&EPA
i! Prntection
Office of Research and
Development
Washington DC 20460
EPA/600/R-97/047
March 1997
Exposure Analysis
Modeling System
(EXAMS II)
User's Guide for Version 2.97.5
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EPA/600/R-97/047
March 1997
EXPOSURE ANALYSIS MODELING
SYSTEM (EXAMS II)
User's Guide for Version 2.97.5
by
Lawrence A. Burns, Ph.D.
Research Ecologist
Ecosystems Research Division
National Exposure Research Laboratory
U.S. Environmental Protection Agency
Athens, Georgia 30605-2700
U.S. Environmental Protection Agency
Perion 5, Library (PL-12J)
77'Wi-st Jsckscn Boulevard, 12th Floor
Chicago, II 60604-3590
Ecosystems Research Division
National Exposure Research Laboratory
U.S. Environmental Protection Agency
Athens, Georgia 30605-2700
Printed on Recycled Paper
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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.
EXAMS-ii
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FOREWORD
Environmental protection efforts are increasingly directed toward preventing adverse health and
ecological effects associated with specific chemical compounds of natural or human origin. As part of
the Ecosystems Research Division's research on the occurrence, movement, transformation, impact, and
control of environmental contaminants, the Ecosystems Assessment 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 the risks associated
with 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, evaluation, 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
Director
Ecosystems Research Division
Athens, Georgia
EXAMS-1H
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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 that 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. This DOS implementation
allows for study of five simultaneous chemical compounds and 100 environmental segments; other
configurations can be created through special arrangement with the author. EXAMS provides analyses
of
Exposure: the expected (96-hour acute, 21-day and long-term chronic) 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.
EXAMS 2.97 includes file-transfer interfaces to the PRZM3 terrestrial model and the FGETS bio-
accumulation model; it is a complete implementation of EXAMS in FORTRAN 90.
This report covers a period from October 1, 1995 to March 31, 1997 and work was completed
as of April 7,1997.
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TABLE OF CONTENTS
Disclaimer ii
Foreword iii
Abstract iv
Introduction to the Exposure Analysis Modeling System (EXAMS) 1
Exposure Analysis in Aquatic Systems 1
The EXAMS program 2
Sensitivity Analysis and Error Evaluation 4
EXAMS Process Models 5
Ecosystems Analysis and Mathematical Systems Models 7
Further Reading 12
EXAMS COMMAND LANGUAGE INTERFACE (CLI) USER'S GUIDE 15
Conventions Used in this Section 15
Overview 15
Entering Commands 16
Command Prompting 17
EXAMS Messages 19
The HELP Command 19
Command Procedures 20
Wild Card Characters 20
Truncating Command Names and Keywords 21
Summary Description of EXAMS' System Commands 21
System Command Descriptions 22
AUDIT 22
CATALOG 24
CHANGE 26
CONTINUE 28
DESCRIBE 32
DO 34
ERASE 37
EXIT 39
HELP 40
LIST 42
NAME 45
PLOT 47
PRINT 53
QUIT 54
READ 55
RECALL 57
RUN 59
SET 60
SHOW 62
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STORE 66
WRITE 68
ZERO 70
EXAMS n Data Dictionary 72
EXAMS data entry template for chemical molar absorption spectra (ABSOR) 104
Implementing the microcomputer MS-DOS Runtime EXAMS 2.97 105
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User's Guide for EXAMS II Version 2.97
Introduction to the Exposure Analysis Modeling System (EXAMS)1
Industrial production of agricultural chemicals, plastics, and pharmaceuticals has increased
steadily over the past four decades. More recently, growth of the chemical industry has been
accompanied by increasing concern over the effects of synthetic chemicals on the environment. The
suspicion has arisen that, in some cases, the benefits gained by using a chemical may not offset the cost
of incidental damage to man's natural life-support system-the biosphere. The toxicity of a chemical
does not of itself indicate that the environmental risks associated with its use are unacceptable, however,
as it is the dose that makes the poison. A rational evaluation of the risk posed by the use and disposal
of synthetic chemicals must begin from a knowledge of the persistence and mobility of chemicals in the
environment, which in turn establish the conditions of exposure leading to absorption of toxicological
dose.
The Exposure Analysis Modeling System (EXAMS), developed at the U.S. Environmental
Protection Agency's research laboratory in Athens, Georgia, is an interactive computer program intended
to give decision-makers in industry and government access to a responsive, general, and controllable tool
for readily deriving and evaluating the behavior of synthetic chemicals in the environment. The research
effort has focused on the development of the interactive command language and user aids that are the
core of EXAMS, and on the genesis of reliable EXAMS mathematical models. EXAMS was designed
primarily for the rapid screening and identification of synthetic organic chemicals likely to adversely
impact aquatic systems. This report is intended to acquaint potential users with the underlying theory,
capabilities, and use of the system.
Exposure Analysis in Aquatic Systems EXAMS was conceived as an aid to those who must execute
hazard evaluations solely from laboratory descriptions of the chemistry of a newly synthesized toxic
compound. EXAMS estimates exposure, fate, and persistence following release of an organic chemical
into an aquatic ecosystem. Each of these terms was given a formal operational definition during the
initial design of the system.
Exposure When a pollutant is released into an aquatic ecosystem, it is entrained in the transport field of
the system and begins to spread to locations beyond the original point of release. During the course of
these movements, chemical and biological processes transform the parent compound into daughter
products. In the face of continuing emissions, the receiving system evolves toward a "steady-state"
condition. At steady state, the pollutant concentrations are in a dynamic equilibrium in which the
loadings are balanced by the transport and transformation processes. Residuals can be compared to the
concentrations posing a danger to living organisms. The comparison is one indication of the risk entailed
by the presence of a chemical in natural systems or in drinking-water supplies. These "expected
1 Additional technical documentation for EXAMS is contained in Burns et al. 1982.
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environmental concentrations" (EECs), or exposure levels, in receiving water bodies are one component
of a hazard evaluation.
Persistence Toxicological and ecological "effects" studies are of two kinds: investigations of short-term
"acute" exposures, as opposed to longer-term "chronic" experiments. Acute studies are often used to
determine the concentration of a chemical resulting in 50% mortality of a test population over a period
of hours. Chronic studies examine sub-lethal effects on populations exposed to lower concentrations
over extended periods. Thus, for example, an EEC that is 10 times less than the acute level does not
affirm that aquatic ecosystems will not be affected, because the probability of a "chronic" impact
increases with exposure duration. A computed EEC thus must be supplemented with an estimate of
"persistence" in the environment. (A compound immune to all transformation processes is by definition
"persistent" in a global sense, but even in this case transport processes will eventually reduce the
pollutant to negligible levels should the input loadings cease.) The notion of "persistence" can be given
an explicit definition in the context of a particular contaminated ecosystem: should the pollutant loadings
cease, what time span would be required for dissipation of most of the residual contamination? (For
example, given the half-life of a chemical in a "first-order" system, the time required to reduce the
chemical concentration to any specified fraction of its initial value can be easily computed.) With this
information in hand, the appropriate duration and pollutant levels for chronic studies can be more readily
decided. More detailed dynamic simulation studies can elicit the probable magnitude and duration of
acute events as well.
Fate The lexicologist also needs to know which populations in the system are "at risk." Populations at
risk can be deduced to some extent from the distribution or "fate" of the compound, that is, by an
estimate of EECs in different habitats of single ecosystems. EXAMS reports a separate EEC for each
compartment, and thus each local population, used to define the system.
The concept of the "fate" of a chemical in an aquatic system has an additional, equally
significant meaning. Each transport or transformation process accounts for only part of the total behavior
of the pollutant. The relative importance of each process can be determined from the percentage of the
total system loadings consumed by the process. The relative importance of the transformations indicate
which process is dominant in the system, and thus in greatest need of accuracy and precision in its
kinetic parameters. Overall dominance by transport processes may imply a contamination of downstream
systems, loss of significant amounts of the pollutant to the atmosphere, or pollution of ground-water
aquifers.
The EXAMS program The need to predict chemical exposures from limited data has stimulated a variety
of recent advances in environmental modeling. These advances fall into three general categories:
• Process models giving a quantitative, often theoretical, basis for predicting the rate of transport
and transformation processes as a function of environmental variables.
• Procedures for estimating the chemical parameters required by process models. Examples
include linear free energy relationships, and correlations summarizing large bodies of
experimental chemical data.
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• Systems models that combine unit process models with descriptions of the environmental forces
determining the strength and speed of these processes in real ecosystems.
The vocabulary used to describe environmental models includes many terms, most of which
reflect the underlying intentions of the modelers. Models may be predictive, stochastic, empirical,
mechanistic, theoretical, deterministic, explanatory, conceptual, causal, descriptive, etc. The EXAMS
program is a deterministic, predictive systems model, based on a core of mechanistic process equations
derived from fundamental theoretical concepts. The EXAMS computer code also includes descriptive
empirical correlations that ease the user's burden of parameter calculations, and an interactive command
language that facilitates the application of the system to specific problems.
EXAMS "predicts" in a somewhat limited sense of the term. Many of the predictive water-quality
models currently in use include site-specific parameters that can only be found via field calibrations.
After "validation" of the model by comparison of its calibrated outputs with additional field
measurements, these models are often used to explore the merits of alternative management plans.
EXAMS, however, deals with an entirely different class of problem. Because newly synthesized chemicals
must be evaluated, little or no field data may exist. Furthermore, EECs at any particular site are of little
direct interest. In this case, the goal, at least in principle, is to predict EECs for a wide range of
ecosystems under a variety of geographic, morphometric, and ecological conditions. EXAMS includes
no direct calibration parameters, and its input environmental data can be developed from a variety of
sources. For example, input data can be synthesized from an analysis of the outputs of hydrodynamic
models, from prior field investigations conducted without reference to toxic chemicals, or from the
appropriate limnological literature. The EECs generated by EXAMS are thus "evaluative" (Lassiter et al.
1978) predictions designed to reflect typical or average conditions. EXAMS' environmental database can
be used to describe specific locales, or as a generalized description of the properties of aquatic systems
in broad geographic regions.
