for w > 0, the decay constant being lambda.
The Strata package should work on UNIX and UNIX-like systems (incl. Linux, NetBSD) in general. (See Downloading Strata.) It is not available for other systems (e.g. MS Windows, Macintosh).
Some annotation in this manual: typewriter font indicates commands to be entered by the user. Names in < angles > indicate controls on a graphic interface. Italicized text usually indicates a file or directory.
The Appendices have information about academic references, downloading Strata (and information on program development and environments), licenses and copyrights and the GNU General Public License, changes from the last release (including patches), known bugs and not-yet-implemented features as of this release, Strata-related mailing lists, and necessary file formats to interface your own models with Strata.
With the executables available, you are ready to begin using the applications.
To create a library from scratch, you might do the following:
To make a similar library later, you could start up with setbasin mybasin. This automatically loads up mybasin.dat and presents you with those parameters. You can then make changes and save back to mybasin.dat (the default choice it presents you with when you click < save > ) or to a different library.
If you're already running setbasin and want to load your library, you can click < load > and type mybasin in the resulting subwindow (and then hit < confirm > ). Setbasin will then have the mybasin.dat parameters. It is not necessary for a library file to be complete. If some parameter is not specified --- either because you used the options to save and load in groups, or (most likely) because new parameters have been added in a new release --- simbasin will use the default values for the unspecified parameters. If you load an incomplete library into setbasin, it will use all the values the library does give, and leave the other parameters as they were before.
filmbasin library tag [-s simulator] [-p plotter] [-f number of frames] [-a]
Library specifies the library in the usual fashion. The tag is a string to affix to the file names to make sure things aren't overridden --- if you make a film from the library mybasin with tag poros, you'll get files named mybasin.film.poros.001.gif etc., which then won't get erased when you run a film from the same library with a different tag (hence different names).
You may optionally specify a plotter (post-processor) with the -p flag. If you do not specify one, it will look for plotbasin (i.e. something named "plotbasin" along your path). You may specify a simulator (processor) with the -s flag. If you don't, it will look for something called simbasin. These two flags are useful if (and only if) you have your own special processor and/or post-processor, or your copies of plotbasin and simbasin are located somewhere not on your path.
You will frequently want to specify the number of frames with the -f flag. If you do not, it defaults to the number of timelines as specified in the library file. If you specify a number greater than this, it will be cut down to this.
If the -a flag was given, filmbasin will prompt you for arguments to pass to the plotter and simulator. Either or both may be left blank. Any arguments you specify will have the same effect as using them directly in the plotter or simulator. For instance, if you specify -p myparams as a plotter argument at this point, and the plotter is plotbasin, it will load the parameter file myparams at startup, that being what plotbasin library -p myparams would do.
The size of the plotbasin window is fixed when started by filmbasin, because the methods we have found so far to turn gifs into real physical films require this size; if people find problems with this it'd be easy enough to change (I don't know why it isn't a settable flag already). You can set whether the timelines are visible, what color data to plot, etc., normally in plotbasin. Set these as desired; they remain fixed throughout the film. You will probably want to run plotbasin normally on the output of simbasin on this library to see what settings produce nice-looking pictures beforehand. Once you are done with the settings on the plotter started up by filmbasin, click on any of the age markings, which will all be zeros, to start it filming. Everything from there is automatic; you can no longer use the plotter controls.
If you are filming the progress of color data, remember that most types automatically scale between the highest and lowest values so far encountered, which means the color scale will change over the course of the film. To avoid this, figure out a range which includes the highest and lowest values you expect to encounter (doing a non-film run first is the best way to do this), set the data to scale between those values in the parameters window, and turn scaling on for that datum. See the plotbasin help entries on color data and scaling for specifics. Also note that data fields frequently assume atypical extreme values during the first few iterations of the simulation, so scaling may result in odd ranges (most notably for porosity, which seems to always have its low end pushed to zero at the start of films).
The files generated will be named in the format (library).film.(tag).(number).gif, where (number) is the number of the frame and gets zero-padded to make them all have the same number of digits (i.e. a 2000-frame picture will have numbers 0001... 0010... etc.). The plotter automatically makes gif rather than xwd files when started by filmbasin.
Note that all this will take a long time to run. If you use the default number of frames, and don't have an unusually coarse-grained or unusually small simulation, expect to leave it running overnight. Also, while a gif file is a highly compressed way to store graphics data, storing thousands of them still takes up a lot of space --- make sure you have room!
