Report Title

A Guide for Using the Transient Ground-Water Flow

Model of the Death Valley Regional Ground-Water Flow

System, Nevada and California

Open-File Report 2006–1104

Prepared in cooperation with the U.S. Department of Energy Office of Environmental

Management, National Nuclear Security Administration, Nevada Site Office, under Interagency

Agreement DE-A52-0NV3944 and Office of Repository Development, under Interagency

Agreement DE-A08-02RW267

U.S. Department of the Interior

U.S. Geological Survey

MODEL COLUMN 

MODEL ROW 

20 40 60 80 100 120 140 160

194

180

160

140

120

100

80

60

40

20

36

37

38

117 116 115

CALIFORNIA

NEVADA

San Bernardino Co 

Inyo Co 

Clark Co 

Lincoln Co 

Esmeralda Co Nye Co 

Amargosa Desert

Pahrump

Valley

Death

Yucca 

Mtn

Pahute

Mesa

Valley 

Devils

Hole

Penoyer

Valley

Nevada Test Site

Furnace

Creek

Tecopa

Beatty

Shoshone

Pahrump

Las

Vegas

A Guide for Using the Transient GroundWater Flow Model of the Death Valley 

Regional Ground-Water Flow System, 

Nevada and California

By Joan B. Blainey, Claudia C. Faunt, and Mary C. Hill

Prepared in cooperation with the U.S. Department of Energy Office of Environmental 

Management, National Nuclear Security Administration, Nevada Site Office, under Interagency 

Agreement DE-A152-01NV13944 and Office of Repository Development, under Interagency 

Agreement DE-A108-02RW12167

Open-File Report 2006–1104

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

P. Lynn Scarlett, Acting Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, Virginia: 2006

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

World Wide Web: http://www.usgs.gov/

Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Blainey, J.B., Faunt, C.C., and Hill, M.C., 2006, A guide for using the transient ground-water flow model of the 

Death Valley regional ground-water flow system, Nevada and California: U.S. Geological Survey Open-File Report 

2006-1104, 26 p. Available at URL: <http://pubs.water.usgs.gov/ofr2006-1104>. 
iii

Contents

Abstract ................................................................................................... 1

Introduction................................................................................................ 1

Purpose and Scope ................................................................................. 4

Overview of Files Required for the DVRFS Model ................................................... 4

MODFLOW Processes.................................................................................... 5

Global (GLO) Process .............................................................................. 5

Name File: Activating Capabilities and Opening Files .................................... 5

Discretization (DIS) File ..................................................................... 6

Space Discretization .................................................................. 6

Time Discretization ..................................................................... 6

Multiplier (MULT) and Zone (ZONE) Files................................................... 6

Ground-Water Flow (GWF) Process ............................................................ 6

Use of Parameters in the Ground-Water Flow Process ....................................... 6

Ground-Water Flow (GWF) Process Packages for the DVRFS Model ........................ 7

Basic (BAS6) Package ..................................................................... 7

Output Control (OC) Option .................................................................. 7

Hydrogeologic-Unit Flow (HUF2) Package ................................................ 7

Horizontal-Flow Barrier (HFB6) Package ................................................ 8

Recharge (RCH) Package .................................................................. 8

Multi-Node Well (MNW1) Package ...................................................... 8

Drain (DRN) Package ........................................................................ 9

Constant-Head Boundary (CHD) Package ................................................ 9

Solver Packages .............................................................................. 9

Observation (OBS) Process ..................................................................... 10

Head Observation (HOB) Package ......................................................... 10

Drain Observation (DROB) Package ...................................................... 11

Constant-Head Flow Observation (CHOB) Package .................................... 11

Sensitivity (SEN) Process ........................................................................ 12

Parameter-Estimation (PES) Process ............................................................ 14

Model Output ............................................................................................. 14

Typical DVRFS MODFLOW-2000 Modes ............................................................... 16

Forward Mode .................................................................................... 16

Parameter-Sensitivity Modes ..................................................................... 18

Parameter-Estimation Mode ..................................................................... 19

Typical Uses of the DVRFS Model ..................................................................... 19

Predictive Pumping Scenarios .................................................................. 19

Converting from a Transient to Steady-State Simulation....................................... 20

Summary ................................................................................................... 23

References Cited.......................................................................................... 23

Appendix A: File Archive Documentation ............................................................ 25
iv

Figures

Figure 1. Map showing geographic and prominent topographic features of the

Death Valley regional ground-water flow system, Nevada and California ......... 2

Figure 2. Map showing simulated discharge areas, major recharge areas,

constant-head boundary flows, and steady-state stress period hydraulic

head in the uppermost active model layer of the Death Valley regional

ground-water flow system, Nevada and California .................................... 3

Figure 3. Graph showing annual discharge from Bennetts and Manse springs in

Pahrump Valley, Nevada, 1875–1998 ...................................................... 11

Tables

Table 1. MODFLOW-2000 packages and processes used in the Death Valley 

regional ground-water flow system model, Nevada and California .................. 4

Table 2. Map coordinates for the Death Valley regional ground-water flow system, 

Nevada and California........................................................................ 6

Table 3. Description of the parameter names in the sensitivity file and the

associated packages and files ............................................................ 13

Table 4. Sensitivity Process and associated factors for Constant-Head Boundary,

Drain, Horizontal-Flow Barrier, and Recharge Packages .............................. 13

Table 5. Select output files produced by MODFLOW-2000 by active processes............... 15

Table 6. Plot symbol codes that identify the observation type in all “underscore”

output files created during forward and parameter-sensitivity mode

simulations ................................................................................. 15

Table 7. Modes of MODFLOW-2000 produced by activating different combinations

of the Sensitivity and Parameter-Estimation Processes, and commonly

used output when the Observation Process is active ................................. 17
Conversion Factors, Datums, and Abbreviations and 

Acronyms

SI to Inch/Pound 

Multiply By To obtain

cubic meter per day (m3/d) 0.2961 acre-foot per year

cubic meter per day (m3/d) 0.0004087 cubic foot per second

cubic meter per day (m3/d) 264.2 gallon per day

kilometer (km) 0.6214 mile

meter (m) 3.281 foot

meter per day (m/d) 3.281 foot per day

meter per day per meter [(m/d)/m] 1 foot per day per foot

square kilometer (km2) 2.417 acre

square kilometer (km2) 0.3861 square mile

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).

Altitude, as used in this report, refers to distance above the vertical datum.
vi

Abbreviations and Acronyms

BAS6 Basic Package

CHD Constant-Head Boundary Package

CHOB Constant-Head Flow Observation Package

DE4 Direct Solution Package

DIS Discretization file

DRN Drain Package

DROB Drain Observation Package

DVRFS Death Valley regional ground-water flow system

GWF Ground-Water Flow Process

GLO Global Process

GMG Geometric Multigrid Package

HFB6 Horizontal-Flow Barrier Package

HOB Head Observation Package 

HGU Hydrogeologic unit

HUF2 Hydrogeologic-Unit Flow Package

KDEP Hydraulic-conductivity depth-dependence

LIST Listing file

LMG Limit to Algebraic Grid Package

MULT Multiplier file

MNW1 Multi-Node Well Package

OBS Observation Process

OC Output Control

PCG Preconditioned Conjugate Gradient Package

PES Parameter-Estimation Process

RCH Recharge Package

SEN Sensitivity Process

SS Specific storage parameter type for the HUF2 Package

SY Specific yield parameter type for the HUF2 Package

USGS United States Geological Survey

UTM Universal Transverse Mercator

WEL1 Well Package

ZONE Zonation file
Abstract

This report is a guide for executing numerical simulations 

with the transient ground-water flow model of the Death 

Valley regional ground-water flow system, Nevada and 

California using the U.S. Geological Survey modular finitedifference ground-water flow model, MODFLOW-2000. 

Model inputs, including observations of hydraulic head, 

discharge, and boundary flows, are summarized. Modification 

of the DVRFS transient ground-water model is discussed for 

two common uses of the Death Valley regional ground-water 

flow system model: predictive pumping scenarios that extend 

beyond the end of the model simulation period (1998), and 

model simulations with only steady-state conditions.

Introduction

The Death Valley regional ground-water flow system 

(DVRFS) model domain encompasses about 100,000 km2 in 

Nevada and California and is bounded by latitudes 35°00’N 

and 38°15’N and by longitudes 115°00’W and 118°00’W 

(fig. 1). Belcher and others (2004), San Juan and others 

(2004), and Faunt and others (2004a, 2004b) documented 

the development of a conceptual understanding of the system 

hydrology and hydrogeology, and ultimately a transient 

ground-water simulation of the DVRFS. Faunt and others 

(2004a) and San Juan and others (2004) described the 

conceptualization of the system hydrology, natural groundwater discharge including evapotranspiration and springs, 

pumpage, ground-water recharge, and water levels (fig. 2). In 

particular, San Juan and others (2004) described model inputs 

and their sources, including the calculation of observations 

(water levels, flows at the model boundary, and natural 

discharge) and observation weights. These observations and 

the associated weights form the basis of the data used to 

calibrate and evaluate the transient numerical flow model.

The transient ground-water flow model of the 

DVRFS simulates steady-state conditions that represent 

predevelopment conditions followed by transient conditions 

from 1913 through 1998 (Faunt and others, 2004b). Recharge 

is constant at average annual values for the entire period of 

simulation; however, the simulated recharge varies spatially. 

