during the
pcen_source operation before integ_linear is called.
SEE ALSO: update_mesh, integ_flat, integ_linear
DOCUMENT gaussian_gate(t0, tsigma, max_trans) sets the drat_gate for the snap function to be a Gaussian centered at time T0, with sigma TSIGMA, and maximum transmission fraction MAX_TRANS.
DOCUMENT gauss_gate(times) gate function used by gaussian_gate. Refer to the source code to learn how to write your own gate function, making proper use of drat_start and drat_stop options in addition to the input times.
SEE ALSO: gaussian_gate, drat_gate
DOCUMENT gauss_int(t) returns time integral of Gaussian specified in call to gaussian_gate.
DOCUMENT ray_info= get_ray_path(path, rt, zt) where PATH is one element of an array returned by track_rays, returns the points where the ray cut the edges of the mesh (ZT, RT). The returned RAY_INFO has two components: RAY_INFO(,1) is the z coordinates and RAY_INFO(,2) is the r coordinates.
SEE ALSO: track_rays
DOCUMENT get_std_limits(rays, slimits) returns slimits suitable for internal routines: 2-by-nrays, with s=0 at point of closest approach to origin
DOCUMENT guess_symmetry, f
or guess_symmetry(f)
guesses the symmetry of the problem in the dump file F based on
the variables f.isymz, f.rt, and f.zt.
If called as a subroutine, prints one of:
"no symmetry", "z=0 reflection symmetry", or "spherical symmetry"
If called as a function, returns 0, 1, or 2, respectively.
DOCUMENT integ_flat(opac, source, rays, mesh, slimits)
or integ_flat(opac, source, ray_paths)
returns ngroup-by-2-by-nrays result, where result(,1,..) is
the transparency factors, and result(,2,..) is the self-emission
for each group on each ray. The input OPAC and SOURCE are the
opacity (an inverse length) and the source function (a specific
intensity). They are mesh-by-ngroups zone centered arrays. The
result has the same units as SOURCE.
In the second form, RAY_PATHS was returned by the track_rays
function.
SEE ALSO: integ_linear, track_rays, form_mesh, streak, snap
DOCUMENT integ_linear(opac, source, rays, mesh, slimits)
or integ_linear(opac, source, ray_paths)
returns ngroup-by-2-by-nrays result, where result(,1,..) is
the transparency factors, and result(,2,..) is the self-emission
for each group on each ray. The input OPAC and SOURCE are the
opacity (an inverse length) and the source function (a specific
intensity). They are mesh-by-ngroups arrays; OPAC is zone centered,
while SOURCE is point centered (using pcen_source). The result
has the same units as SOURCE.
In the second form, RAY_PATHS was returned by the track_rays
function.
The integ_linear routine assumes that the SOURCE function varies
linearly between the entry and exit points from each zone. This
assumption is poor near the turning point, and causes the result
to be a discontinuous function of the ray coordinates, unlike the
integ_flat result.
SEE ALSO: pcen_source, integ_flat, track_rays, form_mesh, streak, snap
DOCUMENT is_present(get_vars(f), name) returns 1 if variable NAME is present in file F, 0 if not.
DOCUMENT pcen_source, opac, source, mesh, drat_nomilne point centers the SOURCE array (in place) using a complicated algorithm involving the OPAC and MESH (from form_mesh and update_mesh). If non-nil, DRAT_NOMILNE must have the same format as the drat_nomilne option.
DOCUMENT reset_options
or reset_options, 1
resets all options for the streak, snap, and streak_save functions
to their default values. With a non-zero, non-nil argument, only
resets options which are currently nil, but have non-nil defaults.
DOCUMENT set_tolerances()
or old_tols= set_tolerances([tol1, tol2, lost_tol])
returns the current tolerances for the ray tracking. Initially,
these are [1.e-3, 1.e-6, 0.0]. In the second form, sets new
tolerances. If any of TOL1, TOL2, or LOST_TOL is zero, that
tolerance is restored to its default value. If TOL1 is less
than zero, the root polishing operation which requires TOL1
and TOL2 is not done at all.
SEE ALSO: track_rays, integ_flat, integ_linear, streak, snap
DOCUMENT snap(f, rays)
or snap(f, rays, slimits)
returns the time-integrated specific intensity for the rad-hydro
problem dumped in file F, on the specified RAYS, with the
specified limits SLIMITS on the transport integrals.
