## TREX Watershed Modeling Framework User’s Manual: Model Theory and Description

Prepared by:
HDR-HydroQual, Inc. 1200 MacArthur Boulevard Mahwah, NJ 07430

In Cooperation With
Colorado State University Department of Civil and Environmental Engineering

Fort Collins, CO 80523-1372

Bureau of Reclamation Flood Hydrology and Meteorology Group, 86-68250, TS C

Denver, CO 80225

First Issued: August 2005
Last Revised: January 2011TREX User’s Manual Page ii

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation



### AUTHORSHIP AND ACKNOWLEDGEMENTS
This document is the user’s manual for the TREX wat ershed model developed at Colorado State University (CSU). TREX is a generali zed watershed rainfall-runoff, sediment transport, and contaminant transport model ing framework. This framework is derived from earlier versions of the CASC2D watersh ed model as developed at CSU (Julien et al. 1995; Johnson et al. 2000; Julien an d Rojas, 2002) with chemical transport and fate processes from the USEPA WASP and IPX seri es of stream water quality models (Ambrose et al. 1993; Velleux et al. 1996; V elleux et al. 2001). The major developers of this code and authors of th is manual are Mark Velleux (CSU) (and now HDR-HydroQual, Inc.), John England (Bureau of Reclamation), and Dr. Pierre Julien (CSU). The contributions of Dr. Rosalia Roja s (CSU) toward TREX code development and for CASC2D-SED source code are grat efully acknowledged. Aditya Maroo (CSU) assisted with programming. Dr. Billy E. Johnson (USACE-ERDC-EL) and Dr. Zhonglong Zhang (SpecPro, Inc.) provided commen ts and technical suggestions for extended framework development. Concepts for develo pment of the simulation relaunch option were contributed by Dr. Veeradej Chynwat (EN SCO, Inc) and Troy Seiler (ENSCO, Inc). James Hallden and Dr. Masa Takamatsu (HydroQual, Inc.) also provided programming support for TREX development. The TREX user’s manual was first developed for the U.S. Army Corps of Engineers, Engineer Research and Development Center, Environme ntal Laboratory. Subsequent revisions were performed in support of the National Oceanic and Atmospheric Administration, National Severe Storms Laboratory. Snow hydrology features were added and supporting manual revisions completed as part of research and development efforts funded by HydroQual, Inc. Code enhancements and manual revisions associated with the October 2009 TREX release were an outgrowt h of a project performed for the American Chemistry Council. Code enhancements and m anual revisions for the July 2010 TREX release were developed for ENSCO, Inc in support of a Department of Defense contract.TREX User’s Manual Page iii

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### TABLE OF CONTENTS
AUTHORSHIP AND ACKNOWLEDGEMENTS.................... ........................................ ii TABLE OF CONTENTS..................................

................................................... .............. iii LIST OF TABLES.....................................

................................................... ..................... vi LIST OF FIGURES ....................................

................................................... ................... vii 1.0 INTRODUCTION ...................................

................................................... ................1 2.0 MODEL THEORY AND PROCESS DESCRIPTIONS.......... ..................................2 2.1 Hydrologic Processes...........................

................................................... ..............2 2.1.1 Precipitation and Interception...............

................................................... ....2 2.1.2 Snowpack and SnowmeltInfiltration and Transmi ssion Loss......................3 2.1.3 Infiltration and Transmission Loss ...........

................................................... 4 2.1.4 Storage ......................................

................................................... ................5 2.1.5 Overland and Channel Flow ....................

................................................... .6 2.2 Sediment Transport Processes ...................

................................................... ........8 2.2.1 Advection-Diffusion ..........................

................................................... .......8 2.2.2 Erosion ......................................

................................................... ..............10 2.2.3 Deposition...................................

................................................... ............14 2.2.4 Soil and Sediment Bed Processes .............. ................................................17 2.3 Chemical Transport and Fate Processes ..........

................................................... 18 2.3.1 Chemical Partitioning and Phase Distribution. ..........................................18 2.3.2 Chemical Advection...........................

................................................... .....21 2.3.3 Erosion and Deposition of Particulate Phase C hemicals ...........................22 2.3.4 Chemical Infiltration and Subsurface Transpor t........................................23 2.3.5 Other Chemical Mass Transfer and Transformati on Processes.................24 3.0 TREX WATERSHED MODELING FRAMEWORK IMPLEMENTATIO N ........25 3.1 Generalized Conceptual Model Framework ......... ..............................................25 3.2 General Description of the Numerical Framework. ............................................29 3.3 TREX Framework Features ........................

................................................... .....29 3.4 Computational Considerations...................

................................................... ......32 3.5 Program Operation..............................

................................................... .............32 4.0 DESCRIPTION AND ORGANIZATION OF MODEL INPUT FIL ES..................35TREX User’s Manual Page iv

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.1 Input File Structure Overview ..................

................................................... .......35 4.2 Main Model Input File..........................

................................................... ...........35 4.2.1 Data Group A: General Controls ............... ................................................36 4.2.2 Data Group B: Hydrologic Simulation Parameter s ...................................37 4.2.3 Data Group C: Sediment Transport Simulation P arameters......................45 4.2.4 Data Group D: Contaminant Transport Simulatio n Parameters ................52 4.2.5 Data Group E: Environmental Properties ....... ...........................................56 4.2.6 Data Group F: Ouput Specification Controls... ..........................................61 4.3 Definitions for Chemical Properties and Reactio n Pathways .............................65 4.4 Definitions for Environmental Properties.......

................................................... .67 4.5 Ancillary Model Input Files....................

................................................... .........68 4.5.1 General Format for Spatial Domain Characteris tics Files (Grid Files) .....68 4.5.2 Description and Organization of Channel Prope rty and Topology Files...69 4.5.3 Description and Organization of Sediment Prop erties and Channel Solids Initial Conditions Files...........................

................................................... .............72 4.5.4 Description and Organization of Channel Chemi cal Initial Conditions Files .............................................

................................................... ....................74 4.5.5 Description and Organization of Environmental Properties Files .............75 4.5.6 Description and Organization of Radar Rainfal l Locations and Radar Rainfall Rates Files...............................

................................................... ..............75 4.5.7 Description and Organization of Space-Time St orm Files........................77 4.5.8 Description and Organization of Environmental Properties Files .............78 4.5.9 Restart Information File and Restart Director y Structure..........................78 5.0 DESCRIPTION AND ORGANIZATION OF MODEL OUTPUT FI LES..............81 5.1 Input Data Echo Report .........................

................................................... ..........81 5.2 Simulation Error Report........................

................................................... ...........81 5.3 Export Time Series Outputs.....................

................................................... ........82 5.4 Point-in-Time Outputs ..........................

................................................... ...........82 5.5 Cumulative Time Outputs........................

................................................... ........82 5.6 Simulation Summary Outputs.....................

................................................... .....82 5.6.1 The Model Dump File..........................

................................................... ...83 5.6.2 Detailed Mass Balance File ...................

................................................... .83 5.6.3 Summary Statistics File ......................

................................................... ....83TREX User’s Manual Page v

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 6.0 DEVELOPMENTAL FEATURES ......................... .................................................84 6.1 Chemical Mass Transfer and Transformation Proce sses....................................84 6.1.1 Chemical Biodegradation......................

................................................... ..84 6.1.2 Chemical Dissolution.........................

................................................... .....85 6.2 Environmental Conditions .......................

................................................... ........86 7.0 PROGRAMMING GUIDE..............................

................................................... ......87 7.1 TREX Programming Overview ......................

................................................... .87 7.2 TREX Availability, Online Resources, and Suppor t ..........................................87 7.3 TREX Program Organization and Description...... .............................................88 7.3.1 Input Functional Unit........................

................................................... ......88 7.3.2 Initialization Functional Unit...............

................................................... ...90 7.3.3 Time Function Update Functional Unit ......... ............................................91 7.3.4 Transport Process Functional Unit............ .................................................91 7.3.5 Integration Functional Unit..................

................................................... ...92 7.3.6 Output Functional Unit .......................

................................................... ....94 7.3.7 Deallocation Functional Unit.................

................................................... .95 7.3.8 Global Declaration and Definition Header File s .......................................96 7.4 Programming Style ..............................

................................................... ............97 7.4.1 Naming Conventions ...........................

................................................... ...97 7.4.2 Internal Documentation and Comments .......... ..........................................97 7.4.3 Maintaining Consistent Programming Style Duri ng Development...........98 8.0 REFERENCES .....................................

................................................... ...............100TREX User’s Manual Page vi

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### LIST OF TABLES Table 3-1. Comparative overview of TREX features. ..

................................................... ..31 Table 3-2. Computers, operating systems, and compil ers used for code development.....32 Table 3-3. TREX simulation restart option command l ine arguments. .............................34TREX User’s Manual Page vii

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### LIST OF FIGURES Figure 2-1. Copper partitioning vs. environmental c onditions (Lu and Allen, 2001). ......21 Figure 3-1. Generalized conceptual model framework.

................................................... ..26 Figure 3-2. TREX Hierarchy and information flow (af ter Ewen et al 2000). ...................30 Figure 7-1. Organization of transport process funct ional units in TREX..........................89 Figure 7-2. Organization of chemical kinetics proce ss modules within TREX. ...............93TREX User’s Manual Page 1

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### 1.0 INTRODUCTION TREX, the T wo-dimensional R unoff, E rosion, and Ex port model, is generalized watershed rainfall-runoff, sediment transport, and contaminant transport modeling framework. This framework is based on the CASC2D wa tershed model (Julien et al. 1995; Johnson et al. 2000; Julien and Rojas, 2002) with chemical transport and fate processes from the USEPA WASP and IPX series of str eam water quality models (Ambrose et al. 1993; Velleux et al. 1996; Velleux et al. 2001). TREX has three main components: 1) hydrology; 2) sediment transport; an d 3) chemical transport and fate. Model theory and process descriptions are presented in Section 2.0. The numerical implementation of the process in the TREX model com puter code is presented in Section 3.0. Descriptions of model input files are presente d in Section 4.0. Descriptions of model output files are presented in Section 5.0. Developm ental features are discussed in Section 6.0. A programming guide, including availability of source code, is presented in Section 7.0. The code has been subjected to extensive testing to ensure accuracy and error-free performance. However, it should be noted that (like most software) TREX is large and complex and coding errors (bugs) may exist. It is a lso important to note that some aspects of the TREX framework and model source code are und er ongoing development. Where possible, developmental features and code are noted . Inclusion of these development portions of the framework is intended to demonstrat e how the basic framework can be readily expanded to permit model use for an even wi der range of conditions than can already be simulated. Nonetheless, users are advise d to carefully review the TREX source code before use to ensure it performs correctly for any given application.TREX User’s Manual Page 2

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### 2.0 MODEL THEORY AND PROCESS DESCRIPTIONS A review of hydrologic and sediment transport proce ss descriptions is informative to illustrate the physics behind individual model proc ess representations. The processes reviewed are specific to those needed to formulate a fully distributed watershed runoff, erosion, and chemical transport and fate modeling f ramework. Major components of the framework are hydrology, sediment transport, and ch emical transport and fate. Each of these major components can be viewed as submodels w ithin the overall framework. The reviews that follow are grouped by submodel.

2.1 HYDROLOGIC PROCESSES The main processes in the hydrologic submodel are: (1) precipitation and interception; (2) snowmelt; (3) infiltration and transmission loss; ( 4) storage; and (5) overland and channel flow.

2.1.1 Precipitation and Interception The hydrologic cycle begins with precipitation. Pre cipitation includes both rainfall and snowfall. When surface air temperatures are near 0° C, precipitation is nearly always snowfall (Eagleson, 1970, Gray and Prowse 1993). Sn owfall can be represented as an equivalent depth (or volume) of water and may be ex pressed as equivalent precipitation. The gross volume of water reaching the near surface is:

s g g A i t V

= ∂ ∂ (2.1)

where: V

g = gross precipitation water volume [L 3 ] i g = gross precipitation rate [L T -1 ] A s = surface area over which precipitation occurs [L 3 ]
t = time [T] Interception is the reduction in the volume of gros s precipitation due to water retention by vegetative cover. As precipitation falls to the sur face, a portion of the gross precipitation at the surface may contact vegetative canopy and ma y be held on foliage by surface tension (Eagleson, 1970). Much of the precipitation falling during the early period of an event may be stored on vegetative surfaces (Linsley et al. 1982). Intercepted water can return to the atmosphere by evaporation. Alternativ ely, intercepted water may reach the land surface when the force of gravity acting of wa ter drops exceeds the surface tension force holding water to plant surfaces. Conceptually , interception may be represented as a volume. Net precipitation volume equals gross preci pitation volume minus the volume lost to interception (Linsley et al. 1982):TREX User’s Manual Page 3

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

## ( )
s

R i i A Et S V + = (2.2)

i g n i g i g n
V V for V V V for V V V

≤ = >

− =

: 0 : (2.3)

where: V

i = interception volume [L 3 ] S i = interception capacity of projected canopy per un it area [L 3 L -2 ] E = evaporation rate [L T -1 ]
t R = precipitation event duration [T] V n = net precipitation volume reaching the surface [L 3 ] Note that when the cumulative gross precipitation v olume that occurs during an event is less than the interception volume, the net precipit ation volume (or depth) reaching the land surface is zero. For single storm events, reco very of interception volume by evaporation can be neglected. Net precipitation vol ume may also be expressed as a net (effective) precipitation rate:

t V A i n

s n ∂ ∂

= 1 (2.4)

where: i n = net (effective) precipitation rate at the surfac e [L T -1 ]

2.1.2 Snowpack and SnowmeltInfiltration and Transmission Loss Snow on the land surface can be quantified in terms of the water content of the snowpack and is expressed as snow-water equivalent (SWE) vol ume or depth (Dingman, 2002). Precipitation that falls as snow is accumulated in the snowpack. Snowmelt occurs as a function of ambient air temperature and incoming sh ortwave solar radiation. Shortwave solar radiation can be scattered by cloud cover, so lar angle, topographic slope and other factors (Dingman, 2002; Liston and Elder, 2006). In coming solar radiation can also be affected by tree canopy, buildings, and other obstr uctions that reduce the open view of the sky (Svensson and Eliasson, 2002; Eliasson and Svensson, 2003; Schnorbus and Alila, 2004). As modified to account for sky view, a snowmelt rate equation that combines temperature and solar radiation effects is (Pelliciotti et al. 2005):



## ( ) ( ) ( )     
≤ >

− − +

−
=
M a M a SR s SV SR M a T S T T for T T for G F F T T F M 0 1 1 α (2.5)

where: M

i = snowmelt rate [L T -1 ]TREX User’s Manual Page 4

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

F T = temperature factor for snowmelt [L T -1 θ -1 ] 1 T a = ambient air temperature [ θ ] T M = temperature at which snowmelt occurs [ θ ] F SR = solar radiation factor for snowmelt [M -1 L T 2 θ -1 ] F SV = sky view factor (proportion of hemisphere visibl e from a point

[dimensionless]

α s = albedo (light reflectance) of snow [dimensionles s] G SR = incoming shortwave solar radiation [M T -3 ]

2.1.3 Infiltration and Transmission Loss Infiltration is the downward transport of water fro m the surface to the subsurface. The rate at which infiltration occurs may be affected b y several factors including hydraulic conductivity, capillary action and gravity (percola tion) as the soil matrix reaches saturation. Many relationships have been used to de scribe infiltration including expressions presented by Green and Ampt (1911), Ric hards (1931), Philip (1957), and Smith and Parlange (1978). The Green and Ampt relat ionship is often used because of its ease of application. This relationship assumes a sh arp wetting front exists between the infiltration zone and soil at the initial water con tent (piston flow) and that the length of the wetted zone increases as infiltration progresse s. Neglecting the depth of ponding at the surface (i.e. assuming that the pressure head i s much smaller than the suction head), the general equation showing the Green and Ampt rel ationship can be expressed as (Li et al. 1976; Julien, 2002): 

## ( )       θ

− + = F S H K f e e c h 1 1 (2.6)

where: f

= infiltration rate [L T -1 ] K h = effective hydraulic conductivity [L T -1 ] H c = capillary pressure (suction) head at the wetting front [L] θ e = effective soil porosity = ( φ - θ r ) [dimensionless] φ = total soil porosity [dimensionless] θ r = residual soil moisture content [dimensionless] S e = effective soil saturation [dimensionless] F = cumulative (total) infiltrated water depth [L]

1 The symbol θ is used to represent the fundamental units of temp erature in the LTM θ system (Dingman, 2002). θ indicates degree and θ -1 indicates degree -1

.TREX User’s Manual Page 5

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Similar to infiltration in overland areas, water in stream channels may be lost to the subsurface by transmission loss. The rate at which transmission loss occurs in a channel may be affected by several factors, particularly hy draulic conductivity. For ephemeral streams, capillary suction head may be significant when stream sediments are unsaturated. Relationships to describe the volume o f transmission loss are presented by Lane (1983). Abdullrazzak and Morel-Seytoux (1983) and Freyberg (1983) use the Green and Ampt (1911) relationship to assess transmission loss. Following the form of the Green and Ampt relationship and accounting for the depth of (ponded) water in the stream channel (hydrostatic head), the transmission loss rate may be expressed as: 

## ( ) ( ) 

     θ

− + + = T S

H H K t e e c w h l 1 1 (2.7)

where: t l

= transmission loss rate [L T -1 ] K h = effective hydraulic conductivity [L T -1 ] H w = hydrostatic pressure head (depth of water in cha nnel) [L] H c = capillary pressure (suction) head at the wetting front [L] θ e = effective sediment porosity = ( φ - θ r ) [dimensionless] φ = total sediment porosity [dimensionless] θ r = residual sediment moisture content [dimensionles s] S e = effective sediment saturation [dimensionless] T = cumulative (total) depth of water transported by transmission

loss [L] During infiltration, water does not completely disp lace all air from soil void spaces. As a consequence of entrapped air, effective hydraulic c onductivities are generally smaller than saturated hydraulic conductivities. Hydraulic conductivities may also be affected by surface crusting in bare soils and macropores in ve getated areas (Rawls et al. 1983; Rawls et al. 1993). For single storm events, recovery of infiltration c apacity by evapotranspiration and percolation can be neglected. Similarly, recovery o f transmission loss capacity by evaporation or other processes can also be neglecte d for single storm events.

2.1.4 Storage Water may be stored in depressions on the land surf ace as small, discontinuous surface pools. Precipitation retained in such small surface depressions is depression storage (Linsley et al. 1982). Water in depression storage may be conceptualized as a volume or, when normalized by surface area, a depth. In effect , the depression storage depth represents a threshold limiting the occurrence of o verland flow. When the water depth isTREX User’s Manual Page 6

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation below the depression storage threshold, overland fl ow is zero. Note that water in depression storage is still subject to infiltration and evaporation. Similar to depression storage in overland areas, wa ter in channels may be stored in depressions in the stream bed (as the channel water depth falls below some critical level, flow is zero and the water surface discontinuous bu t individual pools of water remain). This mechanism is termed dead storage. Note that wa ter in dead storage is still subject to transmission loss and evaporation. For single storm events, recovery of depression sto rage volume by evaporation can be neglected. Similarly, recovery of dead storage volu me by evaporation can also be neglected for single storm events.

2.1.5 Overland and Channel Flow Overland flow can occur when the water depth on the overland plane exceeds the depression storage threshold. Overland flow is gove rned by conservation of mass (continuity) and conservation of momentum. The two- dimensional (vertically integrated) continuity equation for gradually-varied flow over a plane in rectangular (x, y) coordinates is (Julien et al. 1995; Julien, 2002):

e n y x i

W f i dy q dx q dt h
=

+

− = ∂ + ∂ + ∂ (2.8)

where: h = surface water depth [L]

q x , q y = unit discharge in the x- or y-direction = Q x /B x , Q y /B y [L 2 T -1 ] Q x , Q y = flow in the x- or y-direction [L 3 T -1 ] B x , B y = flow width in the x- or y-direction [L] W = unit discharge from/to a point source/sink [L 2 T -1 ] i e = excess precipitation rate [L T -1 ] Momentum equations for the x- and y-directions may be derived by relating the net forces per unit mass to flow acceleration (Julien e t al. 1995; Julien, 2002). In full form, with all terms retained, these equations can be exp ressed in dimensionless form as the friction slope and are known as the Saint Venant eq uations. The full Saint Venant equations may be simplified by neglecting small ter ms that describe the local and convective acceleration components of momentum, res ulting in the diffusive wave approximation (of the friction slope) for the x- an d y-directions:

dx h S S x fx ∂

− = 0 (2.9)TREX User’s Manual Page 7

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation dy h S S y fy ∂

− = 0 (2.10)

where: S

fx , S fy = friction slope (energy grade line) in the x- or y-direction [dimensionless] S 0x , S 0y = ground surface slope in the x- or y-direction [d imensionless] To solve the overland flow equations for continuity and momentum, five hydraulic variables must be defined in terms of a depth-disch arge relationship to describe flow resistance. Assuming that flow is turbulent and res istance can be described using the Manning formulation (in S.I. units), the depth-disc harge relationships are (Julien et al. 1995; Julien, 2002):

β α h q x x = (2.11)

β α h q y y = (2.12)

n S fx
x 2/1

= α (2.13)

n S fy y 2/1

= α (2.14)

where: α x , α y = resistance coefficient for flow in the x- or y-d irection [L 1/3 T -1 ]

β = resistance exponent = 5/3 [dimensionless]

n = Manning roughness coefficient [T L -1/3 ] Similarly, channel flow can occur when the water de pth in the channel exceeds the dead storage threshold. Channel flow is also governed by conservation of mass (continuity) and conservation of momentum. At the watershed it i s convenient to represent channel flows in a watershed as one-dimensional (along the channel in the down-gradient direction). The one-dimensional (laterally and vert ically integrated) continuity equation for gradually-varied flow along a channel is (Julie n et al. 1995; Julien, 2002):

l c q dx Q dt A
= ∂ + ∂ (2.15)

where: A c = cross sectional area of flow [L 2 ]

Q = total discharge [L 3 T -1 ] q l = lateral unit flow (into or out of the channel) [ L 2 T -1 ]TREX User’s Manual Page 8

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W = unit discharge from/to a point source/sink [L 2 T -1 ] Based on the momentum equation for the down-gradien t direction and again neglecting terms for local and convective acceleration, the di ffusive wave approximation may be used for the friction slope (see Eq. 2.9). To solve the channel flow equations for continuity and momentum, the Manning relationship m ay be used to describe flow resistance (Julien et al. 1995; Julien, 2002):

2 /1 3/2 1 f h c S R A n Q = (2.16)

where: R h = hydraulic radius of flow = A c / P c [L] P c = wetted perimeter of channel flow [L]

2.2 SEDIMENT TRANSPORT PROCESSES The movement of water across the overland plane or through a channel network can transport and redistribute soil and sediment throug hout a watershed. The main processes in the sediment transport submodel are: (1) advecti on-diffusion; (2) erosion; (3) deposition; and (4) bed processes (bed elevation re sponse to erosion and deposition).

2.2.1 Advection-Diffusion For the overland plane in two-dimensions (verticall y integrated), the concentration of particles is governed by conservation of mass (sedi ment continuity) (Julien, 1998):

n s d e ty tx s J W J J dy q dx q dt C ˆ ˆ ˆ ˆ ˆ ˆ

=

+

− = ∂ + ∂ + ∂ (2.17)

where: C

s = concentration of sediment particles in the flow [M L -3 ]

tx q ˆ , ty q ˆ = total sediment transport areal flux in the x- or y-direction [M L -2 T -1 ]

e J ˆ = sediment erosion volumetric flux [M L -3 T -1 ]

d J ˆ = sediment deposition volumetric flux [M L -3 T -1 ]

s W ˆ = sediment point source/sink volumetric flux [M L -3 T -1 ]

n J ˆ = net sediment transport volumetric flux [M L -3 T -1 ] The total sediment transport flux in any direction has three components, advective, dispersive (mixing), and diffusive, and may be expr essed as (Julien, 1998):TREX User’s Manual Page 9

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

## ( ) dx

C D R C v q s x s x tx ∂

+

− = ˆ (2.18) 

# ( ) dy

C D R C v q s y s y ty ∂

+

− = ˆ (2.19)

where: v

x , v y = flow (advective) velocity in the x- or y-directi on [L T -1 ] R x , R y = dispersion (mixing) coefficient the x- or y-dire ction [L 2 T -1 ] D = diffusion coefficient [L 2 T -1 ]

v x C s = advective flux in the x-direction = J x [M L -2 T -1 ]

v y C s = advective flux in the y-direction = J y [M L -2 T -1 ]

dx C R s x ∂ = dispersive flux the x-direction [M L -2 T -1 ]

dy C R s y ∂ = dispersive flux the y-direction [M L -2 T -1 ]

dx C D s ∂ = diffusive flux the x-direction [M L -2 T -1 ]

dy C D s ∂ = diffusive flux the y-direction [M L -2 T -1 ]
The dispersive and diffusive flux terms in Eqs. (2. 18) and (2.19) are negatively signed to indicate that mass is transported in the direction of decreasing concentration gradient. Note that both dispersion and diffusion are represe nted in forms that follow Fick’s Law. However, dispersion represents a relatively rapid t urbulent mixing process while diffusion represents a relatively slow a Brownian m otion, random walk process (Holley, 1969). In turbulent flow, dispersive fluxes are typ ically several orders of magnitude larger than diffusive fluxes. Further, flow conditi ons for intense precipitation events are usually advectively dominated as dispersive fluxes are typically one to two orders smaller than advective fluxes. As a result, both the disper sive and diffusive terms may be neglected. Similarly, for the channel plane in one-dimension ( laterally and vertically integrated), the concentration of particles is governed by conservat ion of mass (sediment continuity) (Julien, 1998):

n s d e tx s J

W J J dx q dt C ˆ

ˆ ˆ ˆ ˆ

=

+

− = ∂ + ∂ (2.20)

Individual terms for the channel advection-diffusio n equation are identical to those defined for the overland plane. Similarly, the diff usive flux term can be neglected. TheTREX User’s Manual Page 10

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation dispersive flux is expected to be larger than the c orresponding term for overland flow. However, the channel dispersive flux still may be n egligible relative to the channel advective flux during intense runoff events.

