Minor Bug or Artificial Intelligence Feature in PHAST: 3D Reactive-TransportModel

["Rasmus Jakobsen" <raj@xxxxxxxxx>]

Dear David
PHAST seems to be working fine now - for further optimization here are
some minor quirks

Time control:
I noticed an interesting feature. I had the following couple of lines at
the end of a *.trans.dat file:

PRINT_FREQUENCY
	-HDF_chemistry 1 seconds
	-xyz_chemistry 5000 seconds
	-force_chemistry_print 0

TIME_CONTROL
	-delta_time .25 seconds
	-end_time 10 seconds
END

TIME_CONTROL
	-delta_time 5 seconds
	-end_time 10000 seconds
END

Unintentionally I had left a 1 (forgot to edit it) for the
-HDF_chemistry PRINT_FREQUENCY, though my intention was to set a
-delta_time to 5 seconds (except for the first 10 seconds). What
happened is that PHAST chose to use 1 second as -delta_time. In
principle the safe choice in terms of not missing anything - but it did
increase the simulation time considerably and it also meant that the
output was rather large.
KR
Rasmus 


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-----Original Message-----
From: David L Parkhurst [mailto:dlpark@xxxxxxxx] 
Sent: 13. december 2002 23:40
To: phreeqc_list@xxxxxxxxxxxxxxxxxxxxxx
Subject: PHAST: 3D Reactive-Transport Model

PHAST Release Candidate 1 (Beta test version RC1)

==========
PHAST RC1:
==========

PHAST is a 3D reactive transport model that combines PHREEQC with HST3D,
a
ground-water flow and transport model. Capabilities are limited to
constant
density, constant temperature flow plus a full suite of reaction
capabilities. PHAST uses a purely sequential algorithm that solves first
for the transport of multiple components, reacts each cell of the domain
by
using PHREEQC, and then repeats transport and reaction until each
transient
stress period has been completed.

PHAST beta test version RC1 is now available at
https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phast with executables
for
Windows, Linux, and Sun. No source code is released. The program has
been
extensively tested. No additional features and only minor bug fixes are
anticipated before official release of the program.

Documentation for the flow and transport input is provided in a PDF file
distributed with PHAST. All chemical definitions are identical to
PHREEQC
and you are referred to the PHREEQC User's manual for documentation.

ModelViewer (developed by Paul Hsieh and Scott Charlton) is distributed
with the Windows version. It provides 2D and 3D visualization and
animation
of PHAST results that have been written to the HDF file. ModelViewer has
capabilities to slice, rotate, contour, and animate.

Phastexport is included in the distribution. Phastexport is a Java
program
that extracts data stored in the HDF file and writes the data to an
ascii
file that is suitable for post-processing.


=====================================
MAJOR CHANGES FROM PHAST VERSION 0.3:
=====================================

(1) A few keyword data blocks for the flow and transport data file have
been added or changed. Current data input definitions are available in
the
file phast.pdf in the doc directory of the installation.

(2) Installation of phast is now simplified by using InstallShield
(Windows) and RPM (Linux and Sun).

(3) Scripts (Unix and Windows) have been written to automate the running
of
phastinput and phast.

(4) The HDF file is now written directly while running phast;
previously,
the HDF file was produced from a "selected-output" file by ModelViewer.

(5) The HDF file now contains information on boundary cells (specified
head, leaky, flux, river, and well), which can be visualized by
ModelViewer
with the Features menu.

(6) Flow vectors at nodes are now calculated and may be written to the
HDF
file and visualized.

(7) The output files have been simplified to two main formats: ".O"
files
can be viewed in an editor and usually contain data formatted in 2D
slices,
and ".xyz" files contain data for a single cell on a single line (each
line
contains x, y, z, time , a wet/dry flag, followed by data); .xyz files
are
suitable for spreadsheets and other post processing.

(8) A Java program, phastexport, allows selected data from the HDF file
to
be extracted and written to a file in .xyz format for postprocessing.
Thus,
most data can be stored in and retrieved from the HDF file, minimizing
the
need for writing .O and .xyz files.

(9) Several log files have been merged or eliminated; all errors,
warnings,
input echoing, and log messages are directed to the file prefix.log.

(10) Problems with multilayer rivers have been corrected.

(11) All identified bugs have been fixed.

(12) MPI (LAM and MPICH) has been used to parallelize PHAST. Test
versions
of the parallel program are available on a limited basis by contacting
David Parkhurst (dlpark@xxxxxxxx). No support will be provided for
installing, debugging, or invoking MPI on your system.


=========
PHREEQC:
=========

The current version of PhreeqcI is 2.6.0.1, released May 31, 2002. The
current version of PHREEQC is 2.6, released April 22, 2002.


======
BUGS:
======

Report to dlpark@xxxxxxxxx





Ken Kipp (klkipp@xxxxxxxx)
David Parkhurst (dlpark@xxxxxxxx)

U.S. Geological Survey
Box 25046, MS 413
Denver Federal Center
Denver, CO 80225

Project web page: https://wwwbrr.cr.usgs.gov/projects/GWC_coupled