How do you get an actual film out of the files? There are companies that will take a collection of gif files and hand you film. Check the yellow pages.
There are also various utilities out there that let you view the film on the screen with little or no further processing of the .gif's.
XAnim is one such utility. It's free and fairly widely distributed, so you may well have it already. If not, look at the xanim homepage or ftp to xanim.va.pubnix.com. These have very good directions for getting, compiling, and using xanim.
We didn't write xanim and we haven't used it very much, so we probably won't be able to help if you have questions about it. We have found that xanim displays Strata films nicely when invoked by
xanim -Cd (library).film.(tag).*.gif
though you should note that it takes quite a while to start up to the point of providing a window, and a long time after that to start the animation --- it's loading a lot of data! Also, if there are a lot of gifs it may not be able to store all of them.
MPEG is a standard format for video data. Again, we didn't write it and we don't know much about it, so we'll only say a little about it here. There's a good chance you have the applications mpeg_encode and mpeg_play available on your system. The former can take a bunch of .gif files (among other things) and turn them into an MPEG file; the latter can display an MPEG file as a movie. An HTML link to an MPEG file (with a .mpeg, .mpg, or .mov extension) will provide a click-to-view movie on a webpage.
Mpeg_encode requires as input a parameter file describing what it's supposed to be doing along with the .gif's it's supposed to do it to. We have found that a parameter file that looks like
PATTERN IBBPBBPBBPBBPBB OUTPUT mybasin.mpeg BASE_FILE_FORMAT PPM GOP_SIZE 30 SLICES_PER_FRAME 1 PIXEL HALF RANGE 10 PSEARCH_ALG LOGARITHMIC BSEARCH_ALG CROSS2 IQSCALE 8 PQSCALE 10 BQSCALE 25 REFERENCE_FRAME ORIGINAL YUV_SIZE 640x480 INPUT_CONVERT giftopnm * INPUT_DIR . INPUT mybasin.film.mytag.*.gif [001-250] END_INPUTproduces the correct results. Depending on what graphics converters you have, you may need to change the BASE_FILE_FORMAT and/or INPUT_CONVERT lines. If the above is in mpeg.params, then mpeg_encode mpeg.params will read files mybasin.film.mytag.001.gif thru mybasin.film.mytag.250.gif and produce mybasin.mpeg. Mpeg_play mybasin.mpeg will then display the latter.
At the heart of the simulation is the assumption that sediment transport behaves diffusively (i.e. volumetric flux is proportional to local gradient). For carbonate simulations the sediment source is proportional to water depth, while for clastic simulations the sediment source is a user-specified function. We strongly recommend that you flip through Jordan Flemings (1991), Flemings and Jordan (1989), Flemings and Jordan (1990), and Kaufman et al. (1991) to gain a physical insight into this process. The most useful of these for marine simulations will be Jordan and Flemings (1991).
What follows is a quick description of the important controls. A note on units: any system can be used as long as it is self-consistent. We have personally been working in an m/k/yrs world, and examples are in m/k/yrs units; when plotbasin gives a unit label, it assumes m/k/yrs, so you will need to mentally apply conversion factors there if you use another system.
Epeiric (exponential-depth) sedimentation, where c_1 is
the maximum sedimentation rate and w_0 is the depth of the maximum
sedimentation rate. See Gildner and Cisne (1990).
Oceanic (lag-depth) sedimentation, where c_1 is the maximum
sedimentation rate, c_2 is the exponential decay constant, and w_0 is the
depth of the maximum sedimentation rate. For w < w_0, dsed/dt = c_1.
See the setbasin help entries for details on sealevel files. We recommend that all sealevel files be given a .sea extension.
The file exxon.sea is a special case; it holds the Haq Sealevel Curve, with times given relative to the present. Note that using it may be a bit non-intuitive due to the format of Haq's file. Since it gives time from the present, and the model always uses time from the start of the simulation, it is necessary to use a highly negative time offset, at least as great as the total duration of the simulation. For instance, if the simulation is to run for 20 ma, and the time offset is specified as -100 ma, the portion of the Haq curve from -100 ma to -80 ma will be applied.