EXAMS relies on mechanistic, rather than empirical, constructs for its core process equations
wherever possible. Mechanistic (physically determinate) models are more robust predictors than are
purely empirical models, which cannot safely be extended beyond the range of prior observations.
EXAMS contains a few empirical correlations among chemical parameters, but these are not invoked
unless the user approves. For example, the partition coefficient of the compound on the sediment phases
of the system, as a function of the organic carbon content of its sediments, can be estimated from the
compound's octanol-water partition coefficient. A direct load of the partition coefficient (KOC, see the
EXAMS Data Dictionary) overrides the empirical default estimate, however. (Because EXAMS is an
interactive program in which the user has direct access to the input database, much of this documentation
has been written using the computer variables (e.g., KOC above) as identifiers and as quantities in the
process equations. Although this approach poses some difficulties for the casual reader, it allows the
potential user of the program to see the connections between program variables and the underlying
process theory. The EXAMS data dictionary in this document includes an alphabetical listing and
definitions of EXAMS' input variables.)
EXAMS is a deterministic, rather than a stochastic, model in the sense that a given set of inputs
will always produce the same output. Uncontrolled variation is present both in ecosystems and in
chemical laboratories, and experimental results from either milieu are often reported as mean values and
their associated variances. Probabilistic modeling techniques (e.g., Monte Carlo simulations) can
EXAMS-3
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account, in principle, for this variation and attach an error bound or confidence interval to each
important output variable. Monte Carlo simulation is, however, very time-consuming (i.e., expensive),
and the statistical distributions of chemical and environmental parameters are not often known in the
requisite detail. The objective of this kind of modeling, in the case of hazard evaluations, would in any
case be to estimate the effect of parameter errors on the overall conclusions to be drawn from the model.
This goal can be met less expensively and more efficiently by some form of sensitivity analysis.
Sensitivity Analysis and Error Evaluation EXAMS does not provide a formal sensitivity analysis among
its options: the number of sub-simulations needed to fully account for interactions among chemical and
environmental variables is prohibitively large (Behrens 1979). When, for example, the second-order rate
constant for alkaline hydrolysis of a compound is described to EXAMS via an Arrhenius function, the rate
constant computed for each compartment in the ecosystem depends on at least six parameters. These
include the frequency factor and activation energy of the reaction, the partition coefficient of the
compound (KOC), the organic carbon content of the sediment phase, the temperature, and the
concentration of hydroxide ion. The overall rate estimate is thus as dependent upon the accuracy of the
system definition as it is upon the skill of the laboratory chemist; in this example, the rate could vary six
orders of magnitude as a function of differences among ecosystems. In order to fully map the parameter
interactions affecting a process, all combinations of parameter changes would have to be simulated.
Even this (simplified) example would require 63 simulations (2n-l, where n is the number (6) of
parameters) merely to determine sensitivities of a single component process in a single ecosystem
compartment.
Sensitivity analysis remains an attractive technique for answering a crucial question that arises
during hazard evaluation. This question can be simply stated: "Are the chemical data accurate enough,
and precise enough, to support an analysis of the risk entailed by releases of the chemical into the
environment?" Like many simple questions, this question does not have a simple, definitive answer. It
can be broken down, however, into a series of explicit, more tractable questions whose answers sum to
a reasonably complete evaluation of the significance that should be attached to a reported error bound
or confidence interval on any input datum. Using the output tables and command language utilities
provided by EXAMS, these questions can be posed, and answered, in the following order.
• Which geographic areas, and which ecosystems, develop the largest chemical residuals? EXAMS
allows a user to load the data for any environment contained in his files, specify a loading, and
run a simulation, through a simple series of one-line English commands.
• Which process is dominant in the most sensitive ecosystem(s)? The dominant process, i.e., the
process most responsible for the decomposition of the compound in the system, is the process
requiring the greatest accuracy and precision in its chemical parameters. EXAMS produces two
output tables that indicate the relative importance of each process. The first is a "kinetic profile"
(or frequency scaling), which gives a compartment-by-compartment listing with all processes
reduced to equivalent (hour"1) terms. The second is a tabulation of the overall steady-state fate
of the compound, giving a listing of the percentage of the load consumed by each of the transport
and transformation processes at steady state.
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Given the dominant process, the input data affecting this process can be varied over the reported
error bounds, and a simulation can be executed for each value of the parameters. The effect of parameter
errors on the EECs and persistence of the compound can then be documented by compiling the results
of these simulations.
This sequence of operations is, in effect, a sensitivity analysis, but the extent of the analysis is
controlled and directed by the user. In some cases, for example, one process will always account for
most of the decomposition of the compound. When the database for this dominant process is inadequate,
the obvious answer to the original question is that the data do not yet support a risk analysis. Conversely,
if the dominant process is well defined, and the error limits do not substantially affect the estimates of
exposure and persistence, the data may be judged to be adequate for the exposure analysis portion of a
hazard evaluation.
EXAMS Process Models In EXAMS, the loadings, transport, and transformations of a compound are
combined into differential equations by using the mass conservation law as an accounting principle. This
law accounts for all the compound entering and leaving a system as the algebraic sum of (1) external
loadings, (2) transport processes exporting the compound out of the system, and (3) transformation
processes within the system that degrade the compound to its daughter products. The fundamental
equations of the model describe the rate of change in chemical concentrations as a balance between
increases due to loadings, and decreases due to the transport and transformation processes removing the
chemical from the system.
The set of unit process models used to compute the kinetics of a compound is the central core
of EXAMS. These unit models are all "second-order" or "system-independenf'models: each process
equation includes a direct statement of the interactions between the chemistry of a compound and the
environmental forces that shape its behavior in aquatic systems. Thus, each realization of the process
equations implemented by the user in a specific EXAMS simulation is tailored to the unique characteris-
tics of that ecosystem. Most of the process equations are based on standard theoretical constructs or
accepted empirical relationships. For example, 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 and Sorption lonization of organic acids and bases, complexation with dissolved organic
carbon (DOC), and sorption of the compound with sediments and biota, are treated as thermodynamic
properties or (local) equilibria that alter the operation of 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.
These include the parent uncharged molecule, and singly, doubly, or triply charged cations and anions,
each of which can occur in a dissolved, sediment-sorbed, DOC-complexed, or biosorbed form. The
program computes the fraction of the total concentration of compound that is present in each of the 28
molecular structures (the "distribution coefficients," alpha).
These (alpha) values enter the kinetic equations as multipliers on the rate constants. In this way,
the program accounts for differences in reactivity that depend on the molecular form of the chemical,
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as a function of the spatial distribution of environmental parameters controlling molecular speciation.
For example, the lability of a particular molecule to hydrolytic decomposition may depend on whether
it is dissolved or is sorbed with the sediment phase of the system. EXAMS makes no intrinsic assumptions
about the relative transformation reactivities of the 28 molecular species, with the single exception that
biosorbed species are unavailable to inorganic reactions. These assumptions are controlled through the
structure of the input data describing the species-specific chemistry of the compound.
Transformation Processes EXAMS computes the kinetics of transformations attributable to 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 a pair
of values defining the rate constant as a function of environmental temperatures. For example, the input
data for alkaline hydrolysis of the compound consists of two computer variables: KBH, and EBH. When
EBH is zero, the program interprets KBH as the second-order rate constant. When EBH is non-zero, EBH
is interpreted as the activation energy of the reaction, and KBH is re-interpreted as the pre-exponential
(frequency) factor in an Arrhenius equation giving the second-order rate constant as a function of the
environmental temperature (TCEL) in each system compartment. (KBH and EBH are both actually matrices
with 21 elements; each element of the matrix corresponds to one of the 21 possible molecular species
of the compound, i.e., the 7 ionic species occurring in dissolved, DOC-complexed, or sediment-sorbed
form—as noted above, biosorbed forms do not participate in extra-cellular reactions.)
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 are 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
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compound (Paris, Steen and Burns 1982). This approach is of demonstrated validity for at least some
biolysis processes, and provides the user with a minimal semi-empirical means of distinguishing between
eutrophic an oligotrophic ecosystems. 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 25 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. As with biolysis, this provides the user with a minimal empirical means of
assembling a simulation model that includes specific knowledge of the reductants important to a
particular chemical safety evaluation.
Transport Processes Internal transport and export of a chemical occur in EXAMS via advective and
dispersive movement of dissolved, sediment-sorbed, and biosorbed materials and by volatilization losses
at the air-water interface. EXAMS provides a set of vectors (JFRAD, etc.) that specify the location and
strength of both advective and dispersive transport pathways. Advection of water through the system is
then computed from the water balance, using hydrologic data (rainfall, evaporation rates, stream flows,
groundwater seepages, etc.) supplied to EXAMS as part of the definition of each environment.
Dispersive interchanges within the system, and across system boundaries, are computed from
the usual geochemical specification of the characteristic length (CHARL), cross-sectional area (XSTUR),
and dispersion coefficient (DSP) for each active exchange pathway. EXAMS can compute transport of
synthetic chemicals via whole-sediment bed loads, suspended sediment wash-loads, exchanges with
fixed-volume sediment beds, 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.
Chemical Loadings External loadings of a toxicant can enter the ecosystem via point sources (STRLD),
non-point sources (NPSLD), dry fallout or aerial drift (DRFLD), atmospheric wash-out (PCPLD), and
ground-water seepage (SEELD) entering the system. Any type of load can be entered for any system
compartment, but the program will not implement a loading that is inconsistent with the system
definition. For example, the program will automatically cancel a rainfall loading (PCPLD) 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 error message.
Ecosystems Analysis and Mathematical Systems Models The EXAMS program was constructed from
a systems analysis perspective. Systems analysis begins by defining a system's goals, inputs,
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environment, resources, and the nature of the system's components and their interconnections. The
system goals describe the outputs produced by the system as a result of operating on its input stream.
The system environment comprises those factors affecting system outputs over which the system has
little or no control. These factors are often called "forcing functions" or "external driving variables."