Ground-water pumpage from 1913 to 1998 is a transient stress 

imposed using average annual values. Along some portions of 

the model boundary, constant-head boundary flows represent 

lateral flow from adjacent basins. Ground-water discharge 

from evapotranspiration and spring flow is simulated using 

head-dependent boundaries. DVRFS model input, output, 

and source code are available at the model archive link at 

URL: http://pubs.water.usgs.gov/sir20045205/ (accessed on 

December 22, 2005). A complete list and description of the 

archived model files are provided in the Appendix A (at back 

of report).

The DVRFS model uses the Ground-Water Flow Process 

of MODFLOW-2000 [which is similar to the capabilities of 

MODFLOW-96 (Harbaugh and McDonald, 1996)], as well 

as the Observation and Sensitivity-Analysis Processes of 

MODFLOW-2000 (Hill, 1990; Harbaugh and others, 2000; 

Hill and others, 2000). Subsequent to these publications, 

additional MODFLOW capabilities were developed and used 

in the DVRFS model including the Hydrogeologic-Unit Flow 

(HUF2) Package (Anderman and Hill, 2000, 2003) and the 

Multi-Node Well (MNW1) Package (Halford and Hanson, 

2002). The HUF2 Package allows the modeler to translate the 

hydrogeologic framework into flow model layers by defining 

the geometry of the hydrogeologic units independently of the 

flow model layers. The MNW1 Package simulates pumping 

and injection for wells that penetrate multiple flow model 

layers.

A Guide for Using the Transient Ground-Water Flow Model 

of the Death Valley Regional Ground-Water Flow System, 

Nevada and California

By Joan B. Blainey, Claudia C. Faunt, and Mary C. Hill
Figure 1. Geographic and prominent topographic features of the Death Valley regional ground-water flow system, Nevada and California.

Tonopah

Furnace

Creek

Beatty

Las

Vegas

Shoshone

Baker

Devils

Hole

Amargosa Range

Pahute

Mesa

Pahranagat Range

East Pahranagat Range

North Pahranagat Range

Black

Mtn

Timpahute

 Range

Cactus

Flat

Stonewall

Flat Kawich

Valley Cactus RangeKawich Range

Belted Range

Groom Range

Last Chance Range

Gold

Mtn Half Pint Range

Rainier

Mesa Sarcobatus

Flat

Black Mts

Funeral Mts

Granite Mts

Amargosa Desert

Spring Mts

Pahrump

Valley

Skull Mtn

California

Owlshead Valley

Mts

Frenchman

Flat

Sierra Nevada

Spotted Range

Sheep Range

Panamint Range

Kingston

Range

Soda

Mts

Calico

Hills

Eleana Range

Mercury V

Emigrant

Valley

Tikaboo

Valley

SR SH/LSM

AF

SPH

MQM

RSR

STV

Alkali

Flat Charleston

Peak

Las

Vegas

Valley

MP

IH

Bullfrog

Hills

Fortymile Canyon

MM

Death

Valley

Panamint Valley

Avawatz

Mts

Tecopa

Tonopah

Furnace

Creek

Beatty

Las

Vegas

Shoshone

Baker

Devils

Hole

Amargosa Range

Pahute

Mesa

Pahranagat Range

East Pahranagat Range

North Pahranagat Range

Black

Mtn

Timpahute

 Range

Cactus

Flat

Stonewall

Flat Kawich

Valley Cactus RangeKawich Range

Belted Range

Groom Range

Last Chance Range

Gold

Mtn Half Pint Range

Rainier

Mesa Sarcobatus

Flat

Black Mts

Funeral Mts

Granite Mts

Amargosa Desert

Spring Mts

Pahrump

Valley

Skull Mtn

California

Owlshead Valley

Mts

Frenchman

Flat

Sierra Nevada

Spotted Range

Sheep Range

Panamint Range

Kingston

Range

Soda

Mts

Calico

Hills

Eleana Range

Mercury V

Emigrant

Valley

Tikaboo

Valley

SR SH/LSM

AF

SPH

MQM

RSR

STV

Alkali

Flat Charleston

Peak

Las

Vegas

Valley

MP

IH

Bullfrog

Hills

Fortymile Canyon

MM

CALIFORNIA

KERN CO 

SAN BERNARDINO CO 

INYO CO

CLARK CO 

LINCOLN CO

NYE CO 

ESMERALDA CO

NEVADA

Death

Valley

Panamint Valley

 NV_9GVTP_fig_01

AF = Amargosa Farms

IH = Ibex Hills

MM = Mt. Montgomery

MP = Mormon Point

MQM = Mesquite Mountains

RSR = Resting Spring Range

SH/LSM = Striped Hills/

 Little Skull Mtn

SPH = Sperry Hills

SR = Specter Range

STV = Stewart Valley

Place abbreviations

GREAT BASIN

DESERT

MOJAVE

DESERT

Avawatz

Mts

Tecopa

CALIFORNIA

STUDY

 AREA

NEVADA

Desert boundary

Underground Test Area model boundary 

(IT Corporation, 1996)

Predevelopment Death Valley regional ground-water flow 

 system model boundary (D'Agnese and others, 2002)

Death Valley regional ground-water flow system 

 model boundary

450000 500000 550000 600000 650000

3900000 3950000 4000000 4050000 4100000 4150000 4200000

35°

36°

37°

38°

118° 117° 116° 115°

Nevada Test Site boundary

Yucca Mountain Project model boundary 

(D'Agnese and others, 1997)

Universal Transverse Mercator projection, Zone 11. Shaded-relief 

from 1:250,000-scale Digital Elevation Model (315° azimuth, 

30° altitude); UTM grid in brown.

0

0 20 40 MILES

40 80 KILOMETERS

EXPLANATION

 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Figure 2. Simulated discharge areas, major recharge areas, constant-head boundary flows, and steady-state stress period hydraulic head in the 

uppermost active model layer of the Death Valley regional ground-water flow system, Nevada and California.

CALIFORNIA

NEVADA

Stone CabinRailroad

Garden

Coal

Pahranagat

Sheep

Range

Las

Vegas

SpringMesquite

Owlshead

Panamint

200

800

Silurian

Clayton

Saline

Eureka

1

4

6

2

1

3

2

4

1

7

5

4

3

2

1

4

1

3

1

1

1

2

5

5

3

3

1

2

4

1

3

4

4

3

2

1

3

3

2

2

2

1

2

3

4

2

3

1

12

11

7

5

8

6

9

4

10

2

3

400

200

200

600

1000

1200

2000

2630

2400

1600

1400

1400

1200 1000

800

800

800

600

400

800

800

200

1000

1000

1000

1000

1000

600

1200

1200

800

1400

1200

400

200

200

600

1000

1200

2000

2630

2400

1600

1400

1400

1200 1000

800

800

800

600

400

800

800

200

1000

1000

1000

1000

1000

600

1200

1200

800

1400

1200

1 5

3

4 3 2

Stone CabinRailroad 7

Garden

Coal

EXPLANATION

Direction

of flow

Simulated horizontal-flow barriers

Nevada Test Site boundary

Death Valley regional ground-water flow system 

model grid boundary Simulated discharge areas

200 Simulated steady-state potentiometricsurface contour for layer 1—Contour

interval is 200 meters. Datum is North

American Vertical Datum, 1988

Simulated major recharge areas

Universal Transverse Mercator projection, Zone 11. Shaded-relief 

from 1:250,000-scale Digital Elevation Model (315° azimuth, 

30° altitude); UTM grid in brown.

Colors shown with corresponding 

number indicate Segment Name along 

Death Valley regional ground-water 

flow system model boundary

White and black lines with 

numbers in color indicate 

alternating segments within 

Segment Name (Garden Coal for 

example)

Line with no 

color boxes 

indicates No

flow in and out 

of System Blue boxes indicate 

flow into System

Red boxes indicate 

flow out of System

36°

37°

38°

117° 116° 115°

6

0 20

0 40 80 KILOMETERS

40 MILES

50,000 to 100,000

100,000 to 500,000

500,000 to 1,000,000

1,000,000 to 5,000,000

5,000,000 to 10,000,000

Greater than 10,000,000

Simulated pumping well and total 

withdrawal by model cell, in cubic 

meters per day (1913–98)

Less than 50,000

450000 500000 550000 600000 650000

3950000 4000000 4050000 4100000 4150000 4200000

Introduction 
Purpose and Scope

This report provides the user of the DVRFS transient 

ground-water model a guide for conducting numerical 

simulations with the archived model using MODFLOW2000 (Harbaugh and others, 2000; Hill and others, 2000). 

Both model input and output will be described for forward, 

sensitivity-analysis, and parameter estimation model 

simulations. Additionally, modification of the DVRFS 

transient ground-water model is discussed for two common 

uses of the DVRFS model: predictive pumping scenarios that 

extend beyond the end of the model simulation period (1998), 

and model simulations with only steady-state simulation. 

For both of these model modifications, the required editing 

of MODFLOW-2000 input, including observation files, is 

outlined with examples. This report is designed for users 

familiar with concepts associated with the Ground-Water 

Flow Process of MODFLOW-2000 [which is similar to the 

capabilities of MODFLOW-96 (Harbaugh and McDonald, 

1996)] but perhaps less familiar with the Observation, 

Sensitivity-Analysis, and Parameter-Estimation Processes of 

MODFLOW-2000 (Hill, 1990; Harbaugh and others, 2000; 

Hill and others, 2000).

Overview of Files Required for the 

DVRFS Model

All necessary DVRFS model input is read from one or 

more input data files. MODFLOW-2000 reads ASCII files and 

outputs ASCII (and in some cases binary) files. Input required 

for conducting MODFLOW-2000 simulations with the 

DVRFS model for the Observation, Sensitivity, and ParameterEstimation Processes are shown in table 1. 

