&EPA
United States
Environmental Protection
Agency
Environmental Research
Laboratory
Athens GA 30613-7799
EPA/600/3-89/084
April 1990
Research and Development
Exposure Analysis
Modeling System:
User's Guide for EXAMS II
Version 2.94
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EXPOSURE ANALYSIS MODELING SYSTEM
User's Guide for EXAMS II Version 2.94
by
Lawrence A. Burns, Ph.D.
Research Ecologist
Environmental Research Laboratory
U.S. Environmental Protection Agency
Athens, Georgia 30613-7799
ENVIRONMENTAL RESEARCH LABORATORY
OFFICE OF RESEARCH AND DEVELOPMENT
U.S. ENVIRONMENTAL PROTECTION AGENCY
ATHENS, GEORGIA 30613-7799
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DISCLAIMER
The information in this document has been funded wholly or in part by the
United States Environmental Protection Agency. It has been subject to the
Agency's peer and administrative review, and it has been approved for
publication as an EPA document. Mention of trade names or commercial products
does not constitute endorsement or recommendation for use.
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FOREWORD
Environmental protection efforts are increasingly directed toward
preventing adverse health and ecological effects associated with specific
compounds of natural or human origin. As part of this Laboratory's research
on the occurrence, movement, transformation, impact, and control of
environmental contaminants, the Biology Branch studies complexes of
environmental processes that control the transport, .transformation,
degradation, fate, and impact of pollutants or other materials in soil and
water and develops models for assessing exposures to chemical contaminants.
Concern about environmental exposure to synthetic organic chemicals has
increased the need for techniques to predict the behavior of chemicals
entering the environment as a result of the manufacture, use, and disposal of
commercial products. The Exposure Analysis Modeling System (EXAMS), which has
been undergoing continual development, test, and revision at this Laboratory*
since 1978, provides a convenient tool to aid in judging the environmental
consequences should a specific chemical contaminant enter a natural aquatic
system. Because EXAMS requires no chemical monitoring data, it can be used
for new chemicals not yet introduced into commerce as well as for those whose
pattern and volume of use are known. EXAMS and other exposure assessment,
models should contribute significantly to efforts to anticipate potential
problems associated with environmental pollutants *
Rosemarie C. Russo, Ph.D.
Director
Environmental Research Laboratory
Athens, Georgia
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ABSTRACT
The Exposure Analysis Modeling System, first published in 1982 (EPA-
600/3-82-023), provides interactive computer software for formulating aquatic
ecosystem models and rapidly evaluating the fate, transport, and exposure
concentrations of synthetic organic chemicals—pesticides, industrial
materials, and leachates from disposal sites. EXAMS contains an integrated
Database Management System (DBMS) specifically designed for storage and
management of project databases required by the software. User interaction is
provided by a full-featured Command Line Interface (CLI), context-sensitive
help menus, an on-line data dictionary and CLI users' guide, and plotting
capabilities for review of output data. EXAMS provides 20 output tables which
both document the input datasets and provide integrated results summaries for
aid in ecological risk assessments. •
EXAMS' core is a set of process modules that link fundamental chemical
properties to the limnological parameters that control the kinetics of fate
and transport in aquatic systems. The chemical properties are measurable by
conventional laboratory methods; most are required under various regulatory
authority. When run under the EPA's GEMS or pcGEMS systems, EXAMS accepts
direct output from QSAR software. EXAMS limnological data are composed of
elements historically of interest to aquatic scientists world-wide, so
generation of suitable environmental datasets can generally be accomplished
with minimal project-specific field investigations.
EXAMS provides facilities for long-term (steady-state) analysis of
chronic chemical discharges, initial-value approaches for study of short-term
chemical releases, and full kinetic simulations that allow for monthly
variation in mean climatological parameters and alteration of chemical
loadings on daily time scales. EXAMS has been written in generalized (N-
dimensional) form in its implementation of algorithms for representing spatial
detail and chemical degradation pathways. Implementations under VMS and MS-
DOS allow for study of three simultaneous chemical compounds and 32 or 50
environmental segments, respectively.
EXAMS provides analyses of
Exposure: the expected (long-term chronic, 24-hour and 96-hour acute)
environmental concentrations of synthetic chemicals and their
transformation products,
Fate: the spatial distribution of chemicals in the aquatic ecosystem,
and the relative importance of each transformation and transport process
(important in establishing the acceptable uncertainty in chemical
laboratory data), and
Persistence: the time required for natural purification of the ecosystem
(via export and degradation processes) once chemical releases end.
This report covers a period from April 15, 1985 to September 1, 1989, and work
was completed as of September 1, 1989.
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EXPOSURE ANALYSIS MODELING SYSTEM
User's Guide for EXAMS II Version 2.94
INTRODUCTION
Overview
EXAMS is an interactive computer-based system for specifying and storing
the properties of chemicals and ecosystems, modifying them using simple
commands, and conducting rapid evaluations and error analyses of the probable
aquatic fate of synthetic organic chemicals. EXAMS constructs simulation
models by combining the loadings, transport, and transformations of a chemical
into a set of differential equations, using the law of conservation of mass as
an accounting principle. This is accomplished by computing the total mass of
chemical entering and leaving each, section of a body of water as the algebraic
sum of external loadings, transport processes that distribute chemicals
through the system and export them across its external boundaries, and
transformation processes that convert chemicals to daughter products. The
differential equations are then assembled and solved to give a picture of the
behavior of chemicals in an aquatic ecosystem. The program produces output
tables and simpla graphics describing chemical
\
o exposure: the expected environmental concentrations (EECs)
resulting from a particular pattern of chemical loadings,
o fate: the distribution of the chemical in the system and the
fraction of the loadings consumed by each transport and
transformation process, and
o persistence: the time required for purification of the system (via
export/transformation processes) should the chemical loadings
cease.
EXAMS includes separate mathematical models of the kinetics of the
physical, chemical, and biological processes governing transport and
transformations of chemicals. This set of unit process equations is the
central core of EXAMS. EXAMS' "second-order" or "system-independent" approach
makes it possible to study the fundamental chemistry of materials in the
laboratory and then, based on independent studies of the levels of driving
forces in aquatic systems, evaluate the potential fate of materials in systems
that have not yet been exposed (Baugnman and Burns 1980). EXAMS treats
ionization, and partitioning of the compound with sediments and biota, as
thermodynamic properties or purely local equilibria peculiar to each segment
of the environmental model—as opposed to a treatment as system-wide "global"
equilibria. In this way, EXAMS allows for the impact of spatial variation in
sediment properties, pH, etc. on chemical reactivity. EXAMS computes the
behavior of trivalent organic acids, bases, and ampholytes; each ionic species
can have its own distinctive pattern of sorption and complexation with
naturally occurring particulates and dissolved organic matter. Reaction
pathways can be entered for the production of transformation products, whose
further transport and transformations are then also simulated by EXAMS.
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EXAMS computes the kinetics of transformations by direct photolysis,
hydrolysis, biolysis, and oxidation reactions. The input chemical data for
hydrolytic, biolytic, and oxidative reactions can be entered either as single
valued, second-order rate constants, or as pairs of values defining the rate
constant as an Arrhenius function of the temperature in each segment of the
water body. EXAMS has been designed to accept standard water-quality
parameters and system characteristics that are commonly measured by
limnologists throughout the world, and chemical datasets conventionally
measured or required by United States Environmental Protection Agency
regulatory procedures.
Functional Capabilities
EXAMS is a computer-based system for building models of aquatic
ecosystems and running simulation studies on the behavior of chemical
contaminants. EXAMS' environmental models are maintained in a file composed
of concise ("canonical") descriptions of aquatic systems, in which a body of
water is described as a set of N segments or distinct zones in the system. By
applying the principle of conservation of mass to the transport and
transformation process equations, EXAMS compiles a differential equation for
the net rate of change of chemical concentration in each segment. The
resulting system of N differential equations describes the mass balance for
the entire system. EXAMS includes a descriptor language that simplifies the
specification of system geometry and connectedness. The code is written in a
general (N-segment) form. The software is available in 32-segment (MS-DOS)
and 50—segment (VAX) versions.
The second-order process models used to compute the kinetics of
chemicals are the central core of EXAMS. Each includes a direct statement of
the interactions between the chemistry of a compound and the environmental
forces that shape its behavior in aquatic systems. Most of the process
equations are based on standard theoretical constructs or accepted empirical
relationships. For example, the light intensity in the water column of the
system is computed using the Beer-Lambert law, and temperature corrections for
rate constants are computed using Arrhenius functions. lonization of organic
acids and bases, complexing with dissolved organic carbon (DOC), and sorption
of the compound with sediments and biota, are treated as thermodynamic
properties or (local) equilibria that modify the speed of the kinetic
processes. For example, an organic base in the water column may occur in a
number of molecular species (as dissolved ions, sorbed with sediments, etc.),
but only the uncharged, dissolved species can be volatilized across the
air-water interface.
EXAMS allows for the simultaneous treatment of up to 28 molecular
species of a chemical—the parent uncharged molecule, and singly, doubly, or
triply charged cations and anions, each of which can occur in a dissolved,
DOC-complexed, sediment-sorbed, or biosorbed form. The program computes the
fraction of the total concentration of a compound that is present as each of
the 28 molecular structures ("distribution coefficients," ALPHA). These
values enter the kinetic equations as multipliers on the rate constants. The
program thus completely accounts for differences in reactivity that depend on
the molecular form of the chemical, as a function of the spatial distribution
of environmental parameters controlling molecular speciation. EXAMS makes no
internal assumptions about the relative transformation reactivities of the 28
molecular species. These assumptions are controlled through entry of
species-specific rate constants in the chemical input data.
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EXAMS includes two algorithms for computing the rate of photolytic
transformation of a synthetic organic chemical. These algorithms accommodate
the two more common kinds of laboratory data and chemical parameters used to
describe photolysis reactions. The simpler algorithm requires only an average
pseudo-first-order rate constant (KDP) applicable to near-surface waters under
cloudless conditions at a specified reference latitude (RFLAT). To control
reactivity assumptions, KDP is coupled to nominal (normally unit-valued)
reaction quantum yields (QUANT) for each molecular species of the compound.
This approach makes possible a first approximation of photochemical
reactivity, but neglects the very important effects of changes in the spectral
quality of sunlight with increasing depth in a body of water. The more
complex photochemical algorithm computes photolysis rates directly from the
absorption spectra (molar extinction coefficients) of the compound and its
ions, measured values of the reaction quantum yields, and the environmental
concentrations of competing light absorbers (chlorophylls, suspended
sediments, DOC, and water itself). When using a KDP, please be aware that
data from laboratory photoreactors usually are obtained at intensities as much
as one thousand times larger than that of normal sunlight.
The total rate of hydrolytic transformation of a chemical is computed by
EXAMS as the sum of three contributing processes. Each of these processes can
be entered via simple rate constants, or as Arrhenius functions of
temperature. The rate of specific-acid-catalyzed reactions is computed from
the pH of each sector of the ecosystem, and specific-base catalysis is
computed from the environmental pOH data. The rate data for neutral
hydrolysis of the compound is entered as a set of pseudo-first-order rate
coefficients (or Arrhenius functions) for reaction of the 28 (potential)
molecular species with the water molecule.
EXAMS computes biotransformation of the chemical in the water column,
and in the bottom sediments, of the system as entirely separate functions.
Both functions are second-order equations that relate the rate of
biotransformation to the size of the bacterial population actively degrading
the compound. The second-order rate constants (KBACW for the water column,
KBACS for benthic sediments) can be entered either as single-valued constants
or as functions of temperature. When a non-zero value is entered for the Q10
of a biotransformation (parameters QTBAW and QTBAS, respectively), KBAC is
interpreted as the rate constant at 20 degrees Celsius, and the biolysis rate
in each sector of the ecosystem is adjusted for the local temperature (TCEL).
Oxidation reactions are computed from the chemical input data and the
total environmental concentrations of reactive oxidizing species (alkylperoxy
and alkoxyl radicals, etc.), corrected for ultra-violet light extinction in
the water column. The chemical data can again be entered either as simple
second-order rate constants or as Arrhenius functions. Oxidations due to
singlet oxygen are computed from chemical reactivity data and singlet oxygen
concentrations; singlet oxygen is estimated as a function of the concentration
of DOC, oxygen tension, and light intensity. Reduction is included in the
program as a simple second-order reaction process driven by the user entries
for concentrations of reductants in the system.
Internal transport and export of a chemical occur in EXAMS via advective
and dispersive movement of dissolved, complexed, sediment-sorbed, and
biosorbed materials, and by volatilization losses at the air-water interface.
EXAMS provides a simple set of vectors (JFRAD, etc.) for specifying the
location and strength of both advective and dispersive transport pathways.
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Adyection of water through the system then is computed from the water balance,
using hydrologic data (rainfall, evaporation rates, stream-flows, groundwater
seepages, etc.) supplied as part of the definition of each environment.
Dispersive interchanges within the system, and across system boundaries, are
computed from a conventional geochemical specification of the characteristic
length (CHARL), cross-sectional area (XSTU&), and dispersion coefficient (DSP)
for each active exchange pathway. EXAMS can compute transport of a chemical
via whole-sediment bedloads, suspended sediment wash-loads, ground-water
infiltration, transport through the thermocline of a lake, losses in effluent
streams, etc. Volatilization losses are computed using a two-resistance
model. This computation treats the total resistance to transport across the
air-water interface as the sum of resistances in the liquid and vapor phases
immediately adjacent to the interface.
EXAMS allows for entry of external loadings of chemicals via point
sources, non-point sources, dry fallout or aerial drift, atmospheric wash-out,
and ground-water seepage entering the system. Any type of chemical load can
be entered for any system segment, but the program will not implement a
loading that is inconsistent with the system definition. For example, the
program will automatically cancel a rainfall load entered for the hypolimnion
or benthic sediments of a lake ecosystem. When this type of corrective action
is executed, the change is reported to the user via an information message.
EXAMS provides three operating "modes" of increasing complexity. In the
simplest case (mode 1), EXAMS executes a direct steady-state solution of the
dynamic system equations, thus generating a long-term analysis using a single
set of environmental conditions (e.g., annual average driving forces). In
mode 2, EXAMS makes available initial-value approaches that can be used to set
initial conditions and introduce immediate "pulse" chemical loadings. To the
extent that changes in hydrographic volumes (e.g., during spates) can be
neglected, this mode can be used to evaluate shorter-term transport and
transformation events by segmenting the input datasets and simulation
intervals according to time-slices under full user control. In mode 3, EXAMS
uses a set of 12 monthly values of all environmental parameters, with input
loads that can change monthly and can also include pulse events on individual
dates, to compute the dynamics of chemical contamination over the course of
one or more years' time. The outputs produced by the system are analogous for
all modes of operation, although they differ in detail. For example, in mode
1, a summary table and sensitivity analyses of system fluxes are reported for
steady-state conditions; in mode two the reports are generated for conditions
at the close of each time slice, and in mode 3, the program reports annual (or
interannual) average values and the size and location of exposure extrema.
Basic Assumptions
EXAMS has been designed to evaluate the consequences of longer-term,
primarily time-averaged chemical loadings that ultimately result in
trace-level contamination of aquatic systems. EXAMS generates a steady-state,
average flow field (long-term or monthly) for the ecosystem. The program thus
cannot fully evaluate the transient, concentrated EECs that arise, for
example, from chemical spills. This limitation derives from two factors.
First, a steady flow field is not always appropriate for evaluating the spread
and decay of a major pulse (spill) input. Second, an assumption of
trace-level EECs, which can be violated by spills, has been used to design the
process equations used in EXAMS. The following assumptions were used to build
the program.
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A useful evaluation can be executed independently of the
chemical's actual effects on the system. In other words, the
chemical is assumed not to itself radically change the
environmental variables that drive its transformations. Thus, for
example, an organic acid or base is assumed not to change the pH
of the system; the compound is assumed not to itself absorb a
significant fraction of the light entering the system; bacterial
populations do not significantly increase (or decline) in response
to the presence of the chemical.
EXAMS uses linear sorption isotherms, and second-order (rather
than Michaelis-Menten-Monod) expressions for biotransformation
kinetics. This approach is known to be valid for low
concentrations of pollutants; its validity at high concentrations
is less certain. EXAMS controls its computational range to ensure
that the assumption of trace-level concentrations is not grossly
violated. This control is keyed to aqueous-phase (dissolved)
residual concentrations of the compound: EXAMS aborts any analysis
generating EECs that exceed (the lesser of) 50% of the compound's
aqueous solubility or 10 micromolar (10"^) concentrations of a
dissolved unionized molecular species. This restraint
incidentally allows the program to ignore precipitation, of the
compound from solution and precludes inputs of solid particles of
the chemical.
Sorption is treated as a thermodynamic or, constitutive property of
each segment of the system, that is, sorption/desorption kinetics
are assumed to be rapid compared to other processes. The adequacy
of this assumption is partially controlled by properties of the
chemical and system being evaluated. Extensively sorbed chemicals
tend to be sorbed and desorbed more slowly than weakly sorbed
compounds; desorption half-lives may approach 40 days for the most
extensively bound compounds. Experience with the program has
indicated, however, that strongly sorbed chemicals tend to be
captured by benthic sediments, where their release to the water
column is controlled by their availability to benthic exchange
processes. This phenomenon overwhelms any accentuation of the
speed of processes in the water column that may be caused by the
assumption of local equilibrium.
Input and Output
Input parameters include:
1) A set of chemical loadings on each sector of the ecosystem.
2) Molecular weight, solubility, and ionization constants of the
compound.
3) Sediment-sorption and biosorption parameters: Kp, Koc or Kow,
biomasses, benthic water contents and bulk densities, suspended sediment
concentrations, sediment organic carbon, and ion exchange capacities.
4) Volatilization parameters: Henry's Law constant or vapor pressure
data, wind speeds, and reaeration rates.
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5) Photolysis parameters: reaction quantum yields, absorption spectra,
stratospheric ozone, cloudiness, relative humidity, atmospheric dust
content and air-mass type, scattering parameters, suspended sediments,
chlorophyll, and dissolved organic carbon.
6) Hydrolysis: second-order rate constants or Arrhenius functions for
the relevant molecular species, pH, pOH, and temperatures.
7) Oxidation: rate constants, temperatures, surface oxidant
concentrations, dissolved organic carbon, and oxygen tension.
8) Biotransformation: rate constants, temperatures, bacterial population
densities.
9) Parameters defining strength and direction of advective and
dispersive transport pathways.