2.2.2 Erosion Erosion is the entrainment (gain) of material from a bottom boundary into a flow by the action of water. The erosion flux may be expressed as a mass rate of particle removal from the boundary over time and the concentration ( bulk density) of particles at the boundary:

sb r e C v J = (2.21)
where: J

e = erosion flux [M L -2 T -1 ]

v r = resuspension (erosion) velocity [L T -1 ] C sb = concentration of sediment at the bottom boundary (in the bed)

[M L -3 ] Entrained material may be transported as either bed load or suspended load. However, for overland sheet and rill flows, bedload transport by rolling and sliding may predominate as the occurrence of saltation and full suspension may be limited (Julien and Simons, 1985). Entrainment rates may be estimated from site-specif ic erosion rate studies or, in general, from the difference between sediment transport capa city and advective fluxes:

        

≤ > ρ −

=

s a c s a c b s a c

r C v J for C

v J for C v J

v 0 (2.22)

where: v r

= resuspension (erosion) velocity [L T -1 ] J c = sediment transport capacity areal flux [M L -2 T -1 ]

v a = advective (flow) velocity (in the x- or y-direct ion) [L T -1 ] C s = concentration of sediment entrained in the flow [M L -3 ] ρ b = bulk density of bed sediments [M L -3 ] In the overland plane, particles can be detached fr om the bulk soil matrix by raindrop (splash) impact and entrained into the flow by hydr aulic action when the exerted shear stress exceeds the stress required to initiate part icle motion (Julien and Frenette, 1985; Julien and Simons, 1985). The overland erosion proc ess is influenced by many factors including precipitation (rainfall) intensity and du ration, runoff length, surface slope, soil characteristics, vegetative cover, exerted shear st ress, and particle size. Raindrop impactTREX User’s Manual Page 11

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation may generally be neglected when flow depths are gre ater than three times the average raindrop diameter (Julien, 2002).

2.2.2.1 Soil Erosion Relationships Extensive review of hillslope and watershed-scale s oil erosion models are presented by Aksoy and Kavvas (2005) and Merritt et al. (2003). Soil erosion relationships range in complexity from simple empirical equations to physi cally-based models that are applicable over different spatial and temporal scal es. Common soil erosion relationships include the Universal Soil Loss Equation (USLE) and its variants. The USLE (Wischemeier and Smith, 1978) is an empirical based on a large database of field plot measurements. It was developed to predict soil loss es from agriculture and is designed to estimate long-term average annual soil loss associa ted with sheet and rill erosion using six factors that are associated with climate, soil, topography, vegetation and land use management:

P C LS K R A ˆ

ˆ ˆ = (2.23)
where: A = average annual soil loss due to sheet and rill e rosion

(tons/acre/year) [M L -2 T -1 ] R = rainfall erosivity factor [dimensionless] K ˆ = soil erodibility factor (tons/acre) [dimensionle ss] LS = slope length-gradient factor normalized to a fie ld with a standard

length of 23.2 meters (76.2 ft) and a slope of 9% [ dimensionless] C ˆ = cropping-management factor normalized to a tille d area that is

continuously fallow [dimensionless] P ˆ = conservation practice factor normalized to strai ght-row farming

up and down the slope [dimensionless] The Revised Universal Soil Loss Equation (RUSLE) an d later versions of the RUSLE framework (Renard et al., 1991; Renard et al., 1994 ; Renard et al. 1997) have the same basic form as the original USLE but use extended me thods to calculate how soil erosion factors are determined. In particular, a subfactor approach to determine crop management factors enables RUSLE to be applied to crops and ma nagement systems there were not examined in the original experiments used to develo p the USLE. RUSLE is applicable to one-dimensional hillslopes that do not produce depo sition as a result of changes in slope gradient. RUSLE2 (Foster et al., 2003) provides an approach that estimates erosion on a daily basis and accounts deposition resulting from slope gradient changes on hillslopes. The Modified Universal Soil Loss Equation (MUSLE) ( Williams, 1975) estimates soil erosion loss (yield) for a single storm event by re placing the rainfall erosivity factor with a runoff energy factor determined by flow:TREX User’s Manual Page 12

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation P C LS K Qq Y p e ˆ

ˆ ˆ ) ( β α = (2.24)

where: Y

e = sediment yield from an individual storm (tons/ac re) [M L -2 ] Q v = storm runoff volume (m 3 ) [L 3 ] q p = peak runoff rate (m 3 /s) [L 3 T -1 ]
α = empirical soil erosion coefficient = 11.8 β = empirical soil erosion exponent = 0.56 [dimensio nless] More detailed review of the USLE family of soil ero sion relationships is presented by Kinnell (2010).

2.2.2.2 Overland Sediment Transport Capacity Relationships Building on the initial work of Julien and Simons ( 1985), Prosser and Rustomji (2000) summarized relationships to describe the sediment t ransport capacity of overland flow. A generalized overland flow sediment transport capaci ty equation is:

s s f s S q k q γ

β = (2.25)

where: q s = total sediment transport capacity [M L -1 T -1 ]

k = empirically or theoretically derived coefficient for sediment

transport capacity [M L -1 T -1 ] q = unit flow (discharge) of water [L 2 T -1 ] β s = empirically or theoretically derived exponent fo r discharge

[dimensionless] S f = friction slope (local energy gradient) [dimensio nless] γ s = empirical or theoretically derived exponent for local energy

gradient [dimensionless] The sediment transport capacity coefficient ( k ) represents the combined influence that rainfall intensity, overland flow, and landscape an d particle characteristics such as soil erodibility, infiltration, surface roughness, and v egetative cover have on sediment transport. Extending the review of discharge ( β ) and local energy gradient ( γ ) exponent values presented by Julien and Simons (1985) and co nclude that values of 1.0 ≤ β ≤ 1.8 and 0.9 ≤ γ ≤ 1.8 are generally applicable for use in soil erosi on modeling. Julien (1998, 2002) recommends a modified form of t he Kilinc and Richardson (1973) relationship that includes soil erodibility, cover, and management practice terms from the Universal Soil Loss Equation (USLE) (Meyer and Weis chmeier, 1969) to estimate the total overland sediment transport capacity (for bot h the x- and y-directions):TREX User’s Manual Page 13

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation P C K S q q f s ˆ ˆ ˆ 10 x 542 .1 66.1

035 .2 8 = (2.26)

e s c B q J = (2.27)

where: q s = total sediment transport capacity (kg/m s) [M/LT ]

q = unit flow rate of water = v a h [L 2 T -1 ] S f = friction slope [dimensionless] K ˆ = USLE soil erodibility factor [dimensionless] C ˆ = USLE soil cover factor [dimensionless] P ˆ = USLE soil management practice factor [dimensionl ess] B e = width of eroding surface in flow direction [L]

2.2.2.3 Channel Transport Capacity Relationships In channels, sediment particles can be entrained in to the flow when the exerted shear stress exceeds the stress required to initiate part icle motion. For non-cohesive particles, the channel erosion process is influenced by factor s such as particle size, particle density and bed forms. For cohesive particles, the erosion process is significantly influenced by inter-particle forces (such as surface charges that hold grains together and form cohesive bonds) and consolidation. Total (bed material) load transport capacity relationships account for the both bedload and suspended load com ponents of sediment transport. Yang (1996) and Julien (1998) provide summaries of numerous total load transport relationships. The Engelund and Hansen (1967) relat ionship is considered a reasonable estimator of the total load:



## ( )



# [ ] ( ) 5.0

5.0 1 1 1 05.0        

− −      

− =
p f h

p f a w d G S R gd G S v G G C (2.28)

c t a c A C v J = (2.29)

where: C

w = concentration of entrained sediment particles by weight at the

transport capacity [dimensionless] G = particle specific gravity [dimensionless]

v a = advective (flow) velocity (in the down-gradient direction) [L T -1 ] S f = friction slope [dimensionless] R h = hydraulic radius of flow [L]TREX User’s Manual Page 14

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

g = gravitation acceleration [L T -2 ] d p = particle diameter [L] A c = cross sectional area of flow [L 2 ] C t = concentration of entrained sediment particles at the transport

capacity = 

## ( )



## [ ]

w w C

G G GC

− + 1 10 6 (g/m 3 ) [M L -3 ] It is worth noting that one feature common to both the Kilinc and Richardson (1973) and Engelund and Hansen (1967) relationships is that th e implicit threshold for incipient motion is zero. This means that the transport capac ity of any particle will always be greater than zero, regardless of particle size or t he exerted shear stress, as long as the unit flow or flow velocity and friction slope are non-ze ro. This can lead to inconsistent results when erosion rates are computed from sediment trans port capacities. The inferred erosion rate will almost always be greater than zero becaus e the difference between the transport capacity and advective flux will nearly always be g reater than zero. Consequently, a nonzero erosion rate can be computed even when the exe rted shear stress is far less than the incipient motion threshold for the material. To add ress this limitation, an incipient motion threshold can be added to the modified Kilinc and R ichardson (1973) and Engelund and Hansen (1967) relationships: 

## ( ) P ˆ C ˆ K ˆ S q q . q . f . c s 66 1 035 2 8 10 x 542 1

− = (2.30) 

## ( ) ( ) 

# [ ] ( ) 5 0

5 0 1 1 1 05 0 .

p f h

. p f c a w d G S R gd G S v v G G

. C        

− − −      

− = (2.31)

where: q c = critical unit flow for erosion (for aggregate th e soil matrix) = h v c [L 2 T -1 ]

v c = critical velocity for erosion [L T -1 ] h = surface water depth [L]

2.2.3 Deposition Deposition is the sedimentation (loss) of material entrained in a flow to a bottom boundary by gravity. The deposition process is infl uenced by many factors including particle density, diameter, and shape, and fluid tu rbulence. The deposition flux may be expressed as a mass rate of particle removal from t he water column over time and the concentration of sediment particles that are entrai ned in the flow:

s se d C v J = (2.32)
where: J

d = deposition flux [M L -2 T -1 ]

v se = effective settling (deposition) velocity [L T -1 ]TREX User’s Manual Page 15

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

C s = concentration of sediment particles in the flow [M L -3 ] Coarse particles (>62 μm) are typically inorganic a nd non-cohesive and generally have large settling velocities under quiescent condition s. Numerous empirical relationships to describe the non-cohesive particle settling velocit ies are available. Summaries of relationships and settling velocities are presented by Yang (1996) and Julien (1998). For non-cohesive (fine sand) particles with diameters f rom 62 μ m to 500 μ m, the settling velocity can be computed as (Cheng, 1997):



# ( ) 

# [ ] 5.1

5.0 2
* 5 2.1 25 −

− + = d d v
p s ν (2.33)


## ( ) 3/1

2 * 1 

    

− = ν g G d d p (2.34)

where: v s = quiescent settling velocity [L T -1 ]

ν = kinematic viscosity of water [L 2 T -1 ] d * = dimensionless particle diameter [dimensionless] Medium particles (10 μm < d p <62 μm) can vary in character. Inorganic particles may behave in a non-cohesive manner. In contrast, organ ic particles (potentially including particles with organic coatings) may behave in a co hesive manner. Fine particles (<10 μm) often behave in a cohesive manner. If behavior is largely non-cohesive, settling velocities may be estimated as described by Julien (1998). If the behavior is cohesive, flocculation may occur. Floc size and settling velo city depend on the conditions under which the floc was formed (Burban et al. 1990; Kris hnappan, 2000; Haralampides et al. 2003). When flocculation occurs, settling velocitie s of cohesive particles can be approximated by relationship of the form (Burban et al. 1990):

m f sf ad v = (2.35)

where: v sf

= floc settling velocity (cm/s) [L T -1 ]

a = experimentally determined constant = 8.4 x 10 -3 d f = median floc diameter ( μ m) [L]

m = experimentally determined constant = 0.024 However, depending on fluid shear, particle surface charge, and other conditions, fine particles may not flocculate. Under conditions that limit floc formation, fine particles can have very small, near zero settling velocities.TREX User’s Manual Page 16

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation As a result of turbulence and other factors, not al l particles settling through a column of flowing water will necessarily reach the sediment-w ater interface or be incorporated into the sediment bed (Krone, 1962). Beuselinck et al. ( 1999) suggest that this process also occurs for the overland plane. As a result, effecti ve settling velocities in flowing water can be much less than quiescent settling velocities . The effective settling velocity of a particle can be described as a reduction in the qui escent settling velocity by the probability of deposition (Krone 1962; Mehta et al. 1989):

s dep se v P v = (2.36)

where: v se = effective settling velocity [L T -1 ]

v s = quiescent settling velocity [L T -1 ] P dep = probability of deposition [dimensionless] The probability of deposition varies with shear str ess near the sediment bed and particle size. As particle size decreases or shear stress in creases, the probability of deposition decreases. For non-cohesive particles, the probabil ity of deposition has been described as a function of bottom shear stress (Gessler, 1965; G essler 1967; Gessler, 1971):

dx e P P Y x dep 

# ∫

∞ − − = = 2 5 0 2 1

. π (2.37)
       

− = 1 1
τ τ σ n cd Y , (2.38)

where: P = probability integral for the Gaussian distributi on
σ = experimentally determined constant = 0.57
τ 0 = bottom shear stress [M L -1 T -2 ]
τ cd,n = critical shear stress for deposition of non-cohe sive particles,

defined as the shear stress at which 50% of particl es deposit [M L -1 T -2 ] For coarse particles, the critical shear stress for deposition can be computed from a force balance following the method of van Rijn (1984a,b) as summarized by QEA (1999), with the particle diameter equal to the mean diameter fo r a range of particle size in a class (i.e. d p = d 50 ). For cohesive particles, the probability of depositi on has also been described as a function of bottom shear stress (Partheniades, 1992):TREX User’s Manual Page 17

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation dx e P P Y x dep 

# ∫

∞ − −

− = − = 2 5 0 2 1 1 1 .

π (2.39)

      

      

− = cd

e Y c cd τ τ τ σ 27 1 1 25 0 1

.

, . ln (2.40)

where: σ = experimentally determined constant = 0.49

τ 0 = bottom shear stress [M L -1 T -2 ]
τ cd,c = critical shear stress for deposition of cohesive particles, defined

as the shear stress at which 100% of particles depo sit [M L -1 T -2 ] The probability integrals in Equations 2.37 and 2.3 9 can be approximated as (Abramowitz and Stegun, 1972):



## ( ) 

# ( ) ( ) 0 for 1 0 for 9373 .0 1202 .0 4362 .0 1 3 2

<

− = > +

− − =

Y Y P P Y X X X Y F P (2.41)



## ( ) 2

5 0 2 1 Y e Y F .

− = π (2.42) 

## ( ) 1 3327 0 1 − + = Y X
. (2.43)

2.2.4 Soil and Sediment Bed Processes In response to the difference between bedform trans port, erosion, and deposition fluxes, the net addition (burial) or net loss (scour) of pa rticles from the bed causes the bed surface elevation to increase or decrease. The rise or fall of the bed surface is governed by the sediment continuity (conservation of mass) e quation, various forms of which are attributed to Exner (1925) (see Simons and Sentürk, 1992). Julien (1998) presents a derivation of the bed elevation continuity equation for an elemental control volume that includes vertical and lateral (x- and y-direction) transport terms. Neglecting bed consolidation and compaction processes, and assumin g that only vertical mass transport processes (erosion and deposition) occur, the sedim ent continuity equation for the change in elevation of the soil or sediment bed surface ma y be expressed as:

sb r s se b C

v C v dt z

− = ∂ ρ (2.44)

where: z = elevation of the soil surface or sediment bed [L ]

ρ b = bulk density of soil or bed sediments [M L -3 ]TREX User’s Manual Page 18

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

v se = effective setting (deposition) velocity [L T -1 ] C s = concentration of sediment particles in the water column [M L -3 ]

v r = resuspension (erosion) velocity [L T -1 ] C sb = concentration of sediment particles in the soil or sediment bed

[M L -3 ]

2.3 CHEMICAL TRANSPORT AND FATE PROCESSES The movement of water and sediment across the overl and plane or through a channel network can also transport and redistribute chemica ls throughout a watershed. On the land surface and in channel environments, chemical typically exist in three phases: 1) dissolved in water, 2) bound with dissolved organic compounds (DOC) or other binding ligands or complexation agents; and 3) particle-ass ociated. The pathways that affect chemical movements and interactions in the environm ent depend on the phase in which the chemicals are present. The main processes in th e chemical transport and fate submodel are: 1) chemical partitioning and phase di stribution; 2) advection-diffusion; 3) erosion; 4) deposition; 5) infiltration and 6) and mass transfer and transformation processes (chemical reactions).

2.3.1 Chemical Partitioning and Phase Distribution Many chemicals are hydrophobic and readily partitio n between dissolved, bound, and particle-associated (particulate) phases. Partition ing to bound and particulate phases is a function of chemical affinity for surfaces and ion exchange (ionic chemicals) or organic carbon (neutral chemicals) (Karichoff et al. 1979; Schwarzenbach et al. 1993; Chapra, 1997). The equilibrium distribution of chemicals be tween phases is described by the partition (distribution) coefficient, concentration and binding effectiveness of binding agents, and the concentration of particles or organ ic carbon. Mechanistically, partitioning is a function of the equilibrium rate at which chem icals sorb (move out of the dissolved phase) and desorb (move back into the dissolved pha se). If the rates at which chemicals partition are much faster than the rates of other m ass transfer processes, local equilibrium is assumed to exist and the dissolved, bound and pa rticulate phase chemical concentrations can be expressed in terms of the tot al chemical concentration (sum of phases) (Thomann and Mueller, 1987; Chapra, 1997). Chemicals may partition to all particle types (sorb ents) present in a solution. The equilibrium partition (distribution) coefficient to any particle is defined as (Thomann and Mueller, 1987):

oc n oc n p n p K

f K = = ¶ (2.41)
where: ¶

p n = equilibrium partition (distribution) coefficient for particle “ n ”

[L 3 /M]TREX User’s Manual Page 19

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

K p n = equilibrium partition (distribution) coefficient for particle “ n ”

[L 3 /M] f oc n = fraction organic carbon of particle “ n ” [dimensionless] K oc = organic carbon normalized partition coefficient [L 3 /M] For particulate phases in the water column, equilib rium partition coefficients vary with the concentration of suspended solids as a result o f particle interactions. Particledependent partition coefficients are described as ( Di Toro, 1985):


# ∑ ∑

= = +

= + = N

n x

oc n n oc oc oc N

n x

n p n n p

n px K m f K f

m 1 1 1 ¶ 1 ¶ ¶ ν

ν (2.42)

where: ¶

px n = particle-dependent partition coefficient [L 3 /M]

n = particle index = 1, 2, 3, etc.

m n = concentration of particle “ n ” [M/L 3 ]
ν x = particle interaction parameter [dimensionless] For the bound phase, the equilibrium binding coeffi cient is defined as:

oc D oc e b K f D = ¶ (2.43)
where: ¶ b = equilibrium binding coefficient [L 3 /M] f oc D = fraction organic carbon of DOC [dimensionless] D e = DOC-binding effectiveness coefficient [dimension less] Conceptually, dissolved organic compounds are compo sed entirely of organic carbon ( f oc D = 1). Under those conditions, the equilibrium bind ing coefficient would equal the organic carbon partition coefficient. However, at l east for neutral organic chemical binding in some surface waters (the Great Lakes), o bserved binding coefficients were up to 100 times smaller than K oc (Eadie et al. 1990; Eadie et al. 1992). Also, in s ediment observed binding coefficients were up to 10 times s maller than K oc (Landrum et al. 1985; Landrum et al. 1987; Capel and Eisenreich, 1990). O ne explanation for decreased binding efficiency is photobleaching of DOC by ultraviolet (UV-B) radiation (Kashian et al. 2004). The equilibrium partition coefficient can be used t o describe the fraction of the total chemical that is associated with each phase as foll ows (Thomann and Mueller, 1987; Chapra, 1997):TREX User’s Manual Page 20

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

# ∑

= + + = N

n n

px n b oc d m D f

1 ¶

¶ 1 1 (2.44)



## ∑

= + + = N

n n

px n b oc b oc b m D D f

1 ¶

¶ 1 ¶ (2.45)



## ∑

= + + = N

n n

px n b oc n

px n

n p m D m f

1 ¶

¶ 1 ¶ (2.46)

1
1 = + + 

# ∑

= N

n n p b d f f f (2.47)

where: f

d = fraction of the total chemical in the dissolved phase

[dimensionless] f b = fraction of the total chemical in the DOC-bound phase

[dimensionless]

n = particle index = 1, 2, 3, etc. f p n = fraction of the total chemical in the particulat e phase associated

with particle “ n ” [dimensionless] Equations 2.44-2.46 are presented for the water col umn. For the sediment bed, ¶ p n is used in place of ¶

px n . Lu and Allen (2001) present extensive assessments o f copper partitioning onto suspended particulate matter in river water. They performed a series of adsorption experiments and found that many factors may influence the partition coefficient including pH, total suspended solids concentration, total copper concen tration, dissolved organic matter, particulate organic matter, hardness, and ionic str ength. Their results suggest that adsorption to organic matter binding sites in aqueo us and solid phases plays the biggest role in controlling the extent of copper partitioni ng. However, Lu and Allen (2001) found that the most significant environmental factors aff ecting the value of the partition coefficient were the total suspended solids (TSS) c oncentration and pH. Graphs showing variation of the copper partition coefficient as a function of key environmental conditions are presented in Figure 2-1. Holm et al. (2003) fou nd that cadmium partitioning, like copper, was highly correlated with soil cation exch ange capacity, which is largely determined by organic carbon and clay content. Also , cadmium partition coefficients were found to decrease by an order of magnitude as soil pH decreased from 6.7 to 5.3. Similar behavior is also expected for zinc because, like copper and cadmium, it is divalent. Sauvé et al. (2000, 2003) noted that dist ribution coefficients for cadmium, copper, and zinc and other divalent metals are sens itive to pH. Sauvé et al. (2003)TREX User’s Manual Page 21

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation a) K d as a function of pH and TSS concentration b) K d as a function of pH and copper concentration

c) K d as a function of TSS concentration d) K d as a function of copper concentration and pH Figure 2-1. Copper partitioning vs. environmental c onditions (Lu and Allen, 2001).

reported distribution coefficients (log K d ) values for acidic (pH 4.4) soils were low: Cd log K d = 3.05; Cu log K d = 2.98; and Zn log K d = 2.75. While pH may be the most important variable for partitioning, Sauvé et al. ( 2000, 2003) also noted the importance of organic matter as, after being normalized for pH, s orptive capacities for organic soils were reported to be up to 30 times larger than thos e observed for mineral soils.

2.3.2 Chemical Advection Advection transports all chemical phases. For two-d imensional flow in the overland plane, a chemical continuity (conservation of mass) equation analogous the sediment continuity equation can be written as:

c x c N

n n p b d x xc C v C f f f v J =       + + = 

# ∑

= 1 (2.48)TREX User’s Manual Page 22

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation c y c N

n n p b d y yc C v C f f f v J =       + + = 

# ∑

= 1 (2.49)

where: J

xc , J yc = chemical advective flux x- or y-direction [M/L 2 T]

v x , v y = advective velocity in the x- or y-direction [L/T ]

n = particle index = 1, 2, 3, etc.

v r n = resuspension (erosion) velocity of particle “ n ” [L/T] f d = fraction of the total chemical in dissolved phas e in the water

column [dimensionless] f b = fraction of the total chemical in the bound phas e in the water

column [dimensionless] f p n = fraction of the total chemical in particulate ph ase associated with

particle “ n ” in the sediment column [dimensionless] C c = total chemical concentration in the water column [M/L 3 ] Similarly, for one-dimensional flow in channels a c hemical continuity (conservation of mass) equation analogous the sediment continuity eq uation is identical to Equation 2.48.