Package or process Package or 

process file type Input file name Reference

Global Process (including the discretization 

file (DIS), multiplier file (MULT), name, 

and ZONE files and utility modules)

GLO DIS_WT_CONFINED.txt, MULT.txt, 

NAME.txt, ZONE.txt

Harbaugh and others (2000)

Groundwater Flow Process [including the 

Output Control Option (OC)]

GWF OC.txt Harbaugh and others (2000)

Basic Package BAS6 BAS_active.txt Harbaugh and others (2000)

Hydrogeologic Unit Flow Package 

[including depth decay file (KDEP)]

HUF2 HUF2_CONFINED.txt, KDEP.txt Anderman and Hill (2000, 2003)

Horizontal-Flow Barrier Package HFB6 HFB_final_tr.txt Harbaugh and others (2000)

Recharge Package RCH RCH_tr.txt Harbaugh and others (2000)

Multi-Node Well Package MNW1 MNW_withdrawal_1_7_20.txt1 Halford and Hanson (2002)

Drain Package DRN DRN_tr.txt Harbaugh and others (2000)

Constant-Head Boundary Package CHD CHD_15reg_tr.txt Harbaugh and others (2000)

Preconditioned Conjugate-Gradient 

Package

PCG2 PCG.txt Hill (1990); Harbaugh and others (2000) 

Observation Process [including ConstantHead Flow Observation Package (CHOB), 

Drain Observation Package (DROB), and 

Head Observation Package (HOB)]

OBS OBS.txt, CHOB_15reg.txt, DROB_tr.txt, 

HOBs_sstr.txt

Hill and others (2000)

Sensitivity Process SEN SENSITIVITY.txt Hill and others (2000)

Parameter-Estimation Process PES PES.txt Hill and others (2000)

1

The MNW1 Package has an option to create an equivalent file in the WEL1 Package format. This file, wel_package.wl1, is included in the model archive.

Table 1. MODFLOW-2000 packages and processes used in the Death Valley regional ground-water flow system model, Nevada and California.

[Package or process: BAS6, Basic Package; CHD, Constant-Head Boundary Package; DRN, Drain Package; GLO, Global Process; GWF, Ground-water Flow 

Process; HFB6, Horizontal-Flow Barrier Package; HUF2, Hydrogeologic Unit Flow Package; MNW1, Multi-Node Well Package; OBS, Observation Process; 

PCG2, Preconditioned Conjugate-Gradient Package; PES, Parameter-Estimation Process; RCH, Recharge Package; SEN, Sensitivity Process; ZONE, zone file]

 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
The required input, which is organized into groups of 

related data sets and packages, varies according to the active 

MODFLOW-2000 capabilities. A single model simulation 

or parameter-estimation simulation will not use all files, 

packages, or processes available. Information produced by 

MODFLOW-2000 is written to one or more output data files. 

Input and output are stored in ASCII files or in some cases 

binary files. These files are designed to be read by programs 

such as text editors, and plotting or data analysis routines 

(Harbaugh, 1990; Hanson and Leake, 1999; Winston, 2000). 

Archived input files for the DVRFS model are: 

• Input and output control information [name and Output 

Control (OC) files].

• Finite-difference grid and time discretization [Basic 

(BAS6) Package and Discretization (DIS) File].

• Multiplier (MULT) file.

• Zone (ZONE) file.

• Initial conditions (BAS6 Package).

• Properties of the porous media [Hydrogeologic-Unit 

Flow (HUF2) Package].

• Horizontal-Flow Barrier (HFB6) Package.

• Source term packages:

– Head-independent packages [Well (WEL1), 

Recharge (RCH), and Multi-Node Well (MNW1) 

Packages].

– Head-dependent package [Drain (DRN) Package].

• Time-Variant Specified Head-Package [Constant-Head 

Boundary (CHD) Package).

• Solver (Preconditioned Conjugate Gradient (PCG2) 

Package].

• Utilities for reading array and list data (U2DREL).

• Observation Process (OBS) and Observation Packages 

[Head Observation (HOB), Drain Observation 

(DROB), and Constant-Head Flow Observation 

(CHOB) Packages].

• Sensitivity (SEN) Process.

• Parameter-Estimation (PES) Process.

MODFLOW Processes

MODFLOW is a computer program that simulates 

three-dimensional ground-water flow through porous media 

using the finite-difference method (McDonald and Harbaugh, 

1984, 1988). Each process of MODFLOW-2000, the most 

recent version of MODFLOW, solves an equation with the 

exception of the Global (GLO) Process. The five processes of 

MODFLOW-2000 are: Global (GLO) Process, Ground-Water 

Flow (GWF) Process, Observation (OBS) Process, Sensitivity 

(SEN) Process, and Parameter-Estimation (PES) Process.

In the GLO Process, input arrays define the physical 

system including the altitude and spatial discretization. Input 

data files also describe the model grid geometry, layers, 

time discretization, and program operation. Data describing 

the physical properties of the media and the ground-water 

flow system are input through the various packages of the 

GWF Process. Finite-difference equations are solved by the 

GWF Process to compute a hydraulic head solution based 

on the active processes and packages. Simulated values may 

be compared to observations in the OBS Process. Various 

statistics and sensitivities to the observations are calculated 

in the OBS Process. Upon user initiation, the sensitivity 

equation for hydraulic heads with respect to each parameter 

is calculated throughout the model grid by the SEN Process. 

If both the OBS and SEN Processes are active, observation 

sensitivities may be calculated. With the PES Process active, 

parameter estimation may determine parameter values based 

on optimization of a weighted least-squares objective function 

that evaluates the fit of simulated values to the observations. 

Global (GLO) Process 

The GLO Process controls overall program flow, 

opens files, and reads global data such as space and time 

discretization. The GLO Process has four input files: name, 

discretization, multiplier, and zone files. Instructions for 

preparing the name file, and explanations for the variables 

read in all other files except as noted, are included in the Input 

Instructions section of Harbaugh and others (2000). 

Name File: Activating Capabilities and Opening 

Files

The name file controls the capabilities of MODFLOW2000 utilized during a model simulation. The name file lists 

most of the files used by the GLO, OBS, SEN, and PES 

Processes. MODFLOW capabilities are activated by listing the 

appropriate file type along with the file name and unit number. 

A process or file is not active if a “#” sign appears in the first 

column of the line in the name file (name.txt).

MODFLOW Processes 
Discretization (DIS) File 

Both space and time information are discretized using 

information from the Discretization File, specified as file type 

“DIS”. The length and time units of the model can be specified 

in the discretization file. In the DVRFS model, these units are 

meters and days.

Space Discretization

Information in the DIS file defines the physical size of the 

finite-difference grid. The model grid boundary is rectangular. 

Although the grid can be distorted vertically, model layers 

cannot pinch out to zero thickness. 

The DVRFS model grid is oriented north-south and 

consists of 194 rows and 160 columns with a constant gridcell spacing of 1,500 by 1,500 m (fig. 2 and table 2). Each of 

the 16 model layers generally range in thickness from 50 to 

300 m with model thickness generally increasing with depth 

(Faunt and others, 2004b, table F-1, p. 268). The upper model 

layers simulate relatively shallow saturated ground-water flow 

primarily through basin-fill sediments, volcanic rocks, and 

adjacent mountain ranges. Lower model layers predominantly 

simulate deep ground-water flow through the regional 

carbonate-rock aquifer beneath the basin fill and mountain 

ranges. 

Time Discretization

Time discretization also is specified in the DIS file. The 

fundamental component of time discretization is the time step. 

Time steps are aggregated into stress periods. Time dependent 

input data can vary every stress period. Individual stress 

periods within a single simulation may be either transient or 

steady state. For each stress period, the user specifies the stress 

period length, the number of time steps, and the multiplier 

for the length of successive time steps. For transient stress 

periods, the number of time steps and the time step multiplier 

can affect the accuracy of the solution. The DVRFS model is 

structured with an initial steady-state stress period followed 

by 86 transient stress periods, each one year in duration. Each 

yearly stress period has two time steps. Simulations with more 

time steps did not improve model accuracy (Faunt and others, 

2004b, p. 266).

Multiplier (MULT) and Zone (ZONE) Files

The multiplier file, specified as file type “MULT”, 

defines multiplier arrays for calculation of model-layer 

characteristics from parameter values. Parameters are defined 

in section, “Use of Parameters in the Ground-Water Flow 

(GWF) Process.” The multiplier file may be used to construct 

new arrays by adding and multiplying existing arrays. For 

the DVRFS model, the MULT file is used to represent an 

infiltration array, which is a multiplier for the Recharge 

Package. 

The zone file, specified as file type “ZONE,” defines 

arrays of different zones. Zone arrays may specify cells in a 

layer variable associated with a specific parameter. Parameters 

may be composed of either one or many zones. The DVRFS 

model uses many zone arrays to represent areas of similar 

porous media properties for a given hydrogeologic unit.

Ground-Water Flow (GWF) Process 

The GWF Process includes all aspects of solving the 

ground-water flow equation, including formulation of the 

finite-difference equations, data input, solving the resulting 

simultaneous equations, and model output. The GWF Process 

uses the finite-difference method in which the ground-water 

flow system is divided into a grid of cells. At the center of 

each cell, or node, the finite-difference method is used to 

define a set of simultaneous equations, which are solved for 

head. For steady-state stress periods, the storage term in the 

ground-water flow equation is set to zero.

Use of Parameters in the Ground-Water Flow 

Process

With MODFLOW-2000, parameters may be used 

to define many of the numerous data values that must be 

specified for each model cell. A parameter is a single value 

that is used to determine data values for multiple cells. 