10) System geometry and hydrology: volumes, areas, depths, rainfall,
evaporation rates, entering stream and non-point-source flows and
sediment loads, and ground-water flows.
Although EXAMS allows for the entry of extensive environmental data, the
program can be run with a much reduced data set when the chemistry of a
compound of interest precludes some of.the transformation processes. For
example, pH and pOH data can be omitted in the case of neutral organics that
are not subject to acid or alkaline hydrolysis. EXAMS produces 20 output
tables; these include an echo of the input data, and integrated analyses of
the exposure, fate, and persistence of the chemical or chemicals under study.
The program prints a summary report of the results obtained. Printer-plots of
longitudinal and vertical concentration profiles, as well as time-based
graphics, can be invoked by the user.
System Resource Requirements
EXAMS has been implemented in FORTRAN 77 and can be run on computers
with Fortran compilers that adhere to the full standard. The MS-DOS version
Of EXAMS was compiled under Ryan-McFarland v. 2.,43, and linked with
PLINK86plus version 2.23. The program requires available DOS memory of 435
Kbytes to load plus 32Kb for program operations; its size thus precludes
co-residence with many of the popular, PC "TSR" (terminate and stay resident)
programs. EXAMS is overlaid to run in the DOS environment but, after , : . :
reserving its 32 Kb for program operations, will establish-memory caches in
available extended memory space to minimize disk I/O overhead. . .',
Applications
EXAMS can be used to assess the fate, exposure, and persistence of
synthetic organic chemicals in aquatic ecosystems in which the chemical
loadings can be time-averaged or event loaded, and chemical residuals are at
trace levels. The program has been used, for example, by EPA to evaluate the
behavior of relatively field-persistent herbicides and to evaluate dioxin
contamination downstream from paper mills. EXAMS has been successfully used
to model volatilization of organics in specific field situations and for a
general assessment of the behavior of phthalate esters in aquatic systems.
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EXAMS has been implemented by a number of manufacturing firms for
environmental evaluations of newly synthesized materials and has been used in
an academic setting for both teaching and research. The Bibliography section
of this document lists application and validation studies that can be
consulted for additional detail.
Technical questions; contact the author,
Lawrence A. Burns, Ph.D.
Research Ecologist
US EPA/Athens-ERL
College Station Road
Athens, Georgia 30613-7799 USA
Telephone: (404) 546-3501, (FTS) 250-3501
Documentation and Software Availability
The computer program for version 2.94 of the Exposure Analysis Modeling
System II (EXAMS-II, v. 2.94) is available gratis from the U.S. Environmental
Protection Agency. A user manual is provided with the program; technical
documentation for the program is available from the National Technical
Information Service (NTIS) in the publication
"Exposure Analysis Modeling System (EXAMS): User Manual and System
Documentation" (EPA-600/3-82-023, NTIS PB 82 258096 (US $34.00))
The given price is for purchasers on the North American continent, who can
obtain the document from the
U.S. Department of Commerce
National Technical Information Service "
Springfield, Virginia 22161 USA
NTIS also maintains overseas depositories for the convenience of non-USA
organizations wishing to acquire their publications.
The EXAMS computer program can be obtained from the author at the
address given above. The program is supplied on microcomputer diskette
containing an MS-DOS executable image for use on an IBM PC or "compatible."
To use the PC/MS-DOS run-time version, you will need a microcomputer
(IBM-PC/AT or "Compatible") with at least 51'2 kilobytes of RAM (Random Access
Memory), a 1.2 megabyte or 360 kilobyte diskette drive, a mass-storage device
(5+ megabyte hard disk). Although not required, a math co-processor (80x87)
is strongly recommended. The EXAMS executable image runs under MS-DOS 2.12+
on the Intel 8086 chip family; note that you do NOT need a Fortran compiler.
Along with a request letter, please send one high-density (2S/HD, 5.25 inch)
or two 360 K (2S/DD, 5.25 inch) diskettes. In addition, the software is
available through the Center for Exposure Assessment Modeling (CEAM) bulletin
board system (BBS). The CEAM BBS can be accessed at no charge by calling
(404)-546-3402 (8N1).
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Bibliography
Baughman, G.L., and L.A. Burns. 1980. Transport and transformation of
chemicals: a perspective, pp. 1-17 In: O. Hutzinger (Ed.). The Handbook of
Environmental Chemistry, vol.2, part A. Springer-Verlag, Berlin, Federal
Republic of Germany.
Burns, L.A. 1989. Method 209—Exposure Analysis Modeling System (EXAMS—
Version 2.92). pp. 108-115 In: OECD Environment Monographs No. 27: Compendium
of Environmental Exposure Assessment Methods for Chemicals. Environment
Directorate, Organisation for Economic Co-Operation and Development, Paris,
France.
Burns, Ii.A. 1986. Validation methods for chemical exposure and hazard
assessment models, pp. 148-172 In: Gesellschaft fuer Strahlen- und Umwelt
forschung mbH Muenchen, Projektgruppe "Umwelt gefahrdungspotentiale von
Chemikalien" (Eds.) Environmental Modelling for Priority Setting among
Existing Chemicals. Ecomed, Muenchen-Landsberg/Lech, Federal Republic of
Germany.
Burns, L.A. 1985. Models for predicting the fate of synthetic chemicals in
aquatic systems, pp. 176-190 In: T.P. Boyle (Ed.) Validation and
Predictability of Laboratory Methods for Assessing the Fate and Effects of
Contaminants in Aquatic Ecosystems. ASTM STP 865, American Society for Testing
and Materials, Philadelphia, Pennsylvania.
Burns, L.A. 1983a. Fate of chemicals in aquatic systems: process models and
computer codes, pp. 25-40 In: R.L. Swann and A. Eschenroeder (Eds.) Fate of
Chemicals in the Environment: Compartmental and Multimedia Models for
Predictions. Symposium Series 225, American Chemical Society, Washington,
D.C.
Burns, L.A. 1983b. Validation of exposure models: the role of conceptual
verification, sensitivity analysis, and alternative hypotheses, pp. 255-281
In: W.E. Bishop, R.D. Cardwell, and B.B.' Heidolph (Eds.) Aquatic Toxicology
and Hazard Assessment. ASTM STP 802, American Society for Testing and
Materials, Philadelphia,, Pennsylvania. , . '
Burns, L.A. 1982. Identification and evaluation of fundamental^transport and
transformation process models, pp. 101-126 In: K.L. Dickson, A'.W. Maki, and J.
Cairns, Jr. (Eds.). Modeling the Fate of Chemicals in the Aquatic Environment.
Ann Arbor Science Publ., Ann Arbor, Michigan. , , . ' ...
Burns, L.A., and G.L. Baughman. 1985. Fate modeling, pp. 558-584 In: G.M. Rand
and S.R. Petrocelli (Eds.) Fundamentals of Aquatic Toxicology:. Methods and
Applications. Hemisphere Publ. Co., New York, New York.
Burns, L.A., and D.M. Cline. 1985. Exposure Analysis Modeling System:
Reference Manual for EXAMS II. EPA/600/3-85/038, U.S. Environmental Protection
Agency, Athens, Georgia. 83 pp.
Burns, L.A., D.M. Cline, and R.R. Lassiter. 1982. Exposure Analysis Modeling
System (EXAMS): User Manual and System Documentation. EPA-600/3-82-023, • U.S.
Environmental Protection Agency, Athens, Georgia. 443 pp.
Games, L.M. 1982. Field validation of Exposure Analysis Modeling System
(EXAMS) in a flowing stream. pp. 325-346 In: K.L. Dickson, A.W. Maki, and J.
8
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Cairns, Jr. (Eds.) Modeling the Fate of Chemicals in the Aquatic Environment.
Ann Arbor Science Publ., Ann Arbor, Michigan.
Games, L.M. 1983. Practical applications and comparisons of environmental
exposure assessment models, pp. 282-299 In: W.E. Bishop, R.D. Cardwell, and
B.B. Heidolph (Eds.) Aquatic Toxicology and Hazard Assessment, ASTM STP 802.
American Society for Testing and Materials, Philadelphia, Pennsylvania.
Lassiter, R.R., R.S. Parrish, and L.A. Burns. 1986. Decomposition by
planktonic and attached microorganisms improves chemical fate models.
Environmental Toxicology and Chemistry 5:29-39.
Paris, D.F., W.C. Steen, and L.A. Burns. 1982. Microbial transformation
kinetics of organic compounds, pp. 73-81 In: O. Hutzinger (Ed.). The Handbook
of Environmental Chemistry, v.2, pt.B. Springer-Verlag, Berlin, Federal
Republic of Germany.
Plane, J.M.C., R.G. Zika, R.G. Zepp, and L.A. Burns. 1987. Photochemical
modeling applied to natural waters. pp. 250-267 In: R.G. Zika and W.J. Cooper
(Eds.) Photochemistry of Environmental Aquatic Systems. ACS Symposium Series
327, American Chemical Society, Washington, D.C.
Pollard, J.E., and S.C. Hern. 1985. A field test of the EXAMS model in the
Monongahela River. Environmental Toxicology and Chemistry 4:362-369.
Sanders, P.F., and J.N. Seiber. 1984. Organophosphorus pesticide
volatilization: Model soil pits and evaporation ponds, pp. 279-295 In: R.F.
Kreuger and J.N. Seiber (Eds.) Treatment and Disposal of Pesticide Wastes. ACS
Symposium Series 259, American Chemical Society, Washington, D.C.
Schramm, K.-W., M. Hirsch, R. Twele, and O. Hutzinger. 1988. Measured and
modeled fate of Disperse Yellow 42 in an outdoor pond. Chemosphere 17:587-
595.
Slimak, M.W., and C. Delos. 1982. Predictive fate models: their role in the
U.S. Environmental Protection Agency's water program, pp. 59-71 In: K.L.
Dickson, A.W. Maki, and J. Cairns, Jr. (Eds.) Modeling the Fate of Chemicals
in the Aquatic Environment. Ann Arbor Science Publ., Ann Arbor, Michigan.
Staples, C.A., K.L. Dickson, F.Y. Saleh, and J.H. Rodgers, Jr. 1983. A
microcosm study of Lindane and Naphthalene for model validation, pp. 26-41
In: W.E. Bishop, R.D. Cardwell, and B.B. Heidolph (Eds.) Aquatic Toxicology
and Hazard Assessment: sixth Symposium, ASTM STP 802, American Society for
Testing and Materials, Philadelphia, Pennsylvania.
Wolfe, N.L., L.A. Burns, and W.C. Steen. 1980. Use of linear free energy
relationships and an evaluative model to assess the fate and transport of
phthalate esters in the aquatic environment. Chemosphere 9:393-402.
Wolfe, N.L., R.G. Zepp, P. Schlotzhauer, and M. Sink. 1982. Transformation
pathways of hexachlorocylcopentadiene in the aquatic environment. Chemosphere
11:91-101.
-------
EXAMS COMMAND LANGUAGE INTERFACE (CLI) USER'S GUIDE
This section describes the EXAMS command language, including usage and
reference information. The first part provides an overview of the command
language and its grammar. The second part contains detailed descriptions of
each command. The commands are listed in alphabetical order.
Conventions used in this Section;
Convention
CTRL/x
EXAMS-> LIST 7
•
keyword,...
[keyword]
-------
MODE Analytical Methodology
1 Long-term consequences of continued releases of
chemicals; steady-state analysis.
2 Detailed examination of immediate cpnsequences of
chemical releases; initial-value problems.
3 Intermediate-scale resolution of events over several
years, including effects of seasonal environmental
variability; analysis of time-series data.
Entering Commands
EXAMS commands are composed of English-language words (mostly verbs)
that describe what you want EXAMS to do. Some commands require qualifiers and
parameters. These give EXAMS more information on how to execute the command.
Command parameters describe the object to be acted upon by the command. In
some cases, the object is a keyword (as in the HELP command); in others, it is
an EXAMS data element (SET command) or a section of a file of input data or
analysis results to manipulate (STORE and LIST commands).
Throughout this section, EXAMS commands are printed in uppercase letters
for the sake of clarity. However, EXAMS will accept commands entered in
uppercase, lowercase, or a mixture of uppercase and lowercase letters. Most
EXAMS commands and keywords can be abbreviated to the least number of
characters needed to uniquely distinguish them from other options available.
For example, to end EXAMS you can enter "QUIT", "QUI", "QU", or "Q". The
least number of required characters depends on the context, however, but is
never more than three. For example, the SHOW command includes among its
options both and ; in this case you must enter three
characters for EXAMS to distinguish between them. In EXAMS' "help fields" and
prompts, capitalization is used to show you how many characters are required
for uniqueness.
The following example shows an AUDIT command and EXAMS' response, as
they would appear on a terminal ..-.•-.
EXAMS-> AUDIT ON
All input will now be copied into the file
named ."AUDOUT" on Fortran -Unit Number 4.
EXAMS-> ! This Command File should be renamed file.EXA
.EXAMS->
11
-------
EXAMS analyzes the parts of the above example as follows.
BXAMS->
AUDIT
ON
The EXAMS system prompt for command input; a greater-than (->)
means that EXAMS' command interpreter is ready for a command to
be entered.
The command name, requesting that EXAMS enable/disable the User
Notepad/Command File Creation facility.
An option of the AUDIT command, requesting that the Notepad/
Create facility be enabled.
All input will now b« copied into the file
named "AtJDOUT" on Fortran tJnit Number 4
A message from the AUDIT command, indicating that the command
completed successfully. The command interpreter used the value
of AUDOUT (4) to establish communication With an external file.
The next system command prompt, confirming that the command has
completed its operations (AUDIT has opened communications with
an external file and started recording terminal inputs), and
EXAMS is ready for additional input.
This Command rile should be renamed file.EXA
A comment. Comment lines must begin with an exclamation
point (!) or an asterisk (*). You can use comments, as needed,
to document EXAMS analysis sessions or command procedures.
KXAMS->
EXAM3->
The next EXAMS system command prompt, confirming that the
comment has been recorded in the Notepad/Command file and EXAMS
is ready to accept another command.
Command Prompting •• ..-••;'„
When you enter a command at the terminal-, you need not enter the entire
command on a single line. If you enter a "command that requires that you
specify its range or the object of the requested action, and you do not
include the needed information, EXAMS' command interpreter prokpts you for all
missing information. For example:
EXAMS-> AUDIT
The following AUDIT options are available '
ON
OFf -
Help -
Quit -
— begins a new Audit file,
— ends Audit recording of input commands,
— this message,
— return to the EXAMS prompt.
AUDIT-> ON
12
-------
All input will now be copied into the
file named "AUDOUT" on Fortran unit number 4
In this example, no AUDIT option was entered, so EXAMS prompts for a
more complete specification of the intended action. The line ending with a ->
indicates that EXAMS is waiting for the additional input.
In many cases, EXAMS' prompts do not include an automatic description of
the full range of possible response options. Often, however, entering HELP in
response to the prompt will display a list of available choices, as in the
following example..
EXAMS-> LIST
At the prompt, enter a Table number, "Quit,"
or "Help" to see a catalog of the output tables.
Enter Table Number -> HELP
1 Chemical inputs: FATE Data .
2 Chemical inputs: PRODUCT Chemistry
3 PULSE Chemical Loadings
20 Exposure Analysis SUMMARY
ALL Entire Report
At the prompt, enter a Table number, "Quit,"
or "Help" to see a catalog of the output tables.
Enter Table Number -> 18
Ecosystem: Name of Waterbody
Chemical: Name of chemical
Table 18.01. Analysis of steady-state fate ...
(body of table)
In the example above, LIST is entered without the number of the output table
to be displayed. EXAMS prompts for the missing information; typing HELP in
response to the LIST prompt displays a catalog of EXAMS output tables.
EXAMS Messages
When a command is entered incorrectly, EXAMS displays a descriptive
error message indicating what is wrong. For example, if a data subscript
larger that the maximum available is entered, EXAMS will respond
13
-------
Subscript out-of-range.
You can then retype the command correctly.
Other error messages may be produced during the execution of a command,
or during a simulation or data display sequence. These messages indicate such
things as incomplete environmental data, character data entered where numeric
data are required, or typographic errors during entry of commands. EXAMS will
respond to typographic errors in command entries by displaying:
Command not recognized. Type HELP for command information.
Because the messages are descriptive, it is usually possible to determine what
corrective action is required in order to proceed. When this is not the case,
EXAMS' HELP facility contains a large body of additional and supplementary
information available through the HELP, DESCRIBE, and SHOW commands.
The HELP Command ..
Consulting a printed guide is not the most convenient way to get a
summary of the syntax of a command or a definition of an input datum. EXAMS'
HELP command provides this information in EXAMS' interactive environment. For
example, you can type the command:
EXAMS-> HELP LIST
EXAMS responds by displaying a description of the LIST command, its syntax,
and the options needed to specify the range of the command.
The HELP facility also provides on-line assistance for EXAMS'
data, e.g.,
EXAMS-> HELP QUANT
input
will display the subscript ranges, their meanings, the physical dimensions,
and the English definition of EXAMS chemical input datum "QUANT". This
information is available online for all. EXAMS' input data and control
parameters. The names of all of EXAMS' input variables were selected as
mnemonics for their English-language names. (For example, QUANT is the
photochemical quantum yield.) These mnemonics are used in EXAMS' output
tables; definitions are given in the Data Dictionary of this User Manual as
well as in the on-line HELP. •
EXAMS' Help facility supplies lists of individual topics and subtopics,
The HELP command is described in more detail later in this Section, and a
tutorial explanation of the command is available online by entering
EXAMS-> HELP TUTOR
14
-------
Command Procedures - •
A command procedure is a file that contains a sequence of EXAMS
commands, optionally interspersed with descriptive comments (lines with "!" or
II*H in column one) . By placing sets of frequently-used commands and/or
response options in a command procedure, all the commands in it can be
executed as a group using a single c'ommand. For example, suppose a file
called START.EXA were to contain these command lines and comments:
SET MODE TO 3
SET KCHEM TO 4
SET NYEAR TO 5
RECALL LOAD 7 ,
! Load-UDB Sector 7 is the spray vector study
The four commands in this file can be executed by entering the command
EXAMS-> DO START
or EXAMS-> @START
You do not have to specify the file type of a command procedure when you use
the @ command, so long as the file type is ".EXA"—the default file type for
EXAMS' @ command. You can use another file suffix, if you so inform EXAMS
when you enter the command request. For example, to execute commands in a file
named START.UP
EXAMS-> QSTART.UP .-.•-.
