Input_Instructionsx Input Instructions

Input_Instructions

User Manual:

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Input Instructions and Output Description for

MT3D-USGS Version 1.0.0

Input

Input instructions for the packages that were modified or added in MT3D-USGS are

given below. For convenience, input instructions for MT3DMS Packages have been

reproduced in this document using the original MT3DMS manuals (Zheng and Wang,

1999; Zheng, 2010). Users may need to refer to these original manuals for further details.

NAM File

The Name File contains the names of most input and output files used in a model

simulation and controls the parts of the model program that are active. The Name File is

read on unit 99, which is specified in the MT3DMS/MT3D-USGS main program. The

Name File is constructed as follows:

For each simulation:

1 Record: Ftype, Nunit, Fname, [options]

Format: Free

The Name File contains one of the above records (item 1) for each file. All variables are

free format. The length of each record must be 2,000 characters or less. The records can

be in any order except for the record where Ftype (file type) is ‘LIST’ as described

below.

Comment records are indicated by the # character in column 1 and can be located

anywhere in the file. Any text characters can follow the # character. Comment records

have no effect on the simulation; their purpose is to allow users to provide documentation

about a particular simulation. All comment records after the first item -1 record are

written in the listing file.

Explanation of Variables in the Name File

Ftype - is the file type, which must be one of the following character values. Ftype may

be entered in all uppercase, all lowercase, or any combination.

LIST for the standard MT3DMS/MT3D-USGS output file – the Name File for

MT3DMS/MT3D-USGS must always include a record that specifies ‘LIST’ for Ftype

and the LIST record must be the first non-comment record.

BTN for the MT3D-USGS Basic Transport Package.

FTL for the MODFLOW-produced flow-transport link file.

ADV for the MT3D-USGS Advection Package.

DSP for the MT3D-USGS Dispersion Package.

SSM for the MT3D-USGS Sink/Source Mixing Package.

RCT for the MT3D-USGS Reaction Package.

GCG for the MT3D-USGS Generalized Conjugate-Gradient Solver Package.

TOB for the MT3D-USGS Transport Observation Package.

HSS for the MT3D-USGS HSS Time-Varying Source Package

CTS for the MT3D-USGS Contaminant Treatment System Package.

TSO for reading the adaptive-time-stepping information generated by MF2K-SSPA.

UZT for the MT3D-USGS Unsaturated-Zone Transport Package

LKT for the MT3D-USGS Lake Transport Package

SFT for the MT3D-USGS Stream-Flow Transport Package

DATA(BINARY) for binary (unformatted) files such as those used for input of

concentrations saved in a previous simulation as the initial condition for a continuation

run.

DATA for formatted (text) files such as those used to save formatted concentrations at

observation points and mass budget summaries or for input of data from files that are

separate from the primary package input files.

Various output control options of MT3DMS/MT3D-USGS can be set up to save several

optional output files: the unformatted (binary) concentration file, the formatted

concentration observation file, the formatted mass budget summary file, and the model

configuration file. MT3DMS/MT3D-USGS always assigns default names to these files

with the conventions listed below.

These default names can be overridden, as explained in (Zheng, 2010).

 MT3Dnnn.UCN for the dissolved-phase unformatted concentration files where

nnn is the species index number such as 001 for species 1, 002 for species 2, and

so on;

 MT3DnnnS.UCN for the sorbed-phase or immobile-liquid-phase unformatted

concentration files where nnn is the species index number such as 001 for species

1, 002 for species 2, and so on;

 MT3Dnnn.OBS for the formatted concentration observation files;

 MT3Dnnn.MAS for the formatted mass budget summary files; and

 MT3D.CNF for storing the model configuration (spatial discretization)

information needed by post-processing programs. It is always saved along with

the UCN files.

Nunit - is the FORTRAN unit to be used when reading from or writing to the file. Any

valid unit number on the computer being used can be specified except for the unit

numbers that have been internally reserved by the MT3DMS/MT3D-USGS program. To

use the reserved unit number for a particular file, simply set Nunit associated with that

file to 0. If a reserved unit is used for a file for which the unit is not intended, an error

may occur and the program execution will be terminated. To avoid potential errors, avoid

using any units between 1 and 20, and any units above 100, when specifying units for

those files that do not have a reserved unit number. A complete list of reserved unit

numbers is provided in Table 1.

A negative sign may be assigned to unit numbers 200+ and 300+, that are reserved for

UCN files, to switch off the saving of a particular UCN file.

Fname – is the name of the input/output file, which is a character value. Pathnames may

be specified as part of Fname.

[Options] – optional keywords that may be used for the corresponding input/output file.

FTL file – the following two keywords may be specified in conjunction with the

flow-transport link (FTL) file. Note that if no keyword is specified after the FTL file

name, the FTL file is assumed to be unformatted (binary) by default.

 FREE indicates that the FTL input file for MT3DMS is in list-directed

(free) format, i.e., produced by the LMT6 Package with the option

OUTPUT_FILE_FORMAT set to formatted; and

 PRINT indicates that the content of the flow-transport link file is printed

to the standard output file for checking and debugging purposes. This

option is available in two places: (1) as an option in the NAM file (for

compatibility with MT3DMS) as described here; and (2) as an optional

keyword “FTLPRINT” in the BTN package, described below.

Table 1 – Reserved Unit Numbers for MT3D-USGS Input and Output Files (modified

from table in MT3DMS v5.3 Supplemental User’s Guide)

MT3D-USGS Input/Output Files File Type Reserved Unit

Name File* --- 99

Package Options

Basic Transport* BTN 1

Flow-Transport Link* FTL 10

Advection ADV 2

Dispersion DSP 3

Sink/Source Mixing SSM 4

Contaminant Treatment System CTS 6

Unsaturated-Zone Transport UZT 7

Reaction RCT 8

Generalized Conjugate Gradient GCG 9

Transport Observation TOB 12

HSS Time-Varying Source HSS 13

Time-Step Output TSO 14

Lake Transport LKT 18

Stream Flow Transport SFT 19

Output Files

Output Listing File* LIST 16

Model Configuration File CNF 17

Unformatted Concentration File (dissolved phase) UCN 200+species

index

Unformatted Concentration File(sorbed/immobile

phase)

UCN 300+species

index

Concentrations Observation File OBS 400+species

index

Mass Budget Summary File MAS 600+species

index

* Note – these files are always required for every simulation

ADV Package

Input for the Advection (ADV) package is read on unit INADV = 2, which is preset in the

main program. ADV package is invoked in the NAM file with the use of keyword ADV.

For each simulation:

1 Record: MIXELM, PERCEL, MXPART, NADVFD

Format: I10, F10.0, 2I10

 MIXELM is an integer flag for the advection solution option.

MIXELM = 0, the standard finite-difference method with upstream

or central-in-space weighting, depending on the value of

NADVFD;

= 1, the forward-tracking method of characteristics (MOC);

= 2, the backward-tracking modified method of characteristics

(MMOC);

= 3, the hybrid method of characteristics (HMOC) with MOC or

MMOC automatically and dynamically selected;

= -1, the third-order TVD scheme (ULTIMATE).

 PERCEL is the Courant number (i.e., the number of cells, or a

fraction of a cell) advection will be allowed in any direction in one

transport step.

For implicit finite-difference or particle-tracking-based schemes,

there is no limit on PERCEL, but for accuracy reasons, it is

generally not set much greater than one. Note, however, that the

PERCEL limit is checked over the entire model grid. Thus, even if

PERCEL > 1, advection may not be more than one cell’s length at

most model locations.

For the explicit finite-difference or the third-order TVD scheme,

PERCEL is also a stability constraint which must not exceed one

and will be automatically reset to one if a value greater than one is

specified.

 MXPART is the maximum total number of moving particles

allowed and is used only when MIXELM = 1 or 3.

 NADVFD is an integer flag indicating which weighting scheme

should be used; it is needed only when the advection term is solved

using the implicit finite difference method.

NADVFD = 0 or 1, upstream weighting (default);

= 2, central-in-space weighting.

(Enter item 2 if MIXELM = 1, 2, or 3)

2 Record: ITRACK, WD

Format: I10, F10.0

 ITRACK is a flag indicating which particle-tracking algorithm is

selected for the Eulerian-Lagrangian methods.

ITRACK = 1, the first-order Euler algorithm is used.

= 2, the fourth-order Runge-Kutta algorithm is used; this

option is computationally demanding and may be needed

only when PERCEL is set greater than one.

= 3, the hybrid first- and fourth-order algorithm is used; the

Runge-Kutta algorithm is used in sink/source cells and the

cells next to sinks/sources while the Euler algorithm is

used elsewhere.

 WD is a concentration weighting factor between 0.5 and 1.0. It is used

for operator splitting in the particle tracking-based methods. The value

of 0.5 is generally adequate. The value of WD may be adjusted to

achieve better mass balance. Generally, it can be increased toward 1.0 as

advection becomes more dominant.

(Enter item 3 if MIXELM = 1 or 3)

3 Record: DCEPS, NPLANE, NPL, NPH, NPMIN, NPMAX

Format: F10.0, 5I10

 DCEPS is a small Relative Cell Concentration Gradient below which

advective transport is considered negligible. A value around 10-5 is

generally adequate.

NPLANE is a flag indicating whether the random or fixed pattern is

selected for initial placement of moving particles.

If NPLANE = 0, the random pattern is selected for initial placement.

Particles are distributed randomly in both the horizontal and vertical

directions by calling a random number generator (Figure 18b). This

option is usually preferred and leads to smaller mass balance discrepancy

in nonuniform or diverging/converging flow fields.

If NPLANE > 0, the fixed pattern is selected for initial placement. The

value of NPLANE serves as the number of vertical “planes” on which

initial particles are placed within each cell block (Figure 18a). The fixed

pattern may work better than the random pattern only in relatively

uniform flow fields. For two-dimensional simulations in plan view, set

NPLANE = 1. For cross sectional or three-dimensional simulations,

NPLANE = 2 is normally adequate. Increase NPLANE if more

resolution in the vertical direction is desired.

 NPL is the number of initial particles per cell to be placed at cells where

the Relative Cell Concentration Gradient is less than or equal to DCEPS.

Generally, NPL can be set to zero since advection is considered

insignificant when the Relative Cell Concentration Gradient is less than

or equal to DCEPS. Setting NPL equal to NPH causes a uniform number

of particles to be placed in every cell over the entire grid (i.e., the

uniform approach).

 NPH is the number of initial particles per cell to be placed at cells where

the Relative Cell Concentration Gradient is greater than DCEPS. The

selection of NPH depends on the nature of the flow field and also the

computer memory limitation. Generally, a smaller number should be

used in relatively uniform flow fields and a larger number should be used

in relatively nonuniform flow fields. However, values exceeding 16 in

two-dimensional simulation or 32 in three-dimensional simulation are

rarely necessary. If the random pattern is chosen, NPH particles are

randomly distributed within the cell block. If the fixed pattern is chosen,

NPH is divided by NPLANE to yield the number of particles to be

placed per vertical plane, which is rounded to one of the values shown in

Figure 30.

 NPH is the number of initial particles per cell to be placed at cells where

the Relative Cell Concentration Gradient is greater than DCEPS. The

selection of NPH depends on the nature of the flow field and also the

computer memory limitation. Generally, a smaller number should be

used in relatively uniform flow fields and a larger number should be used

in relatively non-uniform flow fields. However, values exceeding 16 in

two-dimensional simulation or 32 in three-dimensional simulation are

rarely necessary. If the random pattern is chosen, NPH particles are

randomly distributed within the cell block. If the fixed pattern is chosen,

NPH is divided by NPLANE to yield the number of particles to be

placed per vertical plane, which is rounded to one of the values shown in

Figure 30.

 NPMIN is the minimum number of particles allowed per cell. If the

number of particles in a cell at the end of a transport step is fewer than

NPMIN, new particles are inserted into that cell to maintain a sufficient

number of particles. NPMIN can be set to zero in relatively uniform flow

fields and to a number greater than zero in diverging/converging flow

fields. Generally, a value between zero and four is adequate.

 NPMAX is the maximum number of particles allowed per cell. If the

number of particles in a cell exceeds NPMAX, all particles are removed

from that cell and replaced by a new set of particles equal to NPH to

maintain mass balance. Generally, NPMAX can be set to approximately

two times of NPH.

(Enter 4 if MIXELM = 2 or 3)

4 Record: INTERP, NLSINK, NPSINK

Format: 3I10

 INTERP is a flag indicating the concentration interpolation method for

use in the MMOC scheme. Currently, only linear interpolation is

implemented. Enter INTERP = 1.

 NLSINK is a flag indicating whether the random or fixed pattern is

selected for initial placement of particles to approximate sink cells in the

MMOC scheme. The convention is the same as that for NPLANE. It is

generally adequate to set NLSINK equivalent to NPLANE.