Parameter definition includes a parameter name and value, 

and the cells for which the input values are calculated using 

that parameter. The most common and direct approach for 

determining data values from parameters is to set the data 

value equal to the parameter value for multiple cells. In a 

more complex approach, data values are assigned for multiple 

cells with additive contributions from multiple parameters 

Table 2. Map coordinates for the Death Valley regional ground-water 

flow system, Nevada and California.

[Coordinates are calculated at the corner of the finite-difference model grid. 

Coordinates are in Universal Transverse Mercator, Zone 11]

Corner of 

model grid

Grid node

(row, column)

Coordinates (meters)

Northing Easting

Upper left 1, 1 437,000 4,219,000

Upper right 1, 160 677,000 4,219,000

Lower left 194, 1 437,000 3,928,000

Lower right 194, 160 677,000 3,928,000

 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
(Harbaugh and others, 2000, p. 14-19). The DVRFS model 

does not use additive parameters, but in some cases, such as 

the recharge parameters, the data value at a cell is equal to a 

parameter value times a value in a multiplication array. Cellby-cell model input used in MODFLOW 2000 calculations is 

a combination of parameter values specified in the package 

in which the parameters are defined and parameter values 

specified in the SEN Process, and possibly values specified in 

the zone and/or multiplier arrays.

Ground-Water Flow (GWF) Process Packages 

for the DVRFS Model

Harbaugh and others (2000) document the 15 packages 

included in the initial release of MODFLOW-2000. The 

DVRFS model includes 2 packages developed after the initial 

release of MODFLOW-2000: the internal flow package, 

HUF2, (Anderman and Hill, 2000, 2003) and the MNW1 

Package (Halford and Hanson, 2002). The DVRFS model uses 

the Output Control Option and 8 GWF packages: 

1. Basic (BAS6) Package;

2. Output Control (OC) Option;

3. Hydrogeologic-Unit Flow (HUF2) Package; 

4. Horizontal-Flow Barrier (HFB6) Package;

5. Recharge (RCH) Package;

6. Multi-Node Well (MNW1) Package or the Well 

(WEL1) Package);

7. Drain (DRN) Package;

8. Constant-Head Boundary (CHD) Package; and

9. Solver (Preconditioned Conjugate Gradient Package 

(PCG2)) Package.

Basic (BAS6) Package 

The Basic Package, specified as file type “BAS6”, defines 

the initial conditions and some of the boundary conditions of 

the model. Initial conditions consist of starting heads for each 

cell in all model layers. Boundary conditions are specified 

using the array IBOUND. The value of the IBOUND array is 

defined at each cell to indicate that (1) the cell is active and 

head in the cell will be calculated (for a variable-head cell, 

value = 1); (2) the cell is active and head should not change 

from a user-specified value (for a constant- or specified-head 

cell, value = –1); or (3) the cell is inactive and water cannot 

flow through the cell (for a no-flow cell, value = 0).

Output Control (OC) Option

The Output Control Option, specified as file type “OC”, 

is used in conjunction with flags in other packages to write 

head, drawdown, and budget information into separate files 

for specified time steps and stress periods. The OC Option 

overwrites the default for writing heads and the water budget 

to the listing file.

In the DVRFS model, head, drawdown, and budget 

information is printed and saved for the initial steady-state 

stress period and for stress periods 44 and 86 of the transient 

simulation. Stress period 44 is a mid-simulation stress 

period and stress period 86 (representing 1997) is the nextto-last stress period. Head and drawdown information is 

written to data files HEADSOUT.txt (unit number 46) and 

DRAWDOUT.txt (unit number 47).

Hydrogeologic-Unit Flow (HUF2) Package 

The Hydrogeologic-Unit Flow (HUF2) Package, 

specified as file type “HUF2”, is an internal-flow package as 

are the Layer-Property Flow Package (Harbaugh and others, 

2000) and the Block-Centered Flow Package (McDonald and 

Harbaugh, 1988). Internal-flow packages calculate hydraulic 

conductance between cell centers. The HUF2 Package 

translates the hydrogeologic framework into flow model layers 

by optionally defining the geometry of the hydrogeologic units 

(HGUs) independently of flow model layers. In the DVRFS 

model, geometries of the HGUs are complex because of 

considerable structural deformation, which includes folding 

and faulting; model layers in the DVRFS model generally do 

not coincide with HGUs.

 The HUF2 Package calculates effective hydraulic 

properties for all model layers based on hydraulic properties of 

the HGUs. The HUF2 Package determines which HGUs apply 

to a model layer for each flow model grid cell, and calculates 

model-layer horizontal hydraulic conductance using arithmetic 

averaging, vertical hydraulic conductance using harmonic 

averaging, and specific storage using arithmetic averaging 

(Anderman and Hill, 2000, p. 7-10). 

Within a DVRFS model simulation, aquifer transmissivity 

was not changed as water levels declined because changes 

in the saturated thickness were small. This condition is 

documented and specified as the “confined” option in the 

HUF2 Package. Storage values were assigned to the top model 

layer, independent of HGU (Anderman and Hill, 2003, p. 4) 

using the parameter type SYTP. The storage coefficient of the 

top model layer is not multiplied by model layer thickness. 

MODFLOW Processes 
With the HUF2 Package, horizontal hydraulic 

conductivity can be simulated as decreasing with depth 

exponentially using a variable (KDEP) that represents the 

depth decay coefficient (Anderman and Hill, 2003 p. 16-

18). Simulations with depth decay result in relatively more 

permeable values near the land surface and less permeable 

values at depth within a single HGU or in a portion (or zone) 

of an HGU. Values of the depth decay coefficients used in 

the DVRFS model result in substantially reduced hydraulic 

conductivity at depth for most HGUs (Faunt and others, 

2004b, fig. F-35, p. 322).

Horizontal-Flow Barrier (HFB6) Package 

Many fault zones contain a core of low permeability 

gouge, the locus of fault displacement, which acts as a 

barrier to ground-water flow. The capability to simulate thin, 

vertical, and low-permeability geologic features is part of 

the Horizontal-Flow Barrier Package (Hsieh and Freckleton, 

1993), specified as file type “HFB6”. The HFB6 Package 

simulates a ground-water barrier, which is located on the 

boundary between two adjacent finite-difference cells in the 

same layer, by adjusting the hydraulic conductance between 

adjacent cells. 

In the DVRFS model, oftentimes juxtaposition of HGUs 

effectively represented a flow barrier because hydraulic 

properties differed greatly between HGUs. Consequently, 

the barrier to flow did not need to be represented with a 

hydraulic barrier in the HFB6 Package. In some cases, 

important regional faults that influence ground-water flow 

were incorporated into the affected HGUs. For example, thrust 

faults can create a stratigraphic repetition of HGUs that can 

create sharp contrasts in hydraulic conductivity (Faunt and 

others, 2004b, p. 181). Structures interpreted as thin, vertical, 

low-permeability features were represented as 1 m wide (Faunt 

and others, 2004b, p. 269) using the HFB6 Package. HFB6 

parameters with little influence on the simulation of head and 

discharge were removed from the model during calibration. 

Consequently, there are nine HFB6 parameters in the DVRFS 

model that represent eight important regional faults (Faunt and 

others, 2004b table F-15, p. 324 and fig. F-5, p. 273). 

Recharge (RCH) Package 

The Recharge Package, specified as file type “RCH”, 

simulates areally distributed recharge to the ground-water 

system from precipitation that percolates through the 

unsaturated zone to the ground-water system. Distributed 

recharge for the DVRFS model is based on a spatially 

distributed hydrologic model of net infiltration (Hevesi 

and others, 2003). The net infiltration model simulates a 

daily water balance in the unsaturated zone to a maximum 

depth of 6 m, the depth at which the seasonal effects of 

evapotranspiration become insignificant (San Juan and 

others, 2004, p. 115-118). Net infiltration is a reasonable 

approximation of ground-water recharge because most 

of the net infiltration and surface runoff that originates as 

precipitation eventually moves downwards through the 

unsaturated zone to recharge the ground-water system.

Net-infiltration results (Hevesi and others, 2003) were 

modified to create a recharge input for the ground-water 

system that balanced system discharges, the transmissive 

properties of the less permeable rock units at the water table, 

and the variable depth to the water table. Average annual netinfiltration was estimated with simulated net-infiltration from 

1950 to 1999 (Hevesi and others, 2003). Based on the average 

annual net-infiltration rate and the relative permeability of 

rocks in the upper five flow model layers of the DVRFS 

model, a recharge input for the DVRFS model was created 

using nine zones and five recharge parameters. The nine zones 

were created by calculating the recharge rate and the relative 

permeability of rocks in the upper five flow model layers. 

In order to fit the recharge input to the observed discharge, 

recharge was adjusted using a recharge multiplication array 

and recharge parameters based on the nine zones (Faunt and 

others, 2004b, fig. F-35, p. 325 and table F-16, p. 326). The 

values of the five calibrated recharge parameters produced a 

total volume of recharge to the ground-water system that is not 

significantly different from the total volume of net-infiltration; 

for the entire model domain, 92 percent of the estimated netinfiltration was simulated as recharge. 

Multi-Node Well (MNW1) Package 

Simulation of pumpage from wells with the Well (WEL1) 

Package (McDonald and Harbaugh, 1988) is limited to 

withdrawal at specified rates from individual cells. However, 

the Multi-Node Well (MNW1) Package (Halford and Hanson, 

2002) simulates pumpage from wells with screens that span 

multiple layers, partially penetrating wells, and variations 

in intraborehole flow. In the DVRFS region, wells typically 

are completed with screens that span multiple aquifers and 

thus multiple layers in the flow model. The vast majority 

of pumping occurs from model layers 1 through 4 (Faunt 

and others, 2004b, fig. F-8, p. 278). The MNW1 Package 

uses hydraulic conductivity and thickness to portion well 

pumpage between model layers. The DVRFS water budget 

(Faunt and others, 2004b, table F-18, p. 331) includes a 

small component of simulated well pumpage inflows due to 

simulated irrigation-return flows and well injection. A minor 

contribution of the simulated inflows is from intraborehole 

flow between pumping nodes connecting model layers within 

a single well in the MNW1 Package.