2.3.3 Erosion and Deposition of Particulate Phase Chemica ls Chemicals associated with particles in the water co lumn will enter the sediment bed if those particles settle. Similarly, chemicals associ ated with particles in the sediment bed will return to the water column if those particles are entrained (resuspend). The factors that control particle transport between the water c olumn and sediment bed were described in Section 2.2.2. Since particle phase chemicals mo ve with the particles transported, the erosion and deposition fluxes of chemicals are desc ribed as (Thomann and Mueller, 1987): 

# ∑

= = N

n c

n p n r ec C

f v J 1 2

2 (2.50) 

# ∑

= = N

n c

n p n se dc C

f v J 1 1 1 (2.51)

where: J

ec = chemical erosion flux [M/L 2 T] J dc = chemical deposition flux [M/L 2 T]

n = particle index = 1, 2, 3, etc.

v r n = resuspension (erosion) velocity of particle “ n ” [L/T]

v se n = effective settling velocity of particle “ n ” [L/T]TREX User’s Manual Page 23

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation f p1 n = fraction of the total chemical in particulate ph ase associated with

particle “ n ” in the water column [dimensionless] f p2 n = fraction of the total chemical in particulate ph ase associated with

particle “ n ” in the sediment column [dimensionless] C c1 = total chemical concentration in the water column [M/L 3 ] C c2 = total chemical concentration in the soil/sedimen t column [M/L 3 ]

2.3.4 Chemical Infiltration and Subsurface Transport Chemicals associated with the dissolved and bound p hase in the water column will enter the soil or sediment bed if the water transporting those chemicals infiltrates. When chemical partition coefficients are low and a signi ficant fraction of the total chemical mass is in a mobile form, chemical infiltration may be significant. To account for this process, the chemical infiltration flux can be comp uted from the water infiltration flux as: 

## ( ) 1 1 1 1 1 c m i c b d i ic C

f v C f f v J =

+ = (2.52)

where: J

ic = chemical infiltration flux [M/L 2 T]

v i = infiltration rate or transmission loss of water [L/T], previously

defined as f

in Eq. (2.5) or t l in Eq. (2.6) f d1 = fraction of the total chemical in dissolved phas e in the water

column [dimensionless] f b1 = fraction of the total chemical in bound phase in the water column

[dimensionless] f m1 = fraction of the total chemical in the mobile pha se in the water

column [dimensionless] = f d1 + f b1 C c1 = total chemical concentration in the water column [M/L 3 ] Once in the subsurface, infiltrated chemicals would be subject to repartitioning with the chemical mass associated with porewater and particl es in the soil column and transport via groundwater. The flow of groundwater through th e soil also has the potential to leach chemicals from the soil column. Due to adsorption a nd the comparatively high bulk density of particles in the soil, subsurface chemic al transport is subject to retardation (Fetter, 2001). Chemicals subject to retardation tr avel trough the subsurface at rates less than the average linear velocity of water. The reta rdation factor for a chemical in the subsurface is computed as (Fetter, 2001):

p e b K R θ ρ + = 1 (2.53)

where: R = Retardation factor [dimensionless]TREX User’s Manual Page 24

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ρ b = soil bulk density [M/L 3 ] θ e = effective soil porosity (void volume/total volum e)

[dimensionless] K p = chemical equilibrium partition (distribution) co efficient [L 3 /M]

2.3.5 Other Chemical Mass Transfer and Transformation Pro cesses Beyond partitioning and mass transport processes, t he fate of chemicals is potentially influenced by a number of other processes such as b iodegradation, hydrolysis, oxidation, photolysis, and volatilization, and dissolution. Ho wever, for general simulation of elemental metals such as cadmium, copper, and zinc, volatilization, biodegradation, and photolysis do not occur. Hydrolysis and oxidation c an affect the ionic speciation and phase distribution of metallic chemicals but do not affect the total chemical concentration. The effect that possible hydrolysis or oxidation reactions have on phase distributions of metals can be represented in terms of the chemical distribution (partitioning) coefficient.TREX User’s Manual Page 25

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### 3.0 TREX WATERSHED MODELING FRAMEWORK

IMPLEMENTATION

3.1 GENERALIZED CONCEPTUAL MODEL FRAMEWORK A generalized conceptual framework for the TREX wat ershed chemical transport and fate model is presented in Figure 3-1. At present, this framework research focuses on the event transport of metals in surface waters. Conseq uently, several possible processes in the general conceptual framework can be neglected b ecause storm events are short-lived, lasting no more than a few hours. In particular, ma ss transfer and reactions processes such as volatilization, biodegradation, hydrolysis, and photodegradation can be neglected because of the short time scale for simulations or because these processes do not occur for metals. Other processes, such as dispersion and diffusion can also be neglected because at the time scale of event simulations tran sport processes are reasonable expected to be dominated by advection. At the event time sca le, subsurface transport is also neglected. As a result, the transport and fate proc esses most important for the event simulation of metals are:

• Advective water column transport;

• chemical partitioning between water (truly dissolve d), dissolved organic compounds (DOC) (or other binding agents) (bound), and solid (particulate) phases;

• Transport (erosion, deposition, net burial/unburial ) of solids and particulate chemicals;

• Infiltration of dissolved and bound (mobile) phase chemicals;

• External sources and sinks of water, solids and che micals. Dynamic mass balance equations were developed based on the process descriptions presented in Section 2.0. In their most general for m, these mass balance equations form a system of coupled partial differential equations th at are functions of time and space. These equations describe the relationship between m aterial inputs (precipitation or loads) and mass (water depth or constituent concentrations ). To solve these equations, three simplifying assumptions were made and the equations expressed in finite difference form (Thomann and Mueller, 1987; Chapra, 1997):
1. Water column volumes are constant with respect to t ime during any interval ( ∂ V/ ∂ t = 0); 2. Surficial sediments do not move horizontally within the sediment bed; and 3. Chemical partitioning to solids and binding is rapi d relative to other processes (local equilibrium).TREX User’s Manual Page 26

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation a) Overview of hydrology, sediment transport, and c hemical transport and fate submodels

b) Details of chemical transport and fate processes

Figure 3-1. Generalized conceptual model framework.TREX User’s Manual Page 27

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation The state variables in the model framework for the overland plane (denoted with the subscript “ov”) and channel network (denoted with t he subscript “ch”) are: water depth (h), solids concentration (C s ), and chemical concentration (C c ). The corresponding equations for the water column and bed are: Water Depth in the Overland Plane and Channel Netwo rk

c w

c l ovy

y ovx

x e ov A W L q y Q B x Q B i t h +

− ∂ ∂

− ∂ ∂

− = ∂ ∂ 1

1 (3.1) 

## ( )

c w ch l c ch L

W
x Q q t B h +

∂ ∂

− = ∂ ∂ (3.2)

Solids in the Water Column of the Overland Plane an d Channel Network

w s

w c ov s f
w c ov s y w c ov s x w s ov s se w s ov sb r ov s V W V A C v V A C v V A C v V A C v V A C v t C +

− − − − = ∂ ∂

, , , , , , (3.3)

w s

w c ov s f
w c ch s x w s ch s se w s ch sb r ch s V W V A C v V A C v V A C v V A C v t C + +

− − = ∂ ∂

, , , , , (3.4)

Solids in the Soil and Sediment Bed

s s ov sb r s s ov s se ov sb V A C v V A C v t C

,

, ,

− = ∂ ∂ (3.5)

s s ch sb r s s ch s se ch sb V A C v V A C v t C

,

, ,

− = ∂ ∂ (3.6)

Total Chemical in the Water Column of the Overland Plane and Channel Network



## ( )

w c

w s b d ov c ov i w c ov c f
w c ov c y w c ov c x w s p ov c se w s pb ov cb r ov c

V W V A f f C v V A C v V A C v V A C v V A f C v V A f C v t C

+

+

− − − − − = ∂ ∂

,

, , , , , , , (3.7)TREX User’s Manual Page 28

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation



## ( )

w c

w s b d ch c ch i w c ov c f
w c ch c x w s p ch c se w s pb ch cb r ch c

V W V A f f C v V A C v V A C v V A f C v V A f C v t C

+

+

− +

− − = ∂ ∂

,

, , , , , , (3.8)

Total Chemical in the Soil and Sediment Bed

s s pb ov, cb r s s p ov,c se ov, cb V A f C v V A f C v t C

− = ∂ ∂ (3.9)

s s pb ch cb r s s p ch c se ch cb V A f C v V A f C v t C

,

, ,

− = ∂ ∂ (3.10)

where: h = flow depth of water column [L]

C s , C sb = solids concentration in water column and bed [M/ L 3 ] C c , C cb = total chemical concentration in water column and bed [M/L 3 ] Q x , Q y = flow in the x- or y-direction [L 3 /T] q l = lateral unit flow from overland plane to channel (floodplain)

[L 2 /T] L c = length of channel in flow direction [L] A c , A s = cross sectional area in flow direction, bed surf ace area [L 2 ] V w , V s = volume of water and sediments [L 3 ]

v x , v y , v

f = flow velocity in the x- or y-direction and betwe en overland plane and channel (floodplain) [L/T]

v r , v se , v i = resuspension (erosion), effective settling (depo sition), and

infiltration (or transmission loss) velocities [L/T ] f d , f b , f p = dissolved, bound, and particulate chemical fract ions [dimensionless] W w,s,c = material point source/sink: water [L 3 /T], solids, or chemical

[M/T] Each term in the mass balance equations represents a process in the conceptual framework. The variables in each term represent mod el parameters. Thomann and Mueller (1987) and Chapra (1997) provide more detai led presentations of mass balance equations for chemical transport.TREX User’s Manual Page 29

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 3.2 GENERAL DESCRIPTION OF THE NUMERICAL FRAMEWORK To simulate hydrologic, sediment, and chemical tran sport, values must be assigned to each model parameter and the mass balance equations defined by the conceptual model framework must be solved. Numerical integration tec hniques are needed to solve the model equations. TREX uses a finite difference cont rol volume implementation of the generalized mass balance equation. To generate solu tions, the framework computes dynamic mass balances for each state variable and a ccounts for all material that enters, accumulates within, or leaves a control volume thro ugh precipitation excess, external loads, advection, erosion, and deposition. TREX als o features a “semi-Lagrangian” soil/sediment bed layer submodel to account for the vertical distribution of the physical and chemical properties of the overland soil and ch annel sediment columns (see Section 3.3). These equations are solved using Euler’s meth od for numerical integration (Chapra and Canale, 1985):

t t s s s
t

t t t ∆

∂ ∂ + = ∆ + (3.11)

where: t

t s ∆ + = value of model state variable at time t+ ∆ t [L] or [M/L 3 ]

t s = value of model state variable at time t [L] or [M/L 3 ]

t t s ∂ ∂ = value of model state variable derivative at time t [L/T] or [M/L 3 T] ∆ t = time step for numerical integration [T]

3.3 TREX FRAMEWORK FEATURES The initial basis for development of TREX was CASC2 D. As part of the model development process, CASC2D’s underlying hydrologic and sediment transport submodels were significantly enhanced before chemic al transport and fate components were added to create the TREX framework. An overvie w of TREX features is presented in Table 3-1. As part of the overall development ef fort, the entire body of TREX source code is organized to significantly improve code str ucture and modularity and to provide complete, line-by-line documentation. Beyond allowi ng development of chemical transport and fate features to proceed, the TREX co de is structured so that future categories of model features can be added to the fr amework without having to reconstruct the basic code. As presented in Figure 3-2, the cod e is designed so that the calculations for each process at any time level are independent and information is carried forward from hydrology to sediment transport to chemical tr ansport in order to generate a solution. At any time level, flow is assumed to be unaffected by sediment and chemical transport and sediment transport is affected by che mical transport, so calculations for these three components have a natural hierarchy.TREX User’s Manual Page 30

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Figure 3-2. TREX Hierarchy and information flow (af ter Ewen et al 2000).

Within TREX, many features of the original CASC2D c ode were significantly enhanced and many new features were added. In particular, th e TREX code is designed to simulate multiple watershed outlets and to also allow channe l network branching in the upstream and downstream directions. This permits simulation of braided tributaries and distributary flows that might occur around alluvial fans or wher e a river system meets a large receiving waterbody on a low slope. Another signifi cant enhancement is the addition of flow point sources and sinks. Note that TREX does n ot consider groundwater flow processes other than downward flow at the surface b y infiltration or channel transmission loss and through defined soil and sediment layers. However, to account for other water losses or gains, groundwater interactions could be represented as a series of time-variable point sources and sinks. In effect, this feature al lows TREX to be externally coupled with groundwater flow and transport modeling tools such as MODFLOW (Harbaugh et al. 2000), HST3D (Kipp, 1997), and MT3DMS (Zheng and Wa ng, 1999). Another key feature of the enhanced TREX framework is the representation of the bed and bed processes. The bed itself is presented as a vertical stack (layers). Typical water quality modeling approaches use an Eulerian (fixed) frame of reference for all compartments. In contrast, TREX uses what is termed a “semi-Lagrangian” (floating) frame of reference (Velleux et al. 2001). In the Eu lerian approach, the control volume for mass balance calculations is fixed in space and mat erial is advected through the control volume. With respect to the bed, the deposition or erosion of material causes the entireTREX User’s Manual Page 31

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

Table 3-1. Comparative overview of TREX features. Model Component Prior CASC2D Code TREX Code Status General Model Controls Numerical integration time step One time step limited to critical value regardless of flow Series of time step values that can be optimized based on flow Tested
Hydrologic Submodel Water depth initial condition Assumed to be zero but recent code allowed a non-zero flow depth in channels (dry start) User can specify any value for depth overland, in channels, or infiltrated (wet or dry start) Tested

Flow outlets and downstream boundary conditions Limited to one outlet, assumed normal depth Any number of outlets possible, downstream control or normal depth can be specified Partially tested
Floodplain interaction Nascent features in initial code (Julien et al. 1995) but not in recent code (Rojas, 2002). Restored feature and enhanced to compute flooding from water surface elevations Tested

Channel topology: orientation Channel connections limited to four (N-S or E-W) directions Channel connections in all eight raster grid directions Tested
Channel topology: branching Converging branches, limited to two branches upstream Converging and diverging branches with 2-7 branches Tested
Flow point sources and sinks None Point sources for overland plane and channel network. Sources tested, sinks, not. Partially tested
Sediment Transport Submodel Number of particle types Limited to three: sand, si lt, clay Unlimited number of types Tested Floodplain sediment transport None: solids passing through overland part of a floodplain cell instantly move to channel Occurs whenever water depth in overland part of floodplain cell exceeds zero Tested

Channel erosion Limited: only solids deposited during simulation erode; net bed elevation change never < 0 Not restricted; channels can incise and net change in bed elevation can be < 0 Tested

Solids point sources and sinks None Point sources for overland plane and channel network Partially tested Chemical Transport Submodel Number of chemical types None Unlimited Tested Chemical transport and fate None Three-phase partitioning with advection, erosion, deposition Tested
Chemical point sources and sinks None Point sources for overland plane and channel network Partially testedTREX User’s Manual Page 32

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Table 3-2. Computers, operating systems, and compil ers used for code development.

Processor Operating System Development Environment/Compiler Intel Itanium2 (64-bit) Windows XP 64-bit Edition I ntel C++ 8.1 Intel Pentium3 Windows XP Visual C++ 6.0

Intel Pentium4 Windows XP Redhat Enterprise Linux 4 Visual Studio .Net gcc 4.0

Intel Core2 Windows XP Mandriva Linux Visual C++ 6.0, Visual Studio .Net Intel C++ 9.0, PGI C++ AMD Athlon Windows 2000 Visual Studio .Net AMD Opteron 248, x86_64 Fedora Core 5 gcc 4.0.1 AMD Opteron 2220 (dual core) Fedora 8 gcc 4.1.2

frame of reference (all layers in the stack) to adv ect (upward or downward). As control volumes relocate, material is advected between adja cent layers. This advection can affect contaminant distributions in the bed. In the semi-L agrangian approach, the control volume of the surface bed layer is allowed to expan d or contract in response to erosion or deposition. Because the entire frame of reference f or all bed layers is not relocated, the mixing that occurs with the Eulerian approach is el iminated. Velleux et al. (2001) and Imhoff et al. (2003) present further descriptions o f the semi-Lagrangian approach and its details.

3.4 COMPUTATIONAL CONSIDERATIONS The TREX source code is written in C and conforms t o ANSI C99 conventions. The code was compiled and simulations executed on several co mputing systems to ensure a degree of portability. The computers, operating systems, a nd compilers that have been used for code development are presented in Table 3-2. It is worth noting that TREX is a computationally intensive application. Simulations with hydrology, six solids types, and three chemical types on a domain with 34,000 elemen ts required approximately 18.5 CPU hours on a system with a 1.3 GHz Intel Itanium2 (64-bit) processor.

3.5 PROGRAM OPERATION TREX is operated from a command line interface (the command prompt under the Windows operating system or shell prompt in Linux). In its most basic mode of operation, TREX requires that the user specify one argument. This argument is the path and file name of the TREX main input file. The main input file provides basic model input parameters that control a simulation and also contains names of ancillary model input files that delineate specific characteristics of the simulation such as the watershedTREX User’s Manual Page 33

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation boundary mask, elevations, soil classes, and land u se, etc. Descriptions of the main and ancillary input files are presented in Section 4.0. When run from the command prompt under the Windows operating system, the command str eam to begin execution of a TREX simulation is of the form:
C:\trex.exe inputfilename.inp Similarly, when run from a shell prompt under the L inux operating system, the command stream is on the form: /home/username/path/to/input/trex.x inputfilename.inp TREX also has some automated warm/hot start capabli ties (“restart” options) that allow users to simulate a sequence of storm events where final conditions from one event are used as initial conditions for the next. To operate in a mode that permits a warm or hot start, TREX requires that the user specify an argum ent to identify the restart option in addition to the main input file. When run from the command prompt under the Windows operating system, the command stream to begin execu tion of a TREX simulation with a restart option selected is of the form:
C:\trex.exe inputfilename.inp restart# Similarly, when run from a shell prompt under the L inux operating system, the command stream is on the form: /home/username/path/to/input/trex.x inputfilename.inp restart#
where: restart#

is one of the values needed to invoke restart capa bilities. The full list of permissible restart options is summarized in Table 3-3. NOTE: TREX restart options are still under development. During execution, TREX generates a series of output files. Depending on the number of cells in the spatial domain and number of state var iables simulated and the frequency of reporting, the size of model output can be quite la rge (>5 GB). Descriptions of TREX output file types are presented in Section 5.0.TREX User’s Manual Page 34

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Table 3-3. TREX simulation restart option command l ine arguments. Argument Description none No restart files are read or written (default option when no argument is specified) restart0 No initial conditions are read, but final conditions are written to restart files restart1 Initial conditions for a “warm” start read from and final conditions written to restart files restart2 Initial conditions for a “hot” start read from and final conditions written to restart files
Notes 1. For a warm start, initial conditions for soils a nd sediments (solids and chemical concentrations, number of layers, volume, surface area, thickness, etc.) are read from restart files. 2. For a hot start, initial conditions for soils, s ediments, runoff, and surface water (solids and chemical concentrations, number of layers, volume, surface a rea, thickness, etc.) are read from restart files. The warm start option is useful for simulating a se quence of events when the time between storms is so long that runoff depths on the overland plane are z ero and surface water in streams returns to baseflo w conditions. The hot start option is useful when the time between storms is short enough such that runo ff depths are not zero and/or surface water conditions in have not yet returned to baseflow conditions. It should be noted that neither of these restart op tions provide full simulation restart capabilities because conditions for other processes (i.e. interception, infiltrations, transmission loss, etc.) are not wri tten to or read from restart files. Use of any restart option (0, 1, or 2) requires tha t the user provide a “restart-info.txt” file in the “Restart” directory. This file and directory structure are de cribed in Section 4.5.9.TREX User’s Manual Page 35

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### 4.0 DESCRIPTION AND ORGANIZATION OF MODEL INPUT FILES

4.1 INPUT FILE STRUCTURE OVERVIEW TREX has a main input file that controls most aspec ts a simulation. Within this main input file, the inputs are divided into six groupin gs of related parameters (Data Groups AF). The main input file also specifies a number of ancillary input files that are required to operate the model. The ancillary model input files are used to delineate specific characteristics of the simulation such as the water shed boundary mask, elevations, soil classes, and land use, etc. Ancillary files are eac h organized into Data Groups. The organization and content of each Data Group is described in a series of tables presented in the following sections of this manual. Each Data Group is itself divided into records and fields. In general, the name of each va riable, its type, and expected units is described. Variables names starting with “n” descri be the number of elements associated with a parameter (i.e. nsolids = number of solids t ypes, nchems = number of chemicals, ndt = number of time steps, etc.) Variables ending with “opt” are switches that toggle operation of model processes. Variables containing “ic”, “bc”, and “w” are associated with initial conditions (ic), boundary conditions ( bc), and loads/forcing functions (w). Variable types include int (integer), float (floati ng point), char (an unbroken sequence of characters without a space or tab), and string (a s equence of characters that can include spaces and tabs). Inputs are typically specified in metric units (m, m/s, g/m 3 , etc.). Model controls for time steps (dt), printout, initi al conditions (ICs), boundary conditions (BCs), and loads/forcing functions are input as pai red values in a time series (i.e. pairs of {function value at time t, time t}). Time steps and print intervals are step functions (i.e. the input value is used until time t, after which t he next value is used). ICs, BCs, and loads are piecewise linear functions (i.e. values a re linearly interpolated between times specified).