We follow the approach of Sclater
and Christie (1980) and assume porosity is an exponential function of depth:
where f is the fraction of sand (assuming only sand and shale are
present) and the constant parameters are defined below.
We note that the default values from Sclater and Christie (1980) are:
where k is the thermal conductivity (watts per meter degree), T
is
temperature (degrees Celsius), and q is the heat flux (watts per square
meter). Because this is a steady-state problem, given q and k
we can calculate the temperature gradient at any point given any boundary
condition. We choose to set the temperature at the sediment surface by
explicitly specifying the temperature at the air interface and using
to determine the temperature at the sediment-water interface for underwater areas. We can then calculate the temperature at any location.
The thermal conductivity is assumed to vary as a function of lithology and
porosity.
where f is again the fraction of sand in the sand and shale, and
phi is porosity. We work in MKS units (since the thermal quantities only
enter the model in equations with each other, we can safely think of them
all in MKS instead of m/k/yrs with no effect on the numbers), and so our
usual values are (Turcotte and Schubert, 1982)
where the third significant digit has been specified so that areas of sand and shale will be distinguishable when the model runs without compaction (and therefore with zero porosity).
where the TTI which is summed is a continuous version of the empirical
for which n(T) has been found to be crudely approximated by
The fundamental trait here is that the reaction rate doubles with every temperature increase of 10 degrees C.
The TTI value indicates how much the sediment has matured in that time
interval. The Sum TTI is thus the total maturity of the sediment. The
following table shows the usual interpretation of the Sum TTI values.
(Note that these are typically given in megayears, not years.)
Velocities are determined from the Wylie equation
where f is again the fraction of sand in the sediment (ignoring fluid), v_{material} is the velocity of sound through that material. V_b is the resulting bulk velocity and is a selectable data type under < fill > , < log > , and < contour > .
The velocities of sound in sand, shale, and fluid are set in
the parameters window. Typical acoustic velocities are (from Schlumberger,
1987)
Bulk density is determined from
where rho_{material} is the material density and rho_b is the resulting bulk density, which is a viewable data type. Material densities are also specified in the parameters window.
The impedance of a layer of sediment to sound (also selectable data) is
derived as
The reflection coefficients are defined by
and may be made visible with the < misc > menu.
The final signal, consisting of the explosive wavelet (selected in < misc > and visible when relevant in the top left) convolved with the reflection coefficients, may take a few moments to be calculated. It is viewable under < fill > or < log > . (Signal data cannot, of course, be contoured.)
Flemings, P.B. and T.E. Jordan, ``A Synthetic Stratigraphic Model of Foreland Basin Development,'' Journal of Geophysical Research 94: 3851-3866, 1989.
Gildner, R.F. and J.L. Cisne (ed.), ``Quantitative Modeling of Carbonate Stratigraphy and Water-Depth History Using Depth-Dependent Sedimentation Function in Cross, T.A.,'' Quantitative Dynamic Stratigraphy. Prentice Hall, New Jersey, 1990.
Haq, B.U., J. Hardenbol, and P.R. Vail, ``Chronology of fluctuating sea levels since the Triassic,'' Science 235: 1156-1187, 1987.
Hart, B.S., P.B. Flemings, and A. Deshpande, ``Porosity and pressure: Role of compaction disequilibrium in the development of geopressures in a Gulf Coast Pleistocene basin,'' Geology 23 (1): 45-48, 1995.
Jordan, T.E. and P.B. Flemings, ``Large-Scale Stratigraphic Architecture, Eustatic Variation, and Unsteady Tectonism: A Theoretical Evaluation,'' Journal of Geophysical Research, 96 (B4): 6681-6699, 1991.
Kaufman, P., J.P. Grotzinger, and D.S. McCormick, ``Depth-dependent diffusion algorithm for simulation of sedimentation in shallow marine depositional systems in Franseen, E.K.,'' in W.L. Watney, C.G.S.C. Kendall, W. Ross (eds.) Sedimentary modeling: Computer simulations and methods for improved parameter definition, Kansas Geological Survey, 1991.
Log Interpretation Principle/Application, Schlumberger Educational Services. Houston, 1987.
Pegrum, R.M. and A.M. Spencer, ``Hydrocarbon Plays in the northern North Sea,'' in Brooks, J. (ed.) Classic Petroleum Provinces. Geological Society Special Publication, London, 1990.