Wild Card Characters
Some EXAMS commands accept a "wild card" character in the input command
specifications. The asterisk (*) is the only symbol having this function in
EXAMS. Wild card characters are used to refer to a range of data subscripts,
or other entities, by a general name, rather than having to enter a specific
name for each member of the group* Particular uses of wild cards in EXAMS
vary with the individual commands. The command descriptions later in this
Section indicate where wild cards are allowed and their effects.
Truncating Command Names and Keywords
All keywords and names of input data that are entered as command input
can be abbreviated. Only:enough characters to uniquely distinguish a keyword
or datum from others with similar names need be entered (often only one).
15
-------
Summary Description of EXAMS' System Commands
EXAMS Command
AUDIT
CATALOG
CHANGE/SET
CONTINUE
DESCRIBE
DO or @
ERASE
HELP
LIST
NAME
PLOT
PRINT
QUIT
READ/WRITE
RECALL
RUN
SHOW
STORE
ZERO
Summary Description
t
Start/Stop user notepad for recording procedures
List the contents of User Databases (UDBs)
Enter/reset input data and program controls
Resume integration (Modes 2 and 3 only)
Report dimensions and data type of parameter
Execute file of EXAMS commands (file.EXA)
Clear section of stored database (UDB)
Describes access to EXAMS on-line HELP facility
Show tabular results on the screen
Specify the name of a UDB, e.g., CHEM NAME IS ...
Plot results on the screen
Queue tabular results for hardcopy printing
Abort command, or End interactive session
Upload/Download data from non-EXAMS disk files
Activate data from stored database (UDB)
Begin simulation run
Display current data values or control settings
Download current data into stored database (UDB)
Clear chemical loadings, pulses, or residuals
16
-------
AUDIT
Creates a copy of user input commands and responses in an external file.
Related:
Control variables: AUDOUT
Commands: DO
Syntax:
AUDIT
-------
AUDIT-> ON
All input will now be copied into the
file named AUDOUT on Fortran Unit Number 4
This command begins recording of input from the terminal
into an external file. The output will go to a disk file
named "AUDOUT." After leaving EXAMS, this file can be
printed to give a permanent record of the analysis.
2. EXAMS-> AUDIT OFF
The AUDIT option has been terminated.
This command ends copying of EXAMS commands and responses
to the external medium (usually a disk file).
3. EXAMS-> AUDIT ON
All input will now be copied into the
file named "AUDOUT" on Fortran Unit Number 4
EXAMS-> RECALL ENV 2
Selected environment is: Phantom Inlet
EXAMS-> RECALL CHEM 2
Selected compound is: Dichloromucktane
EXAMS-> RECALL CHEM 4 AS 2
Selected compound is: Tetrabromochickenwire ,
EXAMS-> AUDIT OFF
These commands build a file (AUDOUT) that can later be used
as a command file upon entering the EXAMS system. In this
instance, the file would be renamed (e.g., COMMAND.EXA) and
used to execute the above series of commands as a unit—
EXAMS-> DO COMMAND
18
-------
CATALOG
Lists, by accession number, the title of all currently active entries in the
specified User Database (UDB).
Related:
Control variables: none
Commands: ERASE, NAME, RECALL, STORE
Syntax:
CATALOG <0ption>
Options
Chemical
Environment
Load
Product
Prompt:
Options:
Enter Environment, Chemical, Load, Product,
Help, or Quit->
Chemical
Lists the titles, by access number, of chemical databases
currently in the User Database. Each entry corresponds to
a single chemical, and contains the laboratory data des-
cribing ionization and (species-specific) partitioning and
reaction kinetics.
Environment
List the titles, by access number, of environmental data-
bases currently in the User Database. Each entry contains
a "canonical" physical and chemical model of an aquatic
system, including the environmental data needed to compute
reactivity and transport of synthetic chemicals in the
system.
Load
Lists the titles, by access number, of allochthonous
chemical loading patterns stored in the User Database.
These data include monthly values (kg/hour) for stream-
loads, non-point-source loads, groundwater seepage loads,-
precipitation loads, and drift loads of chemicals entering
the aquatic environment, plus specification of pulse
loadings. The pulse load data include the magnitude (kg),
target environmental segment, and scheduling (month and
day) of pulses of synthetic chemicals entering the system.
Product
Lists the titles, by access number, of reaction or
transformation product chemistries stored in the User
Database. These data include the Activity Database num-
bers of chemical parent and product compounds, the number
of the process responsible for the transformation, and the
19
-------
yield efficiency (mole/mole) as an
temperature.
(optional) function of
Description:
The CATALOG command inventories the contents of the specified
User Database (UDB) and lists the titles of active entries on
the terminal screen. Four types of UDBs are available, corres-
ponding to the four options available to the CATALOG command.
The titles are listed by accession number; this number is used
to STORE, RECALL, or ERASE database entries.
Examples:
1. EXAMS-> CATALOG HELP
The CATALOG command requires that you specify either:
1. Environment,
2. Chemical,
3. Load,
4. Product,
5. Help (this option), or
6. Quit.
Enter .Environment, Chemical, Load, Product,
Help, or Quit-> CHEMICAL
Catalog of CHEMICAL parameter sets
UDB No. Name of Entry Volume
1 Chemical Data Entry Template
2 p-Cresol
3 Benz[a]anthracene
EXAMS->
This command lists the contents of the current User Database
for chemical data. Any of these datasets can be loaded into
the Activity Database (ADB) for study, using the RECALL command
and the appropriate access number. The first entry ("Chemical
Data Entry Template") is a blank data area reserved for
entering new chemical data.
20
-------
2. EXAMS-> CATALOG ENVIRON
Catalog of ENVIRONMENTal models
UDB No. Name of Entry Volume
1 Environmental Data Entry Template
2 Pond — AERL code test data
3 Oligotrophic lake — AERL code test data
4 Eutrophic lake — AERL code test data
5 River — AERL code test data
6 Connecticut River estuary
EXAMS->
This command generates a listing of the environmental
datasets present in the User Database. Any of these can be
retrieved for study using a RECALL command and the accession
number. The first entry ("Environmental Data Entry Template")
is a template for entering a new environmental model.
21
-------
CHANGE
Use to enter data into the activity database.
Related:
Coimnands!
DESCRIBE,. HELP
Syntax: CHANGE TO
or SET =
Prompt: Enter name=value command->
Variable: The data entry or variable to be entered can be specified
either as a single datum or, using wild cards (*), as an entire
vector, row/column of a matrix, etc.
Description:
Use the CHANGE command to specify the values of data in the
activity database. "Value" can be any numerical quantity or
literal characters, as appropriate. "Variable" specifies an
individual element of input data or a program control
parameter. Entire vectors, rows/columns of matrices, etc. can
be set to a single uniform value using wild cards (*).
Examples:
1. EXAMS-> CHANGE VOL(53) TO 7E5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 32 elements,
EXAMS> CHANGE VOL(2) TO E
Invalid numeric quantity after TO or =
EXAMS-> CHANGE VOL(2) TO 7E5
This command sets the environmental volume of segment 2 to
7.OE+05 cubic meters. The initial attempt to set the volume of
segment 53 was rejected by EXAMS because the version in use was
set up for environmental models of 32 segments at most. The
DESCRIBE command was used to check the number of subscripts and
the dimensional size of the variable "VOL". The accidental
entry of an alphabetic character ("E") for the volume was
trapped by the CHANGE command; VOL(2) was not altered.
22
-------
2. EXAMS-> HELP TCEL
TCEL is a Real Matrix with 32 rows and 13 columns.
Temperature-CELsius (segment,month) Units: degrees C.
Average temperature of ecosystem segments.
Used (as enabled by input data) to compute effects of
temperature on transformation rates and other properties
of chemicals. " .••-..
EXAMS-> CHANGE TCEL(2,7) TO 24
This command changes the July temperature in segment 2 to 24
degrees C. The HELP command was used to check subscript dimen-
sions, maximum values, the meaning of the subscripts (subscript
#1 denotes the segment, subscript #2, the month), and the
proper units for the input datum (degrees Celsius).
3. EXAMS-> HELP POH
POH is a Real Matrix with 32 rows and 13 columns.
pOH (segment,month) Units: pOH units
The negative value of the power to which 10 is raised in
order to obtain the temporally averaged concentration of
hydroxide [OH"] ions in gram-equivalents per liter.
EXAMS-> CHANGE POH(*,13) TO 6.2
This command sets the average pOH (sector 13) of every
segment to 6.2. .Note use of wild card "*" to specify that all
segments are to be changed. As in the previous example, HELP
was used to check subscript dimensions, units, etc. This step,
of course, is optional.
23
-------
r
CONTINUE
The CONTINUE command resumes EXAMS' simulation analysis of chemical dynamics
beginning from the current state of the system.
Related:
Syntax:
Prompt:
Options:
Description:
Examples:
Control variables: CINT, TINIT, TEND,TCODE, NYEAR
Commands: RUN, SHOW TIME FRAME
CONTINUE
(In Mode 2 only:)
Initial time for integration will be (nn.n) units
Enter ending time of integration, Help,
or Quit->
None. Reply to prompt with a value greater than (nn.n).
The CONTINUE command resumes EXAMS' simulation analysis of
chemical dynamics, beginning from the current state of the
system. Chemical loadings and other input data can be altered
(CHANGEd or SET) between simulation time segments; EXAMS will
re-evaluate equation parameters as needed to incorporate the
changed conditions into the analysis.
CONTINUE cannot be invoked from Mode 1, where it is not approp-
riate. The SHOW TIME FRAME (abbreviate to SH T F) command can
be used to examine the current state of the integrator timer
controls. In Mode 2, the Communications INTerval CINT can be
used to vary the temporal resolution in different segments of
the analysis (see Example 1). In Mode 3, NYEAR, the number of
years in a simulation time segment, can similarly be altered.
1. EXAMS-> SET MODE=>2
EXAMS-> SHOW TIME FRAME
A RUN will integrate from
with output at intervals of
EXAMS-> SET TCODE==2
EXAMS-> SET TEND=10
EXAMS-> SET CINT=0.25
EXAMS-> SH TI F
A RUN will integrate from
with output at intervals of
0., to 24 . Hours
2.00 Hours
0. to 10. Days
0.25 Days
24
-------
EXAMS-> RUN
Simulation beginning for:
Environment: Pond — AERL code test data
Chemical 1: Dichloromucktane
Run complete
EXAMS-> PLOT KIN PL (3,0,0 — see PLOT command)
System: Pond — AERL code test data
Chemical: Dichloromucktane
2.00
1.33
0.667
IBB BBB
I B BBBB BBBB
I
I .
I
I : •
I .,-•... • . .
I :
I ._ ..... • .
I ''.•..• • - ;
I ...
I
I' •.'.'•. ..-..:
BBBB BBBB BBB
B BBBB BBBB BB
BB BBB
0.000
i i i t i i i i _t_ _t_ i
, L . T"! • ~t , T ~ . */ i . , T, ~- -T —•— -^-— — . — — fm , ~ 7 -^— — — ~T
0,000 . 2.00 4.00 6.00 8.00 10.0
1.00 ,; 3.00 •-..< :•,- 5.00
Time, Days
7.00
EXAMS-> SET CINT=1 -
EXAMS-> CONTINUE ;. ' '
Initial time for integration ,will be
Enter ending time of-integration, Help,
or Quit-> 30
Simulation beginning for:
Environment: Pond — AERL code test data
Chemical 1: Dichloromucktane
Run complete.
EXAMS-> SET CINT=10
EXAMS-> ZERO PULSE LOAD
EXAMS-> CONTINUE
Initial time for integration will be
9,00
10.0 Days
30.0 Days
Enter ending time of integration, Help, or Quit-> 90
25
-------
Simulation beginning for:
Environment: Pond — AERL code test data
Chemical 1: Dichloromucktane
Run complete.
EXAMS-> PLOT KINETIC PLOT (3,0,0)
System: Pond — AERL code test data
Chemical: Dichloromucktane
3.49 .IB
I BB
I BB
I B
I BB
2.33 I BB
IB BB
IBBB BBB
I BBB
I BB B
1.16 I B
I B
I BBB
I
I
0.000 I
+ ,+ + + + + + + + + +
0.000 18.0 36.0 54.0 72.0 90.0
9.00 27.0 45.0 63.0 81.0
Time, Days
These commands show the use of the CONTINUE command in Mode 2. The
objective of the analysis was to introduce two pulses of chemical
separated by 10 days and to follow exposure over 90 days. Note the
phased increase in the Communications INTerval CINT from 0.25 to 1
and then 10 days. Note the use of the ZERO command to clear the
pulse load ADB before the simulation of dissimilation from day 30
through day 90. If this were not done, EXAMS would introduce an
additional pulse on day 30.
2. EXAMS-> SET MODE=3
EXAMS-> SHO TI FR
A RUN will integrate from 1 January 1989
through 31 December 1989.
(YEAR1 = 1989, and NYEAR = 1.)
EXAMS-> RUN
Simulation beginning for:
Environment: Pond — AERL code test data
Chemical 1: Dichloromucktane
26
-------
Run complete.
EXAMS-> SHO TI FR
A RUN will integrate from 1 January 1989
through 31 December 1989.
(YEAR1 = 1989, and NYEAR = 1.)
CONTinuation will proceed through 31 December 1990
(NYEAR = 1.)
EXAMS-> SET NYEAR=3
EXAMS-> SH TI F
A RUN will integrate from 1 January 1989
through 31 December 1991.
(YEAR1 = 1989, and NYEAR = 3.)
CONTinuation will proceed through 31 December 1992
(NYEAR = 3.)
EXAMS-> CONTINUE
CONTinuing integration through 31 December 1992.
Simulation beginning for:
Environment: Pond — AERL code test data
Chemical 1: Dichloromucktane
Run complete.
EXAMS->
These commands illustrate the use of the CONTINUE command in
Mode 3. "SHOW TIME FRAME" is used to check the state of the
integrator timer controls.
27
-------
DESCRIBE
Reports the data type, dimensionality, and implemented size of parameters.
Related:
Control variables:
Commands: HELP
Syntax:
DESCRIBE
Parameters:
Any "system parameter"—any chemical or environmental
input datum, control parameter (e.g., MODE, CINT), etc.
Prompt:
Options:
Enter name of input parameter->
Any parameter accessible to the CHANGE and SET commands can be
inspected using the DESCRIBE command.
Description:
The DESCRIBE command returns information about EXAMS' input
data and control parameters. All variables whose values can be
altered using the CHANGE and SET commands can be inspected by
the DESCRIBE command. The information returned by DESCRIBE
includes the data type (real, integer, character), dimension-
ality (scalar, vector, matrix (2-dimensional), table (3-dimen-
sional matrix)) and implemented size in the version of EXAMS in
use. The DESCRIBE command is the first recourse when a CHANGE
or SET command fails.
Examples:
1. EXAMS-> DESR MODE . " . ' .
Command not recognized. Type HELP for command information.
EXAMS-> DESCR ". !,« .
Enter name of input parameter-> MODE
MODE is an Integer Scalar.
These commands establish that "MODE" is an integer scalar.
Note that the initial typing error (DESR) resulted in a "not
recognized" error message followed by return to the EXAMS
prompt.
28
-------
2. EXAMS-> CHANGE VOL(33) TO 7E5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 32 elements.
This command reports that VOL is a real variable, with 32
elements. In this example, the number of segments (NPX) in the
version of EXAMS currently in use is set for 32 at most. Any
(intentional or accidental) attempt to set "KOUNT" to a value
>32, or to enter a value for the VOLume of a segment >32 (e.g.,
VOL(33)) will fail, as illustrated above. DESCRIBE can be used
to check the reason for a failure of the CHANGE or SET command
when a problem with dimension sizes is suspected.
3. EXAMS-> DESCRIBE QUANT
, QUANT is a Real Table with dimensions (3,7,4)
EXAMS-> HELP QUANT
QUANT is a Real Table with dimensions (3,7,4)
QUANTum yield (form,ion,chemical) Units: dimensionless
Reaction quantum yield for direct photolysis of chemicals
— fraction of the total light quanta absorbed by a chemi-
cal that results in transformations. Separate values (21)
for each potential molecular type of each chemical allow
the effects of speciation and sorption on reactivity to
be specified in detail. The matrix of 21 values specifies
quantum yields for the (3) physical forms: (1) dissolved,
(2) sediment-sorbed, and (3) DOC-complexed; of each of (7)
possible chemical species: neutral molecules (1), cations
(2-4), and anions (5-7). (QUANT is an efficiency.)
These commands report the data type and dimensionality of
EXAMS' input "QUANT" (result of "DESCRIBE QUANT") and then
report the meaning of the dimensions and the physical units of
the variable (result of "HELP QUANT"). The local implementation
of EXAMS used in this example has the capacity to simulate the
behavior of no more than four chemicals simultaneously. Thus,
QUANT was DESCRIBEd as consisting of a set of four matrices,
each of (fixed) size (3,7).
29
-------
D O
Executes a command procedure; requests that EXAMS read subsequent input from
a specific file.
Related:
Control variables:
Commands: AUDIT
Syntax:
Prompt:
Parameters:
DO
Enter name of file (no more than nn characters),
Help, or Quit->
name of file
Description:
Specifies the file from which to read a series of EXAMS
commands. If you do not specify a file type suffix, EXAMS
uses a default file type of EXA (e.g., "filename.EXA").
Wild cards are not allowed in the file specification.
Use command procedures to catalog frequently used sequences of
commands. An EXAMS command procedure can contain
o Any valid EXAMS command. The command line can include all
the necessary options and data to build a complete
command (exception: kinetic plots).
•R
o Parameters or response options for a specific command.
When the currently executing command requires additional
parameters, the next line of the command file is searched
for appropriate input.
o Data. When the currently executing command requires
numerical or character data entry, the next line of the
command file is searched for input.
o Comment lines. Any line that contains an exclamation
point (!) or asterisk (*) in column one is ignored by
EXAMS' command interpreter. These lines cam be used as
needed to document the command procedure.
Command procedures must not contain a request to execute
another command procedure. (In other words, a. DO file must not
contain a DO (@) command; EXAMS' DO commands cannot be nested.)
Command procedures can be constructed as external files using
your favorite editor, or they can be constructed interactively
through the EXAMS system command processor, as illustrated
below. The default file type is "EXA", but files of any type
(suffix) can be used if the entire file name is specified when
entering the DO command.
30
-------
Examples:
1.