4.2 MAIN MODEL INPUT FILE Within this main input file, the inputs are divided into six groupings (Data Groups) of related parameters. Data Group A is used to specify general controls for the simulation such as the simulation type and the series of time steps to be used for numerical integration. Data Group B is used to specify parame ters for hydrologic simulations. Data Group C is used to specify parameters for sediment transport simulations. Data Group D is used to specify parameters for chemical transpor t simulations. Data Group E is used to specify parameters for environmental conditions suc h as air temperature and wind speed. Data Group F is used to specify parameters for mode l output control. However, users should note that not all possible combinations of m odel inputs are fully implemented in the model at this time. Users are advised to review the TREX source code.TREX User’s Manual Page 36

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.2.1 Data Group A: General Controls Data Group A: General Controls
Record Description 1 Header1 (string) 2 Header2 (string) 3 “KSIM” (char), ksim (int) {1 = hydrology, 2 = sed iment, 3 = chemical}, “NROWS”

(char), nrows (int), “NCOLS” (char), ncols (int), “ DX” (char), dx (float) (m), “DY” (char), dy (float) (m), “TZERO” (char), tzero (double) (day s) {used for environmental functions such as solar radiation}, “TSTART” (char), tstart ( double) (hrs) {time beyond tzero} Note tzero is the decimal value of the Julian day a t time zero (when the elapsed time is zero)

and tstart is the time along the specified time fun ctions where the simulation starts 4 “DTOPT” (char), dtopt (int) {0 = time steps input by user, 1 = time steps interatively calculated by model without simulation relaunch, 2 = time steps interatively calculated by model with simulation relaunch, 3 = time steps read from external file} Note The timestop option (dtopt) controls how numer ical integration occurs. TREX solves its

govering equations using a first-order, explicit so lver (Euler’s Method). When dtopt = 0, the user must specify the sequence (time series pairs) of time step (dt) values. If a time step is too large, numerical inst ability occurs and simulations will abort. When dtopt = 1, the model interatively calculates a sequence of time steps using Courant numbers determined in overland and channel flow rou ting routines. At any time level, simulations proceed using the time step for the las t successful time iteration. If the time step is too large and the maximum Courant number is exceeded, calculations are repeated using a smaller time step until Courant number cond itions are satisfied. If the time step is too small and Courant numbers fall below the minimu m Courant number, calculations are repeated using a larger time step until Courant num ber conditions are satisfied. The final sequence of calculated time steps is written to fil e for later use. Simulation relaunch does not occur for dtopt = 1 regardless of the ksim valu e input (i.e. ksim is overridden)

. When dtopt = 2, the model calculates a sequence of time steps using Courant conditions in the same manner as for dtopt = 1. Simulation relaun ch occurs if ksim > 1 (and dtopt = 2)

. For the case when ksim = 1 and dtopt = 2, the model will run the simulation, calculate time steps and end as specified. For the case when ksim > 1 and dtopt = 2, the model will override ksim, temporarily set ksim = 1, run the si mulation and determine time steps while performing hydrology calculations only, write time steps to file, reset ksim to its initial value and then relaunch the full simulation (ksim > 1) using the time steps written to file. Caution Automated time-stepping can reduce effort t o develop a full model simulation by reducing

the need to manually repeat simulations to determin e a sequence of time steps. However, run times for individual simulations will increase because calculations for any time level will be repeated as time steps are adjusted and wri tten to file. Once a successful time step sequence for a simulation is generated, users are a dvised to select dtopt = 3 and read those time step values from a file to minimize mode l run time impacts

. if dtopt = 0 5 “NDT” (char), ndt (int) {number of time step valu es}TREX User’s Manual Page 37

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Data Group A: General Controls (continued)
for idt = 1, ndt 6 dt[idt] (float) (s), dttime[idt] (float) (hrs) Note Record 6 is repeated for idt = 1, ndt elseif dtopt = 1 or dtopt = 2 7 “DTMAX” (char), dtmax (float) (s), “MAXCOURANT” ( char), maxcourant (float)

(dimensionless), “RELAXATION” (char), relaxation (f loat) (dimensionless), “ENDTIME” (char), dttime[ndt] (float) (hours) {simu lation end time in hours} 8 DTOUTPUTFILE (char), dtoutputfile (string) elseif dtopt = 3 9 “DTINPUTFILE” (char), dtinputfile (string) ReadDTFile endif dtopt = 0, 1 or 2, 3 10 “NPRINTOUT” (char), nprintout (int) {number of p rint intervals for tabular output} for iprntout = 1, nprintout 11 printout[iprntout] (float) (hrs), printouttime[i prntout] (float) (hrs) Note Record 11 is repeated for iprntout = 1, nprint out 12 “NPRINTGRID” (char), nprintgrid (int) {number of print intervals for grids output}, “GRIDSTART” (char), gridcount {starting value for g rid count, extension for grid files} for iprntgrid = 1, nprintgrid 13 printgrid[iprntgrid] (float) (hrs), printgridtim e[iprntgrid] (float) (hrs) Note Record 13 is repeated for iprntgrid = 1, nprin tgrid 14 “ECHO” (char), echofile (string) {required}

4.2.2 Data Group B: Hydrologic Simulation Parameters Data Group B: Hydrologic Simulation Parameters
Record Description 1 Header (string) 2 “MASK” (char), maskfile (string) call ReadMaskFileTREX User’s Manual Page 38

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Data Group B: Hydrologic Simulation Parameters (con tinued)
3 “ELEVATION” (char), elevationfile (string) (m) call ReadElevationFile 4 “INFOPT” (char), infopt (int) (0 = no infiltratio n, 1 = infiltration) if ksim = 1 {for ksim > 1, see Data Group C} if infopt = 1 {there is infiltration but no sedime nt transport} 5 “NSOILS” (char), nsoils (int) (number of soil typ es) for isoil = 1, nsoils 6 kh[isoil] (float) (m/s), capsh[isoil] (float) (m) , soilmd[isoil] (float) (dimensionless),

soilname[isoil] (string) Note Record 6 is repeated for isoil = 1, nsoils 7 “SOIL_TYPES” (char), soilfile (string) call ReadSoilFile endif infiltopt 8 “NLANDS” (char), nlands (int) (number of land use types) for iland = 1, nlands 9 nmanningov[iland] (float) (n units), interception class[iland] (float) (mm), landname[iland]

(string) Note Record 9 is repeated for iland = 1, nlands 10 “LAND_USE” (char), landusefile (string) call ReadLandUseFile endif ksim = 1 11 “STORAGE_DEPTHS” (char), storagedepthfile (strin g) (m) call ReadStorageDepthFile 12 “CHNOPT” (char), chnopt (int) (0 = no channels, 1 = channels) if chnopt = 1 13 “TPLGYOPT” (char), tplgyopt (int) {0 = compute t opology from channel property file

and link, and node masks, 1 = topology read from to pology file}, “CTLOPT” (char), ctlopt (int) (0 = no transmission loss, 1 = transmi ssion loss) {channel transmission loss option}, “FLDOPT” (char), fldopt (int) {0 = floodpl ain water transfer is from overland to channel only, 1= floodplain water transfer can be i n either direction depending on water surface elevations}, “OUTOPT” (char), outopt (int) {0 = pour water from overland to channel portion of cell before routing overland at outlets, 1 = route water overland before pouring into channel at outlets}TREX User’s Manual Page 39

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Data Group B: Hydrologic Simulation Parameters (con tinued)
if tplgyopt = 0 then 14 “LINK” (char), linkfile (string) call ReadLinkFile 15 “NODE” (char), nodefile (string) call ReadNodeFile 16 “CHANNEL” (char), chanfile (string) {includes ch annel “dead” storage} call ReadChannelFile call ComputeTopology Note Records 14, 15, and 16 are only input if tplgy opt = 0. elseif tplgyopt = 1 17 “TOPOLOGY” (char), topofile (string) {combines t he channel property, and the link and

node masks} {also includes channel “dead” storage} call ReadTopologyFile {for future use...} Note Record 17 is only input if tplgyopt = 1. Warning Option not fully implemented endif tplgyopt if ksim = 1 {for ksim > 1, see Data Group C} if ctlopt = 1 {there is channel transmission loss but no sediment transport} 18 “TRANSMISSION_LOSS_PROPERTIES” (char), channeltl ossfile (string) call ReadTransmissionLossProperties {read none-by- node transmission loss parameter

values} endif ctlopt = 1 endif ksim = 1 endif chnopt 19 (ICov) “INITIAL_WATER_OVERLAND” (char), initialw aterovfile (string) (m) call ReadInitialWaterOverlandFile if infopt = 1 20 (ICsoil) “INITIAL_INFILTRATION” (char), initiali nfiltrationfile (string) (m) call ReadInitialInfiltrationFile endif infopt = 1TREX User’s Manual Page 40

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Data Group B: Hydrologic Simulation Parameters (con tinued)
if (chnopt = 1) then 21 (ICch) “INITIAL_WATER_IN_CHANNELS” (char), initi alwaterchfile (string) (m) call ReadInitialWaterChannelFile 22 (ICsed) “INITIAL_TRANSMISSION_LOSS” (char), init ialtranslossfile (string) (m) call ReadInitalTransmissionLossFile endif chnopt 23 (W) “RAINOPT” (char), rainopt (int) Note rainopt: 0 = uniform in space, 1 = IDW spatial interpolation, 2 = design storm constant in

space from grid index map, 3 = radar data: location s and radar-derived rainrates from files, 4 = design storm basin-average (DAD or SST) input v ia file and distributed via elliptical pattern, 5 = time series grid read. if rainopt = 1 24 “IDWradius” (char), idwradius (float) (m), “IDWe xponent” (char), idwexponent (float)

(dimensionless) endif rainopt =1 if rainopt <= 2 25 “NRAINGAGES” (char), nrg (int) {by default rain is uniform if only one rain gage is

specified and distributed if there is more than one gage} Check if rainopt = 0 and nrg > 1, warn and abort... {if rainopt is zero, then nrg must equal 1} endif rainopt <= 2 if rainopt > 2 or nrg > 0 26 “CONV1” (char), rainconvunits (float), “CONV2” ( char), rainconvtime (float), “SCALE”

(char), rainscale (float) {Note: these scalars are globals as needed for rainopt = 5} endif rainopt > 2 or nrg > 0 if rainopt <=2 if nrg > 0 for irg = 1, nrg 27 “GAGE” (char), rgid[irg] (int), rgx[irg] (float) (m), rgy[irg] (float) (m), nrpairs[irg] (int) for irpairs = 1, nrpairs[irg] 28 rfintensity[irg][ipairs] (float) (m/s), rftime[i rg][ipairs] (float) (hrs) Note Records 27 and 28 are repeated as a group for irg = 1, nrg. Record 26 is repeated for ipairs

= 1, npairs[irg].TREX User’s Manual Page 41

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endif nrg > 0 if rainopt = 2 29 “DESIGN_RAIN_GRID” (char), designraingridfile (s tring) call ReadDesignRainGrid endif rainopt = 2 elseif rainopt = 3 30 “RADAR_RAIN_LOC” (char), radarlocationfile (stri ng) 31 “RADAR_RAIN_RATE” (char), radarrainfile (string) 32 “RADAR_VERIFY” (char), radarverifyfile (string) Note Reading routines called after we read the rada r verify file so that we can write echo output

to verify file. call ReadRadarRainLocations call ReadRadarRainRates (float float float) {pass in units conversions and scale} elseif rainopt = 4 33 “SPACE_TIME_STORM” (char), spacetimestormfile (s tring) call ReadSpaceTimeStorm (float float float) {pass in units conversions and scale} 34 “DAD_GRID” (char), dadstormgridfile (string) {ou tput} {this is grid pointer map of rain

cell locations in space, similar to generated desig nraingridfile} elseif rainopt = 5 35 “RAINGRIDFREQ” (char), raingridfreq (float) (hrs ) 36 “RAINGRIDFILES” (char), raingridfileroot (string ) endif rainopt <= 2 etc. 37a (W) “SNOWOPT” (char), snowopt (int), “MELTOPT” (char), meltopt (int) Note snowopt: 0 = no snowfall, 1 = compute snowfall from rain (precipitation) based on air

temperature, 2 = snow from gages (IDW interpolation in space), 3 = snow on ground from gages (SNOTEL, SNODAS), 4 = time series grid read. Only options 0, 1, 2, and 4 are implemented. meltopt: 0 = no snowmelt, 1 = compute snowmelt base d on modified temperature index, 2+ = options under development. Only options 0 and 1 are implemented. if snowopt > 0 or meltopt > 0 37b “TSNOW” (char), tsnow (float) (°C) {temperature below which precipitation falls as snow

and above which snow begins to melt, can be any val ue but expected value is 0-1 °C}TREX User’s Manual Page 42

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endif snowopt > 0 or meltopt > 0 if meltopt > 0 37c “LATITUDE” (char), latitude (float) (decimal de grees of latitude) {latitude of model

domain. Positive values represent Degrees North and negative values Degrees South} endif meltopt > 0 if snowopt = 2 38 “SnowIDWradius” (char), sidwradius (float) (m), “SnowIDWexponent” (char),

sidwexponent (float) (dimensionless) 39 “NSNOWGAGES” (char), nsg (int) {by default snowf all is uniform if only one snow gage is specified and distributed if there is more than one gage} if nsg > 0 40 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for isg = 1, nsg 41 “GAGE” (char), sgid[isg] (int), sgx[isg] (float) (m), sgy[isg] (float) (m), nspairs[isg] (int) for ispairs = 1, nspairs[isg] 42 sfintensity[isg][ipairs] (float) (m/s), sftime[i rg][ipairs] (float) (hrs) Note Records 41 and 42 are repeated as a group for isg = 1, nsg. Record 42 is repeated for ipairs

= 1, npairs[isg]. Also Note Records 38-42 apply for snowopt involving spatial interpolation of point data. endif nsg > 0 elseif snowopt = 3 Warning Warn user option(s) not implemented... elseif snowopt = 4 43 “SNOWGRIDFREQ” (char), snowgridfreq (float) (hrs ) 44 “CONV1” (char), snowconvunits (float), “CONV2” ( char), snowconvtime (float),

“SCALE” (char), snowscale (float) 45 “SNOWGRIDFILES” (char), snowgridfileroot (string ) endif snowopt = 2, 3, 4... if meltopt > 0 46 “ATMELT” (char), atmelt (float) (m/s/° C), “SRME LT” (char), srmelt (float)

(m/s/(W/m2)) {we might want to switch to reading gr id values rather than a constant...}TREX User’s Manual Page 43

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47 “DEM_SLOPE” (char), slopefile (string) (degrees) call ReadSlopeFile 48 “DEM_ASPECT” (char), aspectfile (string) (degree s) call ReadAspectFile 49 “SKYVIEW” (char), skyviewfile (string) (dimensio nless) call ReadSkyViewFile endif meltopt > 0 if snowopt > 0 or meltopt > 0 50 (ICsnw) “INITIAL_SNOW_OVERLAND” (char), initials nowovfile (string) (m) call ReadInitialSnowOverlandFile endif snowopt > 0 or meltopt > 0 51 (Wov) “NUMBER_OF_OVERLAND_FLOW_POINT_SOURCES” (c har) (Flow point sources

that enter or leave the overland plane by means oth er than rainfall or runoff and which are specified for individual cells, i.e. well, spring, irrigation diversion, etc.), nqwov (int) if nqwov > 0 52 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for i = 1, nqwov 53 qwovrow[i] (int), qwovcol[i] (int), nqwovpairs[i ] (int), qwovdescription[i] (string)

{qwovdescription is read to end of line as characte r} for ipairs = 1, nqovwpairs[i] 54 qwov[i][ipairs] (float) (m3/s), qwovtime[i][ipai rs] (float) (hrs) Note Records 53 and 54 are repeated as a group for i = 1, nqwov. Record 54 is repeated for

ipairs = 1, nqwovpairs[i]. qwov units: m 3 /s. endif nqwov > 0 if chnopt = 1 55 (Wch) “NUMBER_OF_CHANNEL_FLOW_POINT_SOURCES” (ch ar) (Flow point sources

that enter or leave thechannel by means other than rainfall or runoff and which are specified for individual nodes, i.e. mine adit, spr ing, irrigation diversion, etc.), nqwch (int) if nqchw > 0 56 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for i = 1, nqwchTREX User’s Manual Page 44

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57 qwchlink[i] (int), qwchnode[i] (int), nqwchpairs [i] (int), qwchdescription[i] (string)

{qdescription is read to end of line as character} for ipairs = 1, nqwchpairs[i] 58 qwch[i][ipairs] (float) (m3/s), qwchtime[i][ipai rs] (float) (hrs) Note Records 57 and 58 are repeated as a group for i = 1, nqwch. Record 58 is repeated for

ipairs = 1, nqwchpairs[i]. qwch units: m 3 /s. endif nqwch > 0 endif chnopt = 1 59 (BC) “NUMBER_OF_WATERSHED_OUTLETS/BOUNDARIES” (c har) (Locations where

flows leave the model domain via the overland plane and channel network), noutlets (int) for i = 1, noutlets 60 “OUTLET_CELL” (char), iout[i] (int) (m), jout[i] (int) (m), sovout[i] (float)

(dimensionless), dbcopt[i] (int) {0 = normal depth (s f = s o ), 1 = specified water depth time series} if dbcopt[i] > 0 61 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 62 nqbcpairs[i] (int), qbcdescription[i] (string) { qbcdescription is read to end of line as

character} for ipairs = 1, nqbcpairs[i] 63 qbc[i][ipairs] (float) (m), qbctime[i][ipairs] ( float) (hrs) Note Records 60-63 are repeated as a group for i = 1, noutlets. Within this group, Records 61-

63 are only input if dbcopt > 0. If dbcopt > 0, Rec ords 61 and 62 are input once and Record 63 is repeated for ipairs = 1, nqbcpairs[i]. qbc units: m. 64 “NQREPORTS” (char), nqreports (int) for iqreport = 1, nqreports 65 qreprow[iqreport] (int), qrepcol[iqreport] (int) , qarea[iqreport] (float) (km2),

qunitsopt[iqreport] (int) (1 = m3/s, 2= mm/hr), sta tionid (char) Note Record 65 is repeated for iqreport = 1, nqrepo rtsTREX User’s Manual Page 45

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.2.3 Data Group C: Sediment Transport Simulation Paramet ers Data Group C: Sediment Transport Simulation Paramet ers Record Description if ksim >= 2 then (if ksim >= 2, then sediment tra nsport is simulated) 1 Header (string) 2 “NSOLIDS” (char), nsolids (int), “NSGROUPS” (char ), nsgroups (int) Note nsolids = number of particle types, nsgroups = number of reporting groups for solids,

particles in a reported group are summed for a grou p total 3 “ADVOVOPT” (char), advovopt (int), “ADVOVSCALE”, advovscale (float),

“DSPOVOPT” (char), dspovopt (int), “DSPOVSCALE”, ds povscale (float), “DEPOVOPT” (char), depovopt (int), “DEPOVSCALE”, de povscale (float), “ERSOVOPT” (char), ersovopt (int), “ERSOVSCALE”, er sovscale (float), “TNSOVOPT” (char), tnsovopt (int), “TNSOVSCALE”, tn sovscale (float), “ELEVOVOPT” (char), elevovopt (int)
Note advovopt: 0 = advection bypassed, 1 = advection; ds povopt: 0 = dispersion bypassed, 1 =

dispersion; depovopt: 0 = deposition bypassed, 1 = deposition using the fall velocity, 2 = deposition using the fall velocity and the probabil ity of deposition); ersovopt: 0 = erosion bypassed, 1 = transport capacity limited erosion (K ilinc-Richardson), 2 = erosion from excess shear stress (untested); tnsovopt: 0 = no tr ansformations bypassed, 1 = transformations occur; elevovopt: 0 = overland elev ation update calculations bypassed, 1 = overland elevations updated if chnopt > 0 4 “ADVCHOPT” (char), advchopt (int), “ADVCHSCALE”, advchscale (float),

“DSPCHOPT” (char), dspchopt (int), “DSPCHSCALE”, ds pchscale (float), “DEPCHOPT” (char), depchopt (int), “DEPCHSCALE”, de pchscale (float), “ERSCHOPT” (char), erschopt (int), “ERSCHSCALE”, er schscale (float), “TNSCHOPT” (char), tnschopt (int), “TNSCHSCALE”, tnschscale (f loat), “ELEVCHOPT” (char), elevchopt (int)
Note advchopt: 0 = advection bypassed, 1 = advection; ds pchopt: 0 = dispersion bypassed, 1 =

dispersion; depchopt: 0 = deposition bypassed, 1 = deposition using the fall velocity, 2 = deposition using the fall velocity and the probabil ity of deposition; erschopt: 0 = erosion bypassed, 1 = transport capacity limited erosion (E ngelund and Hansen), 2 = erosion from excess shear stress (untested) {other options such as Ackers and White, Yang, etc. can be added here}; tnschopt: 0 = no transformations bypas sed, 1 = transformations occur; elevchopt: 0 = channel bed elevation update calcula tions bypassed, 1 = channel bed elevations updated endif chnopt > 0 Also Note The process options for Records 3 and 4 t oggle use (on or off) of the different process

routines (for sediment transport). However, when ze ro is selected for a process option, the process is bypassed but the user must still enter p rocess parameters (as if the option = 1) as required in later records. 5 Header (string): “PARTICLE GROUP NAMES FOR REPORT ING”TREX User’s Manual Page 46

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for igroup = 1, nsgroups 6 “GROUPNUMBER” (char), particlegroupname[igroup] ( string) Note Record 6 is repeated for igroup = 1, nsgroups. 7 Header (string): “PARTICLE CHARACTERISTICS: ds, G , ws,” {depending on process

options add:} “cncopt, tcdov, tcdch,” ... “groupnum ber, particlename” Particles for isolid = 1, nsolids 8a (general) ds[isolid] (float) (m), spgravity[isolid] (float) ( dimensionless), ws[isolid] (float) (m/s)
if depovopt > 1 or depchopt > 1 or ersovopt > 1 or erschopt > 1 8b (type) cncopt[isolid] (int) (cohesive/non-cohesi ve transport option) {0 = non-cohesive (Gessler),

1 = cohesive (Partheniades)} endif depovopt > 1 or depchopt > 1 or ersovopt > 1 or erschopt > 1 if depovopt > 1 8c (depov) tcdov[isolid] (float) (N/m2 = Pa) endif depovopt > 1 if ersovopt > 1 8d (ersov) tceov[isolid] (float) (N/m2 = Pa), zageo v[isolid] (float) (dimensionless) endif ersovopt > 1 if chnopt > 0 if depchopt > 1 8e (depch) tcdch[isolid] (float) (N/m2 = Pa) endif depchopt > 1 if erschopt = 1 {modified Engelund and Hansen} 8f (ersch = 1) vcch[isolid] (float) (m/s) {critical velocity motio n threshold}
elseif erschopt > 1 8g (ersch > 1) tcech[isolid] (float) (N/m2 = Pa), zagech[isolid] ( float) (dimensionless)
endif erschopt = 1 endif chnopt > 0 8h sgroupnumber[isolid] (int), particlename[isolid] (string)TREX User’s Manual Page 47

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Note Record 8 (a-h) is repeated for isolid = 1, nso lids. if tnsovopt > 0 or tnschopt > 0 9 Header (string): “PARTICLE REACTIONS: abrasion, f locculation, dissolution, etc.” Reactions for i = 1, nsolids 10 “SOLID” (char), isolid (int), “NFIELDS” (char), nfields (int) for ifields = 1, nfields[ichem] 11 ncns (int), fieldname (string) for icns = 1, ncns 12 sname (char), sid (int), svalue (float) 13 “NSYIELDS” (char), nsyields (int) for iyield = 1, nsyields 14 syldfrom[iyield] (int), syldto[iyield] (int), sy ldprocess[iyield] (int), syield[iyield] (float)

(g/g) Note Records 10, 11, 12, and 13 are repeated as a g roup for i = 1, nsolids. Record 10 is input

once. Records 11 and 12 are repeated as a group for iflds = 1, nflds[i]. Within this group, Record 12 is repeated for icns = 1, ncns. Record 13 is input once. Record 14 is repeated for iyield = 1, nyields. endif tnsovopt > 0 or tnschopt > 0 15 (ICov) Header (string): “SOIL CHARACTERISTICS: e rosion parameters, grain size distribution

etc.” 16 “NSOILS” (char), nsoils (int) {number of soil ty pes} Soils for isoil = 1, nsoils if infiltopt = 0 {no infiltration, but there still is sediment transport} if ersovopt <= 1 17 kusle[isoil] (float) (dimensionless), vcov[isoil ] (float) (m/s), porosityov[isoil] (float),

soilname[isoil] (string) {for ksim >1, infopt = 0, and ersovopt = 1, kusle is the only soil parameter specified; cusle and pusle are land use p arameters...} else (ersovopt > 1) 18 mexpov[isoil] (float) (dimensionless), porosityo v[isoil] (float), soilname[isoil] (string) endif ersovopt <= 1 elseif infopt > 0 {both infiltration and sediment transport} if ersovopt <= 1TREX User’s Manual Page 48

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19 kusle[isoil] (float) (dimensionless), vcov[isoil ] (float) (m/s), porosityov[isoil] (float)

(dimensionless), kh[isoil] (float) (m/s), capsh[iso il] (float) (m), soilmd[isoil] (float) (dimensionless), soilname[isoil] (string) else (ersovopt > 1) 20 mexpov[isolid] (float) (dimensionless), porosity ov[isoil] (float) (dimensionless), kh[isoil]

(float) (m/s), capsh[isoil] (float) (m), soilmd[iso il] (float) (dimensionless), soilname[isoil] (string) endif ersovopt <= 1 21a (label) “SoilGSD:” (char) for isoil=1, nsolids 21b (gsd) gsdov[isoil][isolid] (float) Check Compute gsdovtot += gsdov[isoil][isolid]. If gsdovtot != 1.0 then abort. Note Record 17/18/19/20 and 21 are repeated as a gr oup. Only one Record (17 or 18 or 19 or

20) is entered. The record that is entered depends on the values of infopt and ersovopt. The group is repeated for isoil = 1, nsoils. endif infopt = 0 22 Header (string): “LAND USE CHARACTERISTICS: Cusl e, grain size distribution” 23 “NLANDS” (char), nlands (int) {number of land us e types} if ersovopt <= 1 for iland = 1, nlands 24 nmanningov[iland] (float) (n units), interceptio nclass[iland] (float) (mm), cusle[iland]

(float) (dimensionless), pusle[iland] (float) (dime nsionless), landname[iland] (string) else (ersovopt > 1) for iland = 1, nlands 25 nmanningov[iland] (float) (n units), interceptio nclass[iland] (float) (mm), ayov[iland]

(float) (g/cm2), landname[iland] (string) endif ersovopt <= 1 Note Only one Record (24 or 25) is entered. The rec ord that is entered depends on the value of

ersovopt and is repeated for iland = 1, nlands. 26 “LAND_USE” (char), landusefile (string) call ReadLandUseFile 27 Header (string): “SOIL STACK AND LAYER PROPERTIE S: thickness, grain size

distribution”TREX User’s Manual Page 49

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28 “MAXSTACKOV” (char), maxstackov (int), “MINVOLOV ” (char), minvolov (float)

(dimensionless), “MAXVOLOV” (char), maxvolov (float ) (dimensionless), “STKOVOPT” (char), stkovopt (int) {0 = stack does n ot collapse, 1 = stack collapses} 29 “SOIL_STACK” (char), soilstackfile (string) {ini tial number of layers in each grid cell} call ReadSoilStackFile for i = maxstackov to 1 (reverse order) 30 “THICKNESS_LAYERn” (char), thicknessgrid (string ) {thickness values in meters} Read SoilLayerThicknessFile 31 “SOIL_TYPES_LAYERn” (char), soilfile (string) call ReadSoilTypeFile Note The information for Records 30 and 31 is read in reverse order (layer 1 is last). 32 Header (string): “INITIAL SUSPENDED SOLIDS CONCE NTRATIONS IN THE