 NPSINK is the number of particles used to approximate sink cells in the

MMOC scheme. The convention is the same as that for NPH. It is

generally adequate to set NPSINK equivalent to NPH.

(Enter 5 if MIXELM = 3)

5 Record: DCHMOC

Format: F10.0

 DCHMOC is the critical Relative Concentration Gradient for controlling

the selective use of either MOC or MMOC in the HMOC solution

scheme.

The MOC solution is selected at cells where the Relative Concentration

Gradient is greater than DCHMOC.

The MMOC solution is selected at cells where the Relative

Concentration Gradient is less than or equal to DCHMOC.

Input instructions for the ADV package are the same as the original documentation.

Please refer Zheng and Wang (1999) for further details.

BTN Package

Input to the BTN Package is read on unit INBTN=1, which is preset in the main program.

Since the BTN package is needed for every simulation, this input file is always required.

Note that underlined are new features introduced in the current version.

For each simulation:

1 Record: HEADNG(1)

Format: A80

 HEADNG(1) is the first line of any title or heading for the simulation

run. The line should not be longer than 80 characters.

2 Record: HEADNG(2)

Format: A80

 HEADNG(2) is the second line of any title or heading for the simulation

run. The line should not be longer than 80 characters.

3 Record: [Optional Keywords]

Format: Text

Following keywords are available that can be used optionally. Only the

following keywords may appear on this line. If any words other than the

following keywords are encountered, the program will terminate. Ignore

this line if none of the following options are needed.

 MODFLOWSTYLEARRAYS: this keyword enables the use of

MODFLOW-like arrays and array headers, for example, the use of the

keyword ‘(free)’ when reading a 2-dimensional array in free format.

 DRYCELL: this keyword should be used to enable mass transfer through

dry cells, when dry cells can remain active in a flow simulation, as is

possible with MODFLOW-NWT. This option is available only if the

finite-difference method (MIXELM = 0) or the Total Variation

Diminishing (TVD) scheme (MIXELM = −1) is selected in the ADV

Package.

 LEGACY99STORAGE: this keyword is provided for backward

compatibility with MT3DMS. It is recommended that this option should

not be invoked.

 FTLPRINT: this keyword enables printing the content of the flow-

transport link file to the standard output file for checking and debugging

purposes. This option is also available in the NAM file.

 NOWETDRYPRINT: this keyword disables the printing of messages

indicating the “re-wetting” and “drying” of model cells to the standard

output file as a model cell becomes dry or rewets. This option is useful in

keeping the size of standard output file in check.

 OMITDRYCELLBUDGET: this keyword excludes from the global mass

balance calculations, the mass flowing through dry model cells. This

option is recommended when “in” and “out” of dry cells exactly

balances, and overwhelms the global mass budgets, enabling the user to

examine global mass budgets excluding mass flowing through dry cells.

 ALTWTSORB: this keyword provides an alternative formulation to

simulate adsorbed mass. In the absence of this option, by default MT3D-

USGS stores the mass on soil within the non-saturated portion of a model

cell as a “reservoir”. With the use of ALTWTSORB adsorbed mass is

instantaneously created as the water table rises and is lost as the water

table drops via an accounting process so that the mass is conserved.

Details are provided in the MT3D-USGS Version 1 documentation.

3 Record: NLAY, NROW, NCOL, NPER, NCOMP, MCOMP

Format: 6I10

 NLAY is the total number of layers;

 NROW is the total number of rows;

 NCOL is the total number of columns;

 NPER is the total number of stress periods;

 NCOMP is the total number of chemical species included in the current

simulation. For single-species simulation, set NCOMP = 1;

 MCOMP is the total number of “mobile” species. MCOMP must be

equal to or less than NCOMP. For single-species simulation, set

MCOMP=1.

Note that “mobile species” are involved in both transport and reaction

while “immobile” species equal to NCOMPMCOMP are involved in

reaction only. Also, for each species included in NCOMP, MT3DMS

automatically tracks a sorbed or immobile counterpart if a sorption

isotherm or dual-domain mass transfer is specified through the Chemical

Reaction Package. Thus, there is no need to define separate “immobile”

species to simulate sorption or a dual-domain system. The ability to

define separate immobile species is only intended for using MT3DMS

with add-on reaction packages.

4 Record: TUNIT, LUNIT, MUNIT

Format: 3A4

 TUNIT is the name of unit for time, such as DAY or HOUR;

 LUNIT is the name of unit for length, such as FT or M;

 MUNIT is the name of unit for mass, such as LB or KG.

Note that these names are used for identification purposes only and do

not affect the model outcome.

5 Record: TRNOP(10)

(ADV DSP SSM RCT GCG XXX XXX XXX XXX XXX)

Format: 10L2

 This input is not used by MT3D-USGS but is required for backward

compatibility with MT3DMS.

6 Record: LAYCON(NLAY)

Format: 40I2

 LAYCON is a 1-D integer array indicating the type of model layers.

Each value in the array corresponds to one model layer. Enter LAYCON

in as many lines as necessary if NLAY > 40.

LAYCON = 0, the model layer is confined. The layer thickness DZ to be

entered in a subsequent record will be used as the saturated thickness of

the layer.

LAYCON ≠ 0, the model layer is either unconfined or convertible

between confined and unconfined. The saturated thickness, as calculated

by the flow model and saved in the flow-transport link file, will be read

and used by the transport model. (Note that this type corresponds to the

LAYCON values of 1, 2, and 3 of MODFLOW; however, there is no

need to distinguish between these layer types in the transport simulation.)

7 Record: DELR(NCOL)

Format: RARRAY

 DELR is a 1-D real array representing the cell width along rows (Δx) in

the direction of increasing column indices (j). Specify one value for each

column of the grid

8 Record: DELC(NROW)

Format: RARRAY

 DELC is a 1-D real array representing the cell width along columns (Δy)

in the direction of increasing row indices (i). Specify one value for each

row of the grid.

9 Record: HTOP(NCOL,NROW)

Format: RARRAY

 HTOP is a 2-D array defining the top elevation of all cells in the first

(top) model layer, relative to the same datum as the hydraulic heads. For

more details refer to the original MT3DMS User’s Manual (Zheng and

Wang, 1999).

10 Record: DZ(NCOL,NROW) (one array for each layer in the grid)

Format: RARRAY

 DZ is the thickness of all cells in each model layer. DZ is a 3-D array.

The input to 3-D arrays is handled as a series of 2-D arrays with one

array for each layer, entered in the sequence of layer 1, 2, ..., NLAY. For

more details refer to the original MT3DMS User’s Manual (Zheng and

Wang, 1999).

11 Record: PRSITY(NCOL,NROW) (one array for each layer)

Format: RARRAY

 PRSITY is the “effective” porosity of the porous medium in a single

porosity system (see discussions in Chapter 2). Note that if a dual-

porosity system is simulated, PRSITY should be specified as the

“mobile” porosity (i.e., the ratio of interconnected pore spaces filled with

mobile waters over the bulk volume of the porous medium); the

“immobile” porosity is defined through the Chemical Reaction Package.

12 Record: ICBUND(NCOL,NROW) (one array for each layer)

Format: IARRAY

 ICBUND is an integer array specifying the boundary condition type

(inactive, constant-concentration, or active) for every model cell. For

multispecies simulation, ICBUND defines the boundary condition type

shared by all species. Note that different species are allowed to have

different constant-concentration conditions through an option in the

Source and Sink Mixing Package.

If ICBUND = 0, the cell is an inactive concentration cell for all species.

Note that no-flow or “dry” cells are automatically converted into inactive

concentration cells. Furthermore, active cells in terms of flow can be

treated as inactive concentration cells to minimize the area needed for

transport simulation, as long as the solute transport is insignificant near

those cells.

If ICBUND < 0, the cell is a constant-concentration cell for all species.

The starting concentration of each species remains the same at the cell

throughout the simulation. (To define different constant-concentration

conditions for different species at the same cell location, refer to the

Sink/Source Mixing Package.) Also note that unless explicitly defined as

a constant-concentration cell, a constant-head cell in the flow model is

not treated as a constant-concentration cell.

If ICBUND > 0, the cell is an active (variable) concentration cell where

the concentration value will be calculated.

(Enter 13 for each of the NCOMP species)

13 Record: SCONC(NCOL,NROW) (one array for each layer)

Format: RARRAY

 SCONC is the starting concentration (initial condition) at the beginning

of the simulation (unit, ML-3). For multispecies simulation, the starting

concentration must be specified for all species, one species at a time.

14 Record: CINACT, THKMIN

Format: 2F10.0

 CINACT is the value for indicating an inactive concentration cell

(ICBUND = 0). Even if inactive cells are not anticipated in the model, a

value for CINACT still must be submitted.

 THKMIN is the minimum saturated thickness in a cell.

If THKMIN > 0, THKMIN is expressed as the decimal fraction of the

model layer thickness (DZ) below which the cell is considered inactive.

The default value is 0.01 (i.e., 1 percent of the model layer thickness).

If THKMIN < 0, Absolute value of the entered value is used. If the

saturated thickness in a cell falls below the absolute value of THKMIN

then the cell is considered inactive.

15 Record: IFMTCN, IFMTNP, IFMTRF, IFMTDP, SAVUCN

Format: 4I10, L10

 IFMTCN is a flag indicating whether the calculated concentration should

be printed to the standard output text file and also serves as a printing-

format code if it is printed. For more details refer to the original

MT3DMS User’s Manual (Zheng and Wang, 1999).

 IFMTNP is a flag indicating whether the number of particles in each cell

(integers) should be printed and also serves as a printing-format code if

they are printed. The convention is the same as that used for IFMTCN.

 IFMTRF is a flag indicating whether the model-calculated retardation

factor should be printed and also serves as a printing-format code if it is

printed. The convention is the same as that used for IFMTCN.

 IFMTDP is a flag indicating whether the model-calculated, distance-

weighted dispersion coefficient should be printed and also serves as a

printing-format code if it is printed. The convention is the same as that

used for IFMTCN.

 SAVUCN is a logical flag indicating whether the concentration solution

should be saved in a default unformatted (binary) file named

MT3Dnnn.UCN, where nnn is the species index number, for post-

processing purposes or for use as the initial condition in a continuation

run.

If SAVUCN = T, the concentration of each species will be saved in the

default file MT3Dnnn.UCN. In addition, the model spatial discretization

information will be saved in another default file named MT3D.CNF to be

used in conjunction with MT3Dnnn.UCN for post-processing purposes.

The saving of an MT3Dnnn.UCN or an MT3DnnnS.UCN file for a

particular solute, can be switched off by using a negative unit number for

that particular solute in the NAM file. By default SAVUCN = T saves

UCN files for all solutes being simulated.

If SAVUCN = F, neither MT3Dnnn.UCN nor MT3D.CNF is created.

16 Record: NPRS

Format: I10

 NPRS is a flag indicating the frequency of the output and also indicating

whether the output frequency is specified in terms of total elapsed

simulation time or the transport step number. Note that what is actually

printed or saved is controlled by the input values entered in the preceding

record (Record 15).

If NPRS > 0, simulation results will be printed to the standard output text

file or saved to the unformatted concentration file at times as specified in

record TIMPRS(NPRS) to be entered in the next record.

If NPRS = 0, simulation results will not be printed or saved except at the

end of simulation.

If NPRS < 0, simulation results will be printed or saved whenever the

number of transport steps is an even multiple of NPRS.

(Enter 17 only if NPRS > 0)

17 Record: TIMPRS(NPRS)

Format: 8F10.0

 TIMPRS is the total elapsed time at which the simulation results are

printed to the standard output text file or saved in the default unformatted

(binary) concentration file MT3Dnnn.UCN. Note that if NPRS > 8, enter

TIMPRS in as many lines as necessary.

18 Record: NOBS, NPROBS

Format: 2I10

 NOBS is the number of observation points at which the concentration of

each species will be saved at the specified frequency in the default

MT3Dnnn.OBS where nnn is the species index number.

 NPROBS is an integer indicating how frequently the concentration at the

specified observation points should be saved in the observation file

MT3Dnnn.OBS. Concentrations are saved every NPROBS step.

(Enter 19 NOBS times if NOBS > 0)

19 Record: KOBS, IOBS, JOBS

Format: 3I10

 KOBS, IOBS, and JOBS are the cell indices (layer, row, column) in

which the observation point or monitoring well is located and for which

the concentration is to be printed at every transport step in file

MT3Dnnn.OBS. Enter one set of KOBS, IOBS, JOBS for each

observation point.

20 Record: CHKMAS, NPRMAS

Format: L10, I10

 CHKMAS is a logical flag indicating whether a one-line summary of

mass balance information should be printed, for checking and post-

processing purposes, in the default file MT3Dnnn.MAS where nnn is the

species index number.

If CHKMAS = T, the mass balance information for each transport step

will be saved in file MT3Dnnn.MAS.