Examples for an aquatic ecosystem include runoff and sediment erosion from its watershed, insolation,
and rainfall. System resources are defined as those factors affecting performance over which the system
exercises some control. Resources of an aquatic ecosystem include, for example, the pH throughout the
system, light intensity in the water column, and dissolved oxygen concentrations. The levels of these
internal driving variables are determined, at least in part, by the state of the system itself. In other words,
these factors are not necessarily single-valued functions of the system environment. Each of the
components or "state variables" of a system can be described in terms of its local input/output behaviors
and its causal connections with other elements of the system. The systems approach lends itself to the
formulation of mathematical systems models, which are simply tools for encoding knowledge of
transport and transformation processes and deriving the implications of this knowledge in a logical and
repeatable way.
A systems model, when built around relevant state variables (measurable properties of system
components) and causal process models, provides a method for extrapolating future states of systems
from knowledge gained in the past. In order for such a model to be generally useful, however, most of
its parameters must possess an intrinsic interest transcending their role in any particular computer
program. For this reason, EXAMS was designed to use chemical descriptors (Arrhenius functions, pKa,
vapor pressure, etc.) and water quality variables (pH, chlorophyll, biomass, etc.) that are independently
measured for many chemicals and ecosystems.
EXAMS Design Strategy The conceptual view adopted for EXAMS begins by defining aquatic ecosystems
as a series of distinct subsystems, interconnected by physical transport processes that move synthetic
chemicals into, through, and out of the system. These subsystems include the epilimnion and
hypolimnion of lakes, littoral zones, benthic sediments, etc. The basic architecture of a computer model
also depends, however, on its intended uses. EXAMS was designed for use by toxicologists and
decision-makers who must evaluate the risk posed by use of a new chemical, based on a forecast from
the model. The EXAMS program is itself part of a "hazard evaluation system," and the structure of the
program was necessarily strongly influenced by the niche perceived for it in this "system."
Many intermediate technical issues arise during the development of a systems model. Usually
these issues can be resolved in several ways; the modeling "style" or design strategy used to build the
model guides the choices taken among the available alternatives. The strategy used to formulate EXAMS
begins from a primary focus on the needs of the intended user and, other things being equal, resolves
most technical issues in favor of the more efficient computation. For example, all transport and
transformation processes are driven by internal resource factors (pH, temperature, water movements,
sediment deposition and scour, etc.) in the system, and each deserves separate treatment in the model
as an individual state variable or function of several state variables. The strategy of model development
used for EXAMS suggests, however, that the only state variable of any transcendent interest to the user
is the concentration of the chemical itself in the system compartments. EXAMS thus treats all
environmental state variables as coefficients describing the state of the ecosystem, and only computes
the implications of that state, as residual concentrations of chemicals in the system.
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Although this approach vastly simplifies the mathematical model, with corresponding gains in
efficiency and speed, the system definition is now somewhat improper. System resources (factors
affecting performance that are subject to feedback control) have been redefined as part of the system
environment. In fact, the "system" represented by the model is no longer an aquatic ecosystem, but
merely a chemical pollutant. Possible failure modes of the model are immediately apparent. For
example, introduction of a chemical subject to alkaline hydrolysis and toxic to plant life into a
productive lake would retard primary productivity. The decrease in primary productivity would lead to
a decrease in the pH of the system and, consequently, a decrease in the rate of hydrolysis and an increase
in the residual concentration of the toxicant. This sequence of events would repeat itself indefinitely, and
constitutes a positive feedback loop that could in reality badly damage an ecosystem. Given the chemical
buffering and functional redundancy present in most real ecosystems, this example is inherently
improbable, or at least self-limiting. More importantly, given the initial EEC, the environmental
toxicologist could anticipate the potential hazard.
There is a more telling advantage, moreover, to the use of environmental descriptors in
preference to dynamic environmental state variables. Predictive ecosystem models that include all the
factors of potential importance to the kinetics of toxic pollutants are only now being developed, and will
require validation before any extensive use. Furthermore, although extremely fine-resolution (temporal
and spatial) models are often considered an ultimate ideal, their utility as components of a fate model
for synthetic chemicals remains suspect. Ecosystems are driven by meteorological events, and are
themselves subject to internal stochastic processes. Detailed weather forecasts are limited to about nine
days, because at the end of this period all possible states of the system are equally probable. Detailed
ecosystem forecasts are subject to similar constraints (Platt et al. 1977). For these reasons, EXAMS was
designed primarily to forecast the prevailing climate of chemical exposures, rather than to give detailed
local forecasts of EECs in specific locations.
Temporal and Spatial Resolution When a synthetic organic chemical is released into an aquatic
ecosystem, the entire array of transport and transformation processes begins at once to act on the
chemical. The most efficient way to accommodate this parallel action of the processes is to combine
them into a mathematical description of their total effect on the rate of change of chemical concentration
in the system. Systems that include transport processes lead to partial differential equations, which
usually must be solved by numerical integration. The numerical techniques in one way or another break
up the system, which is continuously varying in space and time, into a set of discrete elements. Spatial
discrete elements are often referred to as "grid points" or "nodes", or, as in EXAMS, as "compartments."
Continuous time is often represented by fixing the system driving functions for a short interval,
integrating over the interval, and then "updating" the forcing functions before evaluating the next
time-step. At any given moment, the behavior of the chemical is a complicated function of both present
and past inputs of the compound and states of the system.
EXAMS is oriented toward efficient screening of a multitude of newly invented industrial
chemicals and pesticides. Ideally, a full evaluation of the possible risks posed by manufacture and use
of a new chemical would begin from a detailed time-series describing the expected releases of the
compound into aquatic systems over the entire projected history of its manufacture. Given an
equivalently detailed time-series for environmental variables, machine integration would yield a detailed
picture of EECs in the receiving water body over the entire period of concern. The great cost of this
approach, however, militates against its use as a screening tool. Fine resolution evaluation of synthetic
EXAMS-9
-------
chemicals can probably be used only for compounds that are singularly deleterious and of exceptional
economic significance.
The simplest situation is that in which the chemical loadings to systems are known only as single
estimates pertaining over indefinite periods. This situation is the more likely for the vast majority of new
chemicals, and was chosen for development of EXAMS. It has an additional advantage. The ultimate fate
and exposure of chemicals often encompasses many decades, making detailed time traces of EECs
feasible only for short-term evaluations. In EXAMS, the environment is represented via long-term average
values of the forcing functions that control the behavior of chemicals. By combining the chemistry of
the compound with average properties of the ecosystem, EXAMS reduces the screening problem to
manageable proportions. These simplified "first-order" equations are solved algebraically in EXAMS's
steady-state Mode 1 to give the ultimate (i.e., steady-state) EECs that will eventually result from the input
loadings. In addition, EXAMS provides a capability to study initial value problems ("pulse loads" in Mode
2), and seasonal dynamics in which environmental driving forces are updated on a monthly basis (Mode
3). Mode 3 is particularly valuable for coupling to the output of the PRZM model, which can provide a
lengthy time-series of contamination events due to runoff and erosion of sediments from agricultural
lands.
Transport of a chemical from a loading point into the bulk of the system takes place by advected
flows and by turbulent dispersion. The simultaneous transformations presently result in a continuously
varying distribution of the compound over the physical space of the system. This continuous distribution
of the compound can be described via partial differential equations. In solving the equations, the physical
space of the system must be broken down into discrete elements. EXAMS is a compartmental or "box"
model. The physical space of the system is broken down into a series of physically homogeneous
elements (compartments) connected by advective and dispersive fluxes. Each compartment is a
particular volume element of the system, containing water, sediments, biota, dissolved and sorbed
chemicals, etc. Loadings and exports are represented as mass fluxes across the boundaries of the volume
elements; reactive properties are treated as point processes within each compartment.
In characterizing aquatic systems for use with EXAMS, particular attention must be given the
grid-size of the spatial net used to represent the system. In effect, the compartments must not be so large
that internal gradients have a major effect on the estimated transformation rate of the compound. In other
words, the compartments are assumed to be "well-mixed," that is, the reaction processes are not slowed
by delays in transporting the compound from less reactive to more reactive zones in the volume element.
Physical boundaries that can be used to delimit system compartments include the air-water interface, the
thermocline, the benthic interface, and perhaps the depth of bioturbation of sediments. Some processes,
however, are driven by environmental factors that occur as gradients in the system, or are most active
at interfaces. For example, irradiance is distributed exponentially throughout the water column, and
volatilization occurs only at the air-water interface. The rate of these transformations may be
overestimated in, for example, quiescent lakes in which the rate of supply of chemical to a reactive zone
via vertical turbulence controls the overall rate of transformation, unless a relatively fine-scale
segmentation is used to describe the system. Because compartment models of strongly advected water
masses (rivers) introduce some numerical dispersion into the calculations, a relatively fine-scale
segmentation is often advisable for highly resolved evaluations of fluvial systems. In many cases the
error induced by highly reactive compounds will be of little moment to the probable fate of the chemical
EXAMS-10
-------
in that system, however. For example, it makes little difference whether the photolytic half-life of a
chemical is 4 or 40 minutes; in either case it will not long survive exposure to sunlight.
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.
• 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 (10~5 M) 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. Although solid precipitates have occasionally been treated as a separate, non-reactive
phase in continuous equilibrium with dissolved forms, the efficacy of this formulation has never
been adequately evaluated, and the effect of saturated concentrations on the linearity of sorption
isotherms would introduce several problematic complexities to the simulations.
• 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.
EXAMS-11
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Further Reading
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, Organization for Economic Co-Operation and
Development, Paris, France.
Burns, L.A. 1986. Validation methods for chemical exposure and hazard assessment models, pp.
148-172 In: Gesellschaft fur Strahlen- und Umwelt forschung mbH Miinchen, Projektgruppe "Umwelt
gefahrdungspotentiale von Chemikalien" (Eds.) Environmental Modelling for Priority Setting among
Existing Chemicals. Ecomed, Miinchen-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.
Bums, 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.
EXAMS-12
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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. 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.
Kolset, K., B.F Aschjem, N. Christopherson, A. Heiberg, and B. Vigerust. 1988. Evaluation of some
chemical fate and transport models. A case study on the pollution of the Norrsundet Bay (Sweden), pp.
372-386 In: G. Angeletti and A. Bj0rseth (Eds.) Organic Micropollutants in the Aquatic Environment
(Proceedings of the Fifth European Symposium, held in Rome, Italy October 20-22, 1987). Kluwer
Academic Publishers, Dordrecht.