OVERLAND PLANE: one grid file for each solids type” for isolid=1, nsolids 33 “GRIDFILE_FOR_SOLIDn” (char), initialssovfile (s tring) call ReadInitialSolidsOverland Note Record 32 is input once. Record 33 is repeated for isolid = 1, nsolids if chnopt > 0 34 (ICch) Header (string): “SEDIMENT STACK CHARACTE RISTICS AND LAYER

PROPERTIES: number of layers, thickness, grain size distribution” 35 “MAXSTACKCH” (char), maxstackch (int), “MINVOLCH ” (char), minvolch (float)

(dimensionless), “MAXVOLCH” (char), maxvolch (float ) (dimensionless), “STKCHOPT” (char), stkchopt (int) {0 = stack does n ot collapse, 1 = stack collapses} 36 “SEDIMENT_PROPERTIES_FILE” (char), sedimentprope rtiesfile (string) call ReadSedimentPropertiesFile 37 “INITIAL_SUSP_SOLIDS_CHANNELS” (char), initialss chfile (string) call ReadInitialSolidsChannelFile endif chnopt > 0 for isolid = 1, nsolids 38 (Wpov) “NUMBER_OF_OVERLAND_LOADS_FOR_SOLIDSn” (c har), nswpov[isolid] (int) if nswpov[isolid] > 0TREX User’s Manual Page 50

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39 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for isw = 1, nswpov[isolid] 40 swpovrow[isolid][isw] (int), swpovcol[isolid][is w] (int), nswpovpairs[isolid][isw] (int),

swpovopt[isolid][isw] (int), loadname (string) {rea d to end of line} for iswpair = 1, nswpovpairs[isolid][isw] 41 swpov[isolid][isw][iswpair] (float) (kg/day), sw povtime[isolid][isw][iswpair] (float) (hrs) endif nswch[isolid] > 0 Note Records 38, 39, 40, and 41 are repeated as a g roup for isolid = 1, nsolids. Record 38 is

input once. Record 39 is input once. Records 40 and 41 are repeated as a group for isw = 1, nswpov[isolid]. Record 41 is repeated for iswpai r = 1, nswpovpairs[isolid][isw] for isolid = 1, nsolids 42 (Wdov) “NUMBER_OF_OVERLAND_DISTRIBUTED_LOADS_FOR _SOLIDSn” (char),

nswdov[isolid] (int) if nswdov[isolid] > 0 for isw = 1, nswdov[isolid] 43 “AREAS_FOR_SOLIDSn_WASHOFF_FUNCTIONn” (char), sw dovareafile[isolid][isw]

(string) call ReadSWDovAreaFile 44 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 45 nswdovpairs[isolid][isw] (int), loadname (string ) {read to end of line} for iswpair = 1, nswdovpairs[isolid][isw] 46 swdov[isolid][isw][iswpair] (float) (g/m2/mm rai n), swdovtime[isolid][isw][iswpair]

(float) (hrs) endif nswdov[isolid] > 0 Note Distributed loads are treated as rainfall-driv en “washoff” loads where the load is specified

as a mass per unit area per unit of rain. A grid of washoff areas for each cell must be input as well as a time series for the load. Note Records 42, 43, 44, 45, and 46 are repeated as a group for isolid = 1, nsolids. Record 42 is

input once. Records 43, 44, 45, and 46 are repeated as a group for isw = 1, nswdov[isolid]. Record 46 is repeated for iswpair = 1, nswdovpairs[ isolid][isw] if chnopt > 0 for isolid = 1, nsolidsTREX User’s Manual Page 51

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47 (Wpch) “NUMBER_OF_CHANNEL_LOADS_FOR_SOLIDSn” (ch ar), nswch[isolid] (int) if nswch[isolid] > 0 48 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for isw = 1, nswch[isolid] 49 swchlink[isolid][isw] (int), swchnode[isolid][is w] (int), nswchpairs[isolid][isw] (int),

loadname (string) {read to end of line} for iswpair = 1, nswchpairs[isolid][isw] 50 swch[isolid][isw][iswpair] (float) (kg/day), swc htime[isolid][isw][iswpair] (float) (hrs) Note Records 47, 48, 49, and 50 are repeated as a g roup for isolid = 1, nsolids. Record 47 is

input once. Record 48 is input once. Records 49 and 50 are repeated as a group for isw = 1, nswch[isolid]. Record 50 is repeated for iswpair = 1, nswchpairs[isolid][isw] endif nswch[isolid] > 0 endif chnopt > 0 for ioutlet = 1, noutlets 51 (BC) Header (string) {read to end of line} {Exam ple: “SOLIDS BOUNDARY CONDITIONS FOR OUTLET ioutlet”} if dbcopt[ioutlet] > 0 52 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for isolid = 1, nsolids 53 nsbcpairs[ioutlet][isolid] (int), bcname (string ) {read to end of line} {Example:

“BOUNDARY CONDITIONS FOR SOLID TYPE isolid”} for isbcpair = 1, nsbcpairs[ioutlet] 54 sbc[ioutlet][isolid][isbcpair] (float) (g/m3), s bctime[ioutlet][isolid][isbcpair] (float) (hrs) Note Records 51, 52, 53, and 54 are repeated as a g roup for ioutlet = 1, noutlets. Record 51 is

input once. Records 52, 53, and 54 are only input i f dbcopt[ioutlet] > 0. Record 52 is input once. Records 53 and 54 are repeated as a group for isolid = 1, nsolids. Within this group, Record 54 is repeated for isbcpairs = 1, nsbcpairs[ ioutlet]. endif dbcopt[ioutlet] > 0 55 “NSEDREPORTS” (char), nsedreports (int) for isedreport = 1, nsedreportsTREX User’s Manual Page 52

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56 sedreprow[isedreport] (int), sedrepcol[isedrepor t] (int), sedarea[isedreport] (float) (km2),

sedunitsopt[isedreport] (int) {1 = g/m3, 2 = kg (ma ss transported over the reporting interval)}, stationid (char) Note Record 56 is repeated for isedreport = 1, nsed reports. Reports are for all solids types

simulated endif ksim >= 2

4.2.4 Data Group D: Contaminant Transport Simulation Para meters Data Group D: Contaminant Transport Simulation Para meters
Record Description if ksim >= 3 then (if ksim >= 3, then chemical tra nsport is simulated) 1 Header (string) 2 “NCHEMICALS” (char), nchems (int), “NCGROUPS” (ch ar), ncgroups (int) Note nchems = number of chemical types, ncgroups = number of reporting groups for

chemicals, chemicals in a reported group are summed for a group total 3 Header (string): “CHEMICAL GROUP NAMES FOR REPORT ING” for igroup = 1, ncgroups 4 chemgroupname[igroup] (char) Note Record 4 is repeated for igroup = 1, ncgroups. 5 Header (string): “PROPERTIES FOR CHEMICALS” for ichem = 1, nchems 6 “CHEMICAL n” (char), ichem (int), “NFIELDS” (char ), nflds[ichem] (int),

“GROUPNUMBER” (char), cgroupnumber[ichem] (int), ch emname[ichem] (string) for ifields = 1, nfields[ichem] 7 ncns (int), fieldname (string) for icns = 1, ncns 8 cname (char), cid (int), cvalue (float) 9 “NCYIELDS” (char), ncyields[ichem] (int) for iyield = 1, ncyields 10 cyldfrom[iyield] (int), cyldto[iyield] (int), cy idprocess[iyield] (int), cyield[iyield] (float)

(g/g)TREX User’s Manual Page 53

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Note Records 5, 6, 7, 8, and 9 are repeated as a gr oup for ichem = 1, nchems. Record 5 is input

once. Records 6, 7, and 8 are repeated as a group f or iflds = 1, nflds[ichem]. Within this group, Record 8 is repeated for icns = 1, ncns. Rec ord 9 is input once. Record 10 is repeated for iyield = 1, ncyields. Definitions Chemical Properties and Reaction Pathwa ys are defined in Section 4.3 11 (ICov) Header (string): “INITIAL CHEMICAL CONCEN TRATIONS IN SOIL” for ilayer = maxlayersov, 1, -1 (reverse order, al l possible layers even if null) for ichem = 1, nchems 12 “SOIL_ICs_LAYER_ilayer_CHEMICAL_n” (char), soilc hemfile (string) (mg/kg) call ReadSoilLayerChemicalFile() Note Record 12 is repeated for for ilayer = maxlaye rsov, 1, -1 (reverse order) and ichem = 1,

nchems. One grid file for each chemical repeated fo r each layer. for ichem = 1, nchems 13 Header (string): “INITIAL CHEMICAL CONCENTRATION S IN THE OVERLAND

PLANE WATER COLUMN: one grid file for each chemical type” for ichem=1, nchems 14 “GRIDFILE_FOR_CHEMICALn” (char), initialchemovfi le (string) call ReadInitialChemicalOverland Note Record 13 is input once. Record 14 is repeated for ichem = 1, nchems if chnopt > 0 15 (ICch) Header (string): “INITIAL CHEMICAL CONCEN TRATIONS IN SEDIMENT” 16 “CHEMICAL_SEDIMENT_CONCENTRATION_FILE” (char), s edimentchemfile

(string) (mg/kg) call ReadSedimentChemicalFile 17 “INITIAL_CHEMICAL_CHANNELS” (char), initialchemc hfile (string) call ReadInitialChemicalChannelFile endif chnopt = 1 for ichem = 1, nchems 18 (Wov) “NUMBER_OF_OVERLAND_LOADS_FOR_CHEMICALn” ( char), ncwpov[ichem]

(int) if ncwpov[ichem] > 0 19 “CONV1” (char), conunit (float), “CONV2” (char), contime (float), “SCALE” (char),

scale (float)TREX User’s Manual Page 54

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for icw = 1, ncwpov[ichem] 20 cwpovlink[ichem][icw] (int), cwpovnode[ichem][ic w] (int), ncwpovpairs[ichem][icw]

(int), loadname (string) for icwpair = 1, ncwpovpairs[icw] 21 cwpov[ichem][icw][icwpair] (float) (kg/day), cwp ovtime[ichem][icw][icwpair] (float)

(hrs) Note Records 18, 19, 20, and 21 are repeated as a g roup for ichem = 1, nchems. Record 18 and

19 are each input once. Records 20 and 21 are repea ted for icw = 1, ncwpov[ichem]. Record 21 is repeated for icwpair = 1, ncwpovpairs[ ichem][icw]. Loads input as kg/day. endif ncwpov[ichem] > 0 for ichem = 1, nchems 22 (Wdov) “NUMBER_OF_OVERLAND_DISTRIBUTED_LOADS_FOR _CHEMICALn” (char),

ncwdov[isolid] (int) if ncwdov[ichem] > 0 for icw = 1, ncwdov[ichem] 23 “AREAS_FOR_CHEMICALn_WASHOFF_FUNCTIONn” (char),

cwdovareafile[ichem][icw] (string) call ReadCWDovAreaFile 24 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 25 ncwdovpairs[isolid][isw] (int), loadname (string ) {read to end of line} for icwpair = 1, ncwdovpairs[ichem][icw] 26 cwdov[ichem][icw][icwpair] (float) (g/m2/mm rain ), cwdovtime[ichem][icw][icwpair]

(float) (hrs) endif ncwdov[ichem] > 0 Note Distributed loads are treated as rainfall-driv en “washoff” loads where the load is specified

as a mass per unit area per unit of rain. A grid of washoff areas for each cell must be input as well as a time series for the load. Note Records 22, 23, 24, 25, and 26 are repeated as a group for isolid = 1, nsolids. Record 22 is

input once. Records 23, 24, 25, and 26 are repeated as a group for isw = 1, nswdov[isolid]. Record 26 is repeated for iswpair = 1, nswdovpairs[ isolid][isw] if chnopt > 0 for ichem = 1, nchems 27 (Wch) “NUMBER_OF_CHANNEL_LOADS_FOR_CHEMICALn” (c har), ncwch[ichem] (int)TREX User’s Manual Page 55

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if ncwch[ichem] > 0 28 “CONV1” (char), conunit (float), “CONV2” (char), contime (float), “SCALE” (char),

scale (float) for icw = 1, ncwch[ichem] 29 cwchlink[ichem][icw] (int), cwchnode[ichem][icw] (int), ncwchpairs[ichem][icw] (int),

loadname (string) for icwpair = 1, ncwpovpairs[icw] 30 cwch[ichem][icw][icwpair] (float) (kg/day), cwch time[ichem][icw][icwpair] (float) (hrs) Note Records 27, 28, 29, and 30 are repeated as a g roup for ichem = 1, nchems. Record 27 and

28 are each input once. Records 29 and 30 are repea ted for icw = 1, ncwch[ichem]. Record 30 is repeated for icwpair = 1, ncwchpairs[ichem][i cw]. Loads input as kg/day. endif ncwch[ichem] > 0 endif chnopt > 0 for ioutlet = 1, noutlets if dbcopt[ioutlet] > 0 31 (BC) Header (string) {read to end of line} {Exam ple: “CHEMICAL BOUNDARY CONDITIONS FOR OUTLET ioutlet”} 32 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) for ichem = 1, nchems 33 nsbcpairs[ioutlet][isolid] (int), bcname (string ) {read to end of line} {Example:

“BOUNDARY CONDITIONS FOR CHEMICAL TYPE ichem”} for icbcpair = 1, ncbcpairs[ioutlet] 34 cbc[ioutlet][ichem][icbcpair] (float) (g/m3), cb ctime[ioutlet][ichem][icbcpair] (float) (hrs) Note Records 31, 32, 33, and 34 are repeated as a g roup for ioutlet = 1, noutlets. Record 31 is

input once. Records 32, 33, and 34 are only input i f dbcopt[ioutlet] > 0. Record 32 is input once. Records 33 and 34 are repeated as a group for ichem = 1, nchems. Within this group, Record 34 is repeated for icbcpairs = 1, ncbcpairs[ ioutlet]. endif dbcopt[ioutlet] > 0 35 “NCHEMREPORTS” (char), nchemreports (int) for ichemreport = 1, nchemreports 36 chemreprow[ichemreport] (int), chemrepcol[ichemr eport] (int), chemarea[ichemreport]

(float) (km2), chemunitsopt[ichemreport] (int) {1 = g/m3, 2 = kg (mass transported over the reporting interval)}, stationid (char)TREX User’s Manual Page 56

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Note Record 36 is repeated for: ichemreport = 1, nc hemreports. Reports are for all chemical

types simulated. endif ksim >= 3

4.2.5 Data Group E: Environmental Properties Environmental properties are developmental features that are not fully implemented at this time. For hydrology and sediment transport sim ulations (ksim = 1 or 2), Records 1 and 2 must always be entered. For chemical transpor t simulations (ksim =3), Records 1, 2, 10, and 27 must be entered. If channels are simu lated (chnopt > 0), Record 20 and 37 are also entered. For these records, the required i nput values should each be set to zero until the features of the relevant sections of Data Group E are fully implemented. A more detailed description of environmental functions is presented in Section 4.4 Data Group E: Environmental Properties (ph, water t emp, air temp, etc)
Record Description 1 Header (string) “Data Group E: Environmental Prop erties” 2 “General_Environmental_Properties_NPROPG” (char), npropg (int) for iprop=1, npropg 3 “PROPERTY” (char), pid (int), “CONVUNITS” (char), convunits (float), “SCALE”

(char), scale (float), “NFUNCTIONS” (char), nenvgtf (int) 4 “Cell_Multiplier_Value_Grid” (char), parameterfil e (string)

{value for each cell is used as a multiplier of the time function value for that cell} call ReadGeneralEnvironmentFile(pid, convunits, sc ale) if nenvgtf[iprop] > 0 5 “TimeFunction_Pointer_Grid” (char), tfpointerfile (string)

{identifies which time function (1–nenvgtf[]) is us ed by each cell in the model domain} call ReadGeneralFunctionPointerFile(iprop) for itf=1, nenvgtf[iprop] 6 “TimeFunctionID” (char), tfid (int), “STATIONELEV ” (char), stnelevenvg (float), tfname

(string) Note The station elevation is needed for laspe rate calculations for many parameters such as air

temperature, vapor pressure... 7 “CONV1” (char), convunits (float), “CONV2” (char) , convtime (float), “SCALE” (char),

scale (float)TREX User’s Manual Page 57

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8 “NTFGPAIRS”(char), nenvgtfpairs[iprop][itf] (int) for itfpair = 1, nenvgtfpairs[iprop][itf] 9 envgtf[iprop][itf][itfpair] (float) (units vary), envgtftime[iprop][itf][itfpair] (float) (hrs) Note Units for time function values vary. endif nenvgtf[iprop] > 0 Note Records 3 through 9 are repeated as a group fo r iprop = 1, npropg. Records 3 and 4 are

input once. If nenvgtf[iprop] > 0, Records 5 throug h 9 are input. Record 5 is input once. Records 6, 7, 8, and 9 are repeated as a group for itf = 1, nenvovtf[iprop]. Within this group, Records 6, 7, and 8 are each input once and Record 9 is repeated for itfpairs = 1, nenvgtfpairs[iprop][itf]. if ksim > 2 10 “Overland_Environmental_Properties_NPROPOV” (cha r), npropov (int) for iprop=1, npropov 11 “PROPERTY” (char), pidov (int), “CONV1” (char), convunits (float), “SCALE” (char),

scale (float), “NFUNCTIONS” (char), nenvovtf (int) 12 “Cell_Value_Grid_Layer_n” (char), parameterfile (string) call ReadOverlandEnvironmentFile(pid, 0, conv1, sc ale) if nenvovtf[iprop] > 0 13 “TimeFunction_Pointer_Grid” (char), tfpointerfil e (string) call ReadOverlandFunctionPointerFile(pid, ilayer, conv1, scale) endif nenvovtf[iprop] > 0 for ilayer = maxstackov, 1, -1 {Reverse Order!!} 14 “Cell_Value_Grid_Layer_n” (char), parameterfile (string) call ReadOverlandEnvironmentFile if nenvovtf[iprop] > 0 15 “TimeFunction_Pointer_Grid” (char), tfpointerfil e (string) call ReadOverlandFunctionPointerFile endif nenvovtf[iprop] > 0 if nenvovtf[iprop] > 0 for itf=1, nenvovtf[iprop] 16 “TimeFunctionID” (char), tfid (int), tfname (str ing)TREX User’s Manual Page 58

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17 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 18 “NTFOVPAIRS”(char), nenvovtfpairs[iprop][itf] (i nt) for itfpair = 1, nenvovtfpairs[iprop][itf] 19 envovtf[iprop][itf][itfpair] (float) (units vary ), envovtftime[iprop][itf][itfpair] (float) (hrs) Note Units for time function values vary. Note Records 11 through 19 are repeated as a group for iprop = 1, npropov. Records 11 and 12

are input once. If nenvovtf[iprop] > 0, Record 13 i s input once. Records 14 and 15 are input only if ksim > 1 and are repeated as a group for ilayer = maxstackov, 1, -1 (in reverse order). Within this group, Record 16 is onl y input if nenvovtf[iprop] > 0. Records 16, 17, 18 and 19 are repeated as a group for itf = 1, nenvovtf[iprop]. Within this group, Records 16, 17, and 18 are each input once and Reco rd 19 is repeated for itfpairs = 1, nenvovtfpairs[iprop][itf]. end if nenvovtf[iprop] > 0 if chnopt > 0 20 “Channel_Environmental_Properties_NPROPCH” (char ), npropch (int) for iprop=1, npropch 21 pname (char), pidch (int), fname (char), “CONV1” (char), convunits (float), “SCALE”

(char), scale (float), “NFUNCTIONS” (char) (dummy), nenvchtf (int) 22 “ENV_PROPERTY_FILE_FOR_CHANNEL” (char), paramete rfile (string) {water

column and sediment stack} call ReadChannelEnvironmentFile(pid, 0, conv1, sca le) if nenvchtf[iprop] > 0 for itf=1, nenvchtf[iprop] 23 “TimeFunctionID” (char), tfid (int), tfname (str ing) 24 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 25 “NTFCHPAIRS”(char), nenvchtfpairs[iprop][itf] (i nt) for itfpair = 1, nenvchtfpairs[iprop][itf] 26 envchtf[iprop][itf][itfpair] (float) (units vary ), envchtftime[iprop][itf][itfpair] (float) (hrs) Note Units for time function values vary. Note Records 21, through 26 are repeated as a group for iprop = 1, npropch. Records 21 and 22

are input once. Records 23, 24, 25, and 26 are repe ated as a group for itf = nenvchtf[iprop]. Within this group, Records 23, 24, 25 are input once and Record 26 is repeated for itfpair = 1, nenvchtfpairs[itf].TREX User’s Manual Page 59

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end if nenvchtf > 0 27 “Overland_Particle_Organic_Carbon_FPOCOVOPT” (ch ar), fpocovopt (int) Note fpocovopt is the option for specification of p article organic carbon content:

0 = fpoc for the overland plane not specified (the default value is 1.0, i.e. fpocov[isolid][row][col][layer] = 1.0 and is contan t in space and time) 1 = a grid of values for each particle type with as sociated time functions and pointers is entered for the overland plane (water column and so il stack) and a channel environmental property file with associated time functions and po inters is entered for the channel network if focopt > 0 for isolid=1, nsolids 28 “SOLIDTYPE” (char), pid (int), “SCALE” (char), s cale (float), “NFUNCTIONS” (char),

nfpocovtf (int) {number of FOC time functions for t he specified solids type...} 29 “Cell_Value_Grid_Layer_n” (char), parameterfile (string) call ReadOverlandFpocFile(isolid, 0, conv1, scale) if nfpocovtf[isolid] > 0 30 “TimeFunction_Pointer_Grid” (char), tfpointerfil e (string) call ReadOverlandFpocTFPointerFile(pid, ilayer, co nv1, scale) endif nfpocovtf[isolid] > 0 if ksim > 1 {ksim must be > 1} for ilayer = maxstackov, 1, -1 {Reverse Order!!} 31 “Cell_Value_Grid_Layer_n” (char), parameterfile (string) call ReadOverlandFpocFile if nfpocovtf[isolid] > 0 32 “TimeFunction_Pointer_Grid” (char), tfpointerfil e (string) call ReadOverlandFpocTFPointerFile(isolid) endif nfpocovtf[isolid] > 0 Note Records 31 and 32 are repeated as a block for ilayer=maxstackov, 1, -1 (reverse order). if nfpocovtf[isolid] > 0 for itf=1, nfpovovtf[isolid] 33 “TimeFunctionID” (char), tfid (int), tfname (str ing)TREX User’s Manual Page 60

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34 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 35 “NTFOVPAIRS”(char), nfpocovtfpairs[isolid][itf] (int) for itfpair = 1, nfpocovtfpairs[isolid][itf] 36 fpocovtf[isolid][itf][itfpair] (float) (dimensionle ss: 0

– 1), fpocovtftime[isolid][itf][itfpair]

(float) (hrs) endif nfpocovtf[isolid] > 0 Note Records 28 through 36 are repeated as a group for isolid = 1, nsolids. Within this group,

Records 28, 29, and 30 are input once. Records 31 a nd 32 are repeated as a group for ilayer = maxstackov, 1, -1 (in reverse order). If n fpocovtf[isolid] > 0, Record 33 though 36 are input. Within this group, Records 33, 34, 35 ar e each input once and Record 36 is repeated for itfpairs = 1, nfpocovtfpairs[isolid][i tf]. endif fpocovopt > 0 if chnopt > 0 37 “Channel_Particle_Organic_Carbon_FPOCCHOPT” (cha r), fpocchopt (int) Note fpocchopt is the option for specification of p article organic carbon content:

0 = fpoc for the channel is not specified (the defa ult value is 1.0, i.e. fpocch[isolid][link][node][layer] = 1.0 and is cont ant in space and time) 1 = a channel environmental property file with asso ciated time functions and pointers is entered for the channel network if fpocchopt > 0 38 pname (char), pid (int), “SCALE” (char), scale ( float), “NFUNCTIONS” (char) (dummy),

nfpocchtf (int) 39 “Fpoc_PROPERTY_FILE_FOR_CHANNEL” (char), paramet erfile (string) {water

column and sediment stack} call ReadChannelFpocFile(pid, 0, conv1, scale) if nfpocchtf[iprop] > 0 for itf=1, nfpocchtf[iprop] 40 “TimeFunctionID” (char), tfid (int), tfname (str ing) 41 “CONV1” (char), convunits (float), “CONV2” (char ), convtime (float), “SCALE” (char),

scale (float) 42 “NTFCHPAIRS”(char), nfpocchtfpairs[iprop][itf] ( int) for itfpair = 1, nfpocchtfpairs[iprop][itf]TREX User’s Manual Page 61