The first dimension of RAYS may be length 3, 5, or 6 to represent
the ray(s) in TDG/DIRT coordinates (x,y,theta), "best" coordinates
(x,y,z,theta,phi), or internal coordinates (cos,sin,y,z,x,r),
respectively. The remaining dimensions of RAYS, if any, will be
called "nrays" below.
The SLIMITS parameter, if present, is the value of the s-coordinate
-- position along the ray -- at which to start and stop the
integration of the transport equation. SLIMITS may be nil, a 1-D
array of length 2, or a 2-by-nrays array. Each component of SLIMITS
is [s_start, s_stop]; if s_stop
SEE ALSO: reset_options, streak, streak_save, integ_flat, integ_linear, streak_times, form_rays, best_rays, dirt_rays, internal_rays
DOCUMENT snap_worker(transp, selfem, time) The snap function actually works by replacing the drat_compress with snap_worker. See the source for snap in drat.i for details.
DOCUMENT streak(f, rays)
or streak(f, rays, slimits)
returns the transparency and self-emission as functions of time for
the rad-hydro problem dumped in file F, on the specified RAYS, with
the specified limits SLIMITS on the transport integrals.
The first dimension of RAYS may be length 3, 5, or 6 to represent
the ray(s) in TDG/DIRT coordinates (x,y,theta), "best" coordinates
(x,y,z,theta,phi), or internal coordinates (cos,sin,y,z,x,r),
respectively. The remaining dimensions of RAYS, if any, will be
called "nrays" below.
The SLIMITS parameter, if present, is the value of the s-coordinate
-- position along the ray -- at which to start and stop the
integration of the transport equation. SLIMITS may be nil, a 1-D
array of length 2, or a 2-by-nrays array. Each component of SLIMITS
is [s_start, s_stop]; if s_stop
SEE ALSO: reset_options, snap, streak_save, integ_flat, integ_linear, streak_times, form_rays, best_rays, dirt_rays, internal_rays, apply_funcs
DOCUMENT streak_save, outname, f, rays
or streak_save, outname, f, rays, slimits
or streak_save, outfile, f, rays, slimits
is the same as the streak function, except that the results of
the transport calculation are placed into a PDB file called
OUTNAME, instead of being accumulated in memory. All of the
options for the streak function are available, except for
drat_compress (which is set to streak_saver).
If the first argument is OUTFILE, a file variable instead of a
file name, then that file is used for output. You can create
OUTFILE and add static variables to it with save (but do NOT call
add_record) which streak_save otherwise wouldn't know about.
The output file has history records at the same times as the
input file. Each record contains "time" (a double scalar),
and the two arrays "transp", the transparency (between 0 and 1),
and "selfem", the self emission (which has the same units as
ekap in the file F). The dimensions of transp and selfem
are ngroup-by-2-by-nrays (where nrays represents zero or more
dimensions, copied from the RAYS input array). The RAYS and
SLIMITS inputs are placed into the output file as non-record
variables, and any variables in the drat_static option are
copied form F to the output file. The gb and gav variables
are copied from F into the output file as well. If the drat_glist
option is present, that is stored in the output file also.
OPTIONS: all options available for streak except drat_compress,
drat_gb, drat_gav, drat_static
DOCUMENT streak_saver(transp, selfem, time) The streak_save function actually works by replacing the drat_compress with streak_saver. See the source for streak_saver in drat.i for details.
DOCUMENT streak_times(f) returns the times from file F whic lie between the optional drat_start and drat_stop.
SEE ALSO: drat_start, drat_stop
DOCUMENT ray_paths= track_rays(rays, mesh, slimits) returns array of Ray_Path structs representing the progress of RAYS through the MESH between the given SLIMITS.
SEE ALSO: Ray_Path, integ_flat, get_ray-path
DOCUMENT update_mesh, mesh, rt, zt
or update_mesh, mesh, rt, zt, ireg
updates the opaque MESH object to reflect a new RT, ZT, and
(optionally) IREG. The boundary edges are recomputed and stored
in MESH, as well.
SEE ALSO: form_mesh, integ_flat, integ_linear