Lassiter, R.R. 1982. Testing models of the fate of chemicals in aquatic environments, pp. 287-301 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.
Lassiter, R.R., R.S. Parrish, and L.A. Bums. 1986. Decomposition by planktonic and attached
microorganisms improves chemical fate models. Environmental Toxicology and Chemistry 5:29-39.
Mulkey, L.A., R.B. Ambrose, and T.O. Barnwell. 1986. Aquatic fate and transport modeling techniques
for predicting environmental exposure to organic pesticides and other toxicants—a comparative study.
In: Urban Runoff Pollution. Springer-Verlag, New York.
Paris, D.F., W.C. Steen, and L.A. Bums. 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, 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.
Platt, T., K.L. Denman, and A.D. Jassby. 1977. Modeling the productivity of phytoplankton. pp. 807-856
In: E.D. Goldberg, I.N. McCave, J.J. O'Brian, and J.H. Steele, Eds. Marine Modeling: The Sea, Vol. 6.
Wiley-Interscience: New York.
Reinert, K.H., P.M. Rocchio, and J.H. Rodgers, Jr. 1987. Parameterization of predictive fate models: a
case study. Environmental Toxicology and Chemistry 6:99-104.
Reinert, K.H., and J.H. Rodgers, Jr. 1986. Validation trial of predictive fate models using an aquatic
herbicide (Endothall). Environmental Toxicology and Chemistry 5:449-461.
EXAMS-13
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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.
Schnoor, J.L., C. Sato, D. McKetchnie, and D. Sahoo. 1987. Processes, Coefficients, and Models for
Simulating Toxic Organics and Heavy Metals in Surface Waters. EPA/600/3-87/015, U.S. EPA, Athens,
Georgia.
Sato, C., and J.L. Schnoor. 1991. Applications of three completely mixed compartment models to the
long-term fate of dieldrin in a reservoir. Water Research 25:621-631.
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 hexa-
chlorocylcopentadiene in the aquatic environment. Chemosphere 11:91-101.
EXAMS-14
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EXAMS COMMAND LANGUAGE INTERFACE (CLI) USER'S GUIDE
Introduction 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 Meaning
CTRL/x The phrase CTRL/x indicates that you must press the key labeled CTRL
while simultaneously pressing another key, for example, CTRL/Q.
EXAMS-> LIST 7 Vertical series of periods, or ellipsis, mean that
not all the data EXAMS would display in response to
the particular command is shown, or that not all
the data a user would enter is shown.
keyword,... Horizontal ellipsis indicates that additional key-words, command
parameters, or data can be entered in a command sequence, or that
EXAMS displays additional data as part of the sample output line.
[keyword] Square brackets indicate that the item enclosed is optional, that is, the
entity can be omitted from the command line altogether.
-------
MODE Analytical Methodology
Long-term consequences of continued releases of chemicals; steady-state
analysis.
Detailed examination of immediate consequences of chemical releases;
initial-value problems.
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->
EXAMS analyzes the parts of the above example as follows.
EXAMS-16
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EXAMS-> The EXAMS system prompt for command input; a greater-than (->) means that EXAMS'
command interpreter is ready for a command to be entered.
AUDIT The command name, requesting that EXAMS enable/disable the User Notepad/Command
File Creation facility.
ON An option of the AUDIT command, requesting that the Notepad/Create facility be
enabled.
All input will now be copied into the file
named "AUDOUT" on Fortran Unit 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.
EXAMS-> 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 File should be renamed file.EXA
A comment entered by the user. 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.
EXAMS-> 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
prompts you for all missing information. For example:
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.
EXAMS-17
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AUDIT-> ON
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 Water body
Chemical: Name of chemical
Table 18.01. Analysis of steady-state fate
(body of table)
EXAMS-18
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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
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' input data, e.g.,
EXAMS-> HELP QUANT
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
EXAMS-19
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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
Command Procedures A command procedure is a file that contains a sequence of EXAMS commands,
optionally interspersed with descriptive comments (lines with"!" or "*" 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 command. For example, suppose a file called START.EXA
were to contain these command lines and comments:
SET MODE TO 3
SET KCHEM TO 4
SETNYEARTO5
RECALL LOAD 7
! Loadings UDB Sector 7 is the spray drift 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-> @START.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 describe their effects.
EXAMS-20
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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).
Summarv Description of EXAMS' System Commands
EXAMS Command
AUDIT
CATALOG
CHANGE/SET
CONTINUE
DESCRIBE
DO or @
ERASE
HELP
LIST
NAME
PLOT
PRINT
QUIT
READ
RECALL
RUN
SHOW
STORE
WRITE
ZERO
Summary Description
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 data from non-EXAMS ASCII disk file
Activate data from stored database (UDB)
Begin simulation run
Display current data values or control settings
Download current data into stored database (UDB)
Download data to ASCII disk file
Clear chemical loadings, pulses, or residuals
EXAMS-21
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System Command Descriptions
AUDIT
Creates a copy of user input commands and responses in an external file.
AUDOUT
DO
Related: Control variables:
Commands:
Syntax: AUDIT
-------
ON -- begins a new Audit file,
Off ~ ends Audit recording of input commands,
Help -- this message,
Quit — return to the EXAMS prompt.
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: Dichloroexample
EXAMS-> RECALL CHEM 4 AS 2
Selected compound is: Tetrabromoexample
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., MYCOMAND.EXA) and used
to execute the above series of commands as a unit—
EXAMS-> DO MYCOMAND
EXAMS-23
-------
CATALOG
Lists, by accession number, the title of all current entries in the specified User Database (UDB).
Related:
Syntax:
Prompt:
Options:
Description:
Control variables:
Commands:
none
ERASE, NAME, RECALL, STORE
CATALOG <0ption>
Options: CHEMICAL, ENVIRONMENT, LOAD, PRODUCT
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 describing
ionization and (species-specific) partitioning and reaction kinetics.
ENVIRONMENT
List the titles, by access number, of environmental databases 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 numbers of
chemical parent and product compounds, the number of the process responsible for the
transformation, and the yield efficiency (mole/mole) as an (optional) function of
temperature.
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, corresponding 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.
EXAMS-24
-------
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 example use of the CATALOG 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.
2. EXAMS-> CATALOG ENVIRON
Catalog of ENVlRONMENTal models
UDB No. Name of Entry Volume
1 Environmental Data Entry Template
2 Pond — code test data
3 Connecticut River estuary
This example CATALOG 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.
EXAMS-25
-------
CHANGE
Use to enter data into the activity database (synonymous with SET).
Related: Commands: DESCRIBE, HELP, SET
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( 153) TO 7fi5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 100 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 7.0E+05 cubic meters. The initial attempt
to set the volume of segment 153 was rejected by EXAMS because the version in use was set up for
environmental models of 100 segments at most. The DESCRIBE command was used to check the number
EXAMS-26
-------
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.
2. EXAMS-> HELP TCEL
TCEL is a Real Matrix with 100 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° C. The HELP command was used to
check subscript dimensions, 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 100 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.
EXAMS-27
-------
CONTINUE
The CONTINUE command resumes EXAMS' simulation analysis of chemical dynamics beginning from
the current state of the system.
Related:
Syntax:
Prompt:
Examples:
1.
Control variables:
Commands:
CONTINUE
CINT, TINIT, TEND, TCODE, NYEAR
RUN, SHOW_TIME_FRAME
(In Mode 2 only:)
Initial time for integration will be (nn.n) units
Enter ending time of integration, Help, or Quit->
Options: None
Description
:. 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 appropriate. 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.
EXAMS-> SET MODE=2
EXAMS-> SHOW TIME FRAME
A RUN will integrate from
with output at intervals of
EXAMS-> SETTCODE=2
EXAMS-> SETTEND=10
EXAMS-> SET CINT=0.25
0. to 24. Hours
2.00 Hours
EXAMS-> SH TIF
A RUN will integrate from
with output at intervals of
0. to 10. Days
0.25 Days
EXAMS-28
-------
EXAMS-> RUN
Simulation beginning for:
Environment: Pond — code test data
Chemical 1: Dichloroexample
Run complete
EXAMS-> PLOT KIN PL (3,0,0 - see PLOT command)
System: Pond — code test data
Chemical: Dichloroexample
2.00 I** ***
j *********
j ***********
j * **** **** **
j *****
1.33 I
I
I
I
I
0.667 I
I
I
I
I
0.000 I
-i 1 1 1 (. 1 1 1 H 1 ^
0.000 2.00 4.00 6.00 8.00 10.0
1.00 3.00 5.00 7.00 9.00
Time, Days
EXAMS->SETCINT=1
EXAMS-> CONTINUE
Initial time for integration will be 10.0 Days
Enter ending time of integration, Help, or Quit-> 30
Simulation beginning for:
Environment: Pond — code test data
Chemical 1: Dichloroexample
Run complete.
EXAMS-> SETCINT=10
EXAMS-> ZERO PULSE LOAD
EXAMS-> CONTINUE
EXAMS-29
-------
Initial time for integration will be 30.0 Days
Enter ending time of integration, Help, or Quit-> 90
Simulation beginning for:
Environment: Pond — code test data
Chemical 1: Dichloroexample
Run complete.
EXAMS-> PLOT KINETIC PLOT (3,0,0)
System: Pond — code test data
Chemical: Dichloroexample
3.49 I *
I **
I **
I *
I **
2.33 I **
j* **
j*** ***
I ***
j ** *
1.16 I *
I *
I * * *
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->SHOTIFR
A RUN will integrate from 1 January 1989
EXAMS-30
-------
through 31 December 1989.
(YEARl = 1989, and NYEAR = 1.)
EXAMS-> RUN
Simulation beginning for:
Environment: Pond — code test data
Chemical 1: Dichloroexample
Run complete.
EXAMS-> SHO TI FR
A RUN will integrate from 1 January 1989
through 31 December 1989.
(YEARl = 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.
(YEARl = 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 — code test data
Chemical 1: Dichloroexample
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.
EXAMS-31
-------
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:
Enter name of input parameters
Options: 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), dimensionality (scalar, vector,
matrix (2-dimensional), table (3-dimensional 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 parameters MODE
MODE is an Integer Scalar.