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43 fpocchtf[iprop][itf][itfpair] (float) (dimensionles s: 0

– 1), fpocchtftime[iprop][itf][itfpair]

(float) (hrs) endif fpocchopt > 0 endif ksim > 2

4.2.6 Data Group F: Ouput Specification Controls Data Group F: Ouput Specification Controls
Record Description 1 Header (string) if nqreports > 0 2 Header (string) such as “EXPORT TIME SERIES OUPUT S” 3 “WATER_EXPORT” (char), waterexpfile (string) endif nqreports > 0 if ksim > 1 if nsedreports > 0 4 “SEDIMENT_EXPORT_ROOT” (char), sedexprootfile (st ring) 5 “SEDIMENT_EXPORT_EXT” (char), sedextension (strin g) endif nsedreports > 0 if ksim > 2 if nchemreports > 0 6 “CHEMICAL_EXPORT_ROOT” (char), chemexpfile (strin g) 7 “CHEMICAL_EXPORT_EXT” (char), chemextention (stri ng) endif nchemreports > 0 endif ksim > 2 endif ksim > 1 8 Header (string) such as “POINT-IN-TIME GRID OUPUT S” 9 “RAINFALL_RATES” (char), rainrategrid (string) (P ath and file name) (mm/hr) 10 “RAINFALL_DEPTH” (char), raindepthgrid (string) (Path and file name) (mm) 11 “INFILTRATION_RATE” (char), infrategrid (string) (Path and file name) (mm/hr)TREX User’s Manual Page 62

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12 “INFILTRATION_DEPTH” (char), infdepthgrid (strin g) (Path and file name) (mm) 13 “WATER_DISCHARGE” (char), qgrid (string) (Path a nd file name) (m 3 /s) 14 “WATER_DEPTH” (char), waterdepthgrid (string) (P ath and file name) (m) if snowopt > 1 15 “SWEFALL_RATE” (char), swefallgrid (string) (Pat h and file name) (mm/hr) 16 “SWEFALL_DEPTH” (char), swefalldepthgrid (string ) (Path and file name) (mm) endif snowopt > 1 if meltopt > 0 17 “SWEMELT_RATE” (char), swemeltrategrid (string) (Path and file name) (mm/hr) 18 “SWEMELT_DEPTH” (char), swemeltdepthgrid (string ) (Path and file name) (mm) endif meltopt > 0 if snowopt > 0 or meltopt > 0 19 “SWE_DEPTH” (char), swedepthgrid (string) (Path and file name) (m) endif snowopt > 0 or meltopt > 0 if ksim > 1 20 “SOLID_CONC_WATER_ROOT” (char), solidsconcwaterg ridroot (string) (report for

total and groups) (Path...\root) (g/m 3 ) 21 “SOLID_CONC_SURFACE_LAYER_ROOT” (char), solidsco ncsurfgridroot (string)

(report for total and groups) (Path...\root) (g/m 3 ) if ksim > 2 22 “TOTCHEM_CONC_WATER_ROOT” (char), totchemconcwat ergridroot (string) (report

for total and groups) (Path...\root) (g/m 3 ) 23 “DISCHEM_CONC_WATER_ROOT” (char), dischemconcwat ergridroot (string) (report

for groups) (Path...\root) (g/m 3 ) 24 “BNDCHEM_CONC_WATER_ROOT” (char), bndchemconcwat ergridroot (string)

(report for groups) (Path...\root) (g/m 3 ) 25 “PRTCHEM_CONC_WATER_ROOT” (char), prtchemconcwat ergridroot (string) (report

for groups) (Path...\root) (g/m 3 ) 26 “SRBCHEM_CONC_WATER_ROOT” (char), srbchemconcwat ergridroot (string) (report

for groups) (Path...\root) (mg/kg) 27 “TOTCHEM_CONC_SURFACE_LAYER_ROOT” (char), totche mconcsurfgridroot

(string) (report for total and groups) (Path...\roo t) (g/m 3 )TREX User’s Manual Page 63

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28 “DISCHEM_CONC_SURFACE_LAYER_ROOT” (char), dische mconcsurfgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 29 “BNDCHEM_CONC_SURFACE_LAYER_ROOT” (char), bndche mconcsurfgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 30 “PRTCHEM_CONC_SURFACE_LAYER_ROOT” (char), prtche mconcsurfgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 31 “SRBCHEM_CONC_SURFACE_LAYER_ROOT” (char), srbche mconcsurfgridroot

(string) (report for groups) (Path...\root) (mg/kg) 32 “TOTCHEM_CONC_SUBSURF_LAYER_ROOT” (char), totche mconcsubgridroot

(string) (report for total and groups) (Path...\roo t) (g/m 3 ) 33 “DISCHEM_CONC_SUBSURF_LAYER_ROOT” (char), dische mconcsubgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 34 “BNDCHEM_CONC_SUBSURF_LAYER_ROOT” (char), bndche mconcsubgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 35 “PRTCHEM_CONC_SUBSURF_LAYER_ROOT” (char), prtche mconcsubgridroot

(string) (report for groups) (Path...\root) (g/m 3 ) 36 “SRBCHEM_CONC_SUBSURF_LAYER_ROOT” (char), srbche mconcsubgridroot

(string) (report for groups) (Path...\root) (mg/kg) Note: The subsurface reporting flag (ssrflag) is se t to a non-zero value if one or more of file

names for subsurface reporting is specified (i.e. n ot null). Otherwise, ssrflag = 0. if ssrflag > 0 37 “REPORTING_HORIZON” (char), horizon (float) (m), “SSROPT” (char), ssropt (int) (0

= point concentration; 1 = depth-weighted average c oncentration) Note The reporting horizon represents the depth bel ow grade level that is used to determine the

soil/sediment stack layers where reporting occurs. When ssropt = 0 (point concentrations), the horizon is used to determine which element in t he stack is reported. When ssropt = 1 (depth-weighted average), the concentration reporte d represents an average calculated based on values for all soil/sediment stack layers in the stack from the surface down to the level of the reporting horizon depth. When the repo rting horizon falls within the surface layer of the stack, the point concentration and dep th concention will be equal (and will be equal to surface soil/sediment concentrations speci fied in Records 27-31. endif ssrflag > 0 38 “DISCHEM_FRAC_WATER_ROOT” (char), dischemfracwat ergridroot (string) (report

for total and groups) (Path...\root) (dimensionless ) 39 “BNDCHEM_FRAC_WATER_ROOT” (char), bndchemfracwat ergridroot (string) (report

for groups) (Path...\root) (dimensionless) 40 “MBLCHEM_FRAC_WATER_ROOT” (char), mblchemfracwat ergridroot (string) (report

for groups) (Path...\root) (dimensionless) {mobile = dissolved + bound}TREX User’s Manual Page 64

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41 “PRTCHEM_FRAC_WATER_ROOT” (char), prtchemfracwat ergridroot (string) (report

for groups) (Path...\root) (dimensionless) 42 “DISCHEM_FRAC_SURFACE_LAYER_ROOT” (char), dische mfracsurfgridroot

(string) (report for total and groups) (Path...\roo t) (dimensionless) 43 “BNDCHEM_FRAC_SURFACE_LAYER_ROOT” (char), bndche mfracsurfgridroot

(string) (report for groups) (Path...\root) (dimens ionless) 44 “MOBCHEM_FRAC_SURFACE_LAYER_ROOT” (char), mobche mfracsurfgridroot

(string) (report for groups) (Path...\root) (dimens ionless) {mobile = dissolved + bound} 45 “PRTCHEM_FRAC_SURFACE_LAYER_ROOT” (char), prtche mfracsurfgridroot

(string) (report for groups) (Path...\root) (dimens ionless) 46 “CHEMICAL_INFILTRATION_GRID_ROOT” (char), infche mfluxgridroot (string)

(report for groups) (Path...\root) (dimensionless) endif ksim > 2 47 Header (string) such as “CUMULATIVE TIME GRID OU TPUTS” 48 “NET_ELEVATION_CHANGE” (char), netelevationgrid (string) (Path and filename) (m) 49 “SOLIDS_GROSS_EROSION” (char), solidserosiongrid root (string) (report for groups)

(Path...\root) (kg) 50 “SOLIDS_GROSS_DEPOSITION” (char), solidsdepositi ongridroot (string) (report for

groups) (Path...\root) (kg) 51 “SOLIDS_NET_ACCUMULATION” (char), solidsnetaccum gridroot (string) (report for

groups) (Path...\root) (kg) if ksim > 2 52 “CHEMICAL_GROSS_EROSION” (char), chemerosiongrid root (string) (report for

groups) (Path...\root) (kg) 53 “CHEMICAL_GROSS_DEPOSITION” (char), chemdepositi ongridroot (string) (report

for groups) (Path...\root) (kg) 54 “CHEMICAL_NET_ACCUMULATION” (char), chemnetaccum gridroot (string) (report

for groups) (Path...\root) (kg) endif ksim > 2 endif ksim > 1 49 Header (string) such as “SIMULATION SUMMARY OUPU TS” endif ksim > 2 endif ksim > 1 49 Header (string) such as “SIMULATION SUMMARY OUPU TS”TREX User’s Manual Page 65

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Data Group F: Ouput Specification Controls (continu ed)
50 “DUMP_FILE” (char), dmpfile (string) (Path and f ile name) {optional, not implemented} 51 “MASS_BALANCE” (char), msbfile (string) (Path an d file name) {optional} 52 “SUMMARY_STATISTICS” (char), statsfile (string) (Path and file name) {required} In Data Group F, the units for model output are pre sented as noted above (i.e. mm/hr, mm, m, g/m 3 , g/s, kg, etc.).

4.3 DEFINITIONS FOR CHEMICAL PROPERTIES AND REACTION PATHWAYS At this time, the following chemical properties can be specified in Data Group D. It should be noted that not all chemical processes rou tines that use these properties are implemented. Properties are summarized in groups ac cording to process and pathway: partitioning, biodegradation, dissolution (and prec ipitation), hydrolysis, oxidation (and reduction), photodegradation, radioactive decay, vo latilization, and user-defined reaction. Chemical Properties and Reaction Pathways (Data Gro up D)
CID Name Description Units Default Value Process/Pathway Options (Switches to Activate/Deact ivate Chemical Processes) 100 partopt partitioning: 0 = off, 1 = on N/A 0 200 bioopt biodegradation: 0 = off, 1 = on N/A 0 300 dslopt dissolution: 0 = off, 1 = on N/A 0 400 hydoopt hydrolysis: 0 = off, 1 = on N/A 0 500 oxiopt oxidation: 0 = off, 1 = on N/A 0 600 photoopt photodegradation: 0 = off, 1 = on N/A 0 700 radopt radioactive decay: 0 = off, 1 = on N/A 0 800 volopt volatilization: 0 = off, 1 = on N/A 0 900 udropt user-defined reaction: 0 = off, 1 = on N /A 0 Partitioning (100 series) 100 partopt partitioning: 0 = off, 1 = on N/A 0 110 lkp log partition coefficient L/kg N/A 120 lkb log binding doefficient {partitioning to dissolved organic compounds) L/kg N/A
130 lkoc log organic carbon partition coefficient L /kg OC N/ATREX User’s Manual Page 66

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Chemical Properties and Reaction Pathways (Data Gro up D) (continued)
140 nux particle interaction paramter dimensionless 1.0e+20

Biodegradation (200 series) 200 bioopt biodegradation: 0 = off, 1 = on N/A 0 210 kbiowov first-order biodegradation rate for overland water 1/day none
215 kbiowov second-order biodegradation rate for overland water mL/cells/day none
220 kbiosov first-order biodegradation rate for overland soil 1/day none
225 kbiosov second-order biodegradation rate for overland soil mL/cells/day none
230 kbiowch first-order biodegradation rate for cha nnel water 1/day none
235 kbiowch second-order biodegradation rate for channel water mL/cells/day none
240 kbiosch first-order biodegradation rate for cha nnel sediment 1/day none
245 kbiosch second-order biodegradation rate for channel sediment mL/cells/day none

Dissolution (300 series) 300 dslopt dissolution: 0 = off, 1 = on N/A 0

Hydrolysis (300 series) 400 hydoopt hydrolysis: 0 = off, 1 = on N/A 0

Oxidation (300 series) 500 oxiopt oxidation: 0 = off, 1 = on N/A 0

Photodegradation (300 series) 600 photoopt photodegradation: 0 = off, 1 = on N/A 0TREX User’s Manual Page 67

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Chemical Properties and Reaction Pathways (Data Gro up D) (continued)
Radioactive Decay (300 series) 700 radopt radioactive decay: 0 = off, 1 = on N/A 0

Volatilization (300 series) 800 volopt volatilization: 0 = off, 1 = on N/A 0

User-Defined Reaction (900 series) 900 udropt user-defined reaction: 0 = off, 1 = on N /A 0

4.4 DEFINITIONS FOR ENVIRONMENTAL PROPERTIES At this time, the following environmental propertie s can be specified in Data Group E. It should nonetheless be noted that not all environmen tal or chemical processes routines that use these environmental properties are impleme nted Environmental Properties
PID Name Description Units Default Value General Properties 1 windspeed wind speed m/s 0 2 airtemp air temperature °C 15 3 solarrad incident net solar radiation w/m 2 0 4 cloudcover fraction of sky covered by clouds dime nsionless 0 5 albedo fraction of incident net solar rediation

reflected by the land surface dimensionless 0
Overland/Channel Properties (Runoff/Surface Water a nd Soil/Sediment) 1 cdoc concentration of dissolved organic

compounds (doc) (C doc ) g/m 3 0
2 fdoc effective fraction of doc for binding (f doc ) dimensionless 1 3 hardness hardness g/m 3 0 4 ph pH dimensionless 7TREX User’s Manual Page 68

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Environmental Properties (continued)
5 temperature water, soil/sediment temperature °C 1 5 6 oxrad oxidant/radical concentration g/m 3 0 7 bacteria bacteria concentration g/m 3 0 8 extinction light extinction coefficient 1/m 0 9 udrprop user-defined reaction property vary 0 Overland/Channel Particle Properties for Chemical T ransport and Fate (Particles in Runoff/Surface Water and Soil/Sedimen t) fpocov fraction particulate organic carbon (POC)

of particles in overland water or soil (f poc ) dimensionless 1
fpocch fraction particulate organic carbon (POC)

of particles in channel water or sediment (f poc ) dimensionless 1

4.5 ANCILLARY MODEL INPUT FILES Ancillary input files are used to describe characte ristics of the model domain such as watershed boundary mask, elevations, soil classes, and land uses, etc. Ancillary files for the overland plane are organized as grid files (suc h as those that can be exported from ESRI’s ArcGIS software) that include a header block and a block of grid values specified by row and column. While the exact grid values spec ified in the ancillary files for the overland plane differ, the format for each file is the same. Users should note that the header used for grid files differs slightly from th e native format exported from ArcGIS software. Ancillary files for the channel network a re organized as “channel property files” and “sediment property files”. These files s pecify conditions for each link of the network on a node by node basis. The exact format o f each channel or sediment property files differs slightly according to the type of dat a input.

4.5.1 General Format for Spatial Domain Characteristics F iles (Grid Files) General Format for Spatial Domain Characteristics F iles (Grid Files)
Record Description 1 Header1 (string) 2 “NCOLS” (char), gridcols (int) 3 “NROWS” (char), gridrows (int) 4 “XLLCORNER” (char), xllcorner (float) 5 “YLLCORNER” (char), yllcorner (float)TREX User’s Manual Page 69

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation General Format for Spatial Domain Characteristics F iles (Grid Files) (continued)
6 “CELLSIZE” (char), cellsize (float) 7 “NODATAVALUE” (char), nodatavalue (int) { Note: always use integer -9999 } for i = 1, gridrows for j = 1, gridcols 8 girdvalue[i][j] (int or float depending on grid) {gridvalue is a sample name...} Note Record 8 is repeated for j = 1, grid cols and then repeated again for i = 1, gridrows. Also Note Data input is unformatted. However, a typ ical file will have gridrows number of lines with

gridcols number of entries on each line. Grid Types Grid files are input for: the simulation mask (int) (imask[][]), ground elevation (float)

(elevation[][]), soil types (int) (soiltype[][]), l and use classes (int) (landuse[][]), links (int) (link[][]), nodes (int) (nodes[][]), storage depths in the overland plane (float), initial water depths in the overland plane (float), optional desi gn rainfall grid (rainopt = 2) (int) (designraingridindex[][]),and soil stack elements ( int).

4.5.2 Description and Organization of Channel Property an d Topology Files Channel Property File {input for tplgyopt = 0}
Record Description 1 Header {string} 2 CHANLINKS (char), chanlinks (int) Note The number of links in the network (nlinks) is already known from the link file. This

information is used to check that the channel prope rties file is compatible with the link file. for ilink = 1, nlinks 3 linknum (int) {dummy}, nnodes[ilink] (int) for inode = 1, nnodes[ilink] 4 bwidth[ilink][inode] (float) (m), sideslope[ilink ][inode] (float) (dimensionless),

hbank[ilink][inode] (float) (m), nmanning_ch[ilink] [inode] (float) (n units), sinuosity[ilink][inode] (float) (dimensionless), de adstoragedepth[ilink][inode] (float) (m) Note Records 3 and 4 are repeated as a group for il ink = 1, nlinks. Record 4 is repeated for

inode = 1, nnodes[ilink].TREX User’s Manual Page 70

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation External Channel Topology File {input for tplgyopt = 1} ( Not fully implemented )
Record Description 1 Header {string} 2 nlinks (int) {number of links in network} for ilink = 1, nlinks 3 linknum (int) {dummy}, nnodes[ilink] (int), downs treamlink[ilink] (int) {the downstream

link always starts with the first element of the do wnstream link...} for inode = 1, nnodes[ilink] 4 crow (int), ccol (int), bwidth[ilink][inode] (flo at), sideslope[ilink][inode] (float),

hbank[ilink][inode] (float), nmanningch[ilink][inod e] (float), sinuosity[ilink][inode] (float), deadstorage[ilink][inode] (float) Note Records 3 and 4 are repeated as a group for il ink = 1, nlinks. Record 4 is repeated for

inode = 1, nnodes[ilink].

Channel Initial Water Depth File
Record Description 1 Header {string} 2 CHANLINKS (char), chanlinks (int) Note The number of links in the network (nlinks) is already known from the link file. This

information is used to check that the initial water file is compatible with the link file. for ilink = 1, nlinks 3 linknum (int) {dummy}, nnodes[ilink] (int) for inode = 1, nnodes[ilink] 4 hch0[ilink][inode] (float) (m) Note Records 3 and 4 are repeated as a group for il ink = 1, nlinks. Record 4 is repeated for

inode = 1, nnodes[ilink].TREX User’s Manual Page 71

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Channel Transmission Loss Property File (used only when ksim = 1 and ctlopt > 0)
Record Description 1 Header {string} 2 CHANLINKS (char), chanlinks (int) Note The number of links in the network (nlinks) is already known from the link file. This

information is used to check that the transmission loss file is compatible with the link file. for ilink = 1, nlinks 3 linknum (int) {dummy}, nnodes[ilink] (int) for inode = 1, nnodes[ilink] 4 khsed[ilink][inode] (float) (m/s), capshsed[ilink ][inode] (float) (m), sedmd[ilink][inode]

(float) (dimensionless) {usually zero for initially saturated bed} Note Records 3 and 4 are repeated as a group for il ink = 1, nlinks. Record 4 is repeated for

inode = 1, nnodes[ilink].

Channel Initial Transmission Loss Depth File
Record Description 1 Header {string} 2 CHANLINKS (char), chanlinks (int) Note The number of links in the network (nlinks) is already known from the link file. This

information is used to check that the initial trans mission loss file is compatible with the link file. for ilink = 1, nlinks 3 linknum (int) {dummy}, nnodes[ilink] (int) for inode = 1, nnodes[ilink] 4 translossdepth0[ilink][inode] (float) (m) {depth to wetting front} Note Records 3 and 4 are repeated as a group for il ink = 1, nlinks. Record 4 is repeated for

inode = 1, nnodes[ilink].TREX User’s Manual Page 72

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.5.3 Description and Organization of Sediment Properties and Channel Solids Initial Conditions Files Sediment Properties File: Stack Extent, Thickness, Grain Size Distribution, etc.
Record Description 1 Header {string} 2 “CHANLINKS” (char), chanlinks (int), “CHANSOLIDS” (char), chansolids (int),

“CHANERSCHOPT” (char), chanerschopt (int) {dummy}, “CHANCTLOPT” (char), chanctlopt (int) {dummy} Note The number of links in the network (nlinks) an d number of particle types (nsolids) are

already known from the link file and main input fil e. This information is input to check that the sediment properties file is compatible wit h the channel network and particle types. for ilink = 1, nlinks 3 “LINKNUMBER” (char), linknum (int) {dummy}, “NUMN ODES” (char), channodes

(int) {dummy} for inode = 1, nnodes[ilink] 4a “NODE” (char), nodenum (int) {dummy), “NSTACK” ( char), nstackch0[ilink][inode]

(int) if erschopt > 1 4b “YIELD” (char), aych[ilink][inode] (float) (g/cm 2), “EXPONENT” (char),

mexpch[ilink][inode] (float) (dimensionless) endif erschopt > 1 if ctlopt > 0 4c “KHSED” (char), khsed[ilink][inode] (float) (m/s ), “CAPSHSED” (char),

capshsed[ilink][inode] (float) (m), “SEDMD” (char), sedmd[ilink][inode] (float) (dimensionless) endif ctlopt > 0 Note Record 4 has up to three components. Record 4a is always input. Record 4b is input only if

erschopt > 1. Record 4b is input only if ctlopt > 1

. for ilayer = nstackch0[ilink][inode], 1; ilayer-- {reverse order} 5 “LAYER” (char), layernum (int) {dummy}, “THICKNES S” (char),

hlayerch0[ilink][inode][ilayer] (float) (m) {initia l thickness of the layer}, “WIDTH” (char), bwlayerch0[ilink][inode][ilayer] (float) (m ) {initial bottom width}, “POROSITY” (char), porositych[ilink][inode][ilayer] (float) (d imensionless) Note The width of each layer in the stack (bwlayerc h0) must be less than or equal to the width

of each overlying layer and also less than or equal to the channel bottom width specified in the channel properties file for every link and node in the network. 6a “GSD:” (char)TREX User’s Manual Page 73

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Sediment Properties File: Stack Extent, Thickness, Grain Size Distribution (continued)
for isolid = 1, nsolids 6b gsdch[isolid][ilink][inode][layer] (float) Note Records 3, 4a/b/c, 5, and 6a/b are repeated as a group for ilink = 1, nlinks. Within this

outer block, Records 4a/b/c, 5, and 6a/b are repeat ed for inode=1, nnodes[ilink]. Within this inner block, Records 5 and 6a/b are repeated f or ilayer = nstackch0[ilink][inode], 1 (ilayer--). Within this innermost block, Record 6b is repeated for isolid = 1, nsolids. Check Compute gsdchtot =+ gsd[ilink][inode][isolid] [ilayer] and check that gsdchtot = 1.0. Abort

if gsdchtot != 1.0 for each node of each link...

Channel Initial Suspended Solids File: initial soli ds concentration in channel water
Record Description 1 Header {string} 2 “CHANLINKS” (char), chanlinks (int), “CHANSOLIDS” (char), chansolids (int) Note The number of links in the network (nlinks) an d number of particle types (nsolids) are

already known from the link file and main input fil e. This information is input as a check that the initial solids file is compatible with the channel network and particle types. for ilink = 1, nlinks 3 “LINKNUMBER” (char), linknum (int) {dummy}, “NUMN ODES” (char), channodes

(int) {dummy} for inode = 1, nnodes[ilink] 4 “NODE” (char), nodenum (int) {dummy) for isolid = 1, nsolids 5 csedch[isolid][ilink][inode][0] (float) (g/m 3 ) Note Records 3, 4, and 5 are repeated as a group fo r ilink = 1, nlinks. Within this block, Record

4 and 5 are repeated as a group for inode = 1, nnod es[ilink]. Within this innermost block, Record 5 is repeated for isolid = 1, nsolids.TREX User’s Manual Page 74

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.5.4 Description and Organization of Channel Chemical In itial Conditions Files Chemical Sediment Initial Conditions File: Chemical Concentrations in the Sediment Bed
Record Description 1 Header {string} 2 “CHANLINKS” (char), chanlinks (int), “CHANCHEMS” (char), chanchems (int) Note The number of links in the network (nlinks) an d number of chemicals (nchems) are

already known from the link file and main input fil e. This information is input to check that the chemical conditions file is compatible wit h the channel network and chemicals. for ilink = 1, nlinks 3 “LINKNUMBER” (char), linknum (int) {dummy}, “NUMN ODES” (char), channodes

(int) {dummy} for inode = 1, nnodes[ilink] 4 “NODE” (char), nodenum (int) {dummy), “NSTACK” (c har), nstackch0[ilink][inode]

(int) {dummy} for ilayer = nstackch0[ilink][inode], 1; ilayer-- {reverse order} 5a “LAYER” (char), layernum (int) {dummy} for ichem = 1, nchem 5b “Chemical#” (char) {dummy}, cchemch[isolid][ilin k][inode][layer] (float) (mg/kg) Note Records 3, 4, and 5a/b are repeated as a group for ilink = 1, nlinks. Within this outer

block, Records 4, and 5a/b are repeated for inode=1 , nnodes[ilink]. Within this inner block, Records 5a/b are repeated for ilayer = nstac kch0[ilink][inode], 1 (ilayer--). Within this innermost block, Record 5b is repeated for ich em = 1, nchem.