 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Return flows were simulated because some return flow 

of pumpage by infiltration of excess irrigation, lawn water, 

or septic tank wastewater was anticipated. The magnitude 

and timing of return flow depends on the method (domestic, 

irrigation, or mining, public supply, and commercial) by which 

water is returned to the flow system (San Juan and others, 

2004, p. 114-115). At each withdrawal point, return flow was 

estimated to be 20 percent of the estimated annual pumpage 

(Moreo and others, 2003) lagged by 7 years. All computed 

return flows were assumed to return to the water table at the 

location of the pumped well. 

Drain (DRN) Package 

The Drain Package, specified as file type “DRN”, 

removes water from an aquifer through a head-dependent 

boundary (McDonald and Harbaugh, 1988). For a finitedifference cell specified as a drain cell, ground water is 

simulated as discharging when the simulated head in the cell 

rises above a specified drain altitude. When the head declines 

below the cell altitude, the drain is turned off. Simulated drain 

discharge is calculated as the drain conductance multiplied by 

the difference in altitude between the simulated head and the 

drain. 

In the DVRFS model, evapotranspiration was simulated 

with the drain package for numerical stability. The altitude 

of the drain cells approximates the extinction depth for 

evapotranspiration (Faunt and others, 2004b, p. 271-278). 

Drain altitudes were set equal to 10 m below the lowest 

land-surface altitudes for each group of cells where natural 

discharge is observed (Faunt and others, 2004b, fig. F-7, p. 

275 and table F-4, p. 276-277). Areas of natural discharge 

include wet playas, wetlands with free-standing water or 

surface flow, narrow drainages lined with riparian vegetation, 

and broad areas of phreatophytic shrubs and grass. For 

drain cells representing springs, the drain at that location is 

connected to the topmost occurrence of the lower carbonaterock aquifer, located between model layers 1 and 10.

Data for flows emanating from springs and seeps were 

derived from spring-flow measurements (San Juan and others, 

2004, p. 103-110). Evapotranspiration rates were measured at 

Ash Meadows, Death Valley, and Oasis Valley as a proxy for 

discharge because most ground water discharging from springs 

and seeps is evaporated or transpired locally and is accounted 

for in estimates of evapotranspiration. Discharge simulated 

through the drain cells is compared to measured values in the 

section, “Observation (OBS) Process.”

Constant-Head Boundary (CHD) Package 

At cells defined as constant head, MODFLOW-2000 

calculates flow into and out of the cell as needed to maintain 

the head. In the DVRFS model, lateral boundary flows are 

represented using the Constant-Head Boundary Package, 

specified as file type “CHD”. CHD cells were specified in 

boundary cells that are at or below the regional potentiometric 

surface (Bedinger and Harrill, 2004a, 2004b) to allow 

flow across the boundary (Harrill and Bedinger, 2004). In 

the DVRFS model, the model boundary is not affected by 

simulated pumpage, and heads in the constant-head boundary 

cells do not change over time (Faunt and others, 2004b, table 

F-2, p. 270). Flows simulated through the constant-head 

boundaries are compared against reasonable estimates of flow 

in the section, “Observation (OBS) Process.” 

Solver Packages

Solver Packages, part of the GWF Process, are used 

to arrive at the solution of the finite-difference equations at 

each time-step in a stress period. Many different solvers have 

been written for MODFLOW (Hill, 1990; Harbaugh, 1995; 

Harbaugh and others, 2000). The DVRFS model is archived 

with the Preconditioned Conjugate-Gradient (PCG2) (Hill, 

1990) solver, specified with file type “PCG2”. Two additional 

solvers, Link to Algebraic Multigrid (LMG) solver (Mehl 

and Hill, 2001) and the Geometric Multigrid (GMG) solver 

(Wilson and Naff, 2004), both recently developed, typically 

are 2 to 25 times faster than the PCG (Wilson and Naff, 2004) 

solver. When used with the DVRFS model, the LMG solver 

was faster than the GMG solver for steady-state simulations 

but slower for transient simulations. Due to licensing 

restrictions, the distribution of the LMG solver is limited 

(URL: http://water.usgs.gov/nrp/gwsoftware/modflow2000/

modflow2000.html, accessed December 22, 2005). For steadystate simulations, the GMG solver is often much faster than 

the PCG2 solver.

MODFLOW Processes 
Observation (OBS) Process 

The OBS Process generates simulated (or modelcalculated) values for comparison with measured, or observed, 

values. Additionally, observation sensitivities are calculated 

for use in sensitivity analysis and for regression during 

parameter calibration (Hill and others, 2000). By defining 

an observation value and a weight associated with the 

observation, either as a standard deviation or a coefficient of 

variation (standard deviation divided by the mean), observed 

values can be compared to simulated values to evaluate model 

fit in the context of expected observation accuracy. Statistics 

calculated to quantify this comparison include a weighted 

least-squares objective function (Hill, 1998). In addition, 

when the OBS Process is active, output files are produced for 

comparison of simulated and observed values (Hill and others, 

2000, p. 23).

The OBS Process requires an input file identified by 

file type “OBS”. The tasks of the Observation Process are as 

follows:

1. Read a file (file type OBS) that contains information 

applicable to all observations.

2. Read observed values and information needed 

to calculate associated simulated values. This 

information is provided through input files related 

to the active GWF Processes. For example, if an 

observed flow is represented using the Constant-Head 

Boundary (CHD) Package, an Observation Process 

Constant-Head Boundary Package (specified as file 

type CHOB) input file is needed. 

3. Calculate associated simulated equivalents to the 

observations using hydraulic heads for the entire grid.

4. If the SEN Process is active, calculate the associated 

observation sensitivities using the grid sensitivities 

calculated by the SEN Process.

5. Calculate statistical measures and output files for 

simulated and observed values (Hill, 1998, table 1, 

p. 33).

 Observation inputs for the DVFRS model include: 

(1) head observation file (specified as file type HOB) for 

hydraulic heads and changes in hydraulic head over time, (2) 

drain observation file (specified as file type DROB) for natural 

flows to or from surface-water bodies and diffuse discharge 

areas represented with the DRN Package, and (3) flow 

observations at constant-head boundaries file (specified as file 

type CHOB) for flow to or from a set of constant-head finitedifference cells along parts of the model boundary as specified 

in the CHD Package. 

Head Observation (HOB) Package 

Hydraulic head or head change observations are 

specified in the Head Observation Package, specified as file 

type “HOB”. For each observation, the head observation and 

observation weight are defined by layer(s), row, column, and 

time of the observation. Head observations are located as 

a row and column offset from the node at the center of the 

finite-difference cell (Hill and others, 2000, p. 31-40). In the 

DVRFS model, head observations for wells with water-level 

measurements over multiple years were determined to be 

either affected or not affected by pumping. Head observations 

affected by pumping were simulated as a head change, which 

is calculated as the difference between the observation of 

interest and a reference observation (Hill and others, 2000, p. 

33–34). The reference observation is the measurement prior to 

any pumping effect or the first measurement available.

The open intervals of the wells and boreholes determined 

which model layers were associated with head and headchange observations. Most head and head-change observations 

(82 percent) are from wells completed in the shallow part 

of the flow system (no deeper than model layer 5) and none 

are deeper than model layer 14 (Faunt and others, 2004b, 

fig. F-8, p. 278). For wells open to more than one model 

layer, simulated heads are a weighted average calculated by 

MODFLOW-2000 with user-defined weights (Hill and others, 

2000, p. 34–36). In the DVRFS model, the standard deviation 

of a head observation is based on five potential errors: (1) 

well-altitude error, (2) well-location error, (3) nonsimulated 

transient error, (4) measurement-accuracy error, and (5) 

model-discretization error (San Juan and others, p. 122-132). 

Well-altitude and well-locations errors vary with the type 

of instrument or method used to specify the well location. 

Nonsimulated transient errors result from uncertainty in the 

magnitude of water-level response caused by stresses not 

simulated in the flow model, which typically are seasonal and 

long-term climate changes. A separate method was used to 

calculate the standard deviation of head-change observations 

because differences between simulated and observed head 

changes are expected to be dominated by inaccurate pumpage 

estimates (Faunt and others, 2004b, p. 282). Standard 

deviations for head-change observations less than 1 m were 

assigned a value of 1 m to avoid very small errors that could 

cause numerical instability during calibration. For head change 

observations greater than 1 m, a function was developed that 

produced larger standard deviations for larger head differences 

but also tempered the range in standard deviation between 

large and small head-change observations (Faunt and others, 

2004b, p. 282, eq. 4). 

10 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Drain Observation (DROB) Package 

Drain observations in the Drain Observation Package are 

specified as file type “DROB”. At each finite-difference cell 

specified as a drain cell, discharge observations, observation 

weight, and time of observation are defined. 

In the DVRFS model, ground-water discharge 

observations did not vary during the transient simulation with 

the exception of Manse and Bennetts Springs in Pahrump 

Valley (fig. 1). At this location, changes in discharge have 

been documented during the model simulation period (fig. 3). 

For each of these springs, a single observation occurs during 

the steady-state stress period, and two transient discharge 

observations occur during the stress periods representing 1960 

and 1998. For all other 43 ground-water discharge locations in 

the DROB Package, observations only occur once during the 

stress period representing 1997 (San Juan and others, 2004, p. 