Ross, W.C., D.E. Watts, and J.A. May, ``Insights from Stratigraphic Modeling: Mud-Limited Versus Sand-Limited Depositional Systems,'' AAPG Bulletin 79(2): 231-258, 1995.
Sclater, J.G. and P.A.F. Christie, ``Continental Stretching: An Explanation of the Post-Mid-Cretaceous Subsidence of the Central North Sea Basin,'' Journal of Geophysical Research 85 (B7): 3711-3739, 1980.
Turcotte, D.L, and G. Schubert, Geodynamics: Applications of continuum physics to geological problems. John Wiley & Sons, New York, 1982.
Waples, D.W., Predicting Thermal Maturity, in Geochemistry in Petroleum Exploration. International Human Resources Development Corporation, 1985.
Strata has been successfully used on some DEC MIPS Ultrix, HP/UX v9, SGI, AIX, NetBSD, Linux, Solaris, and SunOS systems; the latter two platforms probably offer the most stability, being the main development environments. It ought to work in UNIX and UNIX-like systems in general. Strata is not available for other systems (e.g. MS Windows, Macintosh).
Copies of this manual in Latex and Postscript are available on the Strata Downloading page along with the Strata source, tutorial, and patches.
You may also retrieve Strata via anonymous ftp from the Penn State sytem:
Unpacking: Most of the material is packed in .tar.gz files. To unpack such a file, either gtar xvfz name.tar.gz if you have gtar (gnu tar) on your system, or else do gunzip name.tar.gz and then tar xvf name.tar. In either case, you will be left with a copy of the tarfile as well as its contents; you'll want to rm the leftover tarfiles.
Gzip: Most UNIX environments have gzip, but it's easy to get if you don't. Like other GNU applications (e.g. gtar), gzip source for various environments is available to anonymous ftp to prep.ai.mit.edu in /pub/gnu. If necessary, gzip -d acts the same as gunzip.
Source Code: The source tarball creates the directory src, and in it a directory for each of the programs, each with its own source. In src there is a configure script which will handle compilation for you. Cd to src and do
This manual does not appear in src, but is available (in LaTeX and Postscript) in man.tar.gz.
Tutorial: This material appears in a tutorial directory. It includes the libraries and data files used in the tutorial. WARNING: the tutorial postscript was made in FrameMaker and has lots of pictures so it is very, very big --- you may have trouble even printing it. You should be able to view it with ghostview and such.
Also please note that the tutorial has not been updated to reflect changes in the package since it was first written! For instance, the tutorial claims that the data files appear elsewhere, whereas they actually appear in the tutorial directory itself. Basically, the information on actually using Strata is accurate, but references to how the package appears is suspect. In case of conflict, this manual is correct.
Revisions: Revisions to Strata will be available in the same places (ftp and WWW); those important enough will be announced to the strata-users list.
Usually, but not always, a revision will be available both as a complete package to take the place of your old Strata and as a patchfile which can be used to patch your old Strata; there will not always be a patchfile. When there is, to patch your copy of Strata, download (and gunzip and untar, just as for the original source) the patches between your version and the latest. Place the resulting patchfile(s) in src. In that directory,
This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program (license.h in the source code); if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
For more information about this package, or to report bugs or be added to the strata-users mailing list, please send email to strata-admin@geosc.psu.edu. You may also wish to contact
Peter B. Flemings
Department of Geosciences
Penn State University
442 Deike Bldg.
University Park, PA 16802
flemings@geosc.psu.edu
John P. Grotzinger
54-816
Department of Earth, Atmospheric, and Planetary Sciences
MIT
Cambridge, MA 02139
grotz@grabau.mit.edu
Jamie Morris
905 Main St. #6
Cambridge, MA 02139
jemorris@mit.edu
Also, the source file license.h contains a copy of the Gnu General Public License, and the source file strata.h contains some excerpts from this manual.