If CHKMAS = F, file MT3Dnnn.MAS is not created.

 NPRMAS is an integer indicating how frequently the mass budget

information should be saved in the mass balance summary file

MT3Dnnn.MAS. Mass budget information is saved every NPRMAS

step.

For each stress period

21 Record: PERLEN, NSTP, TSMULT, [SSFlag]

Format: F10.0, I10, F10.0, [FREE]

 PERLEN is the length of the current stress period. If the flow solution is

transient, PERLEN specified here must be equal to that specified for the

flow model. If the flow solution is steady-state, PERLEN can be set to

any desired length.

 NSTP is the number of time-steps for the transient flow solution in the

current stress period. If the flow solution is steady-state, NSTP = 1.

 TSMULT is the multiplier for the length of successive time steps used in

the transient flow solution; it is used only if NSTP > 1.

If TSMULT > 0, the length of each flow time-step within the current

stress period is calculated using the geometric progression as in

MODFLOW. Note that both NSTP and TSMULT specified here must be

identical to those specified in the flow model if the flow model is

transient.

If TSMULT <= 0, the length of each flow time-step within the current

stress period is read from the record TSLNGH (see record 22). This

option is needed in case the length of timesteps for the flow solution is

not based on a geometric progression in a flow model, unlike

MODFLOW.

 SSFlag is an optional flag to indicate whether the steady-state

transport option should be activated. The option is activated if

SSFlag is set to the keyword SSTATE, which can be any

combination of lower or capital letters.

(Enter 22 if TSMULT <= 0)

22 Record: TSLNGH(NSTP)

Format: 8F10.0

 TSLNGH provides the length of time-steps for the flow solution in the

current stress period. This record is needed only if the length of time-

steps for the flow solution is not based on a geometric progression. Enter

TSLNGH in as many lines as necessary if NSTP > 8.

23 Record: DT0, MXSTRN, TTSMULT, TTSMAX

Format: F10.0, I10, 2F10.0

 DT0 is the user-specified transport step size within each time-step of the

flow solution. DT0 is interpreted differently depending on whether the

solution option chosen is explicit or implicit:

For explicit solutions (i.e., the GCG solver is not used), the program will

always calculate a maximum transport step size which meets the various

stability criteria. Setting DT0 to zero causes the model-calculated

transport step size to be used in the simulation. However, the model-

calculated DT0 may not always be optimal. In this situation, DT0 should

be adjusted to find a value that leads to the best results. If DT0 is given a

value greater than the model-calculated step size, the model-calculated

step size, instead of the user-specified value, will be used in the

simulation.

For implicit solutions (i.e., the GCG solver is used, which is the only

option since version 5.00 of MT3DMS), DT0 is the initial transport step

size. If it is specified as zero, the model-calculated value of DT0, based

on the user specified Courant number in the Advection Package, will be

used. The subsequent transport step size may increase or remain constant

depending on the user-specified transport step size multiplier TTSMULT

and the solution scheme for the advection term.

 MXSTRN is the maximum number of transport steps allowed within one

time step of the flow solution. If the number of transport steps within a

flow time-step exceeds MXSTRN, the simulation is terminated.

 TTSMULT is the multiplier for successive transport steps within a flow

time-step if the GCG solver is used and the solution option for the

advection term is the standard finite-difference method. A value between

1.0 and 2.0 is generally adequate. If the GCG package is not used, the

transport solution is solved explicitly as in the original MT3DMS code,

and TTSMULT is always set to 1.0 regardless of the user-specified input.

Note that for the particle-tracking-based solution options and the third

order TVD scheme, TTSMULT does not apply.

 TTSMAX is the maximum transport step size allowed when transport

step size multiplier TTSMULT > 1.0. Setting TTSMAX=0 imposes no

maximum limit.

CTS Package

Input for the Contaminant Treatment System (CTS) package is read on unit ICTS = 6,

which is preset in the main program. CTS package is invoked in the NAM file with the

use of keyword CTS. The input file is needed only if contaminant treatment systems are

simulated for circulation of mass within a model domain.

For each simulation:

1 Record: MXCTS, ICTSOUT, MXEXT, MXINJ, MXWEL, IFORCE,

ICTSPKG

Format: FREE

 MXCTS is the maximum number of contaminant treatment

systems implemented in a simulation.

 ICTSOUT is the unit number on which well-by-well output

information is written. The default file extension assigned to the

output file is CTO.

 MXEXT is the maximum number of extraction wells specified as

part of a contaminant treatment system.

 MXINJ is the maximum number of injection wells specified as part

of a contaminant treatment system.

 MXWEL is the maximum number of wells in the flow model.

MXWEL is recommended to be set equal to MXWEL as specified

in the WEL file or the MNW2 file.

 IFORCE is a flag to force concentration in treatment systems to

satisfy specified concentration/mass values based on the treatment

option selected without considering whether treatment is necessary

or not. This flag is ignored if “no treatment” option is selected.

If IFORCE = 0, concentration for all injection wells is set to satisfy

treatment levels only if blended concentration exceeds the desired

concentration/mass level for a treatment system. If the blended

concentration in a treatment system is less than the specified

concentration/mass level, then injection wells inject water with

blended concentrations.

If IFORCE = 1, concentration for all injection wells is forced to

satisfy specified concentration/mass values.

 ICTSPKG – is a flag to identify the MODFLOW well (WEL or

MNW2) package that the CTS package will work with, i.e. flow

rates associated with the MODFLOW package identified using this

flag will be used with the CTS package.

ICTSPKG = 0, flow rates from the MNW2 package will be

used.

ICTSPKG = 1, flow rates from the WEL package will be used.

For each stress period:

2 Record: NCTS

Format: FREE

 NCTS is the number of contaminant treatment systems.

If NCTS >= 0, NCTS is the number of contaminant treatment

systems.

If NCTS = -1, treatment system information from the previous

stress period is reused for the current stress period.

For each contaminant treatment system:

3 Record: ICTS, NEXT, NINJ, ITRTINJ

Format: FREE

 ICTS is the contaminant treatment system index number.

 NEXT is the number of extraction wells for the treatment system

number ICTS.

 NINJ is the number of injection wells for the treatment system

number ICTS.

 ITRTINJ is the level of treatment provided for the treatment

system number ICTS. Each treatment system blends concentration

collected from all extraction wells contributing to the treatment

system and assigns a treated concentration to all injection wells

associated with that treatment system based on the treatment

option selected.

If ITRTINJ = 0, no treatment is provided.

If ITRTINJ = 1, same level of treatment is provided to all

injection wells.

If ITRTINJ = 2, different level of treatment can be provided to

each individual injection well.

(Enter 4 NEXT times if NEXT > 0)

4 Record: KEXT, IEXT, JEXT, IWEXT

Format: FREE

 KEXT, IEXT, JEXT are the layer, row, and column numbers of

extraction wells.

 IWEXT is the well index number. This number corresponds to the

well number as it appears in the WEL file of the flow model.

(Repeat record 5 on the same line for each species)

5 Record: QINCTS, (CINCTS(n), n=1,NCOMP)

Format: FREE

 QINCTS is the external flow entering a treatment system. External

flow may be flow entering a treatment system that is not a part of

the model domain but plays an important role in influencing the

blended concentration of a treatment system.

 CINCTS is the concentration with which the external flow enters a

treatment system.

(Enter 6 only if ITRTINJ = 1; Repeat record 6 on the same line for each species)

6 Record: (IOPTINJ(n), CMCHGINJ(n), n=1,NCOMP)

Format: FREE

 IOPTINJ – is a treatment option. Negative values indicate removal

of concentration/mass and positive values indicate addition of

concentration/mass. Treatment is applied at the level of each

individual injection well.

If IOPTINJ = 1, percentage concentration/mass

addition/removal is performed. Percentages must be specified

as fractions. Example, for 50% concentration/mass removal is

desired, -0.5 must be specified.

If IOPTINJ = 2, concentration is added/removed from the

blended concentration. Specified concentration CMCHGINJ is

added to the blended concentration. If the specified

concentration removal, CMCHGINJ, is greater than the

blended concentration, the treated concentration is set to zero.

If IOPTINJ = 3, mass is added/removed from the blended

concentration. Specified mass CMCHGINJ is added to the

blended concentration. If the specified mass removal,

CMCHGINJ, is greater than the blended total mass, the treated

concentration is set to zero.

If IOPTINJ = 4, specified concentration is set equal to the

entered value CMCHGINJ. A positive value is expected for

CMCHGINJ with this option.

 CMCHGINJ is the addition, removal, or specified

concentration/mass values set for the treatment system.

Concentration/mass is added, removed, or used as specified

concentrations depending on the treatment option IOPTINJ.

Note that concentration/mass values as specified by CMCHGINJ

are enforced if the option IFORCE is set to 1. If IFORCE is set to

0, then CMCHGINJ is enforced only when the blended

concentration exceeds the specified concentration CNTE.

(Enter 7 only if IFORCE = 0)

7 Record: (CNTE(n), n=1,NCOMP)

Format: FREE

 CNTE is the concentration that is not to be exceeded for a

treatment system. Treatment is applied to blended concentration

only if it exceeds CNTE, when IFORCE is set to 0.

(Enter 8 NINJ times if NINJ > 0)

8 Record: KINJ, IINJ, JINJ, IWINJ,

(IOPTINJ(n),CMCHGINJ(n), n=1,NCOMP)

Format: FREE

 KINJ, IINJ, JINJ are the layer, row, and column numbers of

injection wells.

 IWINJ is the well index number. This number corresponds to the

well number as it appears in the WEL file of the flow model.

IOPTINJ and CMCHGINJ are entered only if ITRTINJ is set to 2

and are defined above.

Note that concentration/mass values as specified by CMCHGINJ

are enforced at each injection well if the option IFORCE is set to 1.

If IFORCE is set to 0, then CMCHGINJ is enforced only when the

blended concentration exceeds the specified concentration CNTE.

9 Record: QOUTCTS

Format: FREE

 QOUTCTS is the flow rate of outflow from a treatment system to

an external sink. This flow rate must be specified to maintain an

overall treatment system mass balance. QOUTCTS must be set

equal to total inflow into a treatment system minus total outflow to

all injection wells for a treatment system.

DSP Package

Input for the Dispersion (DSP) package is read on unit INDSP = 3, which is preset in the

main program. The DSP package is invoked in the NAM file with the use of keyword

DSP.

For each simulation:

0 Record: [Optional Keywords]

Format: [Free]

Following keywords are available that can be used optionally. Only the

following keywords may appear on this line. If any words other than the

following keywords are encountered, the program will terminate. Ignore

this line if none of the following options are needed. For backward

compatibility, a $ sign must be present in the first column to use the

following keywords.

 MultiDiffusion: (case insensitive) this keywords enables

component-dependent diffusion. The user needs to specify one

diffusion coefficient for each mobile solute component and at each

model cell.

 NOCROSS: this keyword disables cross dispersion terms.

1 Record: AL(NCOL,NROW) (one array for each layer in the grid)

Format: RARRAY

 AL is the longitudinal dispersivity, L, for every cell of

the model grid (unit, L).

2 Record: TRPT(NLAY)

Format: RARRAY

 TRPT is a 1D real array defining the ratio of the horizontal

transverse dispersivity, TH , to the longitudinal dispersivity, L.

Each value in the array corresponds to one model layer. As

reported in Zheng and Wang (1999), various field studies suggest

that TRPT is generally not greater than 0.1.

3 Record: TRPV(NLAY)

Format: RARRAY

 TRPV is the ratio of the vertical transverse dispersitvity, TV, to the

longitudinal dispersivity, L. Each value in the array corresponds

to one model layer. As reported in Zheng and Wang (1999),

various field studies suggest that TRPV is generally not greater

than 0.01.

Set TRPV equal to TRPT to use the standard isotropic dispersion

model (Equation 10 in Chapter 2). Otherwise, the modified

isotropic dispersion model is used (Equation 11 in Chapter 2).

If keyword [MultiDiffusion] is not defined:

4 Record: DMCOEF(NLAY)

Format: RARRAY

 DMCOEF is the effective molecular diffusion coefficient (unit,

L2T-1). Set DMCOEF = 0 if the effect of molecular diffusion is

considered unimportant. Each value in the array corresponds to

one model layer. Enter one array for all solute components.

If keyword [MultiDiffusion] is defined:

4 Record: DMCOEF(NCOL,NROW) (One array for each layer)

Format: RARRAY

 DMCOEF is the effective molecular diffusion coefficient (unit,

L2T-1). Set DMCOEF = 0 if the effect of molecular diffusion is

considered unimportant. Each value in the array corresponds to

one model cell. Repeat the input for each mobile component.

GCG Package

Input to the Generalized Conjugate Gradient (GCG) Package is read on unit INGCG = 9,

which is preset in the main program. Since the release of version 5.00 of MT3DMS, and

now the release of MT3D-USGS, the General Conjugate-Gradient (GCG) solver must be

used.