EXAMS-32
-------
These commands establish that "MODE" is an integer scalar. Note that the initial typing
error (DESK) resulted in a "not recognized" error message followed by return to the
EXAMS prompt.
2. EXAMS-> CHANGE VOL( 133) TO ?E5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 100 elements.
This command reports that VOL is a real variable, with 100 elements. In this example,
the number of segments (NPX) in the version of EXAMS currently in use is set for 100 at
most. Any (intentional or accidental) attempt to set "KOUNT" to a value > 100, or to enter
a value for the VQLume of a segment > 100 (e.g., VOL(133)) 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 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.)
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 DESCRlBEd as consisting of a set of
four matrices, each of (fixed) size (3,7).
EXAMS-33
-------
DO
Executes a command procedure; requests that EXAMS read subsequent input from a specific file.
Related:
Syntax:
Prompt:
Parameters:
Control variables:
Commands:
AUDIT
Description:
DO
Enter name of file (no more than nn characters), Help, or Quit->
name of file
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
Any valid EXAMS command. The command line can include all the necessary options
and data to build a complete command (exception: kinetic plots).
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.
Data. When the currently executing command requires numerical or character data
entry, the next line of the command file is searched for input.
Comment lines. Any line that contains an exclamation point (!) or asterisk (*) in column
one is ignored by EXAMS' command interpreter. These lines can 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.
Examples: 1. EXAMS-> AUDIT ON
All input will now be copied into the
EXAMS-34
-------
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 characters; 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: Dichloroexample
EXAMS/DO-> RECALL LOAD 2
Selected load is: Aedes control spray drift
EXAMS/DO-> ! Load 2 is the Phantom Inlet salt marsh study
EXAMS/DO-> SETKCHEMTO2
EXAMS/DO-> RECALL CHEM 4 AS 2
Selected compound is: Tetrabromoexample
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.
EXAMS-36
-------
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
-------
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.
EXAMS-38
-------
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: EXIT
Prompt: None
Options: None
Description: 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.
EXAMS-39
-------
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:
HELP [keyword]
Prompt:
None
Keyword: Specifies a keyword (a topic or an element of EXAMS input data) that tells EXAMS what
information to display.
• None—if HELP is typed with no keyword, EXAMS lists the keywords that can be
specified to obtain information about other topics.
• Topic-name-describes either a basic EXAMS command, an information page, or
a "system parameter." System parameters 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.
Description: The HELP command provides access to EXAMS' collection of on-line user aids and
information texts. This material includes
• Brief discussions of the syntax and function of each of EXAMS' command words
(RECALL, RUN, etc.)
• Definitions, physical dimensions, and meanings of subscripts for EXAMS' chemical and
environmental input data and control parameters.
• 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.
Examples:
EXAMS-40
-------
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 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.)
You can request information about any input datum (chemical, environmental, control
parameters, analysis parameters) accessible 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.
EXAMS-41
-------
LIST
Displays an EXAMS output table on the terminal screen.
Related: Control variables: FIXFIL
Commands: PLOT, PRINT
Syntax:
LIST
-------
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 Water body
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 Water body
Chemical: Name of FIRST chemical
TABLE 20.01. Exposure analysis summary: 1983—1985.
(body of table)
EXAMS-43
-------
More? (Yes/No/Quit)-> Y
Ecosystem: Name of Water body
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 CONTlNUEd, 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 EXAMS Data Dictionary), and the month of the year, as
follows.
Table
1
4-6, 8,
10,11,13
12
14 (Mode 1/2)
14 (Mode 3)
15-18,20
Sub-tables Examples
1 .cc.i
NN.mm
12.cc.mm
14.cc
14.cc.mm
NN.cc
1.01.1
4.01
10.13
12.01.12
14.01
14.01.12
18.01
20.01
Sub-table Meaning
Table.chemical.ion
Table.month
(13 = annual mean)
Table.chemical.month
Table.chemical
Table.chemical.month
Table.chemical
EXAMS-44
-------
NAME
Use the NAME command to attach unique names to datasets.
Related: Control Variables: MCHEM
Commands: CATALOG, ERASE, STORE, RECALL
Syntax: NAME IS a[aa...] (up to 50 characters), where can be CHEmical,
ENvironment, Load, or PROduct
Prompt: Options available are:
Help - this message.
Quit - return to EXAMS command mode.
= Help
: 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:
Examples:
1.
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".
EXAMS-> CHEM NAME IS Tetrachloroexample
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).
EXAMS-45
-------
2. EXAMS-> SET MCHEM = 2
EXAMS-> CHEM NAME IS Dichloroexample
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.
EXAMS-46
-------
PLOT
Used to plot character graphics for the chemical state of the ecosystem.
Related: Control Variables: MCHEM
Commands: LIST, PRINT
Syntax: PLOT
-------
KINETIC
"KINETIC" plots display the results of integration of the governing equations over the
time spans selected for simulation. These plots also require selection of concentration
variables and either particular segments, or summary "statistics," 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)
Paniculate - Sediment-sorbed (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-> DISSOLVED
The following statistical options are available:
MAX - Maximum concentration
MIN - Minimum concentration
AVE - Average concentration
Help - This message
Quit - Return to the EXAMS prompt
Option-> AVERAGE
EXAMS-48
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EXAMS-> SET MCHEM=2
EXAMS-> PL PO DI AV
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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.
EXAMS-49
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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)
Paniculate - Sediment-sorbed (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
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EXAMS-50
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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 — code test data
Simulation units: Days
Number of segments: 2
1 2
Type of segment (TYPE): 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: average "dissolved" (mg/L)
5 average sorbed (mg/kg)
6 total mass (kg)
Enter parameters, one per line;
enter 0 to end data entry and proceed.
Parameters 3
Parameters 6
Parameters 0
The following parameters are available for each segment:
EXAMS-51
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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)
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 — code test data
Chemical: Methyl Parathion
0.160
0.106
5.322E-02
0.000
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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.
EXAMS-52
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PRINT
Use the PRINT command to queue an output table for hardcopy printing.
Related: Control variables: FIXFIL
Commands: LIST
Syntax: PRINT
-------
QUIT
Use QUIT to abort a command in progress or to end an interactive EXAMS session.
Related: Control variables:
Commands: EXIT
Syntax: QUIT
Prompt: None
Options: None
Description: 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.
EXAMS-54
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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:
Control variables:
Commands:
MODE, MCHEM, PRBEN
WRITE
READ
Enter Environment, Chemical, PRZM, 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 entirely separately from the
main EXAMS User Data Base (UDB), which is contained in a direct access file named
"EXAMS.DAF". Data are transferred directly to the Activity Data Base (foreground
memory ADB) rather than to the User Data Base (UDB) file area, so the STORE command
must be used to transfer data to the UDB from the ADB after invoking READ or they will
be discarded when you exit from EXAMS.
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).
In the PRZM option of the READ command, a set of external loadings generated by the
Pesticide Root Zone Model (PRZM). This facility transfers chemicals exported from the
land surface into an adjacent aquatic system. The PRZM transfer file is a mode 3
construct, in which the first set of loadings contain the application rate of the pesticide,
and the succeeding loadings contain water-borne and sediment-borne chemical transfers
to the aquatic system. The parameter PRBEN (c.f.) controls EXAMS' treatment of
sediment-borne materials. When PRBEN is zero, all sediment-borne materials are
equilibrated with the water column upon entry into the system. When PRBEN is 1.0, all
sediment-borne materials are routed to the benthic zone. PRBEN has a default value of
0.5, based on the observation that, in general, about 50% of sorbed chemical is usually
labile, and about 50% recalcitrant, to rapid re-equilibration in water.
EXAMS-55
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Examples:
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
3. To read a PRZM transfer file, first set MODE to 3, and then read the dataset. Note the
convention for naming of PRZM transfer files—the base name is always "PRZM2EXA" and the
suffix indicates the year—in this case data from 1989 ("D89"). Because EXAMS will accept any
file name for acquisition by the READ command, these files can be renamed to any convenient
file name for archiving or to prevent subsequent PRZM runs from over-writing them.
EXAMS-> READ PRZM PRZM2EXA.D89
EXAMS-56
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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: RECALL [AS ADB#]
Prompt: Enter Environment, Chemical, Load, Product, Help, or Quit->
Command parameters:
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).
Description: 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.
Examples:
EXAMS-57
-------
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:
1
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, Environments,
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->
EXAMS-58
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RUN
The RUN command begins a simulation analysis.
Related: Control Variables: MODE
Commands: CONTINUE
Syntax: RUN
Prompt: None
Description: 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.
Examples:
1. EXAMS-> RECALL CHEMICAL 22
Selected compound is: Dibromoexample
EXAMS-> RECALL ENVIRON 17
Selected environment is: Albemarle Sound—Bogue Bank
EXAMS->SETSTRL(1,1,13)=.01
EXAMS-> RUN
Simulation beginning for:
Environment: Albemarle Sound—Bogue Bank
Chemical 1: Dibromoexample
Run complete.
EXAMS->
In this example, a steady-state (MODE=1) analysis is conducted 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.
EXAMS-59
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SET
Use SET to specify the values of data in the activity database.
Related: Commands: CHANGE (synonym), DESCRIBE, HELP
Syntax: SET
or
SET
Prompt: 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( 167) TO ?E5
Subscript out-of-range.
EXAMS-> DESCRIBE VOL
VOL is a Real Vector with 100 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 7.0E+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 100 segments at most. The DESCRIBE command was used to
EXAMS-60
-------
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.
2. EXAMS-> HELP TCEL
TCEL is a Real Matrix with 100 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°C. The HELP command was
used to check subscript dimensions, 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->HELPPOH
POH is a Real Matrix with 100 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.
EXAMS-61
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SHOW
Use SHOW to display current data values or control settings.
Related: Control Variables: MCHEM, MONTH
Commands: CHANGE, SET
Syntax: SHOW
-------
SHOW DISPERSION displays the input data describing transport in the active (loaded in the ADB)
Environmental dataset. The index vectors (JTURB, ITURB) define the existence of 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.