You may wish to note that the xwd capabilities of the program are derived directly from the xwd source (files xwd_dsimple.c, xwd_dsimple.h, and xwd_here.c of plotbasin), which has the following copyright notice:
XConsortium: copyright.h,v 1.5 89/12/22 16:11:28 rws Exp Copyright 1985, 1986, 1987, 1988, 1989 by the Massachusetts Institute of Technology Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of M.I.T. not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. M.I.T. makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty.Similarly, the gif-making code (gif_here.c of plotbasin) is taken from code with the following licensing / copyright notice:
The Graphics Interchange Format(c) is the copyright property of CompuServe Incorporated. Only CompuServe Incorporated is authorized to define, redefine, enhance, alter, modify or change in any way the definition of the format. CompuServe Incorporated hereby grants a limited, non-exclusive, royalty-free license for the use of the Graphics Interchange Format(sm) in computer software; computer software utilizing GIF(sm) must acknowledge ownership of the Graphics Interchange Format and its Service Mark by CompuServe Incorporated, in User and Technical Documentation. [The rest of the notice concerns software lacking such acknowledgment, so is irrelevant, since here it is.]
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave,
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END OF TERMS AND CONDITIONS
(Strata was patched to v2.11)
(Strata was patched to v2.12)
(Strata was revised to v2.13)
(Strata was patched to v2.14)
Strata-users is the appropriate place for questions about other utilities (like xanim or xv) that might be of use, discussion of what other features would be nice to have in and who wants to pay for them, revelation of clever tricks people have come up with, or anything else having to do with Strata. It is also the main forum in which new releases of Strata will be announced.
As the above implies, adding new features to Strata isn't just a matter of coming up with ideas. The programmer (Jamie Morris), living in Cambridge, MA, would be quite happy to add new things to the package, other commitments permitting, but only if someone has the funding. Send mail to strata-admin or to jemorris@mit.edu if interested.
The librarys.out file must contain the following, in ascii, in order, all numbers being separated by whitespace:
int i, j, k;
Boolean have_data[7];
FILE *fp;
have_data[0] = TRUE; /* elevation */
have_data[1] = compaction; /* porosity, if compaction is on */
have_data[2] = TRUE; /* water depth */
have_data[3] = TRUE; /* max space from neighboring timeline, meters */
have_data[4] = TRUE; /* prevailing diffusion constant */
have_data[5] = did_thermal; /* temperature, if thermal calculations done */
have_data[6] = did_thermal; /* Sum TTI, if thermal calculations done */
for (i = 0; i < 7; ++i) /* loop through the data fields */
if (have_data[i]) /* skip those not calculated */
for (j = 0; j < number of timelines in this slice; ++j)
for (k = 0; k < number of spatial nodes; ++k)
write out datum of field i on timeline j at node k to fp;
where the data should be written as per:
void write_datum(FILE *fp, double x)
{
Boolean negmantis, negexpon; /* mantis / exponent negative? */
unsigned int mantis, expon;
unsigned char buf[3];
double y;
if (negmantis = (x < 0))
x = -x;
else if (!x) {
fwrite("\0\0\0", 1, 3, fp);
return;
}
y = log(x) / .69314718 - 17; /* binary log(x) = ln(x) / ln(2) */
if ((int)y == y) ++y;
if (negexpon = (y < 0))
expon = -y;
else
expon = y;
if (expon > 31)
if (negexpon) {
fwrite("\0\0\0", 1, 3, fp);
return;
}
else {
printf("Simbasin crashes and burns: can't handle %g (too big)\n", x);
exit(1);
}
if (negexpon)
mantis = x * (1 << expon);
else
mantis = ((int)x) >> expon;
buf[1] = (mantis & 65280) >> 8;
buf[2] = mantis & 255;
buf[0] = expon;
if (negexpon) buf[0] += 32;
if (negmantis) buf[0] += 64;
if (mantis & 65536) buf[0] += 128;
fwrite(buf, 1, 3, fp);
}
That is: each datum is expressed as
and written out in three bytes. The first byte gives the exponent (first
five bits), whether the exponent is negative (sixth bit), whether the mantissa
is negative (seventh bit), and the highest (seventeenth) bit of the mantissa
(eighth bit). The second byte gives the ninth through sixteenth bits of the
mantissa, and the third byte gives the first eight bits of the mantissa.
Anything smaller than this dynamic range is written as zero; anything larger
breaks. Note that the max-space-between-timelines data field is saved in meters, and converted by plotbasin to mm/yr, because the conversion factor of .001 / (years per timeline) is generally enough to make the numbers small enough that they all turn into zeros.
See also simbasin's settime.c.
Interactions via filmbasin are more complex; you'll have to look at filmbasin's specs.h for that information.
This manual was written as part of Basin Research at Penn State.
This page maintained by Steven E. Nelson.