For each simulation:

1 Record: MXITER, ITER1, ISOLVE, NCRS

Format: Free

 MXITER is the maximum number of outer iterations; it should be set to

an integer greater than one when nonlinear sorption isotherm is included

in simulation or when the DRYCELL option is used to route solute

through dry cells, as discussed in the documentation.

 ITER1 is the maximum number of inner iterations; a value of 30-50

should be adequate for most problems.

 ISOLVE is the type of preconditioners to be used with the

Lanczos/ORTHOMIN acceleration scheme:

= 1, Jacobi

= 2, SSOR

= 3, Modified Incomplete Cholesky (MIC)

(MIC usually converges faster, but it needs significantly more memory)

 NCRS is an integer flag for treatment of dispersion tensor cross terms:

= 0, lump all dispersion cross terms to the righthand- side (approximate

but highly efficient).

= 1, include full dispersion tensor (memory intensive).

2 Record: ACCL, CCLOSE, IPRGCG

Format: Free

 ACCL is the relaxation factor for the SSOR option; a value of 1.0 is

generally adequate.

 CCLOSE is the convergence criterion in terms of relative concentration;

a real value between 10-4 and 10-6 is generally adequate.

 IPRGCG is the interval for printing the maximum concentration changes

of each iteration. Set IPRGCG to zero as default for printing at the end of

each stress period.

HSS Package

Input for the Hydrocarbon Spill Source (HSS) Package is read on unit INHSS = 13,

which is preset in the main program. The file listed in the name file with “HSS” as the

file type will be read. The input data are read in free format. Input instructions given

below have been reproduced from the original HSS documentation (Zheng et al, 2010).

For a detailed discussion on HSS package, refer to the original documentation (Zheng et

al, 2010).

For each simulation:

1 Record: Comment Line

Format: A80

 Must start with “#” in the first position (column) of a line title or heading

for the simulation run. The line should not be longer than 80 characters.

However, if needed, this line can be repeated as many times as desired.

The header lines are echoed to the standard output listing file.

2 Record: MaxHSSSource, MaxHSSCells, MaxHSSStep, RunOption,

[ShapeOption]

Format: FREE

 MaxHSSSource is the maximum number of HSSM-LNAPL sources

allowed in the current transport simulation. This value is used only

for memory allocation purposes.

 MaxHSSCells is the maximum number of model cells that any

single HSSM-LNAPL source can occupy. A HSSM-LNAPL

source is initially associated with a single model cell. As the oil

lens expands, more model cells may be used to represent the

source, whenever necessary. This value is used only for memory

allocation purposes.

 MaxHSSStep is the maximum number of time steps used to define

any single HSSMLNAPL source, as output from a HSSM run. This

value is used only for memory allocation purposes.

 RunOption is a character flag indicating whether the HSSM model

should be invoked from within MT3DMS or run manually outside

MT3DMS. If ‘RunOption’ is set to “RunHSSM” (case insensitive),

the HSSM code, included with MT3DMS as a dynamic link library

(DLL) module, will be executed from within MT3DMS to simulate

the LNAPL source. If ‘RunOption’ is set to any other value, an

input file defining the LNAPL source must have been generated

from a previous execution of the HSSM code outside MT3DMS.

 [ShapeOption] (Optional) is a character flag indicating the shape of

the source area. Two options can be invoked with this flag:

If ShapeOption = “POLYGON”, shape will be a regular

polygon).

If ShapeOption = “IRREGULAR”, shape is based on an

arbitrary set of points.

Both the options are case insensitive. If left blank, the default

setting (circular shape) for the source in the HSS package will be

used.

3 Record: faclength, factime, facmass

Format: FREE

 faclength is a conversion factor for converting the unit of length

used in HSSM to that used in MT3DMS. For example, if the unit

used in MT3D-USGS is feet while the unit in HSSM is m,

“faclength” should be set equal to 3.28.

 factime is the conversion factor for converting the unit of time

used in HSSM to that used in MT3D-USGS. For example, if the

unit used in MT3D-USGS is minutes while the unit in HSSM is

day, “factime” should be set to 1440.

 facmass is the conversion factor for converting the unit of mass

used in HSSM to that used in MT3D-USGS. For example, if the

unit used in MT3DMS is gram while the unit in HSSM is kg,

“facmass” should be set to 1000.

4 Record: nHSSSource

Format: Free

 nHSSSource is the actual number of HSSM-LNAPL sources

included in the current transport simulation. ‘nHSSSource’ cannot

exceed ‘MaxHSSSource,’ the maximum number of HSSM-

LNAPL sources allowed and specified above.

Read records 5 and 6 for each HSSM-LNAPL source (nHSSSource):

5 Record: HSSFileName, inHSSFile

Format: Free

 HSSFileName is a string of one to 78 non-blank characters

specifying the name of an auxiliary input file defining a specific

HSSM-LNAPL source. ‘HSSFileName’ can include a path;

constraints imposed by a particular computer operating system

regarding file names and paths should be considered when

specifying ‘HSSFileName.’

 inHSSFile is an integer unit number associated with the HSSM-

LNAPL source input file given by ‘HSSFileName.’

If ShapeOption is left blank, specify record 6a:

6a Record: kSource, iSource, jSource, iHSSComp, SourceName

Format: Free

 kSource is the layer index of the initial model cell where a HSSM-

LNAPL source is located.

 iSource is the row index of the initial model cell where a HSSM-

LNAPL source is located.

 jSource is the column index of the initial model cell where a

HSSM-LNAPL source is located.

 iHSSComp is the species index of the LNAPL source in a

multicomponent MT3D-USGS simulation. For example, if

iSSComp = 2, the LNAPL source is intended for species number 2

included in the current simulation.

 SourceName is a string of 1 to 12 nonblank characters used to

identify the HSSM-LNAPL source specified at location ‘kSource,’

‘iSource,’ ‘jSource.’ The identifier need not be unique; however,

identification of HSSM-LNAPL sources in the output files is

facilitated if each source is given a unique name.

This input is backward compatible with MT3DMS. Note that the input

instructions provided with MT3DMS have the two variables –

SourceName and iHSSComp – swapped; the MT3DMS code reads

this input as specified above.

If ShapeOption = ‘POLYGON,’ specify record 6b:

6b Record: kSource, iSource, jSource, iHSSComp, SourceName, nPoint,

nSubGrid

Format: Free

 nPoint is the number of points that define a user defined regular or

irregular polygon. 

 nSubGrid is the number of subdivisions made in the X and Y

directions to calculate approximate area weights of the source

distribution. If ‘nSubGrid’ is set to a negative number, then an

alternate algorithm is used to calculate the area weights.



If ShapeOption = ‘IRREGULAR,’ specify record 6c and 6d:



6c Record: kSource, iHSSComp, SourceName, nPoint, nSubGrid

Format: Free

Read record 6d nPoint times:

6d Record: SourceX, SourceY

Format: Free

 SourceX is the model X coordinate of the points defining a user

specified irregular polygon. SourceX is measured in the positive X

direction.

 SourceY is the model Y coordinate of the points defining a user

specified irregular polygon. ‘SourceY’ is measured in the positive

Y direction. Note that the positive Y direction is opposite to the

direction in which the row numbers increase.

The origin for model coordinates is assumed to be the southwest corner

for the model.

HSS Source Definition File

For each time step computed by the HSSM code:

1 Record: Time, Radius, Sourcemassflux

Format: Free

 Time is the total elapsed time since the beginning of simulation (unit:

day).

 Radius is the radius of the source [L]. If zero or a negative value is

assigned to radius_lnapl, the mass loading source is specified

exclusively at the single finite-difference model cell (kSource, jSource,

iSource) defined in the HSS input file. This input is required but ignored

when ShapeOption is set to ‘IRREGULAR’.

 Sourcemassflux is the rate of contaminant mass flux dissolved into

groundwater from the source (M/T).

LKT Package

Input to the Lake Transport Package is read from a file listed in the name file with “LKT”

as the file type. The input file is needed only if lakes are simulated in the flow model

using the LAK package in MODFLOW and a solution to the transport problem via and

within the lake is desired. If lakes simulated using the LAK package of MODFLOW are

only used as a boundary condition in MT3D-USGS, this package may not be used and the

input for boundary concentration may be entered in the SSM package.

For each simulation:

1 Record: NLKINIT, MXLKBC, ICBCLK, IETLAK

Format: Free

 NLKINIT is an integer value equal to the number of simulated lakes as

specified in the flow simulation.

 MXLKBC is an integer value that must be greater than or equal to the

sum total of boundary conditions applied to each lake.

 ICBCLK is an integer value equal to the unit number on which lake-by-

lake transport information will be printed. This unit number must appear

in the NAM input file required for every MT3D-USGS simulation.

 IETLAK is an integer value specifying whether or not evaporation

as simulated in the flow solution will act as a mass sink.

= 0, Mass does not exit the model via simulated lake evaporation;

≠ 0, Mass may leave the lake via simulated lake evaporation;

2 Record: CINITLAK

Format: RARRAY

 CINITLAK is a vector of real numbers representing the initial

concentrations in the simulated lakes. The length of the vector is equal

to the number of simulated lakes, NLKINIT. Initial lake concentrations

should be in the same order as the lakes appearing in the LAK input file

corresponding to the MODFLOW simulation.

For each stress period:

3 Record: NTMP

Format: I10

 NTMP is an integer value corresponding to the number of specified lake

boundary conditions to follow. For the first stress period, this value must

be greater than or equal to zero, but may be less than zero in subsequent

stress periods.

If NTMP >= 0, NTMP is the number of lake boundary conditions.

If NTMP = -1, lake boundary conditions from the previous stress period are

reused for the current stress period.

(Read item 4 for each NTMP boundary condition)

4 Record: ILKBC, ILKBCTYP, (CBCLK(n), n=1, NCOMP)

Format: Free

 ILKBC is an integer value that is the lake number for which the current

boundary condition will be specified

 ILKBCTYP is an integer value that specifies, for ILKBC, what the

boundary condition type is:

= 1, a precipitation boundary condition. If precipitation to lakes is

simulated in the flow model and a non-zero concentration

(default is zero) is associated with it, use ILKBCTYP = 1;

= 2, a runoff boundary condition. If runoff specified in the LAK

package of MODFLOW has a non-zero concentration (default

is zero) associated with it, use ILKBCTYP = 2. This input is

not the same thing as runoff simulated in the UZF1 package

and routed to a lake (or stream) using the IRNBND array.

 CBCLK is the specified concentration for the current boundary

condition. One entry (on the same line) per species.

RCT Package

Input to the Chemical Reaction Package is read on unit INRCT = 8, which is preset in the

main program. The input file is needed only if chemical reactions are simulated. In

addition, the option for modeling transport in a dual-domain system is specified through

this file.

For each simulation:

1 Record: ISOTHM, IREACT, IRCTOP, IGETSC, IREACTION

Format: 5I10

 ISOTHM is a flag indicating which type of sorption (or dual-

domain mass transfer) is simulated:

= 0, no sorption is simulated;

=1, Linear isotherm (equilibrium-controlled);

=2, Freundlich isotherm (equilibrium-controlled);

=3, Langmuir isotherm (equilibrium-controlled);

=4, First-order kinetic sorption (nonequilibrium);

=5, Dual-domain mass transfer (without sorption);

=6, Dual-domain mass transfer (with sorption).

=-6, Dual-domain mass transfer (with different sorption

coefficients in mobile and immobile domains).

 IREACT is a flag indicating which type of kinetic rate reaction is

simulated:

IREACT = 0, no kinetic rate reaction is simulated;

IREACT = 1, first-order irreversible reaction;

IREACT = 2, MONOD kinetic reaction is simulated;

IREACT = 3, first-order chain reaction is simulated.

IREACT = 100, zeroth-order reaction (decay or production)

Note that options 1 and 2 are not intended for modeling chemical

reactions between species.

 IRCTOP is an integer flag indicating how reaction variables are

entered:

IRCTOP ≥ 2, all reaction variables are specified as 3-D arrays on a

cell-by-cell basis.

IRCTOP < 2, all reaction variables are specified as a 1-D array

with each value in the array corresponding to a single layer. This

option is mainly for retaining compatibility with the previous

versions of MT3DMS.

 IGETSC is an integer flag indicating whether the initial

concentration for the non-equilibrium sorbed or immobile phase of

all species should be read when non-equilibrium sorption

(ISOTHM = 4) or dual-domain mass transfer (ISOTHM = 5, 6, or

-6) is simulated:

IGETSC = 0, the initial concentration for the sorbed or immobile

phase is not read. By default, the sorbed phase is assumed to be in

equilibrium with the dissolved phase (ISOTHM = 4), and the

immobile domain is assumed to have zero concentration (ISOTHM

= 5, 6, or -6).