EXAMS-> AUDIT ON
All input will now be copied into the
file named "AUDOUT" on Fortran Unit Number 4
EXAMS-> RECALL
Enter Environment, Chemical, Load, Product,
Help or Quit-> ENV
Enter environment UDB catalog number,
Help, or Quit-> 2
Selected environment is: Phantom Inlet
EXAMS-> RECALL CHEM 2
Selected compound is: Dichloromucktane
EXAMS-> RECALL LOAD 2
Selected load is: Aedes spray drift
EXAMS-> ! LOAD 2 is the Phantom Inlet salt marsh study
EXAMS-> SET KCHEM TO 2
EXAMS-> RECALL CHEM 4 AS 2
Selected compound is: Tetrabromochickenwire
EXAMS-> AUDIT OFF
These commands build a file (AUDOUT.DAT) that can later be
used as a command file upon entering the EXAMS system. In this
.-:. instance, the file could be renamed (e.g., SETUP.EXA) and used
to execute the'above series of commands as a. unit:
or
EXAMS-> DO SETUP
EXAMS-> @SETUP
The command file appears as follows:
RECALL ' •' i ' , '- ; • '
.7 • •--, ENV . • ; -; -' '••• .---••-.. • '. -i - •-'-.• ••'-'
2
/RECALL CHEM 2
RECALL LOAD 2
! LOAD 2 is the Phantom Inlet salt marsh study
SET KCHEM TO 2
RECALL CHEM 4 AS 2
AUDIT OFF
Note that command files that are constructed interactively will
31
-------
include "AUDIT OFF" as the final instruction. This can, of
course, be removed by editing the file if it is undesirable.
2.
EXAMS-> DO
Enter name of file (no more than nn characters),
Help, or Quit-> HELP
The "DO" or "@" command provides a means of executing
stored EXAMS commands. In response to the prompt, enter
the name of the file that contains the stored commands. A
three-character filename extension of "EXA" is added to
the name if no period is present in the name as entered.
The maximum length for file names is nn chciracters; this
limit includes the .EXA suffix.
Enter name of file (no more than nn characters),
Help, or Quit-> AUDOUT
EXAMS/DO-> ! Audit trail of input sequence from EXAMS.
EXAMS/DO-> RECALL
Enter Environment, Chemical, Load, Product,
Help, or Quit->
EXAMS/DO-> ENV
Enter environment UDB catalog number,
Help, or Quit->
EXAMS/DO-> 2
Selected environment is: Phantom Inlet
EXAMS/DO-> RECALL CHEM 2
Selected compound is: Dichloromucktane
EXAMS/DO-> RECALL LOAD 2
Selected load is: Aedes spray drift
EXAMS/DO-> ! LOAD 2 is the Phantom Inlet salt marsh study
EXAMS/DO-> SET KCHEM TO 2
EXAMS/DO-> RECALL CHEM 4 AS 2 .
Selected compound is: Tetrabromochickenwire
EXAMS/DO-> AUDIT OFF '
The AUDIT option has been terminated.
This command requests execution of the command procedure
constructed, in Example 1 above. The default name (AUDOUT) was
not altered, so the complete file specification was given to
the DO command as the entry parameter. The DO file transfers a
set of two chemicals, an environmental model, and a load
pattern from the stored UDB to the ADB for study and analysis.
32
-------
ERASE
Deletes, by accession number, the data stored at a single sector of a User
Database (UDB) library (chemical, environmental, loadings, product chemistry)
Related:
Control variables:
Commands:
CATALOG, RECALL, STORE
Syntax:
ERASE
-------
I
data include the Activity Database numbers of reactants
and products, the number code of the chemical process, and
yield efficiencies (mole/mole) as an (optional) function
of temperature.
Description:
ERASE deletes the contents of a single sector of the specified
User Database (UDB) library (chemical, environmental, loads, or
product chemistry). The data to be deleted are selected by
choosing the appropriate accession number. (If you work in a
multi-user environment, be sure to avoid erasing others' data.)
Examples:
1. EXAMS-> ERASE ENV 20
Environment 20 erased.
This command erases the data stored at Environmental UDB
sector number twenty. The space is now available for storing
another dataset.
2. EXAMS-> ERASE
Enter Environment, Chemical, Load, Product,
Help, or Quit-> HELP
The ERASE command requires that you specify either:
1. Environment,
2. Chemical,
3. Load,
4. Product,
5. Help (this option), or
6. Quit.
Enter Environment, Chemical, Load, Product,
Help, or Quit-> LOAD
Enter allochthonous loading UDB catalog number,
Help, or Quit-> 10
Load
10 erased.
This command erases the data stored at Loadings UDB sector
number ten. The space is now available for another dataset,
34
-------
EXIT
EXIT can be used as a synonym for QUIT to end an interactive session.
Related:
Control variables:
Commands: QUIT is used to abort commands in progress,
Syntax:
Prompt:
Options:
Description:
EXIT
None
None
If EXIT is entered from the EXAMS prompt command level, EXAMS
stops and returns control to the computer operating system.
Examples:
1. EXAMS-> EXIT
This command terminates an interactive EXAMS session.
35
-------
HELP
Displays, on the terminal, information available in EXAMS' help files. EXAMS
provides descriptions of its commands, input data, control parameters, and
general concepts and analysis procedures.
Related:
Control variables:
Commands:
DESCRIBE
Syntax:
Prompt:
Keyword:
HELP
None
[keyword]
Description:
Specifies a keyword (a topic or an element of EXAMS input data)
that tells EXAMS what information to display.
o None—if HELP is typed with no keyword, EXAMS lists the
keywords that can be specified to obtain information about
other topics.
o Topic-name—describes either a basic EXAMS command, an
information page, or a "system parameter." System param-
eters include chemical and environmental input data,
system control parameters (e.g., CINT), and parameters
that control the current analysis (e.g., IMASS).
Ambiguous abbreviations result in a failure to achieve a
match on the keyword, and an error message is displayed.
The HELP command provides access to EXAMS' collection of on-
line user aids and information texts. This material includes
o Brief discussions of the syntax and function of each of
EXAMS' command words (RECALL, RUN, etc.)
o Definitions, physical dimensions, and meanings of sub-
scripts for EXAMS' chemical and environmental input data
and control parameters.
o A series of information pages providing orientation to the
concepts implemented in the EXAMS program, the range of
capabilities and analyses that can be executed with the
program, and brief expositions on data structures and
program control options.
36
-------
Examples:
1. EXAMS-> HELP
EXAMS includes these system commands:
HELP message text.and list of command and information
topics
Issuing the HELP command without any keywords produces a
list of the HELP topics in EXAMS main command library.
When responding to one of the topics on the list, EXAMS
displays a HELP message on that topic, and a list of subtopics
(if any).
2. EXAMS-> HELP QUOIT .
No information available for this request.
EXAMS->
When you request information for a topic not on file,
EXAMS displays a message to that effect and returns you to the
EXAMS-> prompt.
3. EXAMS-> HELP QUANT
QUANT is a Real Table with dimensions(3,7,4)
QUANTum yield (form,ion,chemical) Units: dimensionless
Reaction quantum yield for direct photolysis of chemicals
— fraction of the total light quanta absorbed by a chemi-
cal that results in transformations. Separate values (21)
for each potential molecular type of each chemical allow
the effects of speciation and sorptibn on reactivity to
be specified in detail. The matrix of 21 values specifies
quantum yields for the (3) physical forms: (1) dissolved,
(2) sediment-sorbed, and (3) DOC-complexed; of each of (7)
possible chemical species: neutral molecules (1), cations
(2-4), and anions (5-7). (QUANT is an efficiency.)
You can request information about any input datum (chemical,
environmental, control parameters, analysis parameters) acces-
sible to the CHANGE and SET commands. EXAMS then displays on
the screen the characteristics of the variable (equivalent to
the results of DESCRIBE), followed by a discussion of the
variable that echoes the entry in the Data Dictionary section
of the EXAMS User Manual.
37
-------
r
LIST
Displays an EXAMS output table on the terminal screen.
Related:
Control variables: FIXFIL
Commands: PLOT, PRINT
Syntax:
LIST
-------
Examples:
1. EXAMS-> LIST
A PRINT, LIST, or PLOT command was issued before executing
a RUN. If results exist from a previous simulation, these
can be accessed after issuing the command:
SET FIXFIL TO 1
EXAMS-> SET FIXFIL TO 1
EXAMS-> LIST
Enter Table Number -> HELP
1 Chemical inputs: FATE Data
2 Chemical inputs: PRODUCT Chemistry
3 PULSE Chemical Loadings
18 Sensitivity Analysis of Chemical FATE
19 Summary TIME-TRACE of Chemical Concentrations
20 Exposure Analysis SUMMARY
ALL Entire Report
Table-> 18
Ecosystem: Name of Waterbody
Chemical: Name of chemical
TABLE 18.01. Analysis of steady-state fate ...
(body of table)
The LIST command requests that output Table 18 from an EXAMS
results file be displayed on the terminal. For illustrative
purposes, it was assumed that the user had left EXAMS and then
returned to inspect Table 18 generated in the previous session.
2. EXAMS-> LIST 20
Ecosystem: Name of Waterbody
Chemical: Name of FIRST chemical
39
-------
r
TABLE 20.01. Exposure analysis summa,ry: 1983—1985.
(body of table)
More? (Yes/No/Quit)-> Y
Ecosystem: Name of Waterbody
Chemical: Name of SECOND chemical
TABLE 20.02. Exposure analysis summary: 1983—1985.
(body of table)
In this example, EXAMS was used to investigate the behavior of two chemicals
over a period of several years, using Mode 3 simulations. The analysis began
with year 1983, and NYEAR was set to 3 to produce an analysis of the period
1983 through 1985. The LIST command requests that all versions of Table 20 in
the analysis file be displayed, with a pause between each for inspection of
the results. In the example, the analyst chose to examine the output for both
chemicals. If the analysis is now CONTINUEd, the current set of tables will
be replaced with new results. The PRINT command should be used to make copies
of all intermediate results you want to save.
The sub-table numbers of EXAMS' output tables identify the
ADB number of the chemical, the indexes of any ions (see SPFLG
in the Dictionary), and the month of the year, as follows.
Table
1
4-6, 8,
10,11,13
Sub-tables
l.cc.i
NN.mm
Examples
1.01.1
4.01
10.13
Sub-table Meaning
Table . chemical . ion
Table. month
(13 = annual mean)
12
12. cc.mni
12.01.12
Table.chemical.month
14 (Mode 1/2) 14. cc
14 (Mode 3) 14.cc.mm
15-18,20 NN.cc
14.01
14.01.12
18.01
20.01
Table . chemical
Table . chemical .month
Table . chemical
40
-------
NAME
Use the NAME command to attach unique names to datasets.
Related:
Syntax:
Prompt:
:
Control Variables: MCHEM
Commands: CATALOG, ERASE, STORE, RECALL
NAME IS a[aa—] (up to 50 characters)
where can be CHEmical, ENvironment,
LOad, or PROduct
Options available are:
Help - this message.
Quit - return to EXAMS command mode.
= Help
- accepted as the new name.
Enter new name->
EXAMS uses these four kinds of datasets:
1. CHEMICAL reactivity and partitioning,
2. ENVIRONMENTal physico/chemical parameters,
3. allochthonous chemical LOADings, and
4. PRODUCT chemistry for generating interconversions
among multiple chemicals in an analysis
Description:
The NAME command is used to -associate unique names with
datasets in the UDB. These names can be STOREd in the
CATALOGS; they are printed in the headers of EXAMS' output
tables. When naming CHEMICAL datasets, the ADB number of the
chemical to be named is given by MCHEM; use "SET MCHEM TO n"
before naming dataset "n".
41
-------
r
Examples:
1. EXAMS-> CHEM NAME IS Tetrachlorochickenwire
The NAME command associates the name "Tetrachloro..." with
the chemical data in the sector of the activity database (ADB)
given by the current value of MCHEM. This name will be printed
on all subsequent appropriate output tables, and it will be
used as a title for the database if the STORE command is used
to download the data into the User Database (UDB).
2. EXAMS-> SET MCHEM =2
EXAMS-> CHEM NAME IS Dichloromucktane
The chemical name command always addresses the MCHEM sector
of the chemical ADB, thus, this example names chemical number 2
to "Dichloro...".
3. EXAMS-> ENVIR NAME IS Pogue Sound
This command names the current environmental dataset "Pogue
Sound". The name will now appear on output tables, and remain
with the dataset if it is downloaded to the UDB permanent
files.
42
-------
PLOT
Used to plot character graphics for the chemical state of the ecosystem.
Related:
Control Variables: MCHEM
Commands: LIST, PRINT
Syntax:
Prompt:
PLOT
Options 1:
POINT
PROFILE
KINETIC
The following options are available:
POint
PRofile -
Kinetic -
Help
Quit
Option->
Vertical concentration profile
Longitudinal concentration profile
List or plot kinetic outputs
This message
Return to the EXAMS program prompt
Plot options: POINT
"POINT" plots are generalized profiles of chemical concentra—
tions. These also require selection of a variable to be dis-
played (total concentration, dissolved concentration,- etc.)
and a "statistical" class (average values, minima, or maxima).
PROFILE
"PROFILE" plots are longitudinal profiles of chemical concen^
trations. These require selection of a concentration variable
(total concentration, dissolved concentration, etc.) and an
environmental sector (water column or benthic sediments). The
abscissa of the resulting plot is set up by increasing segment
number, which in most cases should represent an upstream-down-'
stream progression. When the aquatic model includes both lon>-
gitudinal and vertical segmentation, each section of the plot
begins at the air-water or water/benthic interface and proceeds
vertically downward (the bars are presented along the
abscissa).
43
-------
r
KINETIC
"KINETIC" plots display the results of integration of the
governing equations over the time spans selected for simula-
tion. These plots also require selection of concentration
variables and either particular segments, or summary "statis-
tics," for display. Time is used as the abscissa for the plot.
Description:
Use the PLOT command to display results of the current
analysis. Three kinds of character-graphic PLOTs are
available on-line from EXAMS: POINT, PROFILE, and KINETIC
Each PLOT requires the specification of several options;
these can either be entered on the system command line or
entered in response to EXAMS prompts. The available second-
and third-level options are illustrated in the examples
below. The results available to POINT and PROFILE plots
depend on the Mode used in the simulation. In Mode 1, the
outputs are steady-state concentrations. In Mode 2, the
results are a snap-shot of concentrations as of the end of
the current temporal simulation segment. In Mode 3, the
results are time-averaged concentrations over the most recent
temporal simulation segment of length NYEAR.
Examples:
1. EXAMS-> PLOT POINT
The following concentration options .are available:
Total - mg/L in Water Column,
mg/kg in Benthic Sediments
Dissolved - "Dissolved" (mg/L)
(aqueous + complexes with "dissolved" organics)
Particulate - Sediment-sorbed (mg/kg dry weight)
- Biosorbed (ug/g dry weight)
Chemical mass as grams/square meter AREA
This message
- Return to the EXAMS prompt
Biota
Mass
Help
Quit
Opt±on-> DISSOLVED
The following statistical options are Bailable:
MAX
MIN
AVE
Help
Quit
- Maximum concentration
- Minimum concentration
- Average concentration
- This message
- Return to the EXAMS prompt
44
-------
Option-> AVERAGE
9.00E-T-04
C
0 8.00Er-04
N ,
AC
V E
EN
R T 7.00E-04
A R
G A
E T
• ' I .'
O 6.00E-1-04
N
-I
I
I AAAAAAAAAAA
I A|
I A|
-± A|
I A|
I A|
I A|
I A|
-I A|
I Al
J A|
I A|
I A|
-I A|
I A|
I A|
I A|
I A|
II
1 1
II
ID
|I
IS
IS
|0|
ILI
|V|
|E|
|D|
1 1
|M|
|G|
I/I
ILI
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
IA
5.00E-04
D
I
S
S
O
L
V
E
D
M
|A AAAAAGAAAAA
A| | | |/| | | |A
A||||L||I|A
-+_AAAAAAAAAAA_AAAAAAAAAAA
Water Col Benthic
EXAMS-> SET MCHEM=2
EXAMS-> PL PO
4.00E-04
C
O
N
A C
V E
E N
R T
A R
G A
E T
I
O
N
3.50E-03
3.00E-03
2.50E-03
2.00E-03
AV
-I
I
I
I
I
-I
I
I
I
I .
I
I
I
I
S
S
O
L
AAAAAVAAAAA
D
I
S
AAAAASAAAAA
A| |
A| |
A| I
A| |
A| I
A| |
A! |
1 1
IA
|A
|A
|A
|A
|A
|A
A|
A|
A|
A|
A|
A|
A|
A|
A|
A|
ILI
IDI
I I
I/I
ILI
IA
|A
|A
|A
IA
|A
|A
IA
IA
IA
_AAAAAAAAAAA_
Water Col
AAAAAAAAAAA
Benthic
45
-------
C
T O
O N
T C
A E
L N
T
M R
G A
/ T
L I
O
N
, This example illustrates 'EXAMS' internal prompting for POINT
plots. Note that the analysis included two chemicals; the plot
for chemical number two was obtained by first SETting MCHEM=2.
The second plot was requested via a single command line, thus
bypassing the PLOT prompts.
2. EXAMS-> PLOT PROF
The following concentration options are available:
Total - mg/L in Water Column,
mg/kg in Benthic Sediments
Dissolved - "Dissolved" (mg/L)
(aqueous + complexes with "dissolved" organics)
Particulate - Sediment-sqrbed (mg/kg dry weight)
Biota - Biosorbed (ug/g dry weight)
Mass - Chemical mass as grams/square meter AREA
Help - This message
Quit - Return to the EXAMS prompt
Option-> TOTAL ,
The following options are available:
WATER -, Water Column concentrations
SEDIMENTS - Benthic Sediment concentrations
Help - This message
Quit - Return to the EXAMS prompt
Option-> WATER
8.00E-01
6.00E-01
4.00E-01
2.00E-01 -:
O.OOE+00
•I
I
I
I
I
•I
I
I
I
I
•I
I
I
I
I
•I
I
I
I
I
•+ 001
008
005 006 007 E|E
002 003 004 E|E E|E E|E E|E
EEE EEE EEE EEE EEE EEE EEE
0
E
E
E
E;
09
IE
IE
IE
BE
0
E
E
E
E
E;
10
IE
IE
IE
IE
BE
Oil
E|E
E|E
E|E
E|E
EEE
012
E|E
E|E
E|E
E|E
E|E
EEE
013
E|E
E|E
E|E
E|E
E|E
E|E
E|E
EEE
014
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
HHH
015
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
H|H
HHH
46
-------
The above example illustrates EXAMS' internal prompts for a
PROFILE plot. As with the POINT option, this entire command
could be entered on a single line:
EXAMS-> PLOT PROF TOT WAT
3.