103-110). 

In the DVRFS model, the weight of a ground-water 

discharge observation is represented as a coefficient of 

variation based on Monte Carlo analysis (Laczniak and 

others, 2001; D’Agnese and others, 2002; Faunt and others, 

2004b, p. 283). The coefficients of variation for discharge 

observations range from 0.10 to 0.71 (Faunt and others, 2004b, 

table F-4, p. 276-277).

Constant-Head Flow Observation (CHOB) 

Package 

At finite-difference cells defined as constant head cells, 

the model calculates the flow into and out of cells needed to 

maintain the head. If anything is known about the likely flow 

rate, it is important to include it to constrain model calibration 

(Poeter and Hill, 1997). These flows are input through the 

Constant-Head Flow Observation Package, specified as file 

type “CHOB”.

In the DVRFS model, locations of the constant-head 

flow observations coincide with the locations of the 12 

constant-head boundary parameters that represent segments 

of the model boundary. These 12 segments potentially have 

flow across them based on water budget analyses (Harrill 

and Bedinger, 2004) (fig. 2). Harrill and Bedinger (2004) 

estimated the potential for flow through boundary segments 

of the DVRFS model domain (table A2-9, p. 406-407). 

Constant-head flow observations are specified only during the 

first stress period. Observation weights are calculated from 

specified standard deviations that were based on the method 

used to estimate flow at the boundary (Harrill and Bedinger, 

2004). For boundary-flow estimates based on water-budget 

analyses (Harrill and Bedinger, 2004), the standard deviation 

was set to one-half of the estimated flow value which reflects 

Figure 3. Annual discharge from Bennetts and Manse springs in Pahrump Valley, Nevada, 1875–1998.

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000

YEAR

DISCHARGE, IN THOUSANDS OF CUBIC METERS PER YEAR

Combined measured discharge (Bennetts and Manse Springs)

Measured discharge at Bennetts Spring

Measured discharge at Manse Spring

Pumpage

start

Simulated discharge at Bennetts discharge area

Simulated discharge at Manse discharge area

Combined simulated discharge (Bennetts and Manse discharge areas)

ET-based estimate of natural discharge estimated using vegetation mapped in 1959-61

Model discharge observations at Manse discharge area

Model discharge observations at Bennetts discharge area

0

MODFLOW Processes 11
the large uncertainty in these values. In eight of the segments, 

water budget analyses were not available, so Darcy’s law (with 

the regional potential gradient) and professional judgment 

were used to estimate flow across the boundary (Harrill 

and Bedinger, 2004). In these poorly constrained cases, 

the standard deviation was set to the estimated flow value 

rounded down to the nearest 500 m3/d. For poorly constrained 

boundary-flow estimates, the large standard deviation reflects 

the large uncertainty.

Sensitivity (SEN) Process 

The Sensitivity Process (Hill and others, 2000), specified 

as file type “SEN”, calculates the sensitivity of hydraulic 

heads with respect to parameters. These sensitivities are grid 

sensitivities. If the OBS Process is active, grid sensitivities 

are used to calculate sensitivities for the simulated values 

associated with the observations with respect to a parameter. 

These sensitivities are called observation sensitivities. 

Observation sensitivities are used to calculate a number of 

statistics that can be utilized to: (1) diagnose inadequate data, 

(2) identify parameters that probably cannot be estimated by 

regression using the available observations, and (3) evaluate 

potential new data (Hill and others, 2000). Model output 

for the sensitivity process includes: (1) composite scaled 

sensitivities, (2) dimensionless scaled sensitivities, and (3) 

one-percent scaled sensitivities (Hill, 1998, p. 14-16). Flags 

in the first data row of the SEN Process, in combination with 

processes specified in the name file, control whether the SEN 

Process or PES Process (described in section, “Sensitivity 

(SEN) Process”) are active in MODFLOW-2000.

 In the DVRFS model, parameter values specified in 

the SEN Process are used to calculate the horizontal-flow 

barrier characteristic [(m/d)/m], drain conductance [(m/d)/m], 

hydraulic conductivity (m/d), recharge multiplier (unitless), 

exponential depth decay coefficient (1/m), specific storage 

(1/m), and vertical anisotropy (ratio of horizontal to vertical 

hydraulic conductivity) (unitless) (table 3). All parameters, 

with the exception of the specific storage parameters, were 

log-transformed during parameter estimation.

In the DVRFS model, the SEN Process specifies the value 

of all model parameters with the exception of the simulated 

heads at constant-head boundaries. The SEN Process provides 

one location to change all parameter values. Because the 

simulated lateral boundary flows were not calibration targets, 

constant-head boundary parameters are defined in the CHD 

and CHOB Packages but are not included in the SEN Process 

(effectively a parameter value of 1).

 Generally, in the DVRFS model, the value of a parameter 

in the SEN Process is multiplied by additional values (termed 

factors) in other package(s) to obtain the cell-by-cell model 

input used in MODFLOW-2000 calculations. For example, in 

the HFB6 Package, the parameter value in the SEN Process 

is multiplied by a factor of 1 (table 4). A HFB6 parameter 

is defined as the hydraulic characteristic, which is the flow 

barrier hydraulic conductivity divided by the flow barrier 

width. At cells specified as HFB6 cells, the Factor variable 

is used to calculate the hydraulic characteristic of the flow 

barrier as the product of Factor and the parameter value. All 

hydraulic barriers in the DVRFS model were represented as 

1 m wide (Faunt and others, 2004b, p. 269). Consequently, 

the hydraulic characteristic and the hydraulic conductivity are 

numerically equivalent, and for all cells specified as HFB6 

cells, the value of Factor is 1. 

In other cases, such as the DRN Package, the value of 

the drain parameter in the SEN Process is multiplied by a 

factor other than 1 at each grid cell. In the DRN Package, the 

multiplicative factor represents the fractional area of the cell 

that contributes to natural discharge, evapotranspiration and/or 

spring flow (table 4). It is convenient to represent parameters 

in the DRN Package with a factor other than 1 because drain 

parameters define a conductance that depends on the area 

of the cell contributing discharge. This area dependence 

is represented by the value of the multiplicative factor at 

each drain cell. For each cell specified as a drain cell, the 

variable “Condfact”, the factor used to calculate the hydraulic 

conductance of the drain from the parameter value, is the 

fractional area of the cell that the drain occupies.

In the DVRFS model, recharge is specified by values 

in the MULT and ZONE files, the RCH Package, and SEN 

Process. The distributed net infiltration array (Hevesi and 

others, 2003) input for the DVRFS model is the multiplier 

array rch1_modmd.asc. For each of the five parameters in the 

RCH Package, the parameter value, which varies by zone, is 

multiplied by values in the multiplier array.

 Model input for parameter types not listed in table 4

include hydraulic conductivity (HUF2 Package parameter type 

HK), KDEP, vertical anisotropy (parameter type VANI), and 

specific storage (parameter type SY and SYTP). For these 

parameter types, cell-by-cell model values are calculated with 

the multiplier and zone arrays listed in the HUF2 Package and 

parameter values specified in the SEN Process (Anderman and 

Hill, 2000, 2003).

12  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Table 3. Description of the parameter names in the sensitivity file and the associated packages and files.

[Package/File associated with parameter: DRN, Drain Package; HFB6, Horizontal-Flow Barrier Package; HUF2, Hydrogeologic-Unit Flow Package; KDEP, 

Hydraulic-conductivity depth-dependence parameter; RCH, Recharge Package; SEN, Sensitivity Process. Abbreviations: m/d, meter per day; (m/d)/m, meter 

per day per meter; 1/m, 1 over meter]

Parameter name description (units)

Package/file 

associated with 

parameter

Number of parameters 

defined in the 

SEN process

Parameter name 

prefix or suffix

Fault hydraulic characteristic [(m/d)/m] HFB6 9 B_

Drain conductance [(m/d)/m] DRN 7 _DRN1

Hydraulic conductivity of confining units (m/d) HUF2 8 K1

Hydraulic conductivity of carbonate-rock aquifers (m/d) HUF2 20 K2

Hydraulic conductivity of volcanic-rock units (m/d) HUF2 14 K3

Hydraulic conductivity of basin-fill units (m/d) HUF2 14 K4

Exponential depth decay coefficient (1/m) HUF2, KDEP 10 KDEP or KDP

Recharge multiplier (unitless) RCH 5 RCH_

Specific yield value applied to top model layer (unitless) HUF2 3 SY_

Specific storage (1/m) HUF2 4 STOR_

Vertical anisotropy (unitless) HUF2 6 VANI or VAN1

1Suffix appears at the end of the parameter name in the SEN file.

Table 4. Sensitivity Process and associated factors for Constant-Head Boundary, Drain, Horizontal-Flow Barrier, and Recharge Packages.

[Abbreviations: CHD, Constant-Head Boundary Package; DRN, Drain Package; HFB6, Horizontal-Flow Barrier Package; RCH, Recharge Package; SEN, 

Sensitivity Process; MULT, multiplier file. NA, not applicable. m/d, meter per day; (m/d)/m, meter per day per meter; m, meter]

Package Parameter Type Factor variable Units of the parameter value 

in the SEN Process Comment

CHD Hydraulic head (m) Shdfact1 = Ehdfact2 NA3 Head is the product of Ehdfact2 and the parameter 

value in the SEN Process.

DRN Drain conductance [(m/d)/m] Condfact4 Hydraulic conductance [(m/d)/m] Drain hydraulic conductance5 is the product of 

Condfact and the parameter value in the SEN 

Process. 