IGETSC > 0, the initial concentration for the sorbed phase or

immobile liquid phase of all species will be read.

 IREACTION is an integer flag to select a reaction module. At least

2 species must be simulated when this option is used. Additional

input is needed in needed when this option is used.

If IREACTION=0, no reaction is simulated.

If IREACTION=1, instantaneous EA/ED reaction is simulated

between an ED and an EA.

If IREACTION=2, kinetic reaction is simulated between multiple

EAs and EDs.

(Enter 2A if ISOTHM=1, 2, 3, 4, 6, or -6; but not 5; OR if IREACTION=2)

2A Record: RHOB(NCOL,NROW) (one array for each layer)

Format: RARRAY

 RHOB is the bulk density of the aquifer medium (unit, ML-3).

(Enter 2B if ISOTHM = 5, 6, or -6)

2B Record: PRSITY2(NCOL,NROW) (one array for each layer)

Format: RARRAY

 PRSITY2 is the porosity of the immobile domain, i.e., the ratio of pore

spaces filled with immobile fluids over the bulk volume of the aquifer

medium, when the simulation is intended to represent a dual-domain

system.

(Enter 2C for each of the NCOMP species if IGETSC > 0)

2C Record: SRCONC(NCOL, NROW) (one array for each layer)

Format: RARRAY

 SRCONC is the user-specified initial concentration for the sorbed phase

of a particular species if ISOTHM = 4 (unit, MM-1). Note that for

equilibrium-controlled sorption, the initial concentration for the sorbed

phase cannot be specified.

SRCONC is the user-specified initial concentration for the immobile

liquid phase if ISOTHM = 5, 6, or -6 (unit, ML-3).

SRCONC is not used if ISOTHM = 1, 2, or 3

(Enter 3a for each of the NCOMP species if ISOTHM ≠ 0)

3a Record: SP1(NCOL, NROW) (one array for each layer)

Format: RARRAY

 SP1 is the first sorption parameter. The use of SP1 depends on the type

of sorption selected (i.e., the value of ISOTHM):

For linear sorption (ISOTHM = 1) and nonequilibrium sorption

(ISOTHM = 4), SP1 is the distribution coefficient (Kd) (unit, L3M-1).

For Freundlich sorption (ISOTHM = 2), SP1 is the Freundlich

equilibrium constant (Kf) (the unit depends on the Freundlich exponent

a).

For Langmuir sorption (ISOTHM = 3), SP1 is the Langmuir equilibrium

constant (Kl) (unit, L3M-1).

For dual-domain mass transfer without sorption (ISOTHM = 5), SP1 is

not used, but still must be entered.

For dual-domain mass transfer with sorption (ISOTHM = 6), SP1 is also

the distribution coefficient (Kd) (unit, L3M-1).

For dual-domain mass transfer with sorption (ISOTHM = -6), SP1 is the

mobile domain distribution coefficient ( m

K) (unit, L3M-1).

(Enter 3b for each of the NCOMP species if ISOTHM = -6)

3b Record: SP1IM(NCOL,NROW) (one array for each layer)

Format: RARRAY

 SP1IM is the immobile domain partitioning/distribution coefficient

(im

K) (unit, L3M-1). This option is entered only if ISOTHM = -6, i.e. if

a different partitioning coefficient is simulated for the immobile domain.

(Enter 4 for each of the NCOMP species if ISOTHM ≠ 0)

4 Record: SP2(NCOL,NROW) (one array for each layer)

Format: RARRAY

 SP2 is the second sorption or dual-domain model parameter. The use of

SP2 depends on the type of sorption or dual-domain model selected:

For linear sorption (ISOTHM = 1), SP2 is read but not used.

For Freundlich sorption (ISOTHM = 2), SP2 is the Freundlich exponent

For Langmuir sorption (ISOTHM = 3), SP2 is the total concentration of

the sorption sites available (S) (unit, MM-1).

For non-equilibrium sorption (ISOTHM = 4), SP2 is the first-order mass

transfer rate between the dissolved and sorbed phases (unit, T-1).

For dual-domain mass transfer (ISOTHM = 5, 6, or -6), SP2 is the first-

order mass transfer rate between the two domains (unit, T-1).

(Enter 5 for each species if IREACT > 0)

5 Record: RC1(NCOL, NROW) (one array for each layer)

Format: RARRAY

 If IREACT = 1 or 3, RC1 is the first-order reaction rate for the

dissolved (liquid) phase (unit, T-1). If a dual-domain system is simulated,

the reaction rates for the liquid phase in the mobile and immobile

domains are assumed to be equal.

 If IREACT = 2 (MONOD kinetics), RC1 is the product of total

microbial concentration, Mt (unit, ML-3) and the maximum specific

growth rate of the bacterium, umax (unit, T-1).

 If IREACT = 100 (zeroth-order decay or production), RC1 is the

zeroth-order reaction rate coefficient for the dissolved (liquid)

phase (ML-3T-1) (positive for decay and negative for production).

If a dual-domain system is simulated, the rate coefficients for the

liquid phase in the mobile and immobile domains are assumed

equal.

(Enter 6 for each species if IREACT > 0)

6 Record: RC2(NCOL, NROW) (one array for each layer)

Format: RARRAY

 If IREACT = 1 (first-order kinetic reactions) RC2 is the first-order

reaction rate for the sorbed phase (unit, T-1). If a dual-domain system is

simulated, the reaction rates for the sorbed phase in the mobile and

immobile domains are assumed to be equal. Generally, if the reaction is

radioactive decay, RC2 should be set equal to RC1, while for

biodegradation, RC2 may be different from RC1. Note that RC2 is read

but not used, if no sorption is included in the simulation.

 If IREACT=100 (zeroth-order decay or production), RC2 is the

zeroth-order reaction rate coefficient for the sorbed (solid) phase

(MM-1T-1) (positive for decay and negative for production). If a

dual-domain system is simulated, the rate coefficients for the liquid

phase in the mobile and immobile domains are assumed equal.

(Enter 7 for each species if IREACT = 2)

7 Record: RC3(NCOL, NROW) (one array for each layer)

Format: RARRAY

 RC3 is the half-saturation constant s

K (unit, ML-3). Note that RC3 is

read and used only if IREACT = 2 option to simulate MONOD kinetics

is invoked.

(Enter 8 if IREACT = 3, one line for each of the NCOMP – 1 species)

8 Record: YLD(NCOMP-1)

Format: F10.0

 YLD is the yield coefficient between species. The first value in the array

is for the reaction between species 1 and species 2; the second value for

the reaction between species 2 and 3; and so on. Note that YLD is read

and used only if IREACT = 3 option to simulate first-order chain

reaction is invoked. This option is only available when more than one

species are simulated.

(Enter 9a if IREACTION=1)

9a Record: IED, IEA, F

Format: 2I10, F10.0

 IED is the species number representing the electron donor participating

in the EA/ED reaction.

 IEA is the species number representing the electron acceptor

participating in the EA/ED reaction.

 F is the stoiciometric ratio in the simulated equation

ED + F*EA  Product

(Enter 9b if IREACTION=2)

9b Record: rec_FileName

Format: A500

 rec_FileName is the name of the input file that provides parameter

information relevant to the kinetic reaction module.

rec_FileName

Parameters required for simulating a kinetic reaction are input in a separate file. Below are the

input instructions for that file.

0 Record: [#text]

Format: Free

 This item is optional and can include as many lines as desired, as long as

the first character on each line is #. This line is provided for the user to

include comments.

1 Record: NED, NEA, NSPECIAL, IFESLD

Format: Free

 NED is the number of electron donors.

 NEA is the number of electron acceptors.

 NSPECIAL is the number of special cases.

 IFESLD is an integer flag to simulate solid phase Fe3+.

If IFESLD=0, solid phase Fe3+ is not simulated.

If IFESLD=1, solid phase Fe3+ is simulated.

(Enter 2 NSPECIAL times if NSPECIAL > 0)

2 Record: ISPEC, SPECIAL(ISPEC), EFCMAX

Format: Free

 ISPEC is the sequential order of the species that is treated as a special

case.

 SPECIAL(ISPEC) is the keyword for species number ISPEC. Three

possible keywords are as follows:

SOLID – The solid phase concentration is used; it is for the iron

reduction process. For this case, Fe3+ solid phase will be tracked.

MAXEC – The method of Lu et al. (1999) to deal with the iron

reduction and methanogenesis simulation is used.

STORE – This keyword is for the methanogenesis simulation

only. If the methane concentration is over the maximum express

field capacity (EFC), the additional mass of methane will be

stored, and the result will be output as an unformatted file with a

name of “MT3D_Ad_methane.UCN”. This option uses the

formula developed by Neville and Vlassopoulos (2008).

 EFCMAX is the maximum express field capacity (EFC). If keyword

SOLID is used, then this variable is read but not used.

(Enter 3 NEA times)

3 Record: HSC, IC

Format: Free

 HSC is the half saturation constant.

 IC is the inhibition constants.

(Enter 4 NEA times)

4 Record: DECAYRATE(1:NED)

Format: Free

 DECAYRATE is the decay rate of each electron acceptor corresponding

to each electron donor.

(Enter 5 NEA+NED times)

4 Record: YIELDC(1:NED)

Format: Free

 YIELDC is the yield coefficient of each component corresponding to

each electron donor.

New input requirements

Below is a discussion on input requirements for the revised MT3D-USGS program for

the new reaction package. This section describes in general terms, the input variables

required to complete a simulation that considers multiple electron donors and electron

acceptors, and production of a lower-order ED from the decay of a higher-order ED. The

discussion uses a hypothetical system comprising three EDs and five EAs such that nED

= 3, nEA = 5, and nED + nEA = 8. In this hypothetical, the three EAs are (1) benzene,

(2) MTBE, and (3) TBA. The simulated relationships are as follows: (1) degradation of

benzene, without formation of a product; (2) degradation of MTBE with formation of

TBA [yield coefficient = 1]; and, (3) degradation of TBA, without formation of a

product. This simulation requires that the following inputs be provided:

1. First order decay rates for each ED corresponding to each TEAP

2. Yield coefficients corresponding to:

a. The consumption of each EA due to the degradation of each ED

b. The production of a lower-order ED from the degradation of a higher-

order ED

3. Inhibition constants

4. Half-saturation constants

The inputs for such a simulation are provided as tables, or matrices, in the following

order: decay rates, yield coefficients, inhibition constants, and half-saturation constants.

If it is assumed that the half saturation constant expresses the concentration minimum at

which any activity can occur for that species – i.e., that a single-valued half-saturation

constant applies to each combination of ED and EA - the half-saturation constants can be

provided as a vector with dimensions nED+nEA. Figure 8 is an example matrix of nED

rows and nEA columns that identifies required inputs for the remaining reaction

parameters, and Figure 9 is an example matrix with nED + nEA rows by nED + nEA

columns that the user must fill in when simulating multiple EA and ED reactions.

Finally, Figure 10 shows a non-square, non-symetric matrix with nED rows and nED +

nEA colums that the user must specify when simulating multiple ED and EA reactions.

Table 2 – A matrix of maximum first order decay rates are required input for simulating

multiple EA and ED reactions, an example of which is shown here. Figure 9, below, also

shows input requirements for this type of simulation.

O2 NO

3 FE2 SO

4 CH

BTEX Y Y Y Y Y

MTBE Y Y Y Y Y

TBA Y Y Y Y Y

Table 3 – A matrix of yield coefficients is required for simulating multiple EA and ED

reactions. Although in the general case the matrix could possess nED+nEA rows, on

most occasions the matrix will actually possess nED rows. The entry in the corresponding

cell indicates whether a value needs to be provided. If a value must be provided, it is the

rate of the column species production/consumption due to degradation of 1 unit of the

row species. The entries “+”, “-”, and “N” represent production, consumption, and no

relationship, respectively.

BTEX MTBE TBA O2 NO

3 FE2 SO

4 CH

BTEX N N N - - + - +

MTBE N N + - - + - +

TBA N N N - - + - +

O2 N N N N N N N N

NO3 N N N N N N N N

FE2 N N N N N N N N

SO4 N N N N N N N N

CH3 N N N N N N N N

Table 4 – A matrix of required inhibition constants that must be specified when

simulating multiple EA and ED reactions. Although in the general case the matrix could

possess nED rows, on most occasions the matrix will actually possess only one row; that

is, each species in the reaction possesses a single inhibition constant.

BTEX MTBE TBA O2 NO

3 FE2 SO

4 CH

BTEX N N N + + + + +

MTBE + N N + + + + +

TBA + + N + + + + +

Mass depletion from the system is reported in the global mass balance summary in the

standard output file as a new term called “DECAY OR BIODEGRADATION”. Users

seeking to make use of this option are referred to the input instructions for its

implementation.