JTURB 1 Segment number for dispersion
ITURB 2 Segment number for dispersion
XS TUR m2 5.000E+04 Cross-sectional area of path
CHARL m 2.53 CHARacteristic_Length of path
DSP m2/hr 4.676E-05 Eddy DiSPersion coefficient
Path No.: 1 Vector index for data entry
No more than NCON hydrologic pathways can be specified. If more are needed, this number can
be increased and EXAMS recompiled.
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
SHOWGLOBALS 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 operational MODE: initial values are ignored in Mode 1 as they
have no effect on the analysis results. The value of PRSW also affects the display: when PRSW
is 0, SHOW LOADS returns a summary of annual loadings; when PRSW=1, a month-by-month
EXAMS-63
-------
tabulation is displayed as well. 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. 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 ADB number of CHemical PARent
T PROD 2 ADB number of Transformation PRODuct
N PROC 7 Number of transforming PROCess
R FORM 29 Reactive FORM (dissolved, etc.)
YIELD M/M 0.100 Mole/Mole YIELD of product
EAYLD Kcal 0.000 Enthalpy of yield (if appropriate)
Pathway: 1 Number of the pathway
More detail as to the numbering of NPROC and RFORM is given in the EXAMS Data Dictionary,
which can also be accessed on-line using the HELP command. No more than NTRAN transforma-
tion 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-segment display of the canonical water-quality data
included in the current Environmental ADB dataset. The month to be displayed is set by the
EXAMS-64
-------
current value of MONTH (explicit mean values are denoted by MONTH number 13). The month
is the second subscript of such data as 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,*)
EXAMS-65
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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: STORE [ADB# IN]
Prompt: Enter Environment, Chemical, Load, Product, Help, or Quit->
Command parameters:
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).
Description: 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 by
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.
Examples: 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 current value of MCHEM.
EXAMS-66
-------
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 — 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.
EXAMS-67
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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:
Control variables:
Commands:
MODE, MCHEM
READ
WRITE
Enter Environment, Chemical, Load, 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).
In the LOAD option of WRITE, a set of external chemical loadings are written to an ASCII
file. As with environmental data, the setting of MODE controls the amount of data written
to the file. In Mode 1, only long-term, average data are written from the ADB; in Mode
2, initial conditions are added, and in Mode 3 a full set of monthly loads and daily pulse
loads are written from the ADB to the external file. The first item written to the external
file is the Mode for which the loadings are designed. This datum serves as a check value
when EXAMS reads data from a file of external loadings (see discussion under READ
command.
Examples:
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
EXAMS-68
-------
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 ENV C:\EXAMS\PROJECTX\INLET.DAT
EXAMS-69
-------
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
-------
Selected compound is: Dibromoexample
EXAMS-> RECALL ENVIRON 17
Selected environment is: Albemarle Sound—Bogue Bank
EXAMS-> SET STRL(1,1,13)=.01
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: Dibromoexample
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 allochthonous load of chemical 1 on segment 1 under average
conditions (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
CONTlNUing, 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. Alternatively, 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.
EXAMS-71
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EXAMS II Data Dictionary
ABSER
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.
ADB
Activity DataBase
EXAMS provides for long-term storage of CHEMical, ENVironmental, transformation PRODuct
chemistry, and allochthonous LOADings databases in a User DataBase or UDB. 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 simultaneously, 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: cm'^mole/L)"1
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 molar absorption coefficient of R-H3 (neutral molecule)
ABSOR(w,2,c) is molar absorption coefficient of R-H^ (+1 cation)
ABSOR(w,3,c) is molar absorption coefficient of R-Hj* (+2 cation)
ABSOR(w,4,c) is molar absorption coefficient of R-H^ (+3 cation)
ABSOR(w,5,c) is molar absorption coefficient of R-Hj (-1 anion)
ABSOR(w,6,c) is molar absorption coefficient of R-tT (-2 anion)
ABSOR(w,7,c) is molar absorption coefficient of R3" (-3 anion)
EXAMS-72
-------
ADVPR
ADVection proportion (path) 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
AEC
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.
URTY
AIR mass TYpe (month) Units: letter codes
Select: Rural (default), Urban, Maritime, or Tropospheric
AREA
AREA (segment) Units: m2
Top plan area of each model segment of the water body. 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 TURBiditv (month) Units: km
Equivalent aerosol layer thickness.
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.
EXAMS-73
-------
BACPL
BACterioPLankton population density (segment, month) Units: cfu/mL
Population density of bacteria capable 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) Units: g/cm3
Fresh weight per unit volume of benthic sediments.
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
EXAMS-74
-------
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:
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 synthetic chemicals.
CHPAR
CHemical PARent compound (path) 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.
EXAMS-75
-------
:LOUD
CLOUDiness (month) Units: dimensionless Range: 0—10
Mean monthly cloudiness in tenths of full sky cover.
DEPTH
DEPTH (segment) Units: m
Average vertical depth of each segment.
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.
DIS02
Dissolved o2 (segment, month) Units: mg/L
Concentration of dissolved oxygen (O2) in each segment of ecosystem.
Dissolved Organic Carbon (segment, month) Units: mg/L
Used for computing spectral light absorption and complexation.
DRFLD
DRiFt LoaD (segment, chemical, month) Units: kg/hour
Drift loadings: aerial drift, direct applications, stack fallout (etc.) of chemical on each system
element.
DSP
Dispersion coefficient (path, month) Units: m2/hour
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
EXAMS-76
-------
sediments. In the latter case DSP is a statistical kinetic composite incorporating direct sorption
to the sediment surface, mixing of the sediments by benthos (biorurbation), stirring by demersal
fishes, etc.
See also: CHARL, ITURB, JTURB, XSTUR
EAH
E., for Acid Hydrolysis (form, ion, chemical) Units: kcal/mole
Arrhenius activation energy Ea 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 is non-zero, the second-order rate constant is calculated from:
loe K = KAHCf i c) - 1000 * EAH(form.ion.chemical)
* " 4.58(TCEL(segment,month) + 273.15)
M'V
EAYLD
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, YlELD(p) gives the dimension-
less molar product yield. A non-zero EAYLD(p) invokes a re-evaluation in which YlELD(p) is
interpreted as the Briggsian logarithm of the pre-exponential factor in an Arrhenius-type
function, giving product yield as a function of temperature (varying with position and time)
(TCEL(segment, month)):
log Yield(p) = YIELD(p) - 1000*EAYLD(path)
r 4.58(TCEL(segment,month) + 273.15)
See also: CHPAR, NPROC, RFORM, TPROD, YIELD
EBH
Ea for Base Hydrolysis (form, ion, chemical) Units: kcal/mole
Arrhenius activation energy Ea 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:
EXAMS-77
-------
1000 * EBH(form.ion.chemican
k"' 4.
M'V
loe K = KBHf f i c^
8 k"' 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:
log H = HENRY(chemical) - 1000 * EHEN(chemical)
4.58 (TCEL(segment,month) + 273.15)
EK102
EJ Klo2 (singlet oxygen) (form, ion, chemical) Units: kcal/mole
Arrhenius activation energy for singlet oxygen photo-oxygenation of chemicals. Matrix indices
match those of Klo2, 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 EKlo2
is non-zero, the second-order rate constant is calculated as:
K = Kl O2ff i c) 1000 * EKlo2(form.ion.chemical)
^"' 4.58 (TCEL(segment,month) +273.15)
ELEV
ELEVation Units: meters above mean sea level
Ground station elevation.
ENH
E, 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 pseudo-first-order rate constant is calculated from:
EXAMS-78
-------
i K = KNHff i c) 1000 * ENH(form.ion.chemical)
g 4.58(TCEL(segment,month) + 273.15)
h"1
EOX
E., 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 EOX is
non-zero, the second-order rate constant is calculated from:
loe K = KOXff i c) - 1000 * EOX(form.ion.chemical)
8 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:
loe oK = PKfi c^ - 1000 * EPK(ion.chemical)
4.58 (TCEL(segment,month) + 273.15)
The vector indices for EPK ("c" denotes the chemical) are
EPK( 1 ,c) contains datum for generation of R-H^ from R-H3
EPK(2,c) contains datum for generation of R-H2+ from R-H^
EPK(3,c) contains datum for generation of R-H^ from R-Hf"
EPK(4,c) contains datum for generation of R-Hj from R-H3
EPK(5,c) contains datum for generation of R-H2" from R-Hj
EPK(6,c) contains datum for generation of R3" from R-H2"
EXAMS-79
-------
BRED
E. 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:
los K = KREDCf i c) - 1000 * ERED(form.ion.chemical)
B 4.58(TCEL(segment,month) + 273.15)
ESOL
Enthalpy term for SOLubility (ion, chemical)
Units: kcal/mole
ESOL describes chemical solubility as a function of temperature (TCEL). The matrix indices ("c"
denotes the chemical) denote:
ESOL(l,c) is datum for solubility of neutral molecules
ESOL(2,c) is datum for solubility of singly charged cations
ESOL(3,c) is datum for solubility of doubly charged cations
ESOL(4,c) is datum for solubility of triply charged cations
ESOL(5,c) is datum for solubility of singly charged anions
ESOL(6,c) is datum for solubility of doubly charged anions
ESOL(7,c) is datum for solubility of triply charged anions
R-H,
R-H;
R-H
R-H
R3
EVAPoration (segment, month)
(Monthly) evaporative water losses from ecosystem segments.
Units: mm/month
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:
EXAMS-80
-------
log Va = VAPR(chemical) - 1000*EVPR(chemical)
4.58 (TCEL(segment,month) + 273.15)
FIXFIL
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.
FROG
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 (R-H3) as a function of a property
(organic carbon content) of the sediment.
HENRY'S law constant (chemical) Units: atmosphere-mVmole
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):
log H = HENRY(chemical) - 1000 * EHEN(chemical)
4.58 (TCEL(segment,month) + 273.15)
ICHEM
I CHEMical (event) Units: n/a Range: 1-KCHEM
Event "e" is a pulse of chemical number lCHEM(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 (UDB) (via, for example, the command sequence "RECALL CHEM
7 AS 3") or entered as new data), lCHEM(e) can be SET to 3 to create a pulse load event of that
chemical.