HFB6 Fault hydraulic characteristic 

[(m/d)/m]

Factor = 1.0 Hydraulic conductivity (m/d) Hydraulic characteristic is the product of Factor and 

the parameter value in the SEN Process.

RCH Recharge flux (m/d) NA Unitless multiplier Parameter value in the SEN Process is multiplied 

by the multiplier array6 value at each cell.

1Shdfact is the factor used to calculate the head at the boundary at the start of the stress period. 

2Ehdfact is the factor used to calculate the head at the boundary at the end of the stress period. 

3No CHD parameters are defined in the SEN Process. CHD parameters are defined only in the CHD Package. This is effectively a parameter value of1.0.

4In the DVRFS model, the value of Condfact is the fractional area of a cell that the drain parameter occupies.

5Hydraulic characteristic is the barrier hydraulic conductivity divided by the width of the barrier. In the DVRFS model, the width of all barriers is assumed to 

be 1.0 meter; consequently, the hydraulic characteristic and the hydraulic conductivity are numerically equivalent.

6The multiplier array file is rch1_modmd.asc as specified in the MULT file (mult.txt).

MODFLOW Processes 13
Parameter-Estimation (PES) Process 

The Parameter-Estimation Process (Hill and others, 

2000), specified as file type “PES”, uses a modified GaussNewton method to adjust values of user-selected input 

parameters to minimize the value of the weighted least-squares 

objective function via iteration. The objective function, the 

sum of squared weighted residuals, is used to evaluate the fit 

of simulated to observed values. Residuals are the difference 

between simulated and observed model values (observed 

minus simulated). Weighted residuals in the DVRFS model 

most often reflect a weight equal to the inverse of the standard 

deviation of the observation squared. Thus, squared weighted 

residuals for all types of observations can be summed as 

dimensionless quantities. 

Parameter estimation is initiated using parameter values 

from the SEN Process. Hydraulic heads and sensitivities 

are calculated for each time step. After all time steps are 

computed, simulated values are subtracted from observed 

values to calculate residuals, which are used to compute 

the least-squares objective function. Convergence criteria 

specified in the PES Process include maximum allowable 

values of: (1) the largest fractional change in any of the 

parameter values, and (2) the change in the weighted leastsquares objective function. If either of the two convergence 

criteria is met, parameter estimation converges. If parameter 

estimation does not converge and the maximum number of 

iterations has not been exceeded, updated parameter values 

are used in subsequent parameter-estimation iterations. When 

parameter estimation converges or the maximum number of 

iterations is reached, the PES Process halts.

Model Output

For DVRFS model simulations, MODFLOW-2000 

generates two listing output files (as specified in the name 

file). Most of the output from the GWF and SEN Processes 

is written to the LIST file, while output that applies to the 

overall model simulation is written to the GLOBAL file. The 

LIST file includes allocation information, values used by the 

GWF Process for layers and individual cells to solve the flow 

equation, and calculated model results such as hydraulic head, 

drawdown, and the water budget. When the OBS Process 

is active, the LIST file also contains the model-calculated 

equivalents to the observations and the related statistics. When 

the PES Process is active and a new iteration begins, the LIST 

file is erased and regenerated. As a result, most of the GWF 

and SEN Process output is limited to that produced during the 

most recently executed parameter-estimation iteration. 

The GLOBAL file contains information that applies to 

the model simulation as a whole. This output includes the 

names and types of all input files. Input for the GLO Process 

is echoed in the GLOBAL file. The GLOBAL file includes 

spatial and temporal discretization, and solver information. 

The GLOBAL file also contains parameter definitions read 

from the various packages that define boundary conditions and 

stresses for the GWF Process. Input from active OBS, SEN, 

and PES Processes is echoed to the GLOBAL file. If the OBS, 

SEN, and PES Processes are all active, the GLOBAL output 

file contains:

1. Information about the array storage needed by the 

OBS, SEN, and PES Processes.

2. Information about the definition of parameters and 

observations.

3. Observation-sensitivity tables produced using the 

starting parameter values. Observation sensitivities 

include dimensionless scaled sensitivities and 

composite scaled sensitivities, and (or) one-percent 

scaled sensitivities. 

4. Parameter values and other information from each 

parameter-estimation iteration.

5. Observation sensitivity tables produced using the 

final parameter values. 

6. Parameter variance-covariance and correlation 

matrices.

7. Parameter confidence intervals.

8. A comparison of the parameter values and userdefined reasonable upper and lower limits of the 

parameter value.

9. Summary statistics about the model fit to the 

observations.

The LIST output file contains:

1. Information about the array storage needed by each 

GWF Process Package.

2. Printed arrays of heads for the entire model grid. The 

printed arrays depend on the contents of the GWF 

Process, BAS6 Package, and OC Option.

3. Tables that list observed and simulated values from 

the latest set of parameter values.

4. Observation-sensitivity tables calculated using 

the most recently calculated grid sensitivities. 

Possibilities include dimensionless scaled 

sensitivities, composite scaled sensitivities, and (or) 

one-percent scaled sensitivities.

14  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Table 5. Select output files produced by MODFLOW-2000 by active 

processes.

[Modified from Hill and others, 2000, p. 28. File contents: Observation 

process: For each observation, the listed items are followed by the variables 

OBSNAM and PLOT-SYMBOL. File contents: Parameter estimation outputs 

from MODFLOW-2000, which are inputs for post-processing programs 

RESAN-2000, BEALE-2000, and YCINT-2000 (Hill and others, 2000) are not 

included in this table. Abbreviation: SEN, Sensitivity Process]

Extension File contents

If the Observation Process is active:

_nm Weighted residuals and probability plotting positions

_os Unweighted simulated equivalents and observations

_r Unweighted residuals

_w Weighted residuals

_ww Weighted simulated equivalents and observations

_ws Weighted simulated equivalents and residuals

If the Sensitivity Process also is active, the following files also are 

produced: 

_sc Composite scaled sensitivity for each parameter, 

preceded by the PARNAM.1

_sd Dimensionless scaled sensitivities for each parameter, 

preceded by OBSNAM2 and PLOT-SYMBOL.3

Repeated for each observation. 

_s1 One-percent scaled sensitivities for each parameter, 

preceded by OBSNAM2 and PLOT-SYMBOL3. 

Repeated for each observation. 

If the Parameter-Estimation Process also is active, the following files 

also are produced:

_b Information from each parameter-estimation iteration, 

including parameter values formatted for easy 

substitution into the Sensitivity Process input file, 

sum of squared weighted residuals, maximum 

calculated fractional parameter change and the 

associated parameter number (as listed in the SEN 

file), and value of the Marquardt4 parameter. 

_pa Parameter values for each parameter-estimation 

iteration, formatted for easy production of graphs 

showing parameter values for each iteration. This 

file is not produced until the end of the program; 

to access parameter values as each iteration is 

performed, use the _b file described below. 

_ss Sum of squared weighted residuals for each type of 

observation and prior information and the total; 

values are listed for all parameter-estimation 

iterations. 

1PARNAM is a parameter name that is specified in a Ground-Water Flow 

Process package and the SEN Process.

2OBSNAM are characters used to identify an observation.

3PLOT-SYMBOL is an integer assigned to each observation in an 

observation input file that is echoed to many output files.

4The Marquardt parameter is used to improve regression for ill-posed 

problems (Hill, 1998, p. 8-9).

Table 6. Plot symbol codes that identify the observation type in all 

“underscore” output files created during forward and parameter-sensitivity 

mode simulations.

[Abbreviations: m, meter; Symbol: ≥, greater than or equal to; ≤, less than or 

equal to; >, greater than; =, equal to]

Plot symbol Description

0 Head observation derived from few steady-state 

measurements.

1 Head observation derived from many steady-state 

measurements.

2 Head change observation ≥ 0.1 m and ≤ 1 m, standard 

deviation =1 m.

3 Head change observation < 0.1 m, standard deviation 

=1 m, or discharge observation, or constant head 

observation.

4 Head change observation > 1 m, standard deviation is 

a function of head change observation.

Additional output files are produced by the OBS Process 

(table 5). These files are designed for use by plotting routines 

and other programs (Harbaugh, 1990; Hanson and Leake, 

1999; Winston, 2000). Output files are named using a file 

name base, defined by the user in the OBS Process variable 

OUTNAM. Files are named as OUTNAM followed by a 

period and an extension that begins with an underscore. For 

example, if OUTNAM is “dvr”, the output file names are 

“dvr._os” and so on. These files are collectively referred to as 

the “underscore” output files. 

In all “underscore” output files (dvr._* files) produced 

when the OBS Process is active (table 5), the plot symbol 

variable (PLOT-SYMBOL) is used to identify an observation 

as either a head observation (PLOT-SYMBOL is 0 or 1), a 

head-change observation (PLOT-SYMBOL is 2, 3, or 4), a 

discharge observation (PLOT-SYMBOL is 3), or a constanthead flow observation (PLOT-SYMBOL is 3) (table 6). 

Although the PLOT-SYMBOL value of 3 is used for head 

change, discharge, and constant head flow observations, the 

observation type can be easily identified from the observation 

name (variable OBSNAM). Numeric OBSNAMs indicate head 

change observations; alphabetic OBSNAMs indicate constanthead boundary flows and discharge observations. Furthermore, 

for constant-head flow observations, the OBSNAM begins 

with “C_”. For discharge observations, the OBSNAM 

begins with “OBS” for steady-state observations, “OB” for 

observations in the stress period representing 1960, and “O” 

for observations in the stress period representing 1998.