EXAMS-> PLOT KIN
The following KINETIC options are available:
List - lists selected KINETIC output parameters
Plot - plots selected KINETIC output parameters
Help - this message
Quit - return to the EXAMS prompt
Option-> PLOT
Chemical: Methyl Parathion
Environment: Pond — AERL code test data
Simulation units: Days
Number of segments: 2
Type of segment '(TYPE) :
1 2
L B
The following parameters are available for time-trace plotting
of values averaged over the ecosystem space:
("Dissolved" = aqueous + complexes with "dissolved" organics.)
1 - Water Column: average "dissolved" (mg/L)
2 - average sorbed (mg/kg)
3 - total mass (kg)
4 - Benthic:
5
6
average "dissolved" (mg/L)
average sorbed (mg/kg)
total mass (kg)
Enter parameters, one per line;
enter 0 to end data entry and proceed.
Parameter-> 3
Parameter-> 6
Parameter-> 0
The following parameters are available for each segment":
1 — Total concentration (Water Column, mg/L; benthic, mg/kg)
2 - "Dissolved" (mg/liter of fluid volume)
3 - Sorbed (mg/kg of sediment)
4 - Biosorbed (ug/g)
5 - Mass (grams/square meter of AREA)
47
-------
Enter segment-parameter number pair, one number per line;
enter 0 when data entry is complete; Quit to abort.
Enter segment number > 0
System: Monthly pond — AERL code test data
Chemical: Methyl Parathion
0
0
5
0
.160 I
I
I
I
I
.106 I
I
I
I
I
.322E-02 I
I
I
I
I
BB
B
BB B
B
B B
B B
B B
B B
B CCCC
B CCB
B CC B
BB B C BB
B CC B
B B BC
BCCCCCCC
.000 ICCCCCCCCCCCCCCCCBBCBBB
0.000
73.0 146.
CCC
CCC
CCC
CCCC
BB CCCCC
BBBB CCCCCCCCCC
BBBBBBBBBBBBBBBBBC
219. 292. 365
Time, Days
This example illustrates EXAMS' prompting in KINETIC plots.
The numerical options cannot be entered on the command line,
but must be entered in response to the prompts.
48
-------
PRINT
Use the PRINT command to queue an output table for hardcopy printing.
Related:
Control variables: FIXFIL
Commands: LIST
Syntax:
Prompt:
Options;
PRINT
-------
QUIT
Use QUIT to abort a. command in progress or to end an interactive EXAMS
session.
Related:
Control variables:
Commands: EXIT
Syntax:
Prompt:
Options:
Description:
QUIT
None
None
Entering QUIT at the EXAMS prompt command level will terminate
an interactive session, returning control to the computer's
operating system. QUIT is included as an option of many EXAMS
commands to allow the command to be aborted.
Examples:
1. EXAMS-> AUDIT
The following AUDIT options are available
ON — begins a new audit file,
OFf — ends Audit recording of input commands,
Help — this message,
Quit — return to the Exams prompt.
AUDIT-> QUIT
EXAMS->
This command terminates processing of the AUDIT command and
returns control to the EXAMS prompt command level. The current
status of AUDIT is not altered.
2. EXAMS-> QUIT
This command terminates an interactive EXAMS session.
50
-------
READ
Use the READ command to transfer data from a properly organized non-EXAMS
file into the Activity Data Base (ADB).
Related:
Syntax:
Prompt:
Description:
Examples:
Control variables:
Commands:
MODE, MCHEM
WRITE
READ
Enter Environment, Chemical, Help, or Quit->
The READ command provides a facility for up-loading EXAMS
datasets from external ASCII sequential files. These
non-EXAMS files can be stored separately from the main EXAMS
User Data Base (UDB). Data are transferred to the Activity
Data Base (foreground memory ADB) rather than, directly to the
User Data Base (UDB) file, so the STORE command must be used
to transfer data to the UDB from the ADB after invoking READ.
Under the ENVIRONMENT option of READ, the setting of MODE
controls how many data are read from the external file. When
MODE is 1 or 2, only the dataset sector indicated by the
current value of MONTH is transferred. For example, if
MODE=1 and MONTH=13, explicit mean values (only) will be
uploaded. When MODE=3, the entire ADB dataset ("months" 1
through 13) will be uploaded from the external file called
.
Under the CHEMICAL option of READ, the chemical dataset to be
uploaded from is put into the MCHEM sector of
the Activity Data Base (ADB).
1. Transfer of a single set of values of an environmental
dataset takes place in Mode 1 and 2. In this example, MODE
and MONTH are set to upload average data (only) from a file
called "INLET.DAT" on the default directory; the dataset is
then STOREd in EXAMS' direct access UDB file.
EXAMS-> SET MONTH=13
EXAMS-> SET MODE=1
EXAMS-> READ
Enter Environment, Chemical, Load, Help, or Quit-> EN
Enter name of file, Help, or Quit-> INLET.DAT
2. To continue the above example, an entire monthly dataset
can be read from another file by changing the mode to 3.
Note that a directory other than the default can be specified
as part of the READ command option.
EXAMS-> SET MODE=3
EXAMS-> READ EN C:\EXAMS\PROJECTX\INLET.DAT
51
-------
RECALL
Use RECALL to upload data from the permanent database (UDB) into current
foreground memory (ADB).
Related:
Control Variables: MCHEM
Commands: CATALOG, ERASE, NAME, STORE
Syntax:
Prompt:
RECALL [AS ADB#]
Enter Environment, Chemical, Load, Product,
Help, or Quit->
Command parameters:
Description:
can be Chemical, Environment, Load, or Product
(EXAMS uses these four kinds of datasets.)
AS ADB# is an optional explicit specification of MCHEM
(see Example 1).
UDB# specifies the accession number or location in the User
Database for the source data for transfer to the ADB
(Example 2).
RECALL transfers data from permanent storage (UDB) to
activity databases (ADBs). The data in active use by EXAMS
are held in a foreground memory bank (Activity DataBase or
ADB) with four sectors, one for each datatype required by
EXAMS—
hemical reactivity and partitioning,
nvironmental physical and chemical parameters,
allochthonous chemical oadings, and
roduct chemistry for generating interconversions
among multiple chemicals in an analysis.
When EXAMS is started, the ADB is empty. Use the RECALL
command to transfer data from the permanent User Databases
(UDBs) to foreground memory (ADB).
When an analysis session is ended (QUIT or EXIT), ADBs are
discarded. Use the STORE command to transfer new data from
the ADB to the UDB sector of the same datatype for permanent
retention of the data.
52
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Examples:
1. Because EXAMS can process several chemicals in a single
analysis, the target sector of the chemical activity
database should be specified when using the RECALL command
to activate CHEMICAL data. (This section of the command
should be omitted for other data types.) When the ADB# (an
integer between 1 and KCHEM) is omitted, the chemical data
are transferred to the sector of the activity database given
by the current value of MCHEM. For example, to activate
data from the chemical UDB, putting UDB dataset number 9
into ADB sector 1, and UDB #14 into sector 2:
Either:
EXAMS-> SET MCHEM TO 1
EXAMS-> RECALL CHEMICAL 9 •
EXAMS-> SET MCHEM TO 2
EXAMS-> RECALL CHEMICAL 14
or, equivalently:
EXAMS-> RECALL CHEMICAL 9 AS 1
EXAMS^-> RECALL CHEMICAL 14 AS 2
2. Long-term retention of data required by EXAMS is provided
by storage in the "User Database" (UDB, generally resident on
a physical device—e.g., a hard disk) for Chemicals, Environ-
ments, Loads, or Products. Within each UDB sector, each
dataset is catalogued via a unique accession number (UDB#).
When transferring data to foreground memory (the activity
database or ADB) from a UDB, the source location must be
specified by the name of the UDB sector and the accession
number within the sector. For example, to RECALL an
environmental dataset:
EXAMS-> RECALL ENVIR 2
Selected environment is: Phantom Inlet, Bogue Sound
EXAMS->
53
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RUN
The RUN command begins a simulation analysis.
Related:
Control Variables: MODE
Commands: CONTINUE
Syntax:
Prompt:
Description:
Examples:
RUN
None
The RUN command executes an analysis and creates the output
files accessed by the LIST and PLOT commands. The activity
database (ADB) must be loaded, either via entry of new data or
by RECALL from the UDB, before a RUN can be started.
1. EXAMS-> RECALL CHEMICAL 22
Selected compound is: Dibromomucktane
EXAMS-> RECALL ENVIRON 17
Selected environment is: Albemarle Sound—Bogue Bank
EXAMS-> SET STRL(1,1,13)=.01
EXAMS-> RUN
Simulation beginning for:
Environment: Albemarle Sound--Bogue Bank
Chemical 1: Dibromomucktane
Run complete.
EXAMS->
In this example, a steady-state (MODE=1) analysis is con-
ducted by selecting a chemical -and an environment, imposing a
loading of chemical 1 on segment 1 under average conditions
(i.e., data sector 13, EXAMS initial default value) and
invoking EXAMS' simulation algorithms with the RUN command.
54
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SET
Use to specify the values of data in the activity database.
Related:
Commands: CHANGE (synonym), DESCRIBE, HELP
Syntax:
Prompt:
SET TO
or
SET =
Enter name=value command->
Variable: The data entry or variable to be SET can be specified either as
a single datum or, using wild cards (*), as an entire vector,
row/column of a matrix, etc.
Description:
Use the SET command to specify the values of data in the
activity database. "Value" can be any numerical quantity or
literal, as appropriate. "Variable" specifies an individual
element of input data or a program control parameter. Entire
vectors, rows/columns of matrices, etc. can be set to single
values using wild cards (*). - •-
Examples:
1. EXAMS-> SET VOL(67) TO 7E5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 32 elements.
EXAMS> SET VOL(2) TO E
Invalid numeric quantity after TO.
EXAMS-> SET VOL(2) TO 7E5
This command sets the environmental volume of segment 2 to
7.OE+05 cubic meters. The initial attempt to set the volume of
segment 67 was rejected by EXAMS because the version in use was
set up for environmental models of 32 segments at most. The
DESCRIBE command was used to check the number of subscripts and
the dimensional size of the variable "VOL". The erroneous
entry of an alphabetic for the volume was trapped by the SET
command; the initial value of VOL(2) was not altered.
55
-------
2. EXAMS-> HELP TCEL
TCEL is a Real Matrix *?ith 32 rows and 13 columns.
Temperature-CELsius (segment,month) , Units: degrees C.
Average temperature of ecosystem segments.
Used (as enabled by input data) to compute effects of
temperature on transformation rates and other properties
of chemicals.
EXAMS-> SET TCEL(2,7)=24
This command changes the July temperature in segment 2 to 24
degrees C. The HELP command was used tp check subscript dimen-
sions, maximum values, the meaning of the subscripts (subscript
#1 denotes the segment; subscript #2, the month), and the
proper units for the input datum (degrees Celsius).
3. EXAMS-> HELP POH
POH is a Real Matrix with 32 rows and 13 columns.
pOH (segment,month) Units! pOH units
The negative value of the power to which 10 is raised in
order to obtain the temporally averaged concentration of
hydroxide [OH"] ions in gram-molecules,per liter.
EXAMS-> SET POH(*,13) TO 6.2
This command sets the average pOH (sector 13) of every
segment to 6.2. Note use of wild card "*" to specify that all
segments are to be changed. As in the previous example, HELP
was used to check subscript dimensions, units, etc. This step,
of course, is optional.
56
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SHOW
Use SHOW to display current data values or control settings.
Related:
Syntax:
Prompt:
Control Variables: MCHEM, MONTH
Commands: CHANGE, SET
SHOW
-------
inter-segment dispersive transport paths. A zero in either
vector, when paired with a non- zero value at the
corresponding position in the other index vector, is taken
as a boundary condition with an uncontaminated body of
water. A single element in a dataset might typically be
displayed like the following example.
Segment number for dispersion
Segment number for dispersion
Cross— sectional area of path
CHARacteristic_Length of path
Eddy DiSPersion coefficient
Vector index for data entry
J TURB
I TURB
XS TUR m2
CHARL m
DSP mVhr
Path No . :
1
2
5.000E+04
2.53
4.676E-05
1
No more than NCON hydrologic pathways can be specified.
more are needed, this number can be increased and EXAMS
recompiled.
If
CHEMISTRY
SHOW CHEMISTRY displays the chemical output data currently
in the ADB (foreground memory bank). The sector of the ADB
denoted by the current value of MCHEM is displayed. Within
each sector of the ADB (that is, for each chemical under
active review), the data for each ionic species are
presented separately, and photochemical data are presented
on separate screens.
GEOMETRY
SHOW GEOMETRY returns a segment-by-segment description of
the geometry (volumes, areas, etc.) of the current
ecosystem. The segment number reported with each block of
data is the first subscript for modifying the datum using
CHANGE or SET. The month to be displayed is set by the
current value of MONTH (explicit mean values are denoted by
MONTH number 13): the month is the second subscript of such
data as WIND, STFLO, etc.
GLOBALS
SHOW GLOBALS displays the input data that are "global" in
extent, that is, "global" data apply to all segments of the
current ecosystem.
LOADS
SHOW LOADS displays the current state of allochthonous chemical
loadings. The form of the display depends on the current oper-
ational MODE: initial values are ignored in Mode 1 as they have
no effect on the analysis results. The value of PRSW also af-
fects the display: when PRSW is 0, SHOW LOADS returns a summary
of annual loadings; when PRSW=1, a month-by-month tabulation is
displayed as well. This display may not represent the final
58
-------
values used in the analysis, because EXAMS will modify loads
that result in violation of the linearizing assumptions used to
construct the program. After a RUN has been executed, however,
SHOW LOADS will display the corrected values.
PRODUCTS
SHOW PRODUCTS displays the specifications for product chemistry
currently in the ADB. Each entry is identified and loaded
according to a unique "pathway number." A single element of a
dataset might look like this:
CH PAR 1
T PROD 2
N PROC 7
R FORM 29
YIELD M/M 0.100
EaYLD Kcal 0.000
Pathway: 1
ADB number of CHemical PARent
ADB number of Transformation PRODuct
Number of transforming PROCess
Reactive FORM (dissolved, etc.)
Mole/Mole YIELD of product
Enthalpy of yield (if appropriate)
Number of the pathway
More detail as to the numbering of NPROC and RFORM is given
in the Dictionary, and can be accessed via the HELP command.
No more than NTRAN transformation pathways can be specified.
If more are needed, a special version of EXAMS can be
created.
PLOT
SHOW PLOT examines the contents of the concentration time-
series and steady-state files, and reports the names of the
chemicals and ecosystem used in the analysis.
PULSE LOADS
SHOW PULSE LOADS displays the specifications for
allochthonous pulses of chemicals entering the system. This
display may not represent the final values used in the
analysis, because EXAMS will modify loads that result in
violation of the linearizing assumptions used to construct
the program. Although faulty pulse loads are discarded,
EXAMS does not correct the .input pulse load data, because
the occurrence of load constraint violations depends on the
context (i.e., the size of current stream loadings, etc.).
Thus, unlike SHOW LOADS, the SHOW PULSE display following
execution of a RUN does not display corrected data. The
pulses actually used during an analysis are instead entered
into EXAMS' output tables, where they can be examined using
the LIST and PRINT commands.
QUALITY
SHOW QUALITY returns a segment-by-segme. v display of the
canonical water-quality data included in the current
Environmental ADB dataset. The month to be displayed is set
59
-------
by the current value of MONTH (explicit mean values are
denoted by MONTH number 13). The month is the second
subscript of such data s.'s pH, pOH, etc. The first subscript
is the segment number; thus these data are entered
(CHANGE/SET) as "datum(segment,month)".
TIME FRAME
SHOW TIME FRAME displays the current status of the parameters
needed to control the temporal aspects of a Mode 2 or Mode 3
simulation.
VARIABLES
SHOW VARIABLES displays a list of the names of EXAMS input data
and control parameters. These names must be used to
SET/CHANGE, SHOW values, HELP/DESCRIBE, etc.
Description: Use the SHOW command to examine the current
contents of the ADB, that is, the foreground datasets used
for the current analysis. The SHOW command can be used to
examine clusters of similar data, the values of individual
parameters, or the data contained in entire vectors. Typing
SHOW without an option will display a. list of the available
options.
Examples:
1. The SHOW command can be used to examine the value of single
parameters. For example, the pH of segment 7 of the current
ecosystem during September could be inspected by entering:
EXAMS-> SHOW PH(7,9)
Using wild cards (*), the SHOW command can also be used to
display the data in an entire vector or row/column of a data
matrix. For example, the pH in every segment of the current
ecosystem during September could be displayed by entering:
EXAMS-> SHOW PH(*,9)
and the pH of segment 7 through the year could be displayed by:
EXAMS-> SHOW PH(7,*)
60
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STORE
Use STORE to download current (ADB) data into the permanent database (UDB)
Related:
Control Variables: MCHEM
Commands: CATALOG, ERASE, NAME, RECALL
Syntax:
Prompt:
STORE [ADB# IN]
Enter Environment, Chemical, Load, Product,
Help, or Quit->
Command parameters:
Description:
Examples:
can be Chemical, Environment, Load, or Product
(EXAMS uses these four kinds of datasets.)
ADB# IN is an optional explicit specification of MCHEM
(see Example 1) .
UDB# specifies the accession number or location in the User
Database for storage of the current ADB sector (Example 2).
STORE downloads data from activity databases (ADBs) into the
permanent User DataBases (UDBs). The data in active use by
EXAMS are held in a foreground memory bank . (Activity DataBase
or ADB) with four sectors, one for each datatype required bv
EXAMS: *
CHEMICAL reactivity and partitioning,
ENVIRONMENTal physical and chemical parameters,
allochthonous chemical LOADings, and
PRODUCT chemistry for generating interconversions
among multiple chemicals in an analysis.
When an analysis session is ended (QUIT or EXIT), these data
are discarded. Use the STORE command to transfer data from
the ADB to the UDB sector of the same datatype for permanent
retention of the data.