Channel Initial Suspended Chemical File: initial ch emical concentration in channel water
Record Description 1 Header {string} 2 “CHANLINKS” (char), chanlinks (int), “CHANCHEMS” (char), chanchems (int) Note The number of links in the network (nlinks) an d number of chemical types (nsolids) are

already known from the link file and main input fil e. This information is input as a check that the initial solids file is compatible with the channel network and particle types. for ilink = 1, nlinks 3 “LINKNUMBER” (char), linknum (int) {dummy}, “NUMN ODES” (char), channodes

(int) {dummy}TREX User’s Manual Page 75

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Channel Initial Suspended Chemical File: initial ch emical concentration (continued)
for inode = 1, nnodes[ilink] 4 “NODE” (char), nodenum (int) {dummy) for ichem = 1, nchems 5 cchemch[isolid][ilink][inode][0] (float) (g/m 3 ) Note Records 3, 4, and 5 are repeated as a group fo r ilink = 1, nlinks. Within this block, Record

4 and 5 are repeated as a group for inode = 1, nnod es[ilink]. Within this innermost block, Record 5 is repeated for ichem = 1, nchems.

4.5.5 Description and Organization of Environmental Prope rties Files At this time, ancillary files for environmental pro perties as specified in Data Group E are not fully implemented or documented. Examine the TR EX source for details until code development and documentation efforts are completed

.

4.5.6 Description and Organization of Radar Rainfall Loca tions and Radar Rainfall Rates Files These ASCII file formats were developed by Julie Ja vier, Jim Smith and Mary Lynn Baeck at Princeton University. Radar location and r ainfall rate files are generated by intersecting data from a radar with a watershed and producing a field with constant x- and y-coordinate spacing. This is typically done in-par t with TITAN software from Mike Dixon at NCAR. Radar locations are typically suppli ed in geographic coordinates (latitude and longitude). These must be converted U TM coordinates for use with TREX. There is no check of the radar coordinates relative to the watershed location. The user must ensure that at least one radar cell intersects the watershed. This is typically done in a GIS. These files must be input when rainfall option 3 is selected in Data Group B. Radar Locations File [ReadRadarRainLocations.c]
Record Description 1 Header {string} 2 “RADARCELLSPACING” (char), radarcellw (float), “N RADARCELLS” (char), nrg

(int) Note radar cell spacing is used for the maximum dis tance on restricted nearest neighbor

interpolationTREX User’s Manual Page 76

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Radar Locations File [ReadRadarRainLocations.c] (co ntinued)
for igage = 1, nrg 3 rgx (float), rgy (float) Note rgx and rgy are x and y coordinates of each ra dar cell. Record 3 generally consists of a two

column format in x and y. Read is unformatted. An e xample file is a 200 km x 200 km field at 1km spacing. There are 40000 locations. Th e file is generally a 40000 x 2 array (rows/cols). It has 2 values (x and y) (cols) on ea ch row, with 40000 rows.

Radar Rain Rates File [ReadRadarRainRates.c]
Record Description 1 Header {string} 2 “RADARTIMEINC” (char), timeincrement (float) {min utes}, “RADARDURATION”

(char), stormduration (int) {hours} Note Units for timeincrement must be in minutes. Us e of this fixed increment automatically

assign the time for each intensity value so that we have a "pair" of values (intensity, time). Also, stormduration is a simple surrogate for numbe r of rows in file. The Note the time increment is used in conjunction with the duration to estimate how many rows

there are to read in the file. Later version will j ust scan entire file to determine properties. NOTE The file input is currently limited in that nrpairs is a FIXED length for all radar cell

locations. The current supplied radar fields are un iform in time (same duration and increment at all locations). Unlike the rain data i nput into the main TREX input file, we have no current provision to read nrpairs[irg] so i t is fixed. Later versions may possibly eliminate this restriction. for jrpairs = 1, nrpairs {nrpairs currently input as stormduration} for irgage = 1, nrg 3 rfintensity (float)[irgage][jrpairs] NOTE! The radar rain rate data file is formatted as follo ws: each value on a single row (line)

represents a rainfall intensity at location irgage. The entire row is the intensity at all locations at one time. Each column represents a dif ferent location irgage. Each row represents a single time step (jrpair). Record 3 lo oping order is “opposite” that of rain gages entered into the main TREX input file. Here, we loop over i fastest (inner loop) then j. We loop over columns in the file first then rows , so loop order is OPPOSITE to other rain inputs. However, we assign them to the same ar ray locations. In order to keep consistency throughout rain routines, we have the T REX reading convention: rfintensity[row][column] = rfintensity[i][j] = rfin tensity[nrg][nrpairs]. Record 3 is repeated for jrpairs=1,nrpairs and irgage=1,nrg. An example is a 200 km x 200 km field for one hour at 5 minutes duration. There are 40,00 0 locations (200x200) = nrg on each row. There are 12 rows (60 minutes/5 minutes = 12), so nrpairs =12. The 2D array is then 12 (nrows) x 40000 (ncols).TREX User’s Manual Page 77

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.5.7 Description and Organization of Space-Time Storm Fi les This ASCII file format was developed by John Englan d, Bureau of Reclamation, to read in depth-area duration (DAD) data from the USACE/US BR Storm Catalog. This file must be input when rainfall option 4 is selected in Data Group B. Space-Time Storm File [ReadSpaceTimeStorm.c]
Record Description 1 Header {string} 2 “NUM_DURATIONS” (char), ndurations (int), “MAX_DU R” (char), maxdur (float) Note maxdur is used to limit the duration of the in put storm. We may implement this first by

trial with the user knowing the table explicitly an d only reading in the ndurations. 3 “NUM_AREAS” (char), nareas (int), “MAX_AREA” (cha r), maxarea (float) Note maxara is used to limit the area size for the input storm. We may implement this first by

trial with the user knowing the table explicitly an d only reading in the nareas of interest. 4 “STORM_CENTER_LOCATION” (char), raincenterx (floa t), raincentery (float)

{raincenterx and raincentery are UTM storm center c oordinates; these are fixed scalars for rgx, rgy} {estimate from lat-long in decimal degree s using CORPSCON} 5 “STORM_SHAPE_RATIO” (char), stormelong (float), “ STORM_ORIENT” (char),

stormorient (float) {decimal degrees} Note stormelong is limited from [1.0, 8.0] where 1. 0 will give a circle. stormorient is limited

from [0.0, 360.0] and is defined from positive ordi nate (y-axis) (North) in clockwise direction; see HMR 52 for definitions. for iduration = 2, ndurations {start time is shift ed by one so zero is time 1} 6 dadtime[iduration] (float) {hours} {read n values on one line; local, passed to rftime} end loop over ndurations for iareas = 1, nareas 7 rainarea[iarea] (float) {mi2} {read one value as the first column on the line} for iduration = 2, ndurations 8 daddepth[iarea][iduration] (float) {inches} {read n values on one line, local, pass to

rfintensity after conversion to rate} end loop over ndurations end loop over nareas Note See standard D-A-D sheet to understand format. Data are in U.S. English units as source is

USACE/USBR. Record 6 is on one line. Record 7 is th e first column where nareas equals the number of rows. Record 8 is the cumulative rain fall depths (ndurations long) for that iarea, on the same line as that iarea.TREX User’s Manual Page 78

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 4.5.8 Description and Organization of Environmental Prope rties Files At this time, ancillary files for environmental pro perties as specified in Data Group E are not fully implemented or documented. Examine the TR EX source for details until code development and documentation efforts are completed

.

4.5.9 Restart Information File and Restart Directory Stru cture To use simulation restart capabilities, the user mu st specify a restart option (see Section 3.5 and Table 3-3) as well as an primary restart in formation file. The name and location of the primary restart information file are hardwir ed in the TREX code. When a restart option is used, TREX reads from a file named “resta rt-info.txt” that must be located in a directory named “Restart”, such that the path to th is file is: “Restart/restart-info.txt”. The restart-info.txt file contains the path and names a nd header information for all ancillary files created or read by TREX. Note that the restar t information file and restart directory names are case sensitive. The use of any subdirecto ry paths within the “Restart” directory is at the discretion of the user.

Restart Information File: restart-info.txt (this fi le name is case sensitive)
Record Description 1 Header1 (string) {descriptive header for restart- info.txt file} 2 Header (string) {header for soil stack properties } 3 “SOIL_STACK” (char) {dummy}, restartfile (string) {soil stack file path and name} 4 Header (string) {header for soil stack file} {use d when restart files are written} for ilayer = maxstackov to 1 (reverse order) 5 “SOIL_LAYER_THICKNESS” (char) {dummy}, restartfil e (string) {soil layer thickness

file path and name} 6 Header (string) {header for soil layer thickness file} {used when restart files are written} 7 “SOIL_LAYER_VOLUME” (char) {dummy}, restartfile ( string) {soil layer volume file

path and name} 8 Header (string) {header for soil layer volume fil e} {used when restart files are written} 9 “SOIL_LAYER_MINIMUM_VOLUME” (char) {dummy}, resta rtfile (string) {soil layer

minimum volume file path and name} {soil stack cont rol data} 10 Header (string) {header for soil layer minimum v olume file} {used when restart files are

written}TREX User’s Manual Page 79

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Restart Information File: restart-info.txt (this fi le name is case sensitive) (continued)
11 “SOIL_LAYER_MAXIMUM_VOLUME” (char) {dummy}, rest artfile (string) {soil layer

maximum volume file path and name} {soil stack cont rol data} 12 Header (string) {header for soil layer maximum v olume file} {used when restart files are

written} 13 “SOIL_LAYER_ELEVATION” (char) {dummy}, restartfi le (string) {soil layer elevation

file path and name} {soil stack control data} 14 Header (string) {header for soil layer elevation file} {used when restart files are written} 15 “SOIL_LAYER_TYPE” (char) {dummy}, restartfile (s tring) {soil type file path and

name} {soil type for each cell of this layer} 16 Header (string) {header for soil layer type file } {used when restart files are written}
for isolid = 1 to nsolids 17 “SOIL_LAYER_SOLIDS_CONC” (char) {dummy}, restart file (string) {soil layer solids

concentration file path and name} {concentration of solids type “isolid” in each cell of this layer} 18 Header (string) {header for soil layer solids co ncentration file} {used when restart files are

written} end loop over solids for ichem = 1 to nchems 19 “SOIL_LAYER_CHEM_CONC” (char) {dummy}, restartfi le (string) {soil layer chemical

concentration file path and name} {concentration of chemical type “ichem” in each cell of this layer} 20 Header (string) {header for soil layer chemical concentration file} {used when restart files

are written} end loop over chemicals end loop over soil layers Note Records 5-18 are repeated as a group for ilaye r = maxstackov to 1. Within this outer

block, Records 5-16 are each entered once. Records 17-18 are repeated as a block for isolid = 1 to nsolids. Records 19-20 are repeated a s a block for ichem = 1 to nchems. The entire block is then repeated for each soil layer. 21 Header (string) {header for sediment stack prope rties} 22 “SEDIMENT_STACK” (char) {dummy}, restartfile (st ring) {sediment stack propeties file

path and name} {ancillary file containing all sedim ent stack information such as sediment layer geometry, solids and chemical concentrations, etc. for each node of each link} 23 Header (string) {header for sediment stack prope rties file} {used when restart files are

written} if rstopt = 2TREX User’s Manual Page 80

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Restart Information File: restart-info.txt (this fi le name is case sensitive) (continued)
24 Header (string) {header for overland water prope rties} 25 “OVERLAND_WATER_DEPTH” (char) {dummy}, restartfi le (string) {overland water

depth file path and name} {depth of water in overla nd plane, including overland portion of channel cells} 26 Header (string) {header for overland water depth file} {used when restart files are

written} for isolid = 1 to nsolids 27 “OVERLAND_WATER_SOLIDS” (char) {dummy}, restartf ile (string) {overland water solids concentration file path and name} {concentra tion of solid type “isolid” in overland plane, including overland portion of channel cells } 28 Header (string) {header for overland water solid s concentration file} {used when restart

files are written} end loop over solids Note Records 27-28 are repeated as a group for isol id = 1 to nsolids. for ichem = 1 to nchems 29 “OVERLAND_WATER_CHEM” (char) {dummy}, restartfil e (string) {overland water

chemical concentration file path and name} {concent ration of chemical type “ichem” in overland plane, including overland portion of chann el cells } 30 Header (string) { header for overland water chem ical concentration file} {used when

restart files are written} end loop over chemicals Note Records 29-30 are repeated as a group for iche m = 1 to nchems. 31 Header (string) {header for channel water proper ties} 32 “CHANNEL_WATER” (char) {dummy}, restartfile (str ing) {channel properties file path

and name} {ancillary file containing water depth, s olids concentrations, and chemical concentrations for each node of each link} 33 Header (string) {header for sediment stack prope rties file} {used when restart files are

written}TREX User’s Manual Page 81

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### 5.0 DESCRIPTION AND ORGANIZATION OF MODEL OUTPUT FILES TREX produces six categories of output files that e cho model inputs, report simulation errors, and present a variety of simulation results . These six categories of output are:
1. Input data echo report; 2. Simulation error report; 3. Export times series; 4. Point-in-time grids; 5. Cumulative time grids; and 6. Simulation performance summaries. The names of the specific output files in each cate gory are specified by the user in the main model input file. Descriptions of the output i n each category follow.

5.1 INPUT DATA ECHO REPORT The input data echo report presents a summary (echo ) of all model inputs read by TREX for a simulation. The echo file is useful for debug ging model inputs. If input data are misaligned or other problems with data specified in the main model input file or any ancillary file are detected, the data summarized in the echo file will differ from the data in the input files. A secondary input data echo report, the radar verif ication file, is created when rainfall option (rainopt) 3 is selected in Data Group B and radar rainfall data are used to define precipitation forcing functions. The radar verifica tion file is used to echo the input radar locations and rainfall rates read by the model. The file is also used to print selected intermediate computations so the user can check tha t input data are correctly read by the model and are assigned to the correct locations. Th e following routines write output to the verification file: ReadDataGroupB, ReadRadarRai nLocations, ReadRadarRainRates, and InitializeWater. Intermediate computations and checks that are written to the verification file include: a radar rainfall field i n same units and format as read in (ReadRadarRainRates); rate and time pairs (complete time series) for first and last radar locations to check arrays (ReadRadarRainRates); rad ar grid pointer that determines the TREX model domain cells that each radar gage applie s to (InitializeWater).

5.2 SIMULATION ERROR REPORT The simulation error report presents a summary of n umerical integration errors detected during a run. This file provide information that ma y be helpful for diagnosing model stability errors such as the simulation time at whi ch an error was detected, which modelTREX User’s Manual Page 82

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation routine detected the error, and the cell in which t he error occurred. For a successful simulation, the error file will be empty except for an echo of the main model input file used for the simulation.

5.3 EXPORT TIME SERIES OUTPUTS Export times series are tabular outputs of values o f model state variables at specified points in space (reporting stations) reported over time. Results are output according to the print interval specified in Data Group A of the mai n model input file. Export outputs can be specified for hydrology (water depth or flow at a station), sediment transport (solids concentration or load at a station), and chemical t ransport (chemical concentration or load at a station). Export output files are written in atab-delimited format to facilitate postprocessing and analysis in spreadsheet or statistic al software.

5.4 POINT-IN-TIME OUTPUTS Point-in-time outputs are row-column grid files of model state variables over the entire spatial domain reported at a specific point in time . Results are output according to the grid print interval specified in Data Group A of th e main model input file. Point-in-time outputs can be specified for hydrology (water depth or flow), sediment transport (solids concentrations including the sum of all solids type s), and chemical transport (chemical concentrations by specific phase and phase distribu tion fractions). Point-in-time output files are written in a format that can be directly imported into geographic information system (GIS) software (in particular ESRI’s ArcGIS or Arc/Info) for individual display and the creation of animations (sequential displays of grids for consecutive points in time).

5.5 CUMULATIVE TIME OUTPUTS Cumulative time outputs are row-column grid files o f model state variables over the entire spatial domain reported at the end of the si mulation. Results are output once for the entire time period simulated. Cumulative time outpu ts can be specified for a number of parameters such as the net elevation change and the gross erosion, gross deposition, and net accumulation of solids or chemicals. Cumulative time output files are written in a format that can be directly imported into geographi c information system (GIS) software (in particular ESRI’s ArcGIS or Arc/Info).

5.6 SIMULATION SUMMARY OUTPUTS Simulation summary outputs are divided into three f ormats: 1) a model dump file; 2) a detailed mass balance file; and 3) a summary statis tics file. Each of these formats is described below.TREX User’s Manual Page 83

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 5.6.1 The Model Dump File Note: this output format is not yet implemented. Co mputer code to control when data is written to the dump file exists. However, the dump file write module is just a skeleton. Once implemented, the model dump file will be a bin ary (direct access) file that contains an element-by-element, process-by-process, directio n-by-direction report (dump) for each state variable for all points in space and all poin ts in time in the model domain. A postprocessing program will need to be created to extra ct binary output and write it in tabular or grid form for futher post-processing and analysi s.
5.6.2 Detailed Mass Balance File The detailed mass balance file is a file that conta ins an element-by-element, process-byprocess, direction-by-direction cumulative summary of mass (or volume) that passed through each element (overland cell or channel netw ork node) in the model demain during the simulation period. Mass balance files ar e written in a tab-delimited format to facilitate post-processing and analysis in spreadsh eet or statistical software.

5.6.3 Summary Statistics File Summary statistics file is a simple text file that contains brief summaries of model performance and output for hydrology, sediment tran sport for the sum of all solids types and each solids type simulated, and chemical transp ort for each chemical type simulated. For each output class a simple mass balance is pres ented along with minimum and maximum values for the overland plane and channel n etwork. The overall simulation runtime (wall clock, not CPU time) is also presente d at the end of the file.TREX User’s Manual Page 84

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation



### 6.0 DEVELOPMENTAL FEATURES The TREX framework is designed to be modular to all ow future development and addition of expanded features. Future development p lans call for addition of a wide range of chemical and particle transformation processes. In particular, chemical biodegradation, hydrolysis, oxidation, photolysis, radioactive deca y, volatilization, and dissolution processes may be added to the basic chemical transp ort submodel. Further development plans also include addition of a nutrient submodel to simulate nitrogen, phosphorus, and carbon cycles at the watershed scale. To facilitate future expansion, a number of develop mental features are present in TREX. These developmental features include provisions for :
1. Additional mass transfer and transformation process es for chemicals;
2. Mass transformation processes for solids (such as m ineralization and abrasion);
3. Soil and sediment erosion rate formulations (erosio n rates are presently estimated from transport capacity relationships); and
4. Environmental conditions (such as temperature, wind speed, solar radiation, etc.). While not fully implemented, code for these feature s already exists in TREX in order to provide a template and speed full development. Desc riptions of a number of these developmental features follow.

6.1 CHEMICAL MASS TRANSFER AND TRANSFORMATION PROCESSES As previously noted, future development plans call for addition of a wide range of chemical and particle transformation processes. In particular, chemical biodegradation, hydrolysis, oxidation, photolysis, radioactive deca y, volatilization, and dissolution processes may be added to the basic chemical transp ort submodel. Overviews of most of these processes are presented in the WASP5 (Ambrose et al. 1993) and IPX (Velleux et al. 2001) manuals. However, the basic computer code needed to implement all of these processes already exists within the TREX framework. Further, code for chemical dissolution and simple first-order biodegradation i s fully developed but is untested. Because of their advanced state of development in T REX, overviews of chemical biodegradation and dissolution follow.

6.1.1 Chemical Biodegradation Chemicals that can be metabolized or co-metabolized by bacteria or other microbes may be subject to transformation by biodegradation. The chemical biodegradation flux may be expressed as a simple first-order process as (after Ambrose et al. 1993):TREX User’s Manual Page 85

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

### V C k J ˆ
c

b bc 

### = (6.1)

where: bc



### J ˆ = chemical biodegradation flux [M/T] k b = first-order chemical biodegradation rate [1/T] C c = total chemical concentration in the water column or porewater

[M/L 3 ] V = bulk volume (water and particles) [L 3 ]
6.1.2 Chemical Dissolution Chemicals that exist in a pure solid phase and are not sorbed to particles can enter solution by dissolution. The chemical dissolution f lux may be expressed as a mass rate of transfer from the pure solid phase to the dissolved (aqueous) phase as (Cussler, 1997; Lynch et al. 2003): 

## ( )
c d d sc 

### C

f S k J ˆ

− α = (6.2)

where: sc



### J ˆ = chemical dissolution mass flux [M/T] k d = mass transfer coefficient for chemical dissoluti on [L/T]

= 

### δ

D

D = aqueous phase chemical diffusion coefficient for dissolution [L 2 /T] δ = boundary layer film thickness [L]

α = surface area available for mass transfer between solid and liquid

[L 2 ] S = aqueous solubility of the chemical [M/L 3 ] f d = fraction of the total chemical in the dissolved phase

[dimensionless] C c = total chemical concentration in the water column or porewater

[M/L 3 ] Assuming pure solid phase chemical particles are sp herical, the surface area available for mass transfer can be expressed as a function of the pure solid phase chemical concentration, particle diameter, and particle dens ity as (after Lynch et al. 2003):

p s cp 

### d V C ρ = α 6 (6.3)TREX User’s Manual Page 86

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation where: C cp = pure solid phase chemical concentration (in part icle form) [M/L 3 ]

V = bulk volume (water and particles) [L 3 ] d p = particle diameter [L] ρ p = particle density of pure solid phase chemical [M /L 3 ] Following dissolution from the pure solid phase, di ssolved chemicals are available for mass transfer (i.e. sorption) or transformation. Un der equilibrium conditions, the maximum dissolved phase concentration a chemical ca n attain is the solubility limit. The solubility of a chemical is influenced by several f actors including temperature and the concentrations (activities) of other ions in soluti on. The chemical dissolution reaction pathway may be useful for more detailed simulation of metal precipitates or explosive chemical compounds such as TNT or RDX that can be p resent in a granular, pure solid form.