SFT Package

Input for the SFT package is read from a file listed in the name file with “SFT” as the file

type. The input file is needed only if streams simulated using the SFR2 package in

MODFLOW are activated and a solution to the surface water network transport problem

is desired. If streams simulated using the SFR2 package of MODFLOW are only used as

a boundary condition in MT3D-USGS, this package may not be used and the input for

boundary concentration may be entered in the SSM package. Due to the explicit coupling

of the transport solution of stream nodes and groundwater nodes, it is imperative that the

number of outer iterations (MXITER) for the groundwater transport solution be set

greater than 1.

For each simulation:

1 Record: NSFINIT, MXSFBC, ICBCSF, IOUTOBS, IETSFR

Format: Free

 NSFINIT is the number of simulated stream reaches (in SFR2, the

number of stream reaches is greater than or equal to the number of

stream segments). This is equal to NSTRM found on the first line of the

SFR2 input file. If NSFINIT > 0 then surface-water transport is solved

in the stream network while taking into account groundwater exchange

and precipitation and evaporation sources and sinks. Otherwise, if

NSFINIT < 0, the surface-water network as represented by the SFR2

flow package merely acts as a boundary condition to the groundwater

transport problem; transport in the surface-water network is not

simulated. 

 MXSFBC is the maximum number of stream boundary conditions.

 ICBCSF is an integer value that directs MT3D-USGS to write reach-by-

reach concentration information to unit ICBCSF. This flag is set to 0 and

is not used in the first release of MT3D-USGS (version 1.0).

 IOUTOBS is an integer value that is the unit number of the output file

for simulated concentrations at specified gage locations. The NAM file

must also list the unit number to which observation information will be

written. 

 IETSFR is an integer signifying whether or not mass will exit the

surface-water network with simulated evaporation. If IETSFR = 0, then

mass does not leave via stream evaporation. If IETSFR > 0, then mass is

allowed to exit the simulation with the simulated evaporation. 

2 Record: ISFSOLV, WIMP, WUPS, CCLOSESF, MXITERSF, CRNTSF,

IPRTXMD

Format: Free

 ISFSOLV is an integer value specifying the numerical technique that will

be used to solve the transport problem in the surface water network. The

first release of MT3D-USGS (version 1.0) only allows for a finite-

difference formulation and regardless of what value the user specifies,

the variable defaults to “1”, meaning the finite-difference solution is

invoked.

 WIMP is a real number that ranges between 0.0 and 1.0 and is the stream

solver time weighting factor. Values of 0.0, 0.5, or 1.0 correspond to

explicit, Crank-Nicolson, and fully implicit schemes, respectively.

 WUPS is a real number that ranges between 0.0 and 1.0 and is the space

weighting factor employed in the stream network solver. Values of 0.0

and 1.0 correspond to a central-in-space and upstream weighting factors,

respectively.

 CCLOSESF is a real number and is the closure criterion for the SFT

solver

 MXITERSF is an integer value limiting the maximum number of

iterations the SFT solver can use to find a solution of the stream transport

problem.

 CRNTSF is a real number and is the Courant constraint specific to the

SFT time step, its value has no bearing upon the groundwater transport

solution time step as it is not used in the first release of MT3D-USGS

(version 1.0).

 IPRTXMD is a flag to print SFT solution information to the standard

output file. IPRTXMD = 0 means no SFT solution information is printed;

IPRTXMD = 1 means SFT solution summary information is printed at

the end of every MT3D-USGS outer iteration; and IPRTXMD = 2 means

SFT solution details are written for each SFT outer iteration that calls the

xMD solver that solved SFT equations.

(Enter item 3 for each species)

3 Record: CINITSF(NRCH)

Format: RARRAY

 CINITSF is an array of real numbers representing the initial

concentrations in the surface water network. The length of the array is

equal to the number of stream reaches and starting concentration values

should be entered in the same order that individual reaches are entered

for record set 2 in the SFR2 input file.

(Enter item 4 for each species)

4 Record: DISPSF(NRCH)

Format: RARRAY

 DISPSF is the dispersion coefficient [L2 T-1] for each stream reach in the

simulation and can vary for each simulated component of the simulation.

That is, the length of the array is equal to the number of simulated stream

reaches times the number of simulated components. Values of

dispersion for each reach should be entered in the same order that

individual reaches are entered for record set 2 in the SFR2 input file.

The first NSTRM entries correspond to NCOMP = 1, with subsequent

entries for each NCOMP simulated species.

5 Record: NOBSSF

Format: I10

 Is an integer value specifying the number of surface flow observation

points for monitoring simulated concentrations in streams.

(Read item 6 for each NOBSSF observation location)

6 Record: ISFNOBS

Format Free

 ISFNOBS is the reach number for which to write simulated

concentrations to the file corresponding to the unit number IOUTOBS.

Reach numbers follow the same order that is specified in record set 2 in

the SFR2 input file.

For each stress period:

7 Record: NTMP

Format: I10

 NTMP is an integer value corresponding to the number of specified

stream boundary conditions to follow. For the first stress period, this

value must be greater than or equal to zero, but may be less than zero in

subsequent stress periods.

If NTMP >= 0, NTMP is the number of stream boundary conditions.

If NTMP = -1, stream boundary conditions from the previous stress

period are reused for the current stress period.

(Read item 8 for each NTMP boundary condition)

8 Record: ISFNBC, ISFBCTYP, (CBCSF(n), n=1, NCOMP)

Format: Free

 ISFNBC is an integer value that is the reach number for which the

current boundary condition will be applied.

 ISFBCTYP is an integer value that specifies, for ISFNBC, what the

boundary condition type is:

= 0, a headwater boundary. That is, for streams entering at the

boundary of the simulated domain that need a specified

concentration, use ISFBCTYP = 0;

= 1, a precipitation boundary. If precipitation directly to channels

is simulated in the flow model and a non-zero concentration

(default is zero) is desired, use ISFBCTYP = 1;

= 2, a runoff boundary condition associated with the SFR2 package

of MODFLOW. This is not the same thing as runoff simulated

in the UZF1 package and routed to a stream (or lake) using the

IRNBND array. Users who specify runoff in the SFR2 input

via the RUNOFF variable appearing in either record sets 4b or

6a and want to assign a non-zero concentration (default is

zero) associated with this specified source, use ISFBCTYP=2;

= 3, a constant-concentration boundary. Any reach number may be

set equal to a constant concentration boundary condition.

= 4,

 CBCSF is a real number and is the specified concentration associated

with the current boundary condition entry. Repeat CBCSF for each

simulated species (NCOMP).

SSM Package

Input to the Sink & Source Mixing package is read on unit INSSM=4, which is preset in

the main program. The input file is needed if any sink or source option is used in the

flow model, including the constant-head, general-head, river, drain, recharge,

evapotranspiration, well, multi-node well, stream, lake, and unsaturated zone packages.

For each simulation:

1 Record: FWEL, FDRN, FRCH, FEVT, FRIV, FGHB

Format: 10L2

 These logical flags are no longer needed as the status of various

flow sink/source packages is obtained by MT3D-USGS through

the Flow-Transport Link File produced by MODFLOW. However,

a dummy input line must still be specified in the input file. A blank

line is acceptable.

When MODFLOW-NWT is used to obtain flow solutions for MT3D-

USGS, the LMT package for MODFLOW will store appropriate values

for these flags in the formatted and unformatted flow-transport link file.

If these flags are not specified correctly here, MT3D-USGS will issue a

warning, reset the flags to correct values, and proceed with the

simulation.

2 Record: MXSS, ISSGOUT

Format: 2I10

 MXSS is the maximum number of all point sinks and sources included in

the flow model. Point sinks and sources include constant-head cells,

wells, drains, rivers, and general-head-dependent boundary cells.

Recharge and evapotranspiration are treated as areally distributed sinks

and sources; thus, they should not be counted as point sinks and sources.

MXSS should be set close to the actual number of total point sinks and

sources in the flow model to minimize the computer memory allocated to

store sinks and sources.

 ISSGOUT is the unit number for an optional output file to save the

calculated flux-averaged composite concentrations at multi-node

wells. The name of the output file must be specified through the

Name File as in “DATA ISSGOUT FileName”.

For each stress period:

(Enter item 3 and 4 if recharge (RCH) package is used in the flow simulation)

3 Record: INCRCH

Format: I10

 INCRCH is a flag indicating whether an array containing the

concentration of recharge flux for each species will be read for the

current stress period. If INCRCH ≥0, an array containing the

concentration of recharge flux for each species will be read. If INCRCH

< 0, the concentration of recharge flux will be reused from the last stress

period. If INCRCH < 0 is specified for the first stress period, then by

default, the concentration of positive recharge flux (source) is set equal

to zero and that of negative recharge flux (sink) is set equal to the aquifer

concentration.

(Enter item 4 for each species if INCRCH ≥0)

4 Record: CRCH(NCOL, NROW)

Format: RARRAY

 CRCH is the concentration of recharge flux for a particular species. If the

recharge flux is positive, it acts as a source whose concentration can be

specified as desired. If the recharge flux is negative, it acts as a sink

(discharge) whose concentration is always set equal to the concentration

of groundwater at the cell where discharge occurs. Note that the location

and flow rate of recharge/discharge are obtained from the flow model

directly through the unformatted flow-transport link file.

(Enter item 5 and 6 if evapotranspiration (EVT) or segmented evapotranspiration (ETS)

package is used in the flow simulation)

5 Record: INCEVT

Format: I10

 INCEVT is a flag indicating whether an array containing the

concentration of evapotranspiration flux for each species will be read for

the current stress period.

If INCEVT ≥0, an array containing the concentration of

evapotranspiration flux for each species will be read. If INCEVT < 0,

the concentration of evapotranspiration flux for each species will be

reused from the last stress period. If INCEVT < 0 is specified for the first

stress period, then by default, the concentration of negative

evapotranspiration flux (sink) is set to the aquifer concentration, while

the concentration of positive evapotranspiration flux (source) is set to

zero.

(Enter item 6 for each species if INCEVT ≥ 0)

6 Record: CEVT(NCOL,NROW)

Format: RARRAY

 CEVT is the concentration of evapotranspiration flux for a particular

species. Evapotranspiration is the only type of sink whose concentration

may be specified externally. Note that the concentration of a sink cannot

be greater than that of the aquifer at the sink cell. Thus, if the sink

concentration is specified greater than that of the aquifer, it is

automatically set equal to the concentration of the aquifer. Also note that

the location and flow rate of evapotranspiration are obtained from the

flow model directly through the unformatted flow-transport link file.

(Enter items 7-10 if unsaturated zone (UZF) package is used in the flow simulation)

7 Record: INCUZF

Format: I10

 INCUZF is a flag indicating whether an array containing the

concentration of infiltration flux–applied directly as recharge by virtue of

negative values for IUZFBND–for each species will be read for the

current stress period. If INCUZF ≥0, an array containing the

concentration of infiltration flux for each species will be read. If

INCUZF < 0, the concentration of infiltration flux will be reused from

the previous stress period.

(Enter item 8 for each species if INCUZF ≥0)

8 Record: CUZRCH (NCOL,NROW)

Format: RARRAY

 CUZRCH is the concentration of infiltration flux for a particular species.

Note that the location and flow rate are obtained from the flow model

through the flow-transport link file.

9 Record: INCGWET

Format: I10

 INCGWET is a flag indicating whether an array containing the

concentration of evapotranspiration flux originating from the saturated

zone will be read for the current stress period

If INCGWET≥0, an array containing the concentration of seepage flux

for each species will be read. If INCGWET≥0, the concentration of

seepage flux for each species will be reused from the last stress period. If

INCGWET< 0, the concentration of infiltration flux will be reused from

the last stress period.

(Enter item 10 for each species if INCGWET ≥ 0)

10 Record: CGWET (NCOL, NROW)

Format: RARRAY

CGWET is the concentration of seepage flux for a particular species.

Note that the concentration of a sink cannot be greater than that of the

aquifer at the sink cell. Thus, if the sink concentration is specified greater

than that of the aquifer, it is automatically set equal to the concentration

of the aquifer. Also note that the location and flow rate of seepage are

obtained from the flow model directly through the unformatted flow-

transport link file.

11 Record: NSS

Format: I10

 NSS is the number of point sources whose concentrations need to be

specified. By default, unspecified point sources are assumed to have zero

concentration. (The concentration of point sinks is always set equal to the

concentration of groundwater at the sink location.)

Note that in MT3DMS, point sources are generalized to include not only

those associated with a flow rate in the flow model, but also those

independent of the flow solution. This type of “mass-loading” sources

may be used to include contaminant sources which have minimal effects

on the hydraulics of the flow field.

(Enter item 12 NSS times if NSS > 0)

12 Record: KSS, ISS, JSS, CSS, ITYPE, (CSSMS(n), n=1, NCOMP)

Format: 3I10, F10.0, I10, [free]

 KSS, ISS, JSS are the cell indices (layer, row, column) of the point

source for which a concentration needs to be specified for each species.