1. Because EXAMS can process several chemicals in a single
analysis, the source sector of the chemical activity
database should be specified when using the STORE command to
download CHEMICAL data. (This section of the command should
be omitted for other data types.) When the ADB# (an integer
from 1 to KCHEM) is omitted, the chemical data are taken
from the sector of the activity database given by the
61
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current value of MCHEM. For example, to STORE data in the
UDB, putting ADB sector 1 into the chemical UDB under
catalog/accession 9 and ADB sector 2 into UDB sector 14:
Either:
EXAMS-> SET MCHEM TO 1
EXAMS-> STORE CHEMICAL 9
EXAMS-> SET MCHEM TO 2
EXAMS-> STORE CHEMICAL 14
or, equivalently:
EXAMS-> STORE CHEMICAL 1 IN 9
EXAMS-> STORE CHEMICAL 2 IN 14
2. Long-term retention of data required by EXAMS is
provided by storage in the "User Database" (UDB, generally
resident on a physical device—e.g., a hard disk) for
Chemicals, Environments, Loads, or Products. Within each of
these UDB sectors, each dataset is CATALOGued via a unique
accession number (UDB#). When transferring data between
foreground memory (the activity database or ADB) and a UDB,
the target location must be specified by the name of the UDB
sector and the accession number within the sector. For
example, to STORE the current environmental dataset:
EXAMS-> STORE ENVIR 2
Environment record 2 is in use with
Pond — AERL code test data
Replace?-> NO
Nothing changed.
EXAMS-> STORE ENVIR 14
Environment stored: Phantom Inlet-Bogue Sound Study Data
EXAMS->
Note that EXAMS provides a measure of protection against
accidental overwriting of existing datasets, an important
courtesy in a. multi-user environment.
62
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WRITE
Use the WRITE command to transfer data from the Activity Data Base (ADB)
to an external (non-EXAMS) sequential file.
Related:
Syntax:
Prompt:
Description:
Examples:
Control variables:
Commands:
MODE, MCHEM
READ
WRITE
Enter Environment, Chemical, Help, or Quit->
The WRITE command provides a facility for off-loading EXAMS
datasets into external ASCII sequential files. These
non-EXAMS files can be stored separately from the main EXAMS
User Data Base (UDB). Data are transferred from the
Activity Data Base (foreground memory ADB) rather than
directly from the User Data Base (UDB) file, so the RECALL
command must be used to transfer data from the UDB to the
ADB before invoking WRITE.
Under the ENVIRONMENT option of WRITE, the setting of MODE
controls how many data are stored in the external file.
When MODE is 1 or 2, only the dataset sector indicated by
the current value of MONTH is transferred. For example, if
MODE=1 and MONTH=13, explicit mean values (only) will be
downloaded. When MODE=3, the entire ADB dataset ("months" 1
through 13) will be downloaded to the external file called
.
Under the CHEMICAL option of WRITE, the chemical dataset to
be downloaded to is chosen from the MCHEM
sector of the Activity Data Base (ADB).
1. Transfer of a single set of values of an environmental
dataset takes place ,in Mode 1 and 2. In this example, the data
is RECALLed from the UDB, and MODE and MONTH are set to
download the average data to a file called "INLET.DAT" on the
default directory.
EXAMS-> RECALL ENVIRONMENT 12
Selected environment is: Chinquoteague Inlet
EXAMS-> SET MONTH=13
EXAMS-> SET MODE=1
EXAMS-> WRITE
Enter Environment, Chemical, Load, Help, or Quit-> EN
Enter name of file, Help, or Quit-> INLET.DAT
2. To continue the above example, the entire dataset could
be stored in another file by changing mode to 3. Note that a
directory other than the default can be specified as part of
the WRITE command option.
EXAMS-> SET MODE=3
EXAMS-> WRITE EN C:\EXAMS\PROJECTX\INLET.DAT
63
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ZERO
Use the ZERO command to initialize (set to zero) loadings databases or the
concentration of pollutant chemicals throughout the ecosystem.
Related:
Control variables: MODE
Commands: CONTINUE, RUN
Syntax:
ZERO
-------
EXAMS-> SET IMASS (1)=?2.0
EXAMS-> SET ISEG(1)=14
EXAMS-> SET ICHEM(1)=1
EXAMS-> RUN
Simulation beginning for:
Environment: Albemarle Sound—Bogue Bank
Chemical 1: Dibromomucktane
Run complete.
EXAMS-> ZERO PULSE LOADS
EXAMS-> CONTINUE
In this example, an initial-value (MODE=2) analysis is begun
by selecting a chemical and an environment, imposing an alloch-
thonous load of chemical 1 on segment 1 under average condi-
tions (i.e., data sector 13, EXAMS' initial default value), and
specifying the initial presence (or introduction at time zero)
of 2.0 kg of material in segment 14. At the end of the initial
RUN segment, one might want to examine the output tables, plot
the results, etc. Then, before Continuing, the ZERO command is
used to remove the pulse load specifications. If this were not
done, EXAMS would introduce a second 2.0 kg pulse into segment
14 at the beginning of the continuation segment. Alterna-
tively, the other loadings could have been removed, and the
effect of a series of pulse loads could be studied by issuing
a sequence of CONTINUE commands.
65
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EXAMS II DATA DICTIONARY
ABSER
ADB
ABSolute ERror tolerance of integrators.
When the characteristics of the chemical and ecosystem are such as to
result in "stiff" equations, numerical errors may lead to small negative
numbers in the time series. If desired, the value of ABSER and RELER
can be decreased in order to achieve greater precision in the simulation
outputs.
Activity DataBase
EXAMS provides for long-term storage of CHEMical, Environmental, trans-
formation PRODuct chemistry, and allochthonous LOADings databases in a
User DataBase or XJDB. The actual analyses are conducted on particular
datasets drawn from these files (or entered via SET/CHANGE). Particular
cases are loaded from the UDB into the foreground transient memory of
your computer in an Activity DataBase or ADB, using the RECALL command.
Because EXAMS simulates the behavior of several (MCHEM) chemicals simul-
taneously, the ADB for chemicals has MCHEM separate sectors. These data
are lost when you EXIT from EXAMS, so be sure to STORE any new or
corrected datasets before leaving EXAMS.
ABSOR
ABSORption spectra (wavelength, ion, chemical)
Units: I/cm/(mole/L)
Mean decadic molar light extinction coefficients in 46 wavelength
intervals over 280—825 nm. For wavelength "w" and chemical "c":
ABSOR(w,l,c) is absorption coefficient of (neutral molecule)
ABSOR(w,2,c) "
ABSOR(w,3,c) "
ABSOR(w,4,c) "
ABSOR(w,5,c) "
ABSOR(w, 6, c) "
ABSOR (w, 7,c) "
(1+ cation)
(2+ cation)
(3+ cation)
(1- anion)
(2- anion)
(3- anion)
66
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ADVPR
ADVection PRoportion (path)
AEC
AREA
Units: n/a
Range: > 0 - 1.0
PRoportion of flow ADVected from segment JFRAD that enters ITOAD. The
matching (same subscript) members of JFRAD, ITOAD, and ADVPR define an
advective hydrologic flow pathway. Although usually 1, ADVPR lets one
enter braided channels, etc. The total of ADVPRs for each segment must
sum to either 0 or 1, failing which, EXAMS aborts the RUN. The flow
data can be inspected by typing SHOW ADV; path numbers are given above
each active dataset.. Enter data via CHANGE or SET commands.
Additional information available: JFRAD, ITOAD
Anion Exchange Capacity (segment, month)
Units: meq/100 g (dry)
Anion exchange capacity of sediment phase of each segment. Useful in
relating sediment sorption (partitioning) of anions to a variable
characteristic of system sediments.
AIRTY
AIR mass TYpe (month) , Units: letter codes
Select: Rural (default), Urban, Maritime, or Tropospheric
AREA (segment)
Units: m2
Top plan area of each model segment of the waterbody. For Epilimnion
and Littoral segments, AREA is the area of the air-water interface; for
Hypolimnion segments AREA is the area of the thermocline; for Benthic
segments it is the surface area of'the bottom. In the latter case AREA
may differ from XSTUR in a dispersive exchange pair because of reduction
in exchanging area due to rock outcrops, etc.
ATURB
Atmospheric TURBidity (month)
Equivalent aerosol .layer thickness.
Unit s: km
AUDOUT
While the AUDIT directive is in effect, a copy of user inputs and
responses is written to the file connected to FORTRAN Logical Unit
Number AUDOUT.
67
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BACPL
BACterioPLankton population density (segment, month)
Units: cfu/mL
Population density of bacteria capabl'e of degrading xenobiotics.
The abbreviation "cfu" stands for a "colony forming unit."
BNBAC
BeNthic BACteria (segment, month)
Units: cfu/lOOg dry sediment
Population density of benthic bacteria that degrade xenobiotics.
The abbreviation "cfu" stands for a "colony forming unit."
BNMAS
BeNthic bioMASs (segment, month)
Units: g(dry)/m2
Biomass of small benthos—infauna subject to biosorption.
BULKD
BULK Density (segment, month)
Fresh weight per unit volume of benthic sediments.
Units: g/cm3
CEC
Cation Exchange Capacity (segment, month)
Units: meq/lOOg (dry)
Cation exchange capacity of sediment phase in each segment. Useful in
relating sediment sorption (partitioning) of cations to a variable
characteristic of system sediments.
CHARL
CHARacteristic Length or mixing length (path)
Units: m
Average of segment dimensions normal to the exchange interface linking
segment numbers JTURB(p) and ITURB(p). The matching (same "p"
subscript) members of JTURB, ITURB, CHARL, DSP, and XSTUR together
define a dispersive transport pathway. A given segment may have
different mixing lengths at different interfaces. CHARL can also be
calculated from the distance along a path that connects the centers of
segments JTURB(p) and ITURB(p), passing through the interface whose area
is XSTUR(p).
See also: DSP, ITURB, JTURB, XSTUR
CHEMNA
CHEMical NAme(s) of compounds (50 characters,chemical)
Units: n/a
Do NOT use "CHANGE" or "SET" to enter names! The NAme for a CHEMical is
entered into the database via the command sequence:
68
-------
EXAMS > CHEMICAL NAME IS nnn
where "nnn " can include as many as 50 characters. This name is
associated with chemical library entries and is printed in the header
information of the appropriate output tables.
CHL
CHLorophylls + pheophytins (segment, month)
Units: mg/L
Concentration of chlorophyll plus chlorophyll-like pigments. Used to
compute spectral light absorption coefficients due to pigments which
absorb light from the water column and thus compete with photolysis of
xenobiotics.
CHPAR
CHemical PARent compound (path)
CINT
Units: n/a Range: 1 - KCHEM
CHPAR(p) gives the ADB location of the parent source of TPROD(p). The
matching (same transformation path number "p") members of CHPAR and
TPROD give the location numbers in the active database of the parent
chemical and the transformation product for pathway "p". For example,
"SET CHPAR(p) TO 1", and TPROD(p) to 4, to show that the chemical in ADB
sector 4 is produced via transformation of the chemical in ADB sector 1,
via process data defined by the remaining members of product chemistry
sector "p".
See also: EAYLD, NPROC, RFORM, TPROD, YIELD
Communications INTerval for dynamic simulations.
Units: see TCODE
CINT is the interval between output cycles from the integrators. In
Mode 2, CINT can be set to produce any desired output frequency, so long
as the resulting reporting interval is > 1 hour. When CINT is set to
0, EXAMS (Mode 2) sets CINT to report at the 12 equal-increment periods
most closely matching the duration specified by (TEND - TINIT). CINT is
under full user control only in Mode 2; in Modes 1 and 3 EXAMS itself
sets the value of CINT according to the needs of the analysis.
CLOUD
CLOUDiness (month) Units: dimensionless
Mean monthly cloudiness in tenths of full sky cover.
Range: 0 — 10
DEPTH
DEPTH (segment)
Average vertical depth of each segment.
Units: m
69
-------
DFAC
„ Distribution FACtor (segment, month)
Units: dimensionless ratio
Ratio of optical path length to vertical depth, range 1.0-2.0. A
vertical light beam has a DFAC of 1.0; a fully diffused light field has
a DFAC of 2.0. For whole days, a value of 1.19 is often adequate; EXAMS
defaults to this value when the entry for DFAC is outside the range
1.0-2.0.
DISO2
DOC
Dissolved O2 (segment, month) Units: mg/L
Concentration of dissolved oxygen in each segment of ecosystem.
Dissolved Organic Carbon (segment, month) Units: mg/L
Used for computing spectral light absorption and complexation.
DRFLD
DSP
EAH
DRiFt LoaD (segment, chemical, month)
.Units: kg/hour
Drift loadings: aerial drift, direct applications, stack fallout (etc.)
of chemical on each system element.
DiSPersion coefficient (path, month)
Units: mVhour
Eddy diffusivity to be applied to dispersive exchange pairing "p". The
matching (same "p" subscript) members of JTURB, ITURB, CHARL, and XSTUR
together define a dispersive transport pathway. In the case of
horizontal mixing, DSP is the longitudinal dispersion coefficient; for
vertical mixing it may represent exchange across the thermocline or
exchanges with bottom sediments. In the latter case DSP is a statistical
kinetic composite incorporating direct sorption to the sediment surface,
mixing of the sediments by benthos (bioturbation), stirring by demersal
fishes, etc.
See also: CHARL, ITURB, JTURB, XSTUR
Ea for Acid Hydrolysis (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy of specific-acid-catalyzed hydrolysis of
chemicals. Matrix indices match those of KAH, giving, for each chemical,
data for 3 forms (1: dissolved, 2: solids-sorbed, 3: DOC-complexed) of 7
ionic species (1: neutral; 2, 3, 4: cations; 5, 6, 7: anions). When EAH
70
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is non-zero, the second-order rate constant is calculated from:
1000. * EAH (form,ion,chemical)
log K = KAH(f,i,c) -
(1/M/hour)
4.58 * (TCEL(segment,month) + 273.15)
EAYLD
EBH
EA YieLD (path)
Units: kcal
EAYLD(p) is activation energy Ea to compute transformation product yield
as a. function of environmental temperatures (TCEL). When EA YieLD(p) is
zero, YIELD(p) gives the dimensionless molar product yield. A non-zero
EAYLD(p) invokes a re-evaluation in which YIELD(p) is interpreted as the
pre-exponential factor in an Arrhenius-type function, giving product
yield as a function of spatially and temporally specific temperatures
(TCEL(segment, month)):
1000 * EAYLD(path)
log Yield (p) = YIELD (p)
4.58 * (TCEL(segment,month) + 273.15)
See also: CHPAR, NPROC, RFORM, TPROD, YIELD
Ea for Base Hydrolysis (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy of specific-base catalyzed hydrolysis of
chemicals. Matrix indices match those of KBH, giving, for each chemical,
data for 3 forms (1: dissolved, 2: solids-sorbed, 3: DOC-complexed) of 7
ionic species (1: neutral, 2, 3, 4: cations, 5, 6, 7: anions). When EBH
is non—zero, the second—order rate constant is calculated from:
1000. * EBH (form,ion,chemical)
log K = KBH(f, i,c)
(1/M/hour) 4.58 * (TCEL(segment,month) + 273.15)
EHEN
Enthalpy term for HENry's law (chemical)
Units: kcal/mole
Used to compute Henry's law constants_as a function of TCEL
(environmental temperature). When EHEN is non-zero, the Henry's law
constant (H) affecting volatilization at a particular (segment, month)
is computed from TCEL:
1000 * EHEN(chemical)
log H = HENRY(chemical)
4.58 (TCEL(segment,month) + 273.15)
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EK1O2
Ea K1O2 (singlet oxygen) (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy for singlet oxygen photo-oxygenation of
chemicals. Matrix indices match those of K1O2, giving, for each
chemical, data for 3 forms (1: dissolved, 2: solids-sorbed, 3: DOC-
complexed) of 7 ionic species (1: neutral, 2, 3, 4: cations, 5, 6, 7:
anions). When EK1O2 is non-zero, the second-order rate constant is
calculated as:
log K = Kl02(f,i,c) -
(1/M/hour)
1000. * EK1O2 (form, ion,chemical)
4.58 * (TCEL(segment,month) + 273.15)
EIiEV
ELEVation
Ground station elevation.
Units: meters above mean sea level
ENH
Ea for Neutral Hydrolysis (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy for neutral hydrolysis of chemicals. Matrix
indices match those of KNH, giving, for each chemical, data for 3 forms
(1: dissolved, 2: solids-sorbed, 3: DOC-complexed) of 7 ionic species
(1: neutral, 2, 3, 4: cations, 5, 6, 7: anions). When ENH is non-zero,
the second-order rate constant is calculated from:
log K = KNH(f, i,c) -
(1/M/hour)
1000. * ENH (form,ion,chemical)
4.58 * (TCEL(segment,month) + 273.15)
BOX
Ea oxidation (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy for oxidative transformations of chemicals.
Matrix indices match those of KOX, giving, for each chemical, data for 3
forms (1: dissolved, 2: solids-sorbed, 3:DOC-complexed) of 7 ionic
species (1: neutral, 2, 3, 4: cations, 5, 6, 7: anions). When BOX is
non-zero, the second-order rate constant is calculated from:
log K - KOX(f, i,c) -
(1/M/hour)
1000. * EOX (form, ion,chemical)
4.58 * (TCEL(segment,month) + 273.15)
EPK
Enthalpy term for pK (ion, chemical) Units: kcal/mole
When EPK is non-zero, pK is computed as a function of temperature via:
72
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ERED
ESOL
log pK = PK(i,c)
1000. * EPK(ion,chemical)
4.58 * (TCEL(segment,month) + 273.15)
The vector indices for EPK ("c" the chemical) are:
EPK(l,c) contains datum for generation of S(H4)+ from S(H3)
EPK(2,c) contains datum for generation of S(H5)2+ from S(H4)+
EPK(3,c) " .... ,, „ S(H6)3+ " S(H5)2+
EPK(4,c) " " » » " S(H2)- " S(H3)
EPK(5,c) " " " » » S(H)2- " S(H2)-
EPK(6,c) " " " » » S3- " S(H)2-
Ea REDuction (form, ion, chemical)
Units: kcal/mole
Arrhenius activation energy for reductive transformations of chemicals.
Matrix indices match those of KRED, giving, for each chemical, data for
three forms (1: dissolved, 2: solids-sorbed, 3: DOC-complexed) of seven
ionic species (1: neutral, 2, 3, 4: cations, 5, 6, 7: anions). When
ERED is non-zero, the second-order rate constant is calculated as:
log K = KRED(f,i,c) -
(1/M/hour)
1000. * ERED (form,ion,chemical)
4.58 * (TCEL(segment,month) + 273.15)
Enthalpy term for SOLubility (ion, chemical)
Units: kcal/mole
ESOL describes chemical solubility as a function of temperature (TCEL).
The matrix indices ("c" the chemical) denote:
ESOL(l,c) — datum for solubility of S(H3)
ESOL (2, c) — " " ,,....