See also: IDAY, IMASS, IMON, ISEG
EXAMS-81
-------
IDAY
I DAI (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), lCHEM(e),
iSEG(e), iMON(e), and iDAY(e)) with the same vector subscript describes a single chemical pulse
event. Thus a pulse of chemical lCHEM(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 CONTlNUation 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 lCHEM(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: IDAY, ICHEM, IMASS, ISEG
ISEG
I SEGment (event) Units: n/a Range: 1—KOUNT
Pulse load event "e" loads chemical lCHEM(e) on segment iSEG(e). Any segment can receive a
pulse load. Should the pulse loads increase faefree 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
EXAMS-82
-------
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: O--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 water body. 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 controls the printing of diagnostics from the integrators.
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 IUNIT to 0.
JFRAD
JFRom ADvection (path) 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
EXAMS-83
-------
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 specifica-
tions can be inspected by typing SHOW ADV; pathway numbers are given above each active
dataset. Enter data with SET or CHANGE commands.
See also: rroAD, 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
KAH
K Acid Hydrolysis (form, ion, chemical) Units: per mole [H+] per 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
K BACteria benthos (form, ion, chemical) Units: (cfu/mL)"1 hour"1
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 25° 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—I: neutral, 2-4: cations, and 5-7: anions.
KBACW
K BACterioplankton water (form, ion, chemical) Units: (cfu/mL)"1 hour"1
EXAMS-84
-------
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) Q,0 (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 25 °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.
KBH
K Base Hydrolysis (form, ion, chemical) Units: per mole [OH"] per hour
Second-order rate constant for specific-base-catalyzed hydrolysis of chemicals. When the
matching (same subscripts) Arrhenius activation energy (EBH) 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
K Direct Photolysis (ion, chemical) Units: hour"1
Estimated photolysis rates—use only when ABSOR, the actual light absorption spectra of the
compound in pure water, are unavailable. KDP is an annual average pseudo-first-order photolysis
rate constant under cloudless conditions at RFLAT, where
KDP(l,c) are pseudo-first-order photolysis rate constants of neutral molecules R-H3
KDP(2,c) are pseudo-first-order photolysis rate constants of singly charged cations R-H^
KDP(3,c) are pseudo-first-order photolysis rate constants of doubly charged cations R-Hs"1"
KDP(4,c) are pseudo-first-order photolysis rate constants of triply charged cations R-H3^
KDP(5,c) are pseudo-first-order photolysis rate constants of singly charged anions R-Hj
KDP(6,c) are pseudo-first-order photolysis rate constants of doubly charged anions R-H2"
KDP(7,c) are pseudo-first-order photolysis rate constants of triply charged anions R3
EXAMS-85
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KIEC
Kp for ion Exchange capacity (ion, chemical) Units: Kp (meq/lOOg dry)"1
Coefficient relating sediment partition coefficient Kp of ions to exchange capacity of sediments.
KIEC times the cation exchange capacity CEC(seg, month) (or anion exchange capacity AEC for
anionic species) gives the Kp for sorption of ions with solid phases. This computation is
overridden by explicit (non-zero) values of KPS, i.e., a non-zero value of KPS takes precedence
over a Kp computed by EXAMS using KIEC.
KIEC( 1 ,c) is datum for relating CEC and sorption of singly charged cation R-H^
KlEC(2,c) is datum for relating CEC and sorption of doubly charged cation R-H2*
KiEC(3,c) is datum for relating CEC and sorption of triply charged cation R-H3^
KlEC(4,c) is datum for relating AEC and sorption of singly charged anion R-Hj
KiEC(5,c) is datum for relating AEC and sorption of doubly charged anion R-H2"
KlEC(6,c) is datum for relating AEC and sorption of triply charged anion R3"
KINOUT
Logical Unit Number for writing results of numerical integration to kinetics plotting file.
KNH
K Neutral Hydrolysis (form, ion, chemical) Units: hour"1
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 first-order 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 Ist-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.
KOC
Koc (chemical) Units: [(mg/kg)/(mg/L)] (organic carbon fraction)"1
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 (R-H3) species with those
solids:
EXAMS-86
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Kp(chemical, segment, month) = KOC(chemical) * FROC(segment, month)
KOUNT
Number of segments used to define current ecosystem. Units: n/a
KOW
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.
KOX
K oxidation (form, ion, chemical) Units: per mole [OXRAD] per hour
Second-order rate constants for free-radical (OXRAD) oxidation of chemicals. When the
matching (same subscripts) Arrhenius activation energy (EOX) is zero, KOX is interpreted as the
second-order rate constant. When the matching entry in EOX 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
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 "c" subscript denotes the
chemical; the "ion" subscripts identify:
KPB( 1 ,c) datum for biosorption of neutral molecules R-H3
KPB(2,c) datum for biosorption of singly charged cations R-H^
KPB(3,c) datum for biosorption of doubly charged cations R-H^
KPB(4,c) datum for biosorption of triply charged cations R-H^
EXAMS-87
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KPB(5,c) datum for biosorption of singly charged anions R-H2
KPB(6,c) datum for biosorption of doubly charged anions R-H2"
KPB(7,c) datum for biosorption of triply charged anions R3"
KPDOC
KP Dissolved Organic Carbon (ion, chemical) Units: (ug/g)/(mg/L)
Partition coefficient (Kp) for equilibrium complexation with DOC. The "c" subscript denotes the
chemical; the "ion" subscripts identify:
KPDOC(1 ,c) datum for complexation of neutral molecules R-H3
KPDOC(2,c) datum for complexation of singly charged cations R-H^
KPDOC(3,c) datum for complexation of doubly charged cations R-H2*
KPDOC(4,c) datum for complexation of triply charged cations R-H^
KPDOC(5,c) datum for complexation of singly charged anions R-Hj
KPDOC(6,c) datum for complexation of doubly charged anions R-H2"
KPDOC(7,c) datum for complexation of triply charged anions R3"
KPS
Kg for sediment solids (ion, chemical) Units: (mg/kg)/(mg/L)
Partition coefficients (Kp) for computing sorption with sediments. The "c" subscript denotes the
chemical; the "ion" subscripts identify:
KPS( 1 ,c) datum for sorption of neutral molecules R-H3
KPS(2,c) datum for sorption of singly charged cations R-H^
KPS(3,c) datum for sorption of doubly charged cations R-H2+
KPS(4,c) datum for sorption of triply charged cations R-Hg+
KPS(5,c) datum for sorption of singly charged anions R-H^
KPS(6,c) datum for sorption of doubly charged anions R-H2"
EXAMS-88
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KPS(7,c) datum for sorption of triply charged anions R3
KRED
K REDuction (form, ion, chemical) Units: per mole [REDAG] per 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.
KVQ
KVOlatilization (chemical) Units: dimensionless ratio
Liquid-phase transport resistance, as ratio to reaeration rate.
K102
Klo2 (singlet oxygen) (form, ion, chemical) Units: per M ['O2] per hour
Second-order rate constants for singlet oxygen photo-oxygenation of chemicals. When the
matching (same subscripts) Arrhenius activation energy (EKlo2) is zero, K1O2 is interpreted
as the second-order rate constant. When the matching entry in EK1O2 is non-zero, Klo2 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.
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.
EXAMS-89
-------
LAT
LATitude
Geographic latitude of the ecosystem.
Units: degrees and tenths (e.g., 37.24)
LENG
LENGth (segment)
Length of a reach — used to compute volume, area, depth.
Units: m
LOADNM
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 ...."
LONG
LONGitude
Geographic longitude of the ecosystem.
Units: degrees and tenths (e.g., 154.2)
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 Operational characteristics of EXAMS
1 Long-term (steady-state) analysis.
EXAMS-90
-------
2 Pulse analysis — specifiable initial chemical mass (IMASS) and time frame, time
-invariant environment.
3 Monthly environmental data, daily pulse loads IMASS and monthly chemical loadings
of other types.
MONTH
MONTH Units: n/a
Set MONTH to inspect a specific block of environmental data. Months 1—12 correspond to
January-December; month 13 is average data.
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
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
NPSED
Non-Point-Source SEDiment (segment, month) Units: kg/hour
Non-point-source sediment loads entering ecosystem segments.
NPSFL
EXAMS-91
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Non-Point-Source FLOW (segment, month) Units: mVhour
Non-point-source water flow entering ecosystem segments.
NPSLD
Non-Point-Source LoaD (segment, chemical, month) Units: kg/hour
Chemical loadings entering segments via non-point sources.
NYEAR
Number of YEARS Units: n/a
NYEAR is number of years to be simulated for a mode 3 run.
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 (month) Units: centimeters NTP Typically 0.2--0.3 cm
Mean (monthly) ozone (O3) content of atmosphere.
PCPLD
Precipitation LoaD (segment, chemical, month) Units: kg/hour
Chemical loadings entering each segment via rainfall.
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.
EXAMS-92
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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 oK = PK(i c) - 1000 EPK(ion.chemical)
g P 4.58 (TCEL(segment,month) + 273.15)
The vector indices for PK ("c" denotes the chemical) are
PK(l,c) contains datum for generation of R-H^ from R-H3
PK(2,c) contains datum for generation of R-H2+ from R-H^
PK(3,c) contains datum for generation of R-H^* from R-H2+
PK(4,c) contains datum for generation of R-Hj from R-H3
PK(5,c) contains datum for generation of R-H2 from R-Hj
PK(6,c) contains datum for generation of R3" from R-H2"
PLMAS
PLanktonic bioMASs (segment, month) Units: mg (dry weight)/L
Total plankton subject to biosorption of synthetic chemicals.
POH
pOH (segment, month) Units: pOH units
EXAMS-93
-------
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.
PRBEN
PRoportion of sorbed chemical delivered to BENthic zone Unitless
The PRZM model generates an output file that can be read by the READ command in EXAMS.
PRZM reports, for each runoff date, contaminant dissolved in the flow, and contaminant sorbed
to entrained particulate matter. Use PRBEN (SET to a value between 0.0 and 1.0) to indicate how
much of the sorbed material is to sink through the water column and become incorporated into
the benthic sediments. Based on the generalization that about 50% of sorbed contaminant is
typically quite labile, and 50% is refractory, the default value of PRBEN is set to 0.50.
PRINTR
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
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.).