Special cases for KSS, ISS, and JSS are as follows:

 KSS must be set to 0, to implement a constant concentration

boundary (ITYPE = -1) to be applied on the same layer that the

recharge is applied.

 To specify lake concentration (ITYPE = 26), KSS and ISS must

be set to zero, and JSS must be set equal to the lake number for

which the concentration is specified. Groundwater cells gaining

mass from the lake JSS are internally identified based on

information provided via the flow link file, and the same lake

concentration is used for all gaining groundwater cells connected

to the lake specified using JSS.

 CSS is the specified source concentration or mass-loading rate,

depending on the value of ITYPE, in a single-species simulation. For a

multispecies simulation, CSS is not used, but a dummy value still needs

to be entered here.

Note that for most types of sources, CSS is interpreted as the source

concentration with the unit of mass per unit volume (ML-3), which, when

multiplied by its corresponding flow rate (L3T-1) from the flow model,

yields the mass-loading rate (MT-1) of the source.

For a special type of sources (ITYPE = 15), CSS is taken directly as the

mass-loading rate (MT-1) of the source so that no flow rate is required

from the flow model.

Furthermore, if the source is specified as a constant concentration cell

(ITYPE = -1), the specified value of CSS is assigned directly as the

concentration of the designated cell. If the designated cell is also

associated with a sink/source term in the flow model, the flow rate is not

used.

 ITYPE is an integer indicating the type of the point source as listed

below:

ITYPE = 1, constant-head cell;

= 2, well;

= 3, drain (note that in MODFLOW conventions, a drain is

always a sink, thus, the concentration for drains cannot be

specified if the flow solution is from MODFLOW);

= 4, river;

= 5, general-head-dependent boundary cell;

= 15, mass-loading source;

= -1, constant-concentration cell;

= 21, stream-flow routing (STR);

= 22, reservoir;

= 23, specified flow and head boundary;

= 26, lake;

= 27, multi-node well;

= 28, drain with return flow;

= 30, stream-flow routing (SFR).

For informational purposes, other reserved ITYPE unit numbers

include 7, 8, 29, and 31 for recharge, evapotranspiration,

evapotranspiration with segments, and unsaturated-zone flow,

respectively. Only the numbers listed above may be entered.

Specify the input concentration of an injection well (ISSTYPE=2),

i.e., CSS or CSSMS, as a negative integer code (IC). The absolute

value of the integer code is the single cell location indicator of the

extraction well whose output concentration is used as the input

concentration for the injection well. For an extraction well located

at layer K, row I, and column J, IC is computed as,

 

JINCOLKNROWNCOLIC  11

where NCOL and NROW are the total numbers of columns and

rows.

 (CSSMS(n), n=1, NCOMP) defines the concentrations of a point source

for multispecies simulation with NCOMP > 1. In a multispecies

simulation, it is necessary to define the concentrations of all species

associated with a point source. As an example, if a chemical of a certain

species is injected into a multispecies system, the concentration of that

species is assigned a value greater than zero while the concentrations of

all other species are assigned zero. CSSMS(n) can be entered in free

format, separated by a comma or space between values. Several

important notes on assigning concentration for the constant-

concentration condition (ITYPE = -1) are listed below:

The constant-concentration condition defined in this input file takes

precedence to that defined in the Basic Transport Package input file.

In a multiple stress period simulation, a constant-concentration cell, once

defined, will remain a constant-concentration cell in the duration of the

simulation, but its concentration value can be specified to vary in

different stress periods.

In a multispecies simulation, if it is only necessary to define different

constant-concentration conditions for selected species at the same cell

location, specify the desired concentrations for those species, and assign

a negative value for all other species. The negative value is a flag used

by MT3DMS/MT3D-USGS to skip assigning the constant-concentration

condition for the designated species.

TOB Package

Input for the TOB Package is read from a file listed in the Name File with the

keyword “TOB” as the file type. The input data are arranged and read sequentially in

free format.

For each simulation:

0 Record: Comment

Format: A80

 HEADNG(1) is the first line of any title or heading for the simulation

run. This line can be repeated as many time as desired. The first

character on the line (position 0) must be ‘#’.

1 Record: MaxConcObs, MaxFluxObs, MaxFluxCells

Format: Free

 MaxConcObs is the maximum number of concentration observations

allowed in the current simulation. This value is used for memory

allocation purposes.

 MaxFluxObs is the maximum number of mass-flux observations. It

should be set large enough to accommodate all mass-flux observations at

different mass-flux objects and observation times. This value is used for

memory allocation purposes.

 MaxFluxCells is the maximum number of model cells that makes up a

mass-flux object. This value is used for memory allocation purposes.

2 Record: OUTNAM, inConcObs, inFluxObs, inSaveObs

Format: Free

 OUTNAM is a string of one to 78 nonblank characters. OUTNAM

specifies the base (root) name for three optional output files. The

complete file names are composed of this base name followed by a

period and a three-character extension listed below. The specification of

lower and upper cases in OUTNAM is preserved in generating the file-

name base. OUTNAM can include a path; constraints imposed by a

particular computer operating system regarding file names and paths

should be considered when specifying OUTNAM.

 inConcObs is an integer flag indicating whether the calculated

concentrations at the observation locations should be obtained and saved

to the output file [OUTNAM].OCN. It also serves as the unit number for

the output file [OUTNAM].OCN.

 inFluxObs is an integer flag indicating whether the calculated mass

fluxes at the massflux objects should be obtained and saved to the output

file [OUTNAME].MFX. It also serves as the unit number for the output

file [OUTNAM].MFX.

 inSaveObs is an integer flag indicating whether the calculated

concentrations and mass fluxes at the user-defined observation points

and mass-flux objects should be saved to an unformatted (binary) output

file [OUTNAM].PST. It also serves as the unit number for the output file

[OUTNAM].PST.

Output File Content

[OUTNAM].OCN

Output file containing calculated

concentrations, and optionally, residuals

between the calculated and observed

values, at user-defined observation points

that are screened either in a single layer or

across multiple layers. This text file is

generated only if the flag [inConcObs]

is greater than zero.

[OUTNAM].MFX

Output file containing calculated mass

fluxes into or out of user-defined mass flux

objects, and optionally, residuals between

the calculated and observed values. Each

mass flux object is defined by a group of

model cells containing external

sinks/sources such as wells, rivers, drains,

recharge, and general-head boundaries.

This text file is generated only if the flag

[inFluxObs] is greater than zero.

[OUTNAM].PST

Output file containing calculated

concentrations and mass fluxes at userdefined

observation points and mass-flux

objects. This output file, in binary form, is

intended for post-processing purposes or

for linkage with other modeling programs.

This file is generated only if the flag

[inSaveObs] is greater than zero.

(Enter item 3-5 if inConcObs > 0)

3 Record: nConcObs, CScale, iOutCobs, iConcLOG, iConcINTP

Format: Free

 nConcObs is the number of concentration observations. Observations

made at the same location but different times are considered multiple

observations.

 CScale is the multiplier (scaling factor) for the observed concentrations.

It is used to convert the unit of observed concentrations to the unit of

calculated concentrations used internally in MT3DMS for computing

appropriate residuals.

 iOutCobs is an integer flag indicating what type of output should be

computed and saved.

iOutCobs = 0, calculated concentrations at the observation locations are

saved to the output file [OUTNAM].OCN

iOutCobs > 0, both calculated concentrations and residual errors

between the calculated and observed values are saved to the output

file[OUTNAM].OCN. The statistics of the residual errors is also

computed and saved.

 iConcLOG is an integer flag indicating whether the calculated and

observed concentrations should be converted to the common logarithm

before computing the residual error and related statistics:

iConcLOG = 0, no conversion is done (residual error = calculated –

observed);

iConcLOG > 0, convert the calculated and observed concentration values

to the common logarithmic scale before computing the residual error and

related statistics (residual error = log10Calculated ??log10Observed)..

 iConcINTP is an integer flag indicating whether the calculated

concentration at an observation location should be interpolated from its

neighboring nodal points, if observation location does not coincide with

a nodal point:

iConcINTP = 0, no interpolation is done (the calculated concentration

value at the nearest nodal point is used for comparison with the observed

value);

iConcINTP > 0, perform bilinear interpolation using four neighboring

nodal concentrations in the same model layer.

(Enter item 4-5 inConcObs times)

4 Record: COBSNAM, Layer, Row, Column, iComp, TimeObs, Roff, Coff,

weight, COBS

Format: Free

 COBSNAM is a string of 1 to 12 nonblank characters used to identify the

observation. The identifier need not be unique; however, identification of

observations in the output files is facilitated if each observation is given a

unique COBSNAM.

 Layer is the layer index of the cell in which the concentration

observation is located. If LAYER is less than zero, solute concentrations

from multiple layers are combined to calculate a simulated value. The

number of layers equals the absolute value of LAYER, or |LAYER|.

 Row is the row index of the cell in which the concentration observation

is located.

 Column is the column index of the cell in which the concentration

observation is located.

 iComp is an integer indicating the solute species for which the

concentration observation is made. Integer 1 indicates the first species, 2

the second species, and so on.

 TimeObs is the time since the beginning of simulation to the time of the

current observation. [TimeObs] should be included in the BTN input file

as part of the input array [TIMPRS], i.e., the time to save simulation

results. Otherwise, the calculated concentration is obtained from a time

specified in [TIMPRS] or the end of a stress period that is closest to

[TimeObs]. Note that if [TimeObs] is specified as a negative integer, the

calculated concentration is saved whenever the number of transport steps

is an even multiple of |TimeObs|.

 Roff is the row offset used to locate the observation within a finite-

difference cell. The convention is the same as that used by MODFLOW

(see Figure 1)

 Coff is the column offset used to locate the observation within a finite-

difference cell. The convention is the same as that used by MODFLOW

(see Figure 1)

 Weight is the user-specified weighting factor for computing the residual

error at the current observation, i.e., residual error = (calculated-

observed)*weight. If [weight] is assigned a negative value, the observed

concentration at the target observation point is not used and only the

calculated concentration is saved.

 COBS is the concentration observation for the species defined by

[iComp]. This input item is required regardless of whether the preceding

input item [weight] has been given a positive or negative value.

(Enter item 5 if Layer < 0)

5 Record: mLayer(1), prLayer(1), mLayer(2), prLayer(2), …, mLayer(|Layer|),

prLayer(|Layer|)

Format: Free

 mLayer(i)

is the ith layer number for a multilayer concentration

observation.

 prLayer(i)

is the proportion of the simulated solute concentration in layer

mLayer(i) that is used to calculate a simulated multilayer concentration.

The sum of all prLayer(i) values for a given observation needs to equal

Figure 1. Locating points within a finite-difference cell using ROFF and COFF (after Hill et al., 2000)

1.0. The convention is the same as that used by MODFLOW (see Hill et

al., 2000, p. 35). Note that if the concentration observation is made at a

multi-node well (MNW), the flux-averaged composite concentration for

the MNW wellbore can be computed and saved through the SSM

Package for MT3DMS v5 or later, or MT3D-USGS.

(Enter item 6-9 if inFluxObs > 0)

6 Record: nFluxGroup, FScale, iOutFlux

Format: Free

 nFluxGroup is the total number of mass flux objects. A mass flux object

is defined as a group of model cells needed to represent one mass flux

measurement.

 FScale is the multiplier (scaling factor) for the observed mass flux.

It is used to convert the unit of observed mass flux to the unit of

calculated mass flux observation used internally in MT3DMS for

computing appropriate residuals.

 iOutFlux is an integer flag indicating what type of output should be

computed and saved:

iOutFlux = 0, calculated mass fluxes are saved to the output file

[OUTNAM].MFX;

iOutFlux > 0, both calculated mass fluxes and residual errors between the

calculated and observed values are saved to the output file

[OUTNAM].MFX. The statistics of the residual errors is also computed

and saved.

(Enter item 7-9 nFluxGroup times)

7 Record: nFluxTimeObs, nCells, iSSType

Format: Free

 nFluxTimeObs is the number of times at which mass fluxes are observed

for the current mass-flux object.

 nCells is the total number of cells in the current mass-flux object.

 iSSType is an integer code indicating the type of sinks/sources

constituting the current mass flux object. The [iSSType] codes used here

are the same as those defined for the MT3DMS SSM Package:

issType Code Type of Sink/Source

1 Constant head

2 Well

3 Drain

4 River

5 Head-dependent boundary

6 (Reserved)

7 Recharge

8 Evapotranspiration

9-14 (Reserved)

15 Mass loading

21 Stream-routing

22 Reservoir

23 Specified flow and head boundary

24 Inter-bed storage

25 Transient leakage

26 Lake

27 Multi-node well

28 Drain with return flow

29 Segmented evapotranspiration

30-49 (Reserved)

50 HSS Mass Loading

51 (Reserved)

52 (Reserved)

53 (Reserved)

(Enter item 8 nFluxTimeObs times)

8 Record: FOBSNAM, iComp, FluxTimeObs, weight_fobs, FluxObs

Format: Free

 FOBSNAM is a string of 1 to 12 nonblank characters used to identify the

mass flux observation. The convention is the same as that for

COBSNAM. The first part of FOBSNAM can be used to identify a

common group name, while the rest to distinguish different observations

for the same group.