ESOL(3,c) — " " " "
" " " " S(H6)3+
n ii « .. S(H2)-
" " S(H)2-
ESOL(4,c)
ESOL(5,c)
ESOL(6,c)
ESOL(7,c)
(neutral molecule)
S(H4)+ (1+ cation)
S(H5)2+ (2+ cation)
(3+ cation)
(1- anion)
(2- anion)
S3- (3- anion)
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EVAP
EVAPoration (segment, month) Units: mm/month
(Monthly) evaporative water losses from ecosystem segments.
EVPR
Molar hEat of VaPoRization (chemical)
••Units: kcal/mole
Enthalpy term for computing vapor pressure as a function of TCEL
(environmental temperature (segment,month)). When EVPR is non-zero,
vapor pressure Va is computed from:
1000 * EVPR(chemical)
log Va
VAPR(chemical) -
4.58 (TCEL(segment,month) + 273.15)
FIXFIL
FROG
FIXFIL signals the existence of output data for LISTs and PLOTs.
To access results from a prior run, "SET' FIXFIL to 1." FIXFIL is set to
zero when EXAMS is invoked, so that the LIST and PLOT commands are
protected from attempts to access non-existent output data files. When
results exist from a previous simulation, you can reset FIXFIL to 1 in
order to gain access to them. ,
FRaction Organic Carbon (segment, month)
Units: dimensionless
Organic carbon content of solids as fraction of dry weight. FROC is
coupled to KOC to generate the sediment partition coefficient for
neutral chemicals (SH3) as a function of 'a property (organic carbon
content) of the sediment. f
HENRY
HENRY's law constant (chemical)
Units: ••atmosphere-mYmole
Used in computation of air/water exchange rates (volatilization). If
parameter EHEN is non-zero, HENRY is used as the pre-exponential factor
in computing the Henry's law constant H as a function of environmental
temperatures (TCEL) : ''•
1000 * EHEN(chemical)
log H = HENRY(chemical) -
4.58 (TCEL (segment,month) 4- 273'. 15)
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ICHEM
I CHEMical (event)
Units: n/a
Range: 1 — KCHEM
Event "e" is a pulse of chemical number ICHEM(e) in the active database
ICHEM identifies the location in the Activity Database (ADB) of the
chemical entering the ecosystem via pulse load event "e". When, for
example, chemical data are loaded into ADB sector 3 (whether RECALLed
from the User Database Library (UDL) (via, for example, the command
sequence "RECALL CHEM 7 AS 3") or entered as new data), ICHEM(e) can be
SET to 3 to create a pulse load event of that chemical.
See also: IDAY, IMASS, IMON, ISEG.
IDAY
I DAY (event)
Units: n/a
Range: 1 — 31
Pulse load event "e" takes place on day IDAY(e) of month IMON(e). The
pulse load data are organized by vertical event columns, that is, the
set of pulse load variables (IMASS(e), ICHEM(e), ISEG(e), IMON(e), and
IDAY(e)) with the same vector subscript describes a single chemical
pulse event. Thus a pulse of chemical ICHEM(e), of magnitude IMASS(e),
is released into segment ISEG(e) on day IDAY(e) of month IMON(e).
During mode 2 simulations, IDAY and IMON are inoperative.
See also: ICHEM, IMASS, IMON, ISEG.
IMASS
Initial MASS (event)
Units: kg
IMASS gives the magnitude of chemical pulse load event "e". In mode 2,
pulses are entered at time 0 (i.e., as initial conditions), and at the
outset of each CONTINUation of the simulation. In mode 3, IMON and IDAY
specify the date of the load events. An event recurs in each year of
the RUN or CONTINUed simulation. The pulse load data are organized by
vertical event columns, that is, the series of pulse load variables
(IMASS, ICHEM, ISEG, IMON, and IDAY) with the same vector subscript
describes a single event.
See also: ICHEM, IDAY, IMON, ISEG.
IMON
I MONth (event)
Units: n/a
Range: 1—12
Pulse load event "e" takes place on day IDAY(e) of month IMON(e). The
pulse load data are organized by vertical event columns, that is, the
set of pulse load variables (IMASS(e), ICHEM (e), ISEG(e), IMON(e), and
IDAY(e)) with the same vector subscript describes a single chemical
pulse event. Thus a pulse of chemical ICHEM(e), of magnitude IMASS(e),
75
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is released into segment ISEG(e) on day IDAY(e) of month IMON(e)
During mode 2 simulations, IDAY and IMON are inoperative.
See also: IDAY, ICHEM, IMASS, ISEG. .
XSE6
I SEGment (event)
Units: n/a
Range: 1—KOUNT
Pulse load event "e" loads chemical ICHEM(e) on segment ISEG(e). 'Any
segment can receive a pulse load. Should the pulse loads increase the
FREE concentration of unionized chemical above 10-5 M (or half its
aqueous solubility, whichever is less), the size of the event is
reduced, to avoid violating the linearizing assumptions used to create
EXAMS. The pulse load data are organized by vertical event columns,
that is, the pulse load variables having the same vector subscript
define a single chemical pulse event.
See also: ICHEM, IDAY, IMASS, IMON.
ITOAD
I TO ADvection (path)
Units: n/a Range: 0—-KOUNT (0 = export)
Chemicals are advected to segment ITOAD(p) from segment JFRAD(p). The
matching (same subscript) members of JFRAD, ITOAD, and ADVPR define an
advective hydrologic flow pathway carrying entrained chemicals and
solids through the waterbody. When ITOAD(p) is 0, the pathway advects
water and entrained substances across system boundaries, i.e., ITOAD(p)
- 0 specifies an export pathway. The flow data can be inspected by
typing "SHOW ADV"; path numbers are given above each active dataset.
Enter data with SET or CHANGE commands.
See also: JFRAD, ADVPR
ITURB
I TURbulent dispersion (path)
Units: n/a Range: 0—KOUNT
Segments ITURB(p) and JTURB(p) exchange via turbulent dispersion. The
matching (same "p" subscript) members of ITURB, JTURB, CHARL, DSP, and
XSTUR together define a dispersive transport pathway; ITURB(p) and
JTURB(p) indicate which segments are linked by dispersive transport
pathway "p". A "0" in ITURB paired with a non-zero segment number in
JTURB denotes a boundary condition with a pure (zero chemical) water-
body. The input data can be examined via SHOW TURBULENCE; pathway
numbers are shown with each dataset.
See also: CHARL, DSP, JTURB, XSTUR.
IUNIT
IUNIT controls the printing of diagnostics from the integrators,
76
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IUNIT
Normally zero (off), it may be turned on when problems occur. To
manually set IUNIT to generate integrator diagnostic messages, SET IUNIT
TO 1. The message generator can be disabled at any time by SETting
to 0. - -
JFRAD
J FRom ADvection (path)
KAH
Units: n/a
Range: 1—KOUNT
Chemicals are advected from segment JFRAD(p) to segment ITOAD(p). The
matching (same subscript) members of JFRAD, ITOAD, and ADVPR define an
advective hydrologic flow pathway. EXAMS computes the total net flow
available for advection from segment JFRAD(p). Of the total flow, the
fraction ADVPR(p) flows from segment JFRAD(p) into segment ITOAD(p).
The hydrologic flow carries an entrained mass of chemical along the
pathway. The flow specifications can be inspected by typing SHOW ADV;
pathway numbers are given above each active dataset. Enter data with
SET or CHANGE commands.
See also: ITOAD, ADVPR
JTURB
J TURBulent dispersion (path)
Units: n/a Range: 0—KOUNT
Segments JTURB(p) and ITURB(p) exchange via turbulent dispersion. The
matching (same "p" subscript) members of JTURB, ITURB, CHARL, DSP, and
XSTUR together define a dispersive transport pathway; JTURB(p) and
ITURB(p) indicate which segments are linked by dispersive transport
pathway "p". A "0" in JTURB paired with a non-zero segment number in
ITURB denotes a boundary condition with a pure (zero chemical) water-
body. The input data can be examined via SHOW TURBULENCE; pathway
numbers are shown with each dataset.
See also: CHARL, DSP, ITURB, XSTUR
KAcid Hydrolysis (form, ion, chemical).
Units: per mole [H*] /hour
Second-order rate constant for specific-acid-catalyzed hydrolysis of
chemicals. When the matching (same subscripts) Arrhenius activation
energy (EAH) is zero, KAH is interpreted as the second-order rate
constant. When the matching entry in EAH is non-zero, KAH is
interpreted as the (Briggsian) logarithm of the frequency factor in an
Arrhenius equation, and the 2nd-order rate constant is computed as a
function of segment temperatures TCEL. Matrix indices refer to three
forms—1: aqueous, 2: solids-sorbed, and 3: DOC-complexed; by seven
ions—1: neutral, 2-4: cations, and 5-7: anions.
KBACS
KBACteria benthoS (form, ion, chemical)
Unit a: 1/(cfu/mL)/hr
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Second-order rate constants—-benthic sediment bacterial biolysis of
chemicals normalized by "colony forming units" (cfu) per mL. When the
matching (same subscripts) Q10 (QTBAS) is zero, KBACS is interpreted as
the second-order rate constant. When the matching entry in QTBAS is
non-zero,KBACS is interpreted as the numerical value of the
second-order rate constant at 20 degrees C, and local values of the
rate constant are computed as a function of temperature (TCEL) in each
ecosystem segment. Indices refer to four forms—1: aqueous, 2:
solids-sorbed, 3: DOC-complexed, and 4: bio-sorbed; by seven ions—1:
neutral, 2-4: cations, and 5-7: anions.
KBACW
KBH
KBACterioplankton Water (form, ion, chemical)
Units: I/ (cfu/mL)/hr
Second-order rate constants K for water column bacterial biolysis of
chemicals normalized by "colony forming units" (cfu) per mL. When the
matching (same subscripts) Q10 (QTBAW) is zero, KBACW is interpreted as
the second-order rate constant. When the matching entry in QTBAW is
non-zero,KBACW is interpreted as the numerical value of the
second-order rate constant at 20 degrees C, and local values of the
rate constant are computed as a function of temperature (TCEL) in each
ecosystem segment. Indices refer to four forms—1: aqueous, 2:
solids-sorbed, 3: DOC-complexed, and 4:bio-sorbed; by seven ions—1:
neutral, 2-4: cations, and 5-7: anions.
KBase Hydrolysis (form, ion, chemical)
Units: per mole [OH"]/hour
Second-order rate constant for specific-base-catalyzed hydrolysis of
chemicals. When the matching (same subscripts) Arrhenius activation
energy (BBH) is zero, KBH is interpreted as the second-order rate
constant. When the matching entry in EBH is non-zero, KBH is
interpreted as the (Briggsian) logarithm of the frequency factor in an
Arrhenius equation, and the 2nd-order rate constant is computed as a
function of segment temperatures TCEL. Matrix indices refer to three
forms—1: aqueous, 2: solids-sorbed, and 3: DOC-complexed; by seven
ions—1: neutral, 2-4: cations, and 5-7: anions.
KCHEM
Number of chemicals under review in current study.
Units: n/a
KDP
KDirect Photolysis (ion, chemical)
Units: I/hour
Estimated photolysis rates—use only when ABSOR is unavailable. KDP is
an annual average for cloudless conditions at RFLAT, where
KDP(l,c) refer to photolysis of neutral molecules S(H3)
KDP(2,c) " " " " singly charged cations S(H4)+
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KDP(3,c)
KDP(4,c)
KDP(5,c)
KDP(6,c)
KDP(7,c)
doubly charged cations S (H5) 2+
triply charged cations S(H6)3+
singly charged anions S(H2)~
doubly charged anipns S(H)2-
triply charged anions S3-
KIEC
Kp for Ion Exchange Capacity (ion, chemical) Units: Kp/(meq/lOOg dry)
Coefficient relating Kp of ions to exchange capacity of sediments. . KIEC
times CEC(seg, month) (or AEC) gives Kp for sorption of ions with solid^
phases. Overridden by explicit (non-zero) values of KPS.
KIEC(l,c) contains datum for relating sorption of S(H4)+ to C.E,C.
KIEC (2, c) " " " " " " S(H$)2+ "
KIEC (3, C) " " " " " " S(H6)3+ "
KIEC(4,c) " " " " " » S(H2)- to A.B.q.
KIEC (5, c) " " " " " " S(H)2- "
KIEC (6, c) " " " " " " S3«- "
KINOUT
Logical Unit Number for writing results of numerical integration to
kinetics plotting file.
KNH
KNeutral Hydrolysis (form, ion, chemical)
Units: I/hour
Pseudo-first-order rate constants for neutral hydrolysis of chemicals,
When the matching (same subscripts) Arrhenius activation energy (ENH) is
zero, KNH is interpreted as the second-o-rder rate constant. When the
matching entry in ENH is non-zero, KNH is interpreted as the (Briggsian)
logarithm of the frequency factor in an Arrhenius equation, and the 2nd^-
order rate constant is computed as a function of segment temperatures
TCEL. Matrix indices refer to three forms—1: aqueous, 2: solidsr-
sorbed, and 3: DOC-complexed; by seven ions—1: neutral, 2-4: cations,
and 5-7: anions.
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KOC
Koc(chemical)
Units: ((mg/kg)/(mg/L)) / (organic carbon fraction)
KOC is partition coefficient (Kp) keyed to organic carbon content
FROC(s, m) of the sediment solids in each (s) segment, during each (m)
month of simulation of chemical behavior in the system. Multiplication
of KOC by the organic carbon fraction FROC(s) of the solids in each
segment yields the partition coefficient (Kp) for sorption of unionized
(SH3) species with those solids:
Kp(chemical, segment, month) = KOC(chemical) * FROC(segment, month)
KOUNT
Number of segments used to define current ecosystem.
Units: n/a
ROW
KOX
KO2
Octanol-Water partition coefficient (chemical)
Units: (mg/L)/(mg/L)
Kow is an experimentally determined chemical descriptor. Kow (KOW(c))
can be used to estimate Koc (c.f.), and thus relate the Kp of a chemical
to the organic carbon content of sediments.
K oxidation (form, ion, chemical)
Units: per mole [OXRAD] /hour
Second-order rate constants for free-radical (OXRAD) oxidation of
chemicals. When the matching (same subscripts) Arrhenius activation
energy (BOX) is zero, KOX is interpreted as the second-order rate
constant. When the matching entry in BOX is non-zero, KOX is
interpreted as the (Briggsian) logarithm of the frequency factor in an
Arrhenius equation, and the 2nd-order rate constant is computed 'as a
function of segment temperatures TCEL. Matrix indices refer to three
forms—1: aqueous, 2: solids-sorbed, and 3: DOC-complexed; by seven
ions—1: neutral, 2-4: cations, and 5-7: anions.
KO2(segment, month)
Units: cm/hour
Oxygen exchange constant or piston velocity at?20- degrees C in each
ecosystem segment.
KPB
KP for Biomass (ion, chemical)
Units: (ug/g) / (mg/L)
Partition coefficient (Kp) for computing equilibrium biosorption. The
"ion" subscripts ("c" is the chemical) identify:
KPB(l,c) — datum for biosorption of S(H3)
(neutral molecule)
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KPB(2,c) — datum for biosorption of S(H4)+ (1+ cation)
KPB(3,c) -- " " " " S(H5)2+ (2+ cation)
KPB(4,c) — " " " " S(H6)3+ (3+ cation)
KPB(5,c) — " " " " S(H2)- (1- anion)
KPB<6,c) ~ " " " " S(H)2- (2- anion)
KPB(7,c) -- " " " " S3- (3- anion)
KPDOC
KPS
KPDissolved Organic Carbon (ion, chemical)
Units: (ug/g)/(mg/L)
Partition coefficient (Kp) for equilibrium complexation with DOC. The
"ion" subscripts ("c" is the chemical) identify:
KPDOC (l,c) — datum for complexation of S(H3)
KPDOC(2,c) — datum for complexation of S(H4) +
KPDOC(3,c) — " " "
KPDOC(4,c) — " " "
KPDOC(5,c) — " " "
KPDOC(6,c) — " " "
KPDOC(7,c) — " " "
KP for Sediment solids (ion, chemical)
(neutral molecule)
(1+ cation)
S(H5)2+ (2+ cation)
S(H6)3+ (3+ cation)
(1- anion)
(2- anion)
(3- anion)
Units: (mg/kg)/(mg/L)
S(H2)-
S(H)2-
S3-
Partition coefficients (Kp) for computing sorption with sediments .• The
"ion" subscripts ("c" is the chemical) identify:
KPS(l,c) — datum for sorption of S(H3)
KPS(2,c) — datum for sorption of S(H4)+
KPS (3,c)
KPS(4,c)
KPS (5,c)
KPS(6,c)
KPS(7,c)
11 S (H5) 2+
" S(H6)3+
" S(H2)-
" S(H)2-
- " S3-
(neutral molecule)
(1+ cation)
(2+ cation)
(3+ cation)
(1— anion)
(2- anion)
(3- anion)
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KRED
KREDuction (form, ion, chemical)
KVO
K102
LAT
Units: per mole [REDAG] /hour
Second-order rate constants for REDucing AGent chemical reduction of
compounds. When the matching (same subscripts) Arrhenius activation
energy (ERED) is zero, KRED is interpreted as the second-order rate
constant. When the matching entry in ERED is non-zero, KRED is
interpreted as the (Briggsian) logarithm of the frequency factor in an
Arrhenius equation, and the 2nd-order rate constant is computed as a
function of segment temperatures TCEL. Matrix indices refer to three
forms—1: aqueous, 2: solids-sorbed, and 3: DOC-complexed; by seven
ions—1: neutral, 2-4: cations, and 5-7: anions.
KVOlatilization (chemical) Units: dimensionless ratio
Liquid-phase transport resistance, as ratio to reaeration rate.
K1O2(singlet oxygen) (form, ion, chemical)
Units: per M [1O2] /hr
Second-order rate constants for singlet oxygen photo-oxygenation of
chemicals. When the matching (same subscripts) Arrhenius activation
energy (EK1O2) is zero, K1O2 is interpreted as the second-order rate
constant. When the matching entry in EK1O2 is non-zero, K1O2 is
interpreted as the (Briggsian) logarithm of the frequency factor in an
Arrhenius equation, and the 2nd-order rate constant is computed as a
function of segment temperatures TCEL. Matrix indices refer to three
forms—1: aqueous, 2: solids-sorbed, and 3: DOC-complexed; by seven
ions—1: neutral, 2-4: cations, and 5-7: anions.