6.2 ENVIRONMENTAL CONDITIONS The rates at which chemical mass transfer and trans formation processes occur often change as environmental conditions vary. Basic hydr ologic processes such as evapotranspiration and soil moisture can change and environmental conditions vary. To facilitate development of more detailed chemical fa te process representations or longterm hydrological impacts on chemical transport and fate, provisions to add a series of spatially and temporally varying time functions to represent environmental conditions exist in the TREX framework. While further developm ent is needed to fully activate these features, code exists to represent environmen tal conditions such as wind speed, air temperature, solar radiation, the concentration of dissolved organic carbon (DOC) or other binding agents, the fraction organic carbon o r partitioning effectiveness of both dissolved and particulate sorbents for partitioning , hardness, pH, water temperature, the concentration of oxidants, the concentration (popul ation density) of bacteria, and light extinction properties. The developmental code for e nvironmental conditions is organized to permit representation of any number or type of e nvironmental properties as needed. For example, additional properties such as relative humidity or the atmospheric concentration of a chemical can be readily added wi thin the existing framework structure.TREX User’s Manual Page 87

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation



### 7.0 PROGRAMMING GUIDE

7.1 TREX PROGRAMMING OVERVIEW TREX has a modular design to support future expansi ons and enhancements. With a basic degree of familiarity, users can customize mo st functions of the frameworks to create highly specialized application to address a broad range of watershed hydrological, sediment transport, and chemical transport and fate issues. However, some caution is appropriate. TREX is a complex program. No guarante es are made regarding either the suitability of TREX for constructing a specific wat ershed model application or the computational performance of the code. Although sub stantial efforts have been taken to examine all aspects of the code, users are strongly advised to carefully examine the TREX source code and all model inputs and outputs t o ensure proper operation. The authors would appreciate receiving notification of any comments, potential programming errors, bug reports, other problems enc ountered with the TREX program, or desired enhancements. Notification may be sent b y standard mail, telephone, or email to:

Mark Velleux HydroQual, Inc. 1200 MacArthur Boulevard Mahwah, NJ 07430 John F. England, Jr. Bureau of Reclamation Flood Hydrology Group, 86-68250 Bldg. 67, Denver Federal Center Denver, CO 80225 Dr. Pierre Julien Department of Civil Engineering Colorado State University B205 Enginring Research Center Fort Collins, CO 80523 (201) 529-5151 (303) 445-2541 (970) 491-8450 mvelleux@hydroqual.com jengland@usbr.gov pierre@eng r.colostate.edu

7.2 TREX AVAILABILITY, ONLINE RESOURCES, AND SUPPORT The TREX source code, some example input and output files, and user’s manual are available for download from Dr. Julien’s web site a t Colorado State University: http://www.engr.colostate.edu/%7Epierre/ce_old/Proj ects/TREX%20Web%20Pages/TR EX-Home.html The web site also includes references to reports an d journal articles on TREX and applications with TREX. Velleux et al. (2008) prese nt an overview of TREX. A metals transport study using TREX is described in Velleux (2005) and Velleux et al. (2006). Extreme flood modeling of the Arkansas River with T REX is presented in England (2006) and England et al. (2007).TREX User’s Manual Page 88

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation The authors may periodically update the TREX distri bution bundle on this web site as development continues. Example application files (t est cases) are also included. The current examples include hydrology and sediment tra nsport for the October 17, 1981 storm event on the Goodwin Creek, Mississippi water shed, a hypothetical chemical transport example based on the Goodwin Creek settin g, and demonstrations of extreme storm rainfall options applied to the Arkansas Rive r, Colorado. The hydrology and sediment transport examples for the Goodwin Creek s ite are of note because they allow comparison to results obtained using CASC2D-SED des cribed by Johnson et al. (2000), Julien and Rojas (2002), and Rojas et al. (2008). Please note that TREX was developed for academic an d research use. TREX is not officially supported by Colorado State University, the Bureau of Reclamation, or HydroQual, Inc. This means that users should not ex pect support beyond receiving the program, example files, and user’s manual via the w eb site unless special arrangements are made with the authors.

7.3 TREX PROGRAM ORGANIZATION AND DESCRIPTION TREX is a modular program and is comprised of subpr ocess groups that are organized into functional units for input, initialization, ti me function update, transport process, integration, output, and deallocation. The main pro gram (trex) calls processes to:
1. Read inputs; 2. Initialize variables; 3. Compute hydrologic (water) transport, sediment (sol ids) transport, and chemical transport from the simulation iterative time loop; 4. Compute hydrologic (water) mass balance, sediment ( solids) mass balance, and chemical mass balance from the simulation iterative time loop; 5. Write outputs; and 6. Deallocate memory and end execution. The transport process functional units for hydrolog ic transport, sediment transport, and chemical transport and fate are the core of TREX. T hese units appear within the model iterative time loop of TREX. The organization of th e transport process functional units is presented in Figure 7-1. Descriptions of the main c omponents of each functional unit within TREX follow. Descriptions of data included i n global header files also follows.

7.3.1 Input Functional Unit The input functional unit reads user-specified data from the main model input file, as organized into Data Groups A-F, as well as any anci llary input files required for a simulation. The major modules within this functiona l unit are:TREX User’s Manual Page 89

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation trex

ChemicalTransport

ChannelChemicalAdvection ChannelChemicalDeposition

ChannelChemicalDispersion

ChannelChemicalErosion ChannelChemicalKinetics

ChannelChemicalTransmissionLoss

FloodplainChemicalTransfer OverlandChemicalAdvection

OverlandChemicalDeposition

OverlandChemicalDispersion

OverlandChemicalErosion OverlandChemicalInfiltration OverlandChemicalKinetics SolidsTransport

ChannelSolidsAdvection

ChannelSolidsDeposition

ChannelSolidsDispersion

ChannelSolidsErosion ChannelSolidsKinetics

ChannelSolidsTransportCapacity

FloodplainSolidsTransfer OverlandSolidsAdvection OverlandSolidsDeposition

OverlandSolidsDispersion

OverlandSolidsErosion OverlandSolidsKinetics

OverlandSolidsTransportCapacity WaterTransport

ChannelWaterRoute

FloodplainWaterTransfer Infiltration Interception

OverlandWaterRoute Rainfall

TransmissionLoss

Figure 7-1. Organization of transport process funct ional units in TREX.TREX User’s Manual Page 90

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation • ReadInputFile

• ReadDataGroupA

• ReadDataGroupB

• ReadDataGroupC

• ReadDataGroupD

• ReadDataGroupE

• ReadDataGroupF At the time TREX is executed, the user must specify the name of the main model input file (and may also specify a restart option). The m ain model input file is specified as an argument to the program as described in Section 3.5 . The main input file name is stored in global memory and TREX calls ReadInputFile to in itiate data input processing operations. As TREX reads Data Groups A-F, a series of utility and secondary modules are called to read any required ancillary input fil es. The name assigned to each of these secondary modules provides a shorthand description of the module function and use. For example, ReadMaskFile is called to read the row-col umn grid format file that defines the spatial domain of a simulation. The model echo file is produced as output by the this unit.

7.3.2 Initialization Functional Unit The initialization functional unit allocates memory and assigns initial values to variables needed for simulation. The modules within this func tional unit, organized by the transport process (water, solids, chemical) for which they in itialize variables, are:

• Initialize

• InitializeWater

• InitializeSolids

• InitializeChemical

• InitializeEnvironment

• TimeFunctionInit

• TimeFunctionInitWater

• TimeFunctionInitSolids

• TimeFunctionInitChemical

• TimeFunctionInitEnvironment

• ComputeInitialState

• ComputeInitialStateWater

• ComputeInitialStateSolids

• ComputeInitialStateChemicalTREX User’s Manual Page 91

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Once all model inputs are read, the initialization functional unit initializes all remaining primary and secondary variables that are not define d at the time the main model inputs are read. In addition, this functional unit also cr eates all basic output file types that will be used during the simulation. For example, the exp ort, detailed mass balance, and summary statistics files are created by this functi onal unit.

7.3.3 Time Function Update Functional Unit The time function update functional unit assigns va lues in time for each time function specified by the user. The modules within this func tional unit, organized by transport process (water, solids, chemical), are:

• UpdateTimeFunction

• UpdateTimeFunctionWater

• UpdateTimeFunctionSolids

• UpdateTimeFunctionChemical

• UpdateEnvironment
This functional unit is called from the simulation iterative time loop within TREX. Userspecified time functions such as the rainfall inten sity (rate) as a gage location, the flow from a point source of water, or the load from a ch emical point source are updated for use each time step during the simulation. Values in tim e are updated between times defined by user input using linear interpolation. Outputs f rom this functional unit may be subsequently interpolated over space or applied at a point as needed by the modules comprising the transport functional unit.

7.3.4 Transport Process Functional Unit The transport process functional unit computes rate s and fluxes for each hydrological, sediment transport, and chemical transport process specified by the user. The modules within this functional unit, organized by transport process (water, solids, chemical), are:

• WaterTransport

• Rainfall

• Interception

• Infiltration, TransmissionLoss

• OverlandWaterRoute, ChannelWaterRoute

• FloodplainWaterTransfer

• SolidsTransport

• OverlandSolidsKinetics, ChannelSolidsKinetics

• OverlandSolidsDeposition, ChannelSolidsDepositionTREX User’s Manual Page 92

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation • OverlandSolidsAdvection, ChannelSolidsAdvection

• OverlandSolidsDispersion, ChannelSolidsDispersion

• OverlandSolidsTransportCapacity, ChannelSolidsTrans portCapacity

• OverlandSolidsErosion, ChannelSolidsErosion

• FloodplainSolidsTransfer

• ChemicalTransport

• OverlandChemicalKinetics, ChannelChemicalKinetics

• OverlandChemicalInfiltration, ChannelChemicalInfilt ration

• OverlandChemicalDeposition, ChannelChemicalDepositi on

• OverlandChemicalAdvection, ChannelChemicalAdvection

• OverlandChemicalDispersion, ChannelChemicalDispersi on

• OverlandChemicalErosion, ChannelChemicalErosion

• FloodplainChemicalTransfer
This functional unit is called from the simulation iterative time loop within TREX. Transport rates and fluxes for each process for eac h state variable in each overland cell and each channel node are computed for the surface water as well as all layers in the soil and sediment column for each time step during the s imulation. Further details regarding the organization of the kinetics (mass transfer and transformation reactions) modules for chemical fate are presented in Figure 7-2. the chem ical kinetics subunits include process modules for partitioning, biodegradation, hydrolysi s, oxidation, photolysis, radioactive decay, a user-defined reaction, volatilization, dis solution, and transformation yields between chemical state variables.

7.3.5 Integration Functional Unit The integration functional unit performs numerical integration to compute values for each state variable over time using the rates and fluxes for each hydrological, sediment transport, and chemical transport process computed by the transport process and time function update functional units. The modules withi n this functional unit, organized by transport process (water, solids, chemical), are:

• WaterBalance

• OverlandWaterDepth

• ChannelWaterDepth

• SolidsBalance

• OverlandSolidsConcentration

• ChannelSolidsConcentrationTREX User’s Manual Page 93

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation

OverlandChemicalKinetics

OverlandChemicalBiodegradation

OverlandChemicalDissolution

OverlandChemicalHydrolysis

OverlandChemicalOxidation OverlandChemicalPartitioning

OverlandChemicalPhotolysis

OverlandChemicalRadioactive

OverlandChemicalUDReaction

OverlandChemicalVolatilization

OverlandChemicalYield ChannelChemicalKinetics

ChannelChemicalBiodegradation

ChannelChemicalDissolution

ChannelChemicalHydrolysis

ChannelChemicalOxidation ChannelChemicalPartitioning

ChannelChemicalPhotolysis

ChannelChemicalRadioactive

ChannelChemicalUDReaction

ChannelChemicalVolatilization

ChannelChemicalYield Figure 7-2. Organization of chemical kinetics proce ss modules within TREX.TREX User’s Manual Page 94

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation • SolidsBalance

• OverlandSolidsConcentration

• ChannelSolidsConcentration

• ChemicalBalance

• OverlandChemicalConcentration

• ChannelChemicalConcentration

• NewState

• NewStateWater

• NewStateSolids

• NewStateChemical

• NewStateStack
This functional unit is called from the simulation iterative time loop within TREX. The model state variables are water depth, solids conce ntration, and chemical concentration. Mass balances are performed by summing the volume a nd mass fluxes for each state variable to computing new values for depth or conce ntration. The new state of the domain (water depths, solids concentrations, chemic al concentrations, as well as soil or sediment stack volumes) is then stored. At the end of the simulation iterative time loop, utility functions to determine maximum and minimum depths and concentrations are called, the new domain state is set as the current state, and then the simulated time is advanced one time step.

7.3.6 Output Functional Unit The output functional unit writes program results t o a range of user-specified output files. The modules within this functional unit are:

• WriteTimeSeries

• WriteTimeSeriesWater, WriteTimeSeriesSolids, WriteT imeSeriesChemical

• WriteGrids

• WriteGridsWater, WriteGridsSolids, WriteGridsChemic al

• WriteDumpFile

• WriteEndGrids

• WriteEndGridsWater, WriteEndGridsSolids, WriteEndGr idsChemical

• ComputeFinalState

• ComputeFinalStateWater, ComputeFinalStateSolids, Co mputeFinalStateChemical

• WriteMassBalance

• WriteMassBalanceWater, WriteMassBalanceSolids, Writ eMassBalanceChemicalTREX User’s Manual Page 95

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation • WriteSummary

• WriteSummaryWater, WriteSummarySolids, WriteSummary Chemical With the exception of the WriteEndGrid series of mo dules, this functional unit is called from the simulation iterative time loop within TREX . The WriteEndGrids modules are once at the end of the simulation immediately follo wing the simulation iterative time loop. Each time these modules are called, user-spec ified output is written to file. The WriteTimesSeries modules write to files that hold c omma separated values written line by line to form a sequence of model results at spec ified points in space organized by time. For example, one possible time series output is the water depth or total suspended solids concentrations at a reporting station. The W riteGrid modules write to grid (rowcolumn) output files that hold values for all point s in space for a single time in a format. Grid outputs are written in sequence at a user-spec ified frequency. For example, one possible sequence of grid output is the water depth s over the model domain at simulation times of the simulation start (time = 0), 10 minute s, 20 minutes, etc. The WriteEndGrid modules write to files similar to regular grid outp uts except that a single grid that holds the difference between start and end conditions ove r the model domain for the entire simulation is written. The ComputeFinalState module s compute conditions for primary and secondary model variables as needed to prepare detailed mass balance and summary statistics reports. The WriteMassBalance modules wr ite to a single file that holds a detailed mass balance for all state variables. The WriteSummary nodules write to a single file that holds summary detail and simulation stati stics for all state variables.

7.3.7 Deallocation Functional Unit The deallocation functional unit performs end of si mulation memory deallocation simulation clean-up tasks. The modules within this functional unit are:

• FreeMemory

• FreeMemoryWater

• FreeMemorySolids

• FreeMemoryChemical

• FreeMemoryEnvironment

• SimulationError

• RunTime The FreeMemory series of modules of functional unit are called from SimulationError when an trapped error condition occurs or following the simulation iterative time loop within TREX. These modules deallocate memory alloca ted for primary and secondary variables. At the end of a successful simulation, R unTime is called to determine the wall clock time (not CPU time) elapsed from the start to the end of the simulation.TREX User’s Manual Page 96

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 7.3.8 Global Declaration and Definition Header Files TREX is designed to operate around large, globally available (common) data blocks. The categories of global data blocks, organized by tran sport function, are:

• trex_general_declarations, trex_general_definitions

• trex_water_declarations, trex_water_definitions

• trex_solids_declarations, trex_solids_definitions

• trex_chemical_declarations, trex_chemical_definitio ns

• trex_environmental_declarations, trex_environmental _definitions Each category of global data is used by a specific layer of the framework. The framework layers are: general model controls, hydrology, sedi ment transport, and chemical transport. In TREX, information is always (and only) passed fo rward from one layer to the next. Declarations files specify included C library files (e.g. stdio.h, math.h, etc.), function prototypes, macros, and external file pointers and variable declarations. Definitions files provide definitions for all externally declared fil e pointers and variables. General declarations specify information regarding general model controls. Water declarations specify information regarding hydrology. Solids dec larations specify information regarding sediment transport. Chemical declarations specify information regarding chemical transport and fate. Environmental declarat ions specify information regarding environmental conditions. To make information available to a layer, the globa l declarations file for that layer must be included in all modules of the layer. The genera l declarations are common to, and used by, all program layers. The hydrology layer uses th e general and water declarations. The sediment transport layer uses the general, water, a nd solids declarations. The chemical transport layer uses the general, water, solids, ch emical, and environmental declarations. Note that for the present state of development, env ironmental conditions only affect chemical transport and fate. As environmental condi tion feature developments continue, the environmental category may be divided into sepa rate groups for hydrology, sediment transport, and chemical transport. For example, win d speed, air temperature, and relative humidity functions might be used by the hydrology l ayer to compute evapotranspiration and evaporation of surface water while soil tempera ture might be used by the sediment transport layer to compute mineralization rates of organic particles. It is also important to note that information is ne ver passed backwards between layers. For example, the hydrology layer does not and shoul d not have access to global data for sediment or chemical transport. Similarly, sediment transport does not and should not have access to global data for chemical transport a nd fate. This layered data access and management approach is useful for maintaining frame work modularity. Future layers, such as nutrient transport or eutrophication, can b e readily added without establishing confusing crosslinks between layers.TREX User’s Manual Page 97

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 7.4 PROGRAMMING STYLE To enhance readability, comprehension, and facilita te future development, a consistent programming style has been used for all TREX code d evelopment. The authors believe continued use of a consistent programming style is critical for future code maintenance and development. Descriptions of the key convention s of the TREX programming style follow.

7.4.1 Naming Conventions All variable names in the code are lower case (e.g. nsolids, advsedchoutflux, etc.). All programs module names are a mixture of upper and lo wer case (e.g. WaterTransport, ChannelChemicalKinetics, etc.). All macros are uppe r case (e.g. MAXNAMESIZE, TOLERANCE, etc.). Variable names are descriptive. A s a short hand, variables for the overland plane include “ov” and those for the chann el network include “ch”. Variables for water depth have “h” and flow have “q” in their names. Variables for sediment transport variables include “sed” and those for che mical transport include “chem”. Flux and mass terms include “flux” and “mass”, respectiv ely. Transport process variables also include three character identifiers to denote the s pecific process with which the variable is associated: “adv” for advection, “dsp” for dispe rsion, “dep” for deposition, “ers” for erosion, or “dsl” for dissolution, etc. In addition to identifiers such as “ov”, “adv”, and “flux”, transport variables also include “out” or “ in” to identify the direction of transport. Each of these name elements are typically concatena ted to form the full variable name. For example, the flux of suspended solids transport ed out of an overland cell by advection would be “advsedovoutflux”. Through use o f a consistent naming convention, new state variables and process modules can be adde d to the framework by using existing modules as templates and using a simple search and replace to include the names of new variables.

7.4.2 Internal Documentation and Comments The TREX code is extensively documented. Every modu le includes initial comments that identify the module name, purpose and methods, inpu ts, outputs, controls, modules called, calling module(s), routine author(s), revis ion history (if any), and date. Further, virtually every line of code has a comment to expla in the line-by-line operation of the module. Wherever additional information is needed t o explain the basis of an operation, a comment block delimited by the string “Note:” occur s and is followed by more in-depth documentation. Comment blocks delimited by the stri ng “Developer’s Note:” identify areas that may be the subject of future framework d evelopment efforts. The beginning, interior, and concluding brackets of loop and if structures each have comments to clearly identify the structures. Also, each unit of code within a loop or if structure is indented with tabs to provide further visual cues as to which structure controls the code. The start and end of all loop structures are identified the strings “loop” and “end loop”, respectively. The start and end of all if st ructures are identified the strings “if” and “end if”, respectively.TREX User’s Manual Page 98

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 7.4.3 Maintaining Consistent Programming Style During Dev elopment In many settings, it is common for a computer progr am code development team to change over time. This is particularly true in a setting s uch as a university where computer code is shared among different generations of students a nd projects. Under such conditions, it is common for code to rapidly mutate until it becom es so unintelligible that sometimes even the immediate code author(s) cannot clearly fo llow or explain its operation. The experience of the authors is that computer code han dled on an informal or ad hoc basis by a changing array of developers quickly becomes unma nageable. To achieve a higher degree of long-term manageability and maintainabili ty over time, the authors strongly recommend that future developers continue to use th e programming style conventions employed during initial TREX development. Continued adherence to naming conventions and use o f extensive, line-by-line comments in the code is essential for future maintainability . In addition to providing information regarding program operation, use of consistent comm ents and variable names also greatly facilitates program testing and debugging. Use of e stablished programming conventions allows newly developed modules to be rapidly screen ed for the occurrence potential bugs such as incorrect variable name references. For exa mple a common programming error is to reference variables for the channel network in a module for overland plane (or vice versa). Consider a solids transport module where va riables csedch and advsedchoutflux have been incorrectly used instead of csedov and ad vsedovoutflux. By adhering to variable naming conventions, a module can be search ed (case sensitive) for the occurrence of the string “sedch” since overland pro cess variables use the string “sedov” and it is very rare for an overland module to ever reference conditions in the channel network. Similarly, the occurrence of the string “s edov” rather than “chemov” would be rare in chemical process modules. Care should also be taken to prevent “cross-wiring” of program layers. The global data structure needed for any model layer (hydrology, se diment transport, etc.) should contain all variables needed for that layer to operate. In terms of program flow, information should only be passed forward. The global data stru cture for a later model layer should never be used or available to an earlier model laye r. It is worth reiterating that an important feature o f the TREX framework is that all source code for the program is extensively documented. The importance of comprehensive, lineby-line program documentation for future code maint enance and development cannot be understated. All too often during development effor ts, internal code documentation is neglected when programmers add code without adding corresponding, detailed comments for the perceived “speed and ease” of development. This inevitably leads to generation of poorly written, undocumented code. Even if the orig inal authors of undocumented code are available and can still decipher it in the futu re, it becomes exceedingly difficult for other programmers to manage such code over time. Th e challenges of managing poorly written and poorly documented code are often diffic ult to overcome and can be costly in terms of lengthened development time cycles. The co nsequence of earlier shortcuts taken for “speed and ease” is often that the same body of code ends up being repeatedly redeveloped by subsequent generations of developers . It the further experience of theTREX User’s Manual Page 99

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation authors that code that cannot be fully documented a t the time it is first written is in many instances poorly conceived, often poorly structured , and typically leads to effort wasted redeveloping code. For these and many other reasons , the importance of maintaining complete and comprehensive internal documentation o f all program code cannot be overemphasized.TREX User’s Manual Page 100

Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation 

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Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Eadie, B., N. Morehead, and P. Landrum. 1990. Three -phase partitioning of hydrophobic organic compounds in Great Lakes waters. Chemospher e, 20(1-2):161-178. Eadie, B., N. Morehead, V. Klump, and P. Landrum. 1 992. Distribution of hydrophobic organic compounds between dissolved and particulate organic matter in Green Bay waters. Journal of Great Lakes Research, 18(1):91-9 7. Eagleson, P.S. 1970. Dynamic Hydrology. McGraw-Hill Book Company, New York, New York. 462 pp. Eliasson, I., and Svensson, M.K. 2003. Spatial air temperature variations and urban land use – a statistical approach. Meteorological Applic ations, 10(2):135-149. Engelund, F., and Hansen, E. 1967. A monograph on s ediment transport in alluvial streams. Teknisk Vorlag, Copenhagen, Denmark. 62 pp

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Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Julien, P.Y., and Simons, D.B. 1985. Sediment trans port capacity of overland flow. Transactions of the American Society of Agricultura l Engineers, 28(3):755-762. Karickhoff, S.W., Brown, D.S., and Scott, T.A. 1979 . Sorption of hydrophobic pollutants on natural sediments. Water Research, 13(3):241-248

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Last Revised: January 2011 HDR-HydroQual, Inc. with Colorado State University and Reclamation Lu, Y., and Allen, H. 2001. Partitioning of copper onto suspended particulate matter in river waters. Science of the Total Environment 277( 1-3):119-132. Lynch, J., Brannon, J., Hatfield, K., and Delfino, J. 2003. An exploratory approach to modeling explosive coumpond persistence and flux us ing dissolution kinetics. Journal of Contaminant Hydrology, 66(3-4):147-153. Mehta, A., McAnally, W., Hayter, E., Teeter, A., He ltzel, S., and Carey, W. 1989. Cohesive sediment transport. II: application. Journ al of Hydraulic Engineering, 115(8):1094-1112. Merritt, W.S., Letcher, R.A., and Jakeman. A.J. 200 3. A review of erosion and sediment transport models. Environmental Modelling and Softw are, 18(8-9):761-799. Meyer, L.D., and Weischmeier, W.H. 1969. Mathematic al simulation of the process of soil erosion by water. Transactions of the American Society of Agricultural Engineers, 12(6):754-762. Partheniades, E. 1992. Estuarine sediment dynamics and shoaling processes. In: Handbook of Coastal and Ocean Engineering, Volume 3 : Harbours, Navigation Channels, Estuaries, and Environmental Effects, pp. 985-1071. Herbich, J. B., Ed. Gulf Publishing Company, Houston, Texas. Pellicciotti, F., Brock, B., Strasser, U., Burlando , P., Funk, M., and Corripio, J. 2005. An enhanced temperature-index glacier melt model inclu ding the shortwave radiation balance: development and testing for Haut Glacier d ’Arolla, Switzerland. Journal of Glaciology, 51(175):573-587. Phillip, J.R. 1957a. The theory of infiltration: 1. The infiltration equation and its solution. Soil Science, 83:345-357. QEA. 1999. PCBs in the Upper Hudson River, Volume 2 : A model of PCB Fate, Transport, and Bioaccumulation. Prepared for Genera l Electric, Albany, New York. Prepared by Quantitative Environmental Analysis, LL C, Montvale, New Jersey. Job Number GENhud:131. May. Rawls, W.J., Brakensiek, D.L., and Miller, N. 1983. Green-Ampt infiltration parameters from soils data. Journal of Hydraulic Engineering, 109(1):62-69. Rawls, W.J, Ahuja, L.R., Brakensiek, D.L., and Shir mohammadi, A. 1993. “Infiltration and Soil Movement.” In: Handbook of Hydrology, Maid ment, D.R., ed. McGrawHill, Inc., New York, New York. pp 5.1-5.51. Renard, K.G., Foster, G.R., Weesies, G.A., and Port er, J.P. 1991. RUSLE: revised universal soil loss equation. Journal of Soil and W ater Conservation, 46(1):30-33.TREX User’s Manual Page 105

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