 FluxTimeObs is the time since the beginning of simulation to the

time of the current mass flux observation. [FluxTimeObs] should

be included in the BTN input file as part of the input array

[TIMPRS], i.e., the time to save simulation results. Otherwise, the

calculated mass flux is obtained from a time specified in

[TIMPRS] or the end of a stress period that is closest to

[FluxTimeObs]. Note that if [FluxTimeObs] is specified as a

negative integer, the calculated mass flux is saved whenever the

number of transport steps is an even multiple of |FluxTimeObs|.

 weight_fobs is the user-specified weighting factor for computing the

residual error at the current mass-flux object, i.e., residual error =

(calculated-observed)*weight. If [weight_fobs] is assigned a negative

value, the observed mass flux at the target massflux object is not used

and only the calculated mass flux is saved.

 FluxObs is the observed solute mass flux, QC [dimension, MT-1], for the

user-specified species [iComp]. The mass flux observation is negative

when the mass is leaving the groundwater system, and positive when the

mass is entering the groundwater system. This input item is required

regardless of whether the preceding input item [weight_fobs] has been

given a positive or negative value.

(Enter item 9 nCells times for current mass flux object)

9 Record: kcell, icell, jcell, factor

Format: Free

 kcell is the layer index of a sink/source cell included in the current mass

flux object.

 icell is the row index of a sink/source cell included in the current mass

flux object.

 jcell is the column index of a sink/source cell included in the current

mass flux object.

 Factor is the weighting factor for the mass flux calculated at the specified

cell location (jcell, icell, kcell). [factor] = 1.0 under most circumstances,

i.e., the specified cell belongs to a single mass-flux object. However, the

mass flux calculated at one specific cell can be assigned to one or more

mass-flux objects that cover portions of the cell. In that case, [factor] can

be less than 1.0. Regardless, the sum of [factor] values at a single cell for

multiple mass-flux objects should add up to 1.0.

OUTPUT INFORMATION

As pointed out previously, three optional output files may be created depending

on how the output options are specified in the input file to the TOB Package. These files

are:

1) a text file with the 3-letter extension “.OCN” which contains the calculated

concentrations, and if requested, the residuals between the calculated and 17

observed values, at the user-specified observation locations. This text file is

generated only if the concentration observation flag [inConcObs] is specified in the

TOB input file as greater than zero.

2) a text file with the 3-letter extension “.MFX” which contains the calculated mass

fluxes into or out of user-defined mass flux objects, and if requested, the residuals

between the calculated and observed values. Each mass flux object is defined by a

group of model cells containing external sinks/sources such as wells, rivers, drains,

recharge, and general-head boundaries. This text file is generated only if the mass

flux observation flag [inFluxObs] is specified in the TOB input file as greater than

zero.

3) an unformatted (binary) file with the 3-letter extension “.PST” which contains the

calculated concentrations and/or mass fluxes at user-defined observation points.

The records in the PST binary output file are in the form of [cobsnam, TimeObs, CCal]

for concentration observations where cobsnam is the name of the concentration

observation as a string of 12 characters , and TimeObs and CCal are real numbers

indicating the observation time and the calculated concentration value.

The records in the PST binary output file are in the form of [fobsnam, TimeFluxObs,

FluxCal] for mass-flux observations where fobsnam is the name of the mass-flux

observation as a string of 12 characters , and TimeFluxObs and FluxCal are real numbers

indicating the observation time and the calculated mass flux.

This output file is intended for post-processing purposes or for linkage with other

modeling programs. The file is generated only if the output flag [inSaveObs] is specified

in the TOB input file as greater than zero.

UZT Package

Input for the UZT package is read from a file listed in the name file with “UZT” as the

file type. The input data are read in free format. Input instructions are given below

For each simulation:

1 Record: HEADNG(1)

Format: A80

 HEADNG(1) is the first line of any title or heading for the simulation

run. This line can be repeated as many time as desired. The first

character on the line (position 0) must be ‘#’.

2 Record: ICBCUZ, IET

Format: Free

 ICBCUZ is the unit number to which unsaturated-zone concentration

will be written out.

 IET is a flag that indicates whether or not ET is being simulated in the

UZF1 flow package. If ET is not being simulated, IET informs the FMI

package not to look for UZET and GWET arrays in the flow-transport

link file.

IET = 0, ET is not simulated by UZF1 (IETFLG = 0)

IET > 0, ET is simulated by UZF1 (IETFLG ≠ 0)

3 Record: IUZFBND(NROW,NCOL)

Format: IARRAY

 IUZFBND is an array of integer values specifying which row/column

indicies variably-saturated transport will be simulated in.

IUZFBND > 0 indicates that variably-saturated transport will be

simulated.

IUZFBND = 0 means variably-saturated transport will not be simulated.

IUZFND < 0 corresponds to IUZFBND < 0 in the UZF1 input package,

meaning that user-supplied values for FINF are specified recharge.

4 Record: WC(NROW,NCOL) (one array for each layer)

Format: RARRAY

 WC is an array of starting water contents. For cells above the water

table, this value can range between residual and saturated water contents.

In cells below the water table, this value will be equal to saturated water

content (i.e., effective porosity).

5 Record: SDH(NROW,NCOL) (one array for each layer)

Format: RARRAY

 SDH is the starting saturated thickness for each cell in the simulation.

SDH = 0 in cells residing above the starting water table, is equal to the

cell thickness for cells where the water table is above the top elevation of

the cell. For cells in which the water table resides, SDH is equal to the

water table elevation minus the bottom elevation of the cell.

For each stress period:

6 Record: INCUZINF

Format: I10

 INCUZINF is a flag indicating whether an array containing the

concentration of infiltrating (FINF) flux for each species will be read for

the current stress period. If INCUZINF ≥ 0, an array containing the

concentration of infiltrating flux for each species will be read. If

INCUZINF < 0, the concentration of infiltrating flux will be reused from

the previous stress period. If INCUZINF < 0 is specified for the first

stress period, then by default the concentration of positive infiltrating

flux (source) is set equal to zero. There is no possibility of a negative

infiltration flux being specified. If infiltrating water is rejected due to an

infiltration rate exceeding the vertical hydraulic conductivity, or because

saturation is reached in the unsaturated zone and the water table is

therefore at land surface, the concentration of the runoff will be equal to

CUZINF specified next. The runoff is routed if IRNBND is specified in

the MODFLOW simulation.

(Enter item 7 for each species if INCUZINF ≥ 0)

7 Record: CUZINF

Format: RARRAY

 CUZINF is the concentration of the infiltrating flux for a particular

species.

8 Record: INCUZET

Format: I10

 INCUZET is a flag indicating whether an array containing the

concentration of evapotranspiration flux originating from the unsaturated

zone will be read for the current stress period.

If INCUZET ≥0, an array containing the concentration of

evapotranspiration flux originating from the unsaturated zone for each

species will be read. If INCUZET < 0, the concentration of

evapotranspiration flux for each species will be reused from the last

stress period. If INCUZET < 0 is specified for the first stress period,

then by default, the concentration of negative evapotranspiration flux

(sink) is set to the aquifer concentration, while the concentration of

positive evapotranspiration flux (source) is set to zero.

(Enter item 9 for each species if INCUZET ≥ 0)

9 Record: CUZET

Format: RARRAY

 CUZET is the concentration of ET fluxes originating from the

unsaturated zone. As a default, this array is set equal to 0 and only

overridden if the user specifies INCUZET > 1. If empirical evidence

suggest volatilization of simulated constituents from the unsaturated

zone, this may be one mechanism for simulating this process, though it

would depend on the amount of simulated ET originating from the

unsaturated zone.

10 Record: INCGWET

Format: I10

 INCGWET is a flag indicating whether an array containing the

concentration of evapotranspiration flux originating from the saturated

zone will be read for the current stress period.

If INCGWET ≥0, an array containing the concentration of

evapotranspiration flux originating from the saturated zone for each

species will be read. If INCGWET < 0, the concentration of

evapotranspiration flux for each species will be reused from the last

stress period. If INCUZET < 0 is specified for the first stress period,

then by default, the concentration of negative evapotranspiration flux

(sink) is set to the aquifer concentration, while the concentration of

positive evapotranspiration flux (source) is set to zero.

(Enter item 11 for each species if INCGWET ≥ 0)

11 Record: CGWET

Format: RARRAY

 CGWET is the concentration of ET fluxes originating from the saturated

zone. As a default, this array is set equal to 0 and only overridden if the

user specifies INCUZET > 1.

Output

For a detailed description of output files and output generated by MT3DMS, please refer

to the original MT3DMS manuals (Zheng and Wang, 1999; Zheng, 2010). Additional

output generated by MT3D-USGS is described below.

New options added in MT3D-USGS are echoed to the standard output files with a brief

description.

Output Files

A number of output files are generated based on various options introduced in MT3D-

USGS. The output files, their formats, and the options that produce the output files are as

follows.

CTO file

The CTO file contains a well-by-well printout of the mass balance related to the CTS

package. CTO file is a formatted ASCII output file optionally generated by modified

MT3DMS. This file is generated if the flag ICTSOUT is set to a unit number when the

CTS package is used. ICTSOUT can be set to zero if the CTO file is not desired. See the

input instruction of CTS package for more details. CTO is the extension provided to the

output file using the same filename that is specified for the CTS input file by replacing

the file extension.

The output to this file is printed in the following format.

 Stress period, flow time step, transport time step, time step size, contaminant

treatment system (CTS) index, well index number, layer, row, column, species, flow

rate, concentration, and mass.

 3I10,1X,G14.7,6I10,3(1X,G14.7)

Budget Terms

CTS Mass Balance

If the contaminant treatment system (CTS) package is implemented in a simulation, a

separate overall mass balance that is specific to the treatment systems is reported in the

standard output file. The treatment system specific mass balance reports separate terms

for mass extracted from the groundwater system via extraction wells that enters the

treatment systems, mass entering the treatment systems from external sources, mass

addition or removal as a result of specified treatment options, mass leaving the treatment

systems that is injected back into the groundwater system, and mass leaving the treatment

systems to external sinks. Mass entering and leaving a treatment system also appears in

the global mass budget summary of the standard output file.

SFT Mass Balance

If the stream-flow transport (SFT) package is implemented in a simulation, a separate

overall mass balance that is specific to the stream reaches is reported in the standard

output file. Mass entering and leaving the stream nodes also appears in the global mass

budget summary of the standard output file.

LKT Mass Balance

If the lake transport (LKT) package is implemented in a simulation, a separate overall

mass balance that is specific to the lakes is reported in the standard output file. Mass

entering and leaving the lakes also appears in the global mass budget summary of the

standard output file.

Mass Balance Summary

In the modified version of MT3DMS, a few new terms were introduced to the global

mass balance summary written to the standard output file. Following are the new terms

that were added:

 If the contaminant treatment system (CTS) package is implemented in a

simulation, a separate term is reported as ‘TREATMENT SYSTEM’ in the

standard output file. The treatment system IN and OUT terms in the overall mass

balance account for mass entering via injection wells and mass leaving via

extraction wells that are associated with treatment systems respectively.

 Storage change due to flow solution was calculated but not reported in the

original MT3DMS. This term however, was added to the total IN and total OUT

reported in the standard output file. The term is reported as ‘MASS STOR

(FLOW MODEL): ’ in the mass balance summary.

 If keyword OMITDRYCELLBUDGET is not invoked in the BTN file, then mass

flowing through dry cells is included and reported to the standard output file mass

balance summary. The term is reported as ‘INACTIVE CELLS(ICBND=0):’.

 If instantaneous EA/ED reaction is invoked, then the mass lost from the system as

a result of the reaction is reported as ‘EA-ED REACTION:’ in the mass balance

summary of the standard output file.

 If kinetic reaction is invoked, then the mass budget for the reaction terms is

reported as ‘DECAY OR BIODEGRADATION’ in the mass balance summary of

the standard output file.

 If UZF is used then mass associated with infiltration or discharge is reported as

‘INFILTRATION/DISCHARGE’ and mass associated with evapotranspiration

from UZF is reported as ‘UZ AND GW ET’.

 SFR influx and out-flux terms are reported as ‘STREAM’ in the mass balance

summary of the standard output file.

 LAK influx and out-flux terms are reported as ‘LAKE’ in the mass balance

summary of the standard output file.

Input_Instructionsx Input Instructions

Input_Instructions

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