LAMAX
LAMbda MAXimum (ion, chemical)
Units: nanometers
Wavelength of maximum absorption of light by each ionic species, or
wavelength of maximum overlap of solar spectrum and chemical's
absorption spectrum (of each ion). Indices match with KDP matrix. LAMAX
selects the wavelengths used to compute light extinction factors for
photochemical transformation, in those cases where the absorption
spectrum of the compound is not available, but the results of simple
photochemical experiments can be used as a coarse estimate of rates of
photochemical transformations (i.e., KDP > 0.0). When set to zero,
LAMAX defaults to 300 nm.
LATitude
Units: degrees and tenths (e.g., 37.24)
Geographic latitude of the ecosystem.
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LENG
LENGth (segment)
Length of a reach — used to compute volume, area, depth.
Units: m
LOADNM
LONG
LOADings database NaMe (50 characters)
Units: n/a
Do NOT use "CHANGE" or "SET" to enter names! The NaMe for a LOADings
database is entered via the command sequence:
EXAMS > LOAD NAME IS nnn...
where "nnn... " can include as many as 50 characters. This name is
associated with chemical loadings database library entries, so that load
patterns can be found in the catalog. The Ith character can be
corrected with a CHANGE or SET command. For example, to repair the 7th
character, "SET LOADNM(7) TO ... ."
LONGitude Units: degrees and tenths (e.g., 154.2)
Geographic longitude of the ecosystem. '
MCHEM
M CHEMical
Number of chemical in activity data base.
Units: n/a
MODE
MODE sets the operating "mode" of EXAMS.
Three operating modes are available; these are selected by SETting MODE
to 1, 2, or 3.
MODE
MONTH
Operational characteristics of EXAMS
1 • , Long-term (steady-state) analysis. , .
2 Pulse analysis -- specifiable initial chemical mass ..,
(IMASS) and time frame, time-rinvariant environment.,
3 Monthly environmental data, daily pulse loads IMASS
and monthly chemical loadings of other types. '
MONTH Units: n/a
Set MONTH to inspect a specific block of environmental data.
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MWT
Gram Molecular WeighT (chemical)
Units: g/mole
Molecular weight of the neutral species of each study chemical. Changes
in molecular weight due to ionization are neglected.
NPROC
NPSED
NPSFL
NPSLD
NYEAR
Number of PROCess (path) Units: n/a Range: 1—9
Signals the type of process transforming CHPAR(p) into TPROD(p).
NPROC can be set to the following:
1 —> specific acid hydrolysis
2 —> neutral hydrolysis
3 —> specific base hydrolysis
4 —> direct photolysis
5 —> singlet oxygen reactions
6 —> free radical oxidation
7 —> water column bacterial biolysis
8 —> benthic sediment bacterial biolysis
9 —> reductions, e.g., reductive dechlorination
See also: CHPAR, EAYLD, RFORM, TPROD, YIELD
Non-Point-Source SEDiment (segment, month) Units: kg/hour
Non-point-source sediment loads entering ecosystem segments.
Non-Point-Source FLow (segment, month) Units: mVhour
Non-point-source water flow entering ecosystem segments.
Non-Point-Source LoaD (segment, chemical, month) Units: kg/hour
Chemical loadings entering segments via non-point sources.
Number of YEARs Units: n/a
NYEAR is number of years to be simulated for a mode 3 run.
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OXRAD
OXidant RADicals (month)
Units: moles/L
Concentration of environmental oxidants in near-surface waters (e.g.,
peroxy radicals). EXAMS computes segment-specific oxidant
concentrations using ultra-violet light extinction in the system.
OZONE
OZONE (month) Units: centimeters NTP Typically 0.2 — 0.3 cm
Mean (monthly) ozone (O3) content of atmosphere.
PCPLD
Precipitation LoaD (segment, chemical, month)
Chemical loadings entering each segment via rainfall.
Units: kg/hour
PCTWA
PerCenT WAter (segment, month)
Units: dimensionless
Percent water in bottom sediments of benthic segments. Elements of
these vectors that correspond to water column segments are not used
(dummy values). PCTWA should be expressed as the conventional soil-
science variable (the fresh weight : dry weight ratio times 100); all
values must be greater than or equal to 100. An entry in PCTWA that is
less than 100.0 for a benthic segment raises an error condition, and
control is returned to the user for correction of the input data.
PH
pH (segment, month)
Units: pH units
The negative value of the power to which 10 is raised in order to obtain
the temporally averaged concentration of hydronium ions [H3O+] in gram-
equivalents per liter.
PK
pK (ion, chemical)
Negative of base-10 logarithm of acid/base dissociation constants. When
the matching value in the EPK matrix is zero, PK(i, c) is taken as the
pK value. (To "match" is to have the same subscript values.) When
EPK(i, c) is non-zero, PK is taken as the base-10 logarithm of the pre-
exponential factor in the equation for pK as a function of environmental
temperature TCEL, that is,
log pK = PK(i,c) -
1000 EPK(ion,chemical)
4.58 (TCEL (segment,month) -f 273.15)
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The vector indices for PK ("a" the chemical) are:
PK(l,c) contains datum for generation of S(H4)+ from S(H3)
PK(2,c) " " " " " S(H5)2+ from S(H4) +
PK(3,c) " " " " " S(H6)3+ " S(H5)2+
PK(4,c) " " " " " S(H2)- " S(H3)
PK(5,C) " " " " " S(H)2- " S(H)-
PK(6,C) " " " " " S3- " S(H)2-
PLMAS
PLanktonic bioMASs (segment, month) Units: mg (dry weight)/L
Total plankton subject to biosorption of xenobiotic chemicals.
POH
pOH (segment, month)
Units: pOH units
The negative value of the power to which 10 is raised in order to obtain
the temporally averaged concentration of hydroxide [OH"] ions in gram-
equivalents per liter.
PRINTR
h
Logical Unit Number used for printing results on a line printer.
PRODNM
PRODuct chemistry database NaMe (50 characters)
Units: n/a
Do NOT use "CHANGE" or "SET" to enter names! The NaMe for a PRODuct
chemistry database is entered via the command sequence:
EXAMS > PRODUCT NAME IS nnn
where "nnn... " can include as many as 50 characters. This name is
associated with product chemistry database library entries, so that
databases can be found in the catalog. Use a CHANGE or SET command to
repair single characters in the name. For example, to repair character
seven, enter "SET PRODNM(7) TO ... ."
PRSW
PRint Switch
Units: n/a
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PRSW is a switch for controlling printing options. In mode 3, when PRSW
is set to 0 (the default), average values of the environmental
parameters are recorded in the run log. When PRSW is 1, a separate
table is produced for each (monthly) data set, except for those values
which are invariant (VOL etc.).
QTBAS
"Qi
Q Ten BActeria benthos (form, ion, chemical)
Units: dimensionless
Q10 values for benthic bacterial biolysis (see KBACS) of chemical.
is the increase in the second-order rate, constant due to a 10 C
increase in temperature. Indices refer to 28 molecular spp: 4 forms —
1: aqueous, 2: solids-sorbed, 3: DOC-complexed, and 4: bio-sorbed; by 7
ions — 1: neutral, 2-4: cations, and 5-7: anions. When QTBAS is non-
zero, the matching (same subscripts) rate constant is computed as:
Kbacs(f,i,c) = QTBAS(f,i,c)
(TCEL(seg,month)-20)/10
KBACS(f,i,c)
QTBAW
Q Ten BActeria Water (form, ion, chemical)
QUANT
Units: dimensionless
Qio values for bacterioplankton biolysis (see KBACW) of chemical.
"Qio" is the increase in the second-order rate constant due to a 10 C
increase in temperature. Indices refer to 28 molecular spp: 4 forms —
1: aqueous, 2: solids-sorbed, 3: DOC-complexed, and 4: bio-sorbed; by 7
ions 1: neutral, 2-4: cations, and 5-7: anions. When QTBAW is non-
zero, the matching (same subscripts) rate constant is computed as:
(TCEL(seg,month)-20)/10
Kbacw(f,i,c) = QTBAW(f,i,c) * KBACW(f,i,c)
QUANTum yield (form, ion, chemical)
Units: dimensionless
Reaction quantum yield for direct photolysis of chemicals — fraction of
the total light quanta absorbed by a chemical that results in
transformations. Separate values (21) for each potential molecular type
of each chemical allow the effects of speciation and sorption on
reactivity to be specified in detail. The matrix of 21 values specifies
quantum yields for the (3) physical forms: (1) dissolved, (2) sediment-
sorbed, and (3) DOC-complexed; of each of (7) possible chemical species:
neutral molecules (1), cations (2-4), and anions (5-7). (QUANT is an
efficiency.)
RAIN
RAINfall (month)
Average (monthly) rainfall in geographic area of system.
Units: mm/month
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RANUNT
Logical Unit Number for the UTILITY file support.
/
The UTILITY file is used for retrieving and storing chemical and
environmental parameters, for supporting the on-line assistance
facility, and to support the SYSTEM PARAMETERS operations.
REDAG
REDucing AGents (segment, month) Units: moles/L
Molar concentration of reducing agents in each system segment.
RELER
RELative ERror tolerance for integrators.
When the characteristics of the chemical and ecosystem are such as to
result in "stiff" equations, numerical errors may lead to small negative
numbers in the time series. If desired, the value of ABSER and RELER
can be decreased in order to achieve greater precision in the simulation
outputs.
RFLAT
ReFerence LATitude (ion, chemical)
Units: degrees (e.g., 40.72)
(RFLAT - LAT) corrects for N/S displacement of the ecosystem LAT from
the location (RFLAT) of a matched (same subscript) KDP.
RFLAT(l,c) refer to photolysis of neutral molecules
S(H3)
RFLAT(2,c)
RFLAT(3,C)
RFLAT(4,c)
RFLAT(5,c)
RFLAT(6,C)
RFLAT(7,C)
singly charged cations S(H4)+
doubly charged cations S(H5)2+
triply charged cations S(H6)3+
singly charged anions S(H2)-
doubly charged anions S(H)2-
triply charged anions S3-
RFORM
Reactive FORM (path)
Units: n/a Range: 1—32
RFORM gives the reactive molecular form (ionic species in each of the
possible sorptive states) of CHPAR(p) resulting in product TPROD(p).
The table shows the value of RFORM for each molecular entity, including
values for total dissolved (29), solids-sorbed (30), etc.
88
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Ionic spp.
& valence
Neutral
Cations
(0)
(1+) (2+) (3+)
Anions Total
(1-) (2-) (3-) (all)
Forms;
Dissolved
Solids-sorbed
DOC-complexed
Biosorbed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
See also: CHPAR, EAYLD, NPROC, TPROD, YIELD
RHUM
Relative HUMidity (month)
Units: %, i.e., saturation = 100% R.H.
Mean (monthly) relative humidity during daylight hours. Data typical of
daylight hours are needed because their primary use is to characterize
light transmission in the atmosphere.
RPTOUT
Logical Unit Number for data written to tabular report file.
SEELD
SEEpage LoaD (segment, chemical, month)
Units: kg/hour
Chemical loadings entering the system via "interflows" or seepage (all
sub-surface water flows entering the system, (usually) via a benthic
segment).
SEEPS
SEEPage flows (segment, month)
Units: mVhour
Interflow (subsurface water flow, seepage) entering each segment. SEEPS
usually enter via a benthic segment. SEEPS are assumed to lack an
entrained sediment flow, that is, they are flows of water only.
SOL
SOLubility (ion, chemical)
Units: mg/L
Aqueous solubility of each species (neutral molecule + all ions). When
the matching value in the ESOL matrix is zero, SOL(i, c) is taken as the
aqueous solubility in mg/L. (To "match" is to have the same subscript
values.) When ESOL(i, c) is non-zero, SOL(i, c) is taken as the base-10
logarithm of the pre-exponential factor of the equation describing the
MOLAR solubility of the species as a function of environmental
temperature (TCEL). The vector indices for SOL are given in the text
describing ESOL. Solubility must be specified, because it is used as a
constraint on loads.
89
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SPFLG
SPecies FLaGs (ion, chemical) — can be "1" (exists) or "0".
This vector of "flags" or "switches" shows which ions exist. Set the
flags ("SET SPFLG(i, c) TO 1") when entering chemical data in order to
show EXAMS the ionic structure of the chemical.
SPFLG(l) set (=1) signals that the neutral molecule S(H3) exists.
SPFLG(2) set signals existence of singly charged cation S(H4)+
SPFLG(3)
SPFLG(4)
SPFLG(5)
SPFLG(6)
SPFLG(7)
doubly
triply
singly
doubly
triply
" S(H5)2+
" S(H6)3+
anion S(H2)-
" S(H)2-
S3-
SSOUT
Logical Unit Number for data written to plotting file containing EXAMS'
steady-state chemical concentrations.
STFLO
STream FLOws (segment, month)
Units: m3/hour
Flow into head reach of river or estuary; segment tributaries and creeks
or other streamflows entering a lake or pond. Note that STFLO
represents stream flow entering system segments from external sources
ONLY. EXAMS itself computes hydrologic flows among segments that are
part of the waterbody being studied, via the specified advective and
dispersive flow patterns (see JFRAD, JTURB, etc.) Therefore, DO NOT
compute net water balances for each segment and enter these into the
database—enter ONLY those flows entering the system across external
boundaries!
STRLD
STReam LoaD (segment, chemical, month) Units: kg/hour
Chemical loadings entering ecosystem segments via stream flow.
STSED
STream-borne SEDiment (segment, month)
Stream-borne sediment load entering ecosystem segments.
Units: kg/hour
90
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SUSED
Suspended SEDiment (segment, month) Units: mg/L
Suspended particulate matter —- applicable to the water column only.
SYSTYP
Name of aquatic ecoSYStem TYPe (50 characters) Units: n/a
Do NOT use "CHANGE" or "SET" to enter names! The name of a waterbody is
entered into the database via the command sequence:
EXAMS > ENVIRONMENT NAME IS nnn...
where "nnn " can include as many as 50 characters. This, name is
associated with environmental library entries (the UDB catalog) and is
printed in the header information of the appropriate output tables. Use
SET and CHANGE to correct single characters in the name. For example,
to correct the seventh character in a name, "CHAN SYSTYP(7) TO ... ."
TCEL
Temperature CELsius (segment, month)
Units: degrees C
Average temperature of ecosystem segments. Used (as enabled by input
data) to compute effects of temperature on transformation rates and
other properties of chemicals.
TCODE
The value of Time CODE sets the units of TINIT, TEND, and CINT.
TCODE can be SET to 1 (hours), 2 (days), 3 (months), or 4 (years).
TCODE is under full user control only in Mode 2. In mode 2, TCODE
controls the time frame of the study. For example, given TINIT=0
TEND=24., and CINT=2.; CHANging TCODE from 1 to 3 converts a 0-24 hour
study into 0-24 months, with bimonthly reports. In mode 1, EXAMS
selects the units for reporting results, from the probable half-life of
the study chemical(s). In mode 3, a RUN encompasses one year or longer,
and the timing is set to produce standard outputs.
TEND
Time END for a dynamic simulation segment.
Units: see TCODE
A simulation segment encompasses the period TINIT through TEND. At the
end of each integration, TINIT is reset to TEND. The simulation can be
extended by invoking the "CONTINUE" command; EXAMS will then request a
new value of TEND. Pulse loads (IMASS) and longer-term chemical loads
(STRLD, NPSLD, etc.) can be modified or deleted during the pause between
simulation segments.
91
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TINIT
Time INITial for a dynamic simulation segment.
Units: see TCODE
A simulation RUN encompasses the period TINIT through TEND. At the end
of each integration, TEND is transferred to TINIT. The simulation
results can be evaluated, and the study continued via the "CONTINUE"
command. EXAMS will note the new value of TINIT and request a new
endpoint. Pulse and other chemical loadings can be modified or deleted
between simulation segments.
TPROD
Transformation PRODuct (path)
Units: n/a Range: 1-KCHEM
The
TPROD(p) — ADB location of the transformation product of CHPAR(p).
matching (same transformation path number "p") members of CHPAR and
TPROD give the location numbers in the active database of the parent
chemical and the transformation product for pathway "p". For example,
SET CHPAR(p) TO 1, and TPROD(p) to 4, to show that the chemical in ADB
sector 4 is produced via transformation of the chemical in ADB sector 1,
via process data defined by the remaining members of product chemistry
sector "p".
See also: CHPAR, EAYLD, NPROC, RFORM, YIELD
TTYIN
Logical Unit Number for interactive input commands.
TTYOUT
Logical Unit Number for output error messages and warnings, and for
EXAMS' interactive responses.
TYPE
UDB
Segment TYPE (segment)
Units: letter codes
Letter codes designating segment types used to define ecosystems,
Available types: Littoral, Epilimnion, Hypolimnion, and Benthic.
User DataBase
Long-term retention of data required by EXAMS is provided by storage in
the "User Database" (UDB, generally resident on a physical device,
e.g., a hard disk) for CHEMICALS, ENVIRONMENTS, LOADs, or PRODUCTS.
Within each of these UDB sectors, each dataset is CATALOGued via a
unique accession number (UDB#). When transferring data between
foreground memory (the activity database or ADB) and a UDB, the target
location must be specified by the name of the UDB sector and the
accession number within the sector. For example, to STORE the current
pattern of chemical loadings: STORE LOAD 7. Similarly, to retrieve or
RECALL data from a UDB into the ADB for use in an analysis, one could
enter: RECALL LOAD 7.
92
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VAPR
VAPoR pressure (chemical)
Units: Torr
is zero (0) but
HENRY
VAPR / 760.
SOL / MWT
-------
XSTUR
XSection for TURbulent dispersion (path)
Units: m2
XSTUR is cross-sectional area of a dispersive exchange interface at the
boundary between segments JTURB<£) and ITURB(p). The matching (same p
subscript) members of JTURB, ITURB, CHARL, DSP, and XSTUR collectively
define a dispersive transport pathway. The exchange constant E(p) is
computed as:
E(p) (mVhour) = DSP (p) XSTUR (p) / CHARL (p)
See also: CHARL, DSP, ITURB, JTURB
YEAR1
YEAR 1
Starting year for mode 3 simulation (e.g., 1985)
Units: n/a
YIELD
YIELD of product (path)
Units: mole/mole
YIELD(p) is the product yield from the transformation pathway "p" with
dimensions mole of transformation product TPROD(p) produced per mole of
parent compound CHPAR(p) reacted (dimensionless).
See also: CHPAR, EAYLD, NPROC, RFORM, TPROD
1990/7AS-159/OOA5!
94
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