OTBAS
o_Ten BActeria benthos (form, ion, chemical) Units: dimensionless
Q10 values for benthic bacterial biolysis (see KBACS) of chemical. "Q]0" is the increase in the
second-order rate constant due to a 10°C increase in temperature. Indices refer to 28 molecular
EXAMS-94
-------
spp: 4 forms—1-.aqueous, 2:solids-sorbed, 3:DOC-complexed, and 4: bio-sorbed; by 7 ions-
—Irneutral, 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)-25)/10 * KBACS(f,i,c)
OTBAW
Q Ten BActeria water (form, ion, chemical) Units: dimensionless
Q10 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-haqueous, 2:solids-sorbed, 3:DOC-complexed, and 4: bio-sorbed; by 7 ions-
-hneutral, 2-4:cations, and 5-7:anions. When QTBAW is non-zero, the matching (same
subscripts) rate constant is computed as:
KBACW(f,i,c) = QTBAW(f,i,c)(TCEL(se8'mon*>25'10 * KBACW(f,i,c)
OUANTum 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
RAlNfall (month) Units: mm/month
Average (monthly) rainfall in geographic area of system.
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
EXAMS-95
-------
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 North or South displacement of the ecosystem LATitude from the
location (RFLAT) of a photochemical study used to develop a matched (same subscript) KDP
pseudo-first-order rate constant.
RFLAT(1 ,c) refer to photolysis of neutral molecules R-H3
RFLAT(2,c) refer to photolysis of singly charged cations R-H^
RFLAT(3,c) refer to photolysis of doubly charged cations R-H
RFLAT(4,c) refer to photolysis of triply charged cations R-H^
RFLAT(5,c) refer to photolysis of singly charged anions R-Hj
RFLAT(6,c) refer to photolysis of doubly charged anions R-H2"
RFLAT(7,c) refer to photolysis of triply charged anions R3
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.
EXAMS-96
-------
Ionic species
Valence
Forms:
Dissolved
Solids-sorbed
DOC-complexed
Biosorbed
Neutral
0
1
2
3
4
Cations
1+
5
6
7
8
2+
9
10
11
12
3+
13
14
15
16
Anions
1-
17
18
19
20
2-
21
22
23
24
3-
25
26
27
28
Total
(all)
29
30
31
32
RHUM
See also: CHPAR, EAYLD, NPROC, TPROD, YIELD
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.
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).
SEEPage flows (segment, month)
Units: m /hour
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.
EXAMS-97
-------
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.
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)=l")
when entering chemical data in order to show EXAMS the ionic structure of the chemical. When
EXAMS starts, only SPFLG(1,*) are set, i.e., the default chemical structure is a neutral (non-
ionizing) molecule. As additional SPFLG are set, EXAMS displays the additional chemical data
tables needed to display the properties of the ionic species.
set SPFLG(1 ,c)=l to signal existence of a neutral molecule R-H3
set SPFLG(2,c)=l to signal existence of a singly charged cation R-H^
set SPFLG(3,c)=l to signal existence of a doubly charged cation R-H2+
set SPFLG(4,c)=l to signal existence of a triply charged cation R-Hg+
set SPFLG(5,c)=l to signal existence of a singly charged anion R-H^
set SPFLG(6,c)=l to signal existence of a doubly charged anion R-H2"
set SPFLG(7,c)=l to signal existence of a triply charged anion R3"
SPRAY
SPRAY drift from agricultural chemicals Unitless percentage
The PRZM model generates an output file that can be read by the READ command in EXAMS.
PRZM3 reports, for each application date, the application rate and the percentage drift to adjacent
aquatic ecosystems. Use SPRAY to set a drift percentage for earlier versions of PRZM. EXAMS
defaults SPRAY to 10%. Note that values of SPRAY are entered as percentages rather than as
fractions.
EXAMS-98
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)UT
Logical Unit Number for data written to plotting file containing EXAMS' steady-state chemical
concentrations.
STream FLOWS (segment, month) Units: mVhour
Flow into head reach of river or estuary; segment tributaries and creeks or other stream flows
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 water body 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) Units: kg/hour
Stream-borne sediment load entering ecosystem segments.
SUSED
suspended SEDiment (segment, month) Units: mg/L
Suspended paniculate 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 water body 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 environmen-
tal 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,
EXAMS-99
-------
EXAMS-> CHAN SYSTYP(7) TO ...
Temperature in CELSJUS (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 lime 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.
TINIT
lime iNirial 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
TPROD(p) — ADB location of the transformation product of CHPAR(p). The matching (same
transformation path number "p") members of CHPAR and TPROD give the location numbers in the
EXAMS-100
-------
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
Segment TYPE (segment) Units: letter codes
Letter codes designating segment types used to define ecosystems.
Available types: Littoral, Epilimnion, Hypolimnion, and Benthic.
UDB
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.
VAPR
VAPOR pressure (chemical) Units: Ton-
Used to compute Henry's law constant when HENRY datum is zero (0) but VAPR is non-zero:
HENRY = (VAPR/760) / (SOL/MWT)
If the associated molar heat of vaporization (EVPR) is non-zero, VAPR is taken as the base-10
logarithm of the pre-exponential factor in an exponential function describing vapor pressure as
a function of temperature (TCEL).
EXAMS-101
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VOL
VQLume (segment) Units: m3
Total environmental volume of ecosystem segments.
WIDTH
WIDTH (segment) Units: m
Average bank-to-bank distance—for computing volume, area, depth of lotic systems described
via length, width, and cross-sectional areas.
WIND
wiNDspeed (segment, month) Units: m/second
Average wind velocity at a reference height of ten centimeters above the water surface.
Parameter is used to compute a piston velocity for water vapor (Liss 1973, Deep-Sea Research
20:221) in the 2-resistance treatment of volatilization losses.
XSA
Cross-sectional (XS) Area (segment) Units: m2
Area of water body in section along advective flowpath.
XSTUR
X Section for TURbulent dispersion (path) Units: m2
XSTUR is cross-sectional area of a dispersive exchange interface at the boundary between
segments JTURB(p) 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) (nrVhour) = DSP(p) xSTUR(p) / CHARL(p)
See also: CHARL, DSP, ITURB, JTURB
YEARl
YEAR 1 Units: n/a
Starting year for mode 3 simulation (e.g., 1985).
EXAMS-102
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YIELD
YIELD of product (path) Units: mole per 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
EXAMS-103
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Implementing the microcomputer MS-DOS Runtime EXAMS 2.97
The diskette contains EXAMS program files stored in a combined archival
compressed format. The files require a total of about 600 Kb of mass storage
for transfer to your hard disk, plus an additional ten megabytes for storage
of the files as they are retrieved from the Archives,plus additional working
space for the files produced while EXAMS runs.
The disk includes, besides the file README.XMS you are now reading,
o A file for installing the EXAMS program, in file INSTXMS.EXE
o the task image in file EXAMS.EXE, which allows space for five simul-
taneous chemicals (or one chemical and two degradation products,
etc.), and environmental models of up to one hundred segments;
o the unformatted direct access data- and help-file EXAMSDAF.TPL,
with space for 25 chemical datasets, 10 environmental datasets,
5 external chemical load series, and 5 product chemistries.
This file is a template file and should be protected via the DOS
command ATTRIB +R if at all possible.
o an EXAMS command file for testing the installation, in TEST.EXA;
o TESTOUT.XMS, a sample output for comparison with the results of your test
run
o a file for assisting in the interpretation of error messages, and
o the User's Guide for EXAMS 2.97. File EXAMS.WPD is in WordPerfects.1 format.
EXAMS.TXT is ANSI, and EXAMS.ASC is ASCII, Generic Word Processor format.
(Printed copies of the manual are not always available.)
o EXAMS makes use of the Phar Lap DOS-extender to access extended
memory. EXAMS will require time to set up its virtual memory
system when loaded from DOS; load time can usually be reduced by running
as a Windows task. When running in a DOS session under Windows95 set all
memory properties to "Auto" except DPMI memory. Set DPMI memory to 65535.
First, make sure that your IBM PC/AT 386/486/Pentium or "Compatible"
measures up to the following minimum hardware and software specifications.
o appropriate diskette drive (for installation only)
o 10 megabyte available mass storage (hard disk)
o 80x87 math co-processor
o MS-DOS version 5.0 or higher
If your machine does not conform to these minimum specifications, the
EXAMS program WILL NOT execute properly.
- more -
EXAMS-105
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Then, to install the program
1. Transfer the contents of the diskette to your hard disk in some
suitable subdirectory or partition.
a. Set the default drive to the mass
storage device (e.g., hard disk "C") : C:
b. Create an EXAMS directory: MKDIR EXAMS
(N.B. if installing as part of PIRANHA, the PIRANHAXEXAMS
directory already exists--do NOT create another EXAMS directory)
c. Request verification of copy results: VERIFY ON
d. Change default directory to EXAMS: CD\EXAMS
or to PIRANHA EXAMS subdirectory CD\PIRANHA\EXAMS
e. Transfer the files from the diskette
(e.g., drive "A") to the hard disk: COPY A:*.*
f. Execute the file INSTXMS.EXE to
recover files from the archives: INSTXMS
g. Protect the direct access file
template from accidental corruption: ATTRIB +R EXAMSDAF.TPL
h. Create a working copy of the file:
(N.B. Skip this step if upgrading PIRANHA)
COPY EXAMSDAF.TPL EXAMS.DAF
2. Start the EXAMS program from the EXAMS directory.
a. Start the EXAMS program: EXAMS
b. When you reach the EXAMS system
prompt, start the test command file: EXAMS-> DO TEST
3. When the test run finishes compare the outcome (in file REPORT) with the
file TESTOUT supplied with the program:
FC REPORT.XMS TESTOUT.XMS
Files TESTOUT.XMS and TEST.EXA are not needed for routine
operation of EXAMS and can be deleted, as can file INSTXMS.EXE.
4. EXAMS uses Logical Unit Number (LUN) Seven, writing to device
PRN, for its Print command. As part of starting the program under DOS,
you may wish to make the DOS print routine memory-resident (i.e., set up
a print spooler) before starting EXAMS.
a. Load the DOS print routine (optional) PRINT
b. Start the EXAMS program: EXAMS
EXAMS-106