Model Output 15
Typical DVRFS MODFLOW-2000 Modes

The source code used in the DVRFS model (mf2k_13_00-dp.exe) is MODFLOW-2000 version 1.13 compiled to run in 

double precision. A model simulation is conducted by executing “mf2k_13_00-dp.exe” in a DOS window and entering “name.

txt” when prompted for the name file. The source code is available from the USGS website at URL: http://pubs.water.usgs.

gov/sir20045205/, accessed on December 22, 2005, under model archive. Single precision simulations result in inaccurate water 

budgets due to rounding errors. The most recent version of MODFLOW-2000, version 1.15.01, is available at URL: http://water.

usgs.gov/nrp/gwsoftware/modflow2000/modflow2000.html, accessed on December 22, 2005. The executable file available at the 

website is single precision, and the source code must be recompiled in double precision. 

Various simulation modes are available in MODFLOW-2000 depending on the file types activated in the name file, and 

the values assigned to variables in the SEN and PES Processes. In general, four types of model modes are thought to be most 

relevant to simulations with the DVRFS model: (1) forward with observations and parameter-value substitution, (2) parameter 

sensitivity with observations, (3) sensitivity-analysis, and (4) the parameter-estimation mode (table 7) (Hill and others, 2000, p. 

12). The two parameter-sensitivity modes (modes 2 and 3) produce similar output files; however, depending on the parametersensitivity mode, different statistics are written to the GLOBAL file (table 6). 

For discussion, it is assumed that the OBS Process is always active, and parameter-value substitution (values from the SEN 

Process are always used) occurs. In all modes, a LIST file and a GLOBAL file are created. However, different information is 

written to these two files depending on the mode and which processes (OBS, SEN, PES) are active (table 6). 

Forward Mode 

Forward mode generally is the simplest mode and also is the mode most similar to MODFLOW-96. To execute a simulation 

in forward mode with observations and parameter-value substitution (Hill and others, 2000, p. 12), include the SEN and PES 

Process file types in the name file (for example, see the archived model name file). In the SEN Process (SENSITIVITY.txt), set 

the second variable (first data row, second column entry variable INSENALL) to –1. Shown below are the first few lines of the 

SEN Process with the ISENALL variable shaded in gray:

# SEN Package Line 0: Text 

100 -1 0 100 Line 1: NPLIST ISENALL IUHEAD MXSEN 

0 0 0 3 Line 2: IPRINTS SEN_ISENSU (binary or text file = unit 42) SEN_ISENPU 

(text file = unit 43) ISENFM.

The forward mode with observations and parameter value substitution can generate head and drawdown arrays for 

contouring, water-budget terms, and the fit of simulated equivalents to observations. Model time steps for which output is saved 

and printed are determined by the OC Option. In the DVRFS model, arrays of simulated head and drawdown by layer and 

time, as specified in the OC Option, are contained in the files HEADSOUT.TXT and DRAWDOWN.TXT, respectively. The 

HEADSOUT.txt and DRAWDOWN.txt files are specified as the file type “DATA” in the name file.

Output files created in the forward mode with observations and parameter value substitution include GLOBAL, LIST, 

HEADSOUT.txt, DRAWDOUT.txt and the “underscore” output files (dvr._* files) are listed in table 5. 

16  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Table 7. Modes of MODFLOW-2000 produced by activating different combinations of the Sensitivity and Parameter-Estimation Processes, and 

commonly used output when the Observation Process is active.

[Modified from Hill and others, 2000, p. 12. Abbreviations: OBS, Observation Process; PES, Parameter-Estimation Process; SEN, Sensitivity Process]

Active?

Mode Commonly used model output Model output filenames

OBS PES SEN

Forward Mode

YES NO or 

YES

YES1 Forward with 

Observations and 

Parameter-Value 

Substitution

Head contour maps Depends on print flags

Water-budget terms Depends on print flags

Fit of simulated equivalents to observations _os, _ww, _ws, _r, _w, and _nm

Parameter-Sensitivity Modes

YES NO YES Parameter Sensitivity 

with Observations

Fit of simulated equivalents to observations _os, _ww, _ws, _r, _w, and_nm

One-percent scaled sensitivity maps (set 

print flags in SEN file)

GLOBAL file or _s1 (depends on 

print flags)

Composite scaled sensitivities _sc

Prediction scaled sensitivities 3_s1

YES YES2 YES Sensitivity Analysis Fit of simulated equivalents to observations _os, _ww, _ws, _r, _w, and _nm

Composite scaled sensitivities _sc

Prediction scaled sensitivities 3_s1

Parameter 95-percent linear confidence 

intervals

GLOBAL file

Parameter standard deviations GLOBAL file

Parameter coefficient of standard deviations GLOBAL file

Parameter correlation coefficients GLOBAL file

Parameter covariance matrix GLOBAL file

Calculated error variance GLOBAL file

Standard error of the regression GLOBAL file

Parameter-Estimation Mode

YES YES YES Parameter Estimation Optimal parameter values or, if optimal 

values are not achieved, data from 

parameter-estimation iterations to 

diagnose problems.

GLOBAL file, _pc, and _pa

1ISNEALL<0 in the Sensitivity Process input file.

2MAX-ITER=0 in the Parameter-Estimation Process input file.

3One-percent scaled sensitivities in this file are often used as prediction scaled sensitivities. Predictions scaled sensitivities can be calculated from one-percent 

scaled sensitivities (Hill, 1998, p. 15-17).

Typical DVRFS MODFLOW-2000 Modes 17
Parameter-Sensitivity Modes

To execute a model simulation in a parameter-sensitivity mode, activate the SEN Process and inactivate the PES Process 

in the name file (parameter sensitivity with observations mode), or make the PES Process active with the variable MAX-ITER 

set to zero (sensitivity-analysis mode). To calculate sensitivities for all parameters, activate the parameter sensitivity with 

observations mode by setting the second variable (ISENALL) in the first data row of the SEN Process to 1. The first few lines of 

the SEN Process are shown below with the ISENALL variable shaded in gray:

# SEN Package Line 0: Text(Line 3: PARNAM ISENS LN B BL BU BSCAL)

100 1 0 100 Line 1: NPLIST ISENALL IUHEAD MXSEN 

0 0 0 3 Line 2: IPRINTS SEN_ISENSU (binary or text file=unit 42) 

SEN_ISENPU (text file = unit 43) ISENFM

B_LVVSZ_1 01 �.0E-4 0.100000E-0��7 10.0000 0.100000E-0�

B_HWY95� 0 12.�95E-4 0.100000E-0��7 10.0000 0.100000E-0�

B_DVFC_FCR 0 1 1.0E-��7 0.100000E-0��7 10.0000 0.100000E-0�

B_LVVSZ_IS 0 1 1.1E-8 0.100000E-0��7 10.0000 0.100000E-0�

B_LVVSZ_I2 0 1 4.1�9E-8 0.100000E-0��7 10.0000 0.100000E-0�

B_PAHRUMP 0 1 5.52E-��7 0.100000E-0��7 10.0000 0.100000E-0�

B_DV_N 0 1 2.4E-7 0.100000E-07 10.0000 0.100000E-08

Calculating sensitivities for individual parameters, or a subset of parameters, is much faster than calculating sensitivities 

for all parameters. If only a part of the DVRFS modeling area is of interest to a user, sensitivities can be calculated only for 

parameters in the subarea of interest. To calculate sensitivities for only select parameters, set the second variable (INSENALL) 

in the first data row of the SEN Process to 0. Next, for each parameter for which sensitivity output is desired, set the second 

column (variable ISENS) to 1. Shown below are the first few lines of the SEN Process with the ISENALL variable shaded in 

gray. As designated by the Boolean flag in the second column (variable ISENS), sensitivities will only be calculated for the fault 

conductance parameters B_HWY95 and B_DV_N:

# SEN Package Line 0: Text(Line 3: PARNAM ISENS LN B BL BU BSCAL)

100 0 0 100 Line 1: NPLIST ISENALL IUHEAD MXSEN 

0 0 0 3 Line 2: IPRINTS SEN_ISENSU (binary or text file=unit 42) 

SEN_ISENPU (text file = unit 43) ISENFM

B_LVVSZ_1 01 �.0E-4 0.100000E-07 10.0000 0.100000E-0�

B_HWY95� 1 12.95E-4 0.100000E-07 10.0000 0.100000E-0�

B_DVFC_FCR 0 1 1.0E-7 0.100000E-0��7 10.0000 0.100000E-0�

B_LVVSZ_IS 0 1 1.1E-8 0.100000E-07 10.0000 0.100000E-0�

B_LVVSZ_I2 0 1 4.19E-8 0.100000E-07 10.0000 0.100000E-0�

B_PAHRUMP 0 1 5.52E-7 0.100000E-0��7 10.0000 0.100000E-0�

B_DV_N 1 1 2.4E-7 0.100000E-07 10.0000 0.100000E-08

In addition to all the output created in the forward mode, additional output files (dvr._sc, dvr._sd, and dvr._s1) are produced 

when the SEN Process is active (table 7). These output files list composite scaled sensitivities (dvr._sc) and dimensionless 

scaled sensitivities (dvr._sd) for each selected parameter, and prediction scaled sensitivities (dvr._s1) for each observation for 

each selected parameter. Statistics written to the GLOBAL file in the parameter-sensitivity mode that are not produced during a 

forward model simulation include the calculated error variance, the standard error of the regression, and parameter correlation 

coefficients (Hill, 1998). 

18  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Parameter-Estimation Mode

To execute a model simulation in parameter-estimation mode, activate the SEN and PES Processes in the name file. In the 

PES Process, also set the variable MAX-ITER to 1. Parameter-sensitivity mode output includes one-percent scaled sensitivity 

arrays (set additional print flags in the SEN Process and OC Option), the fit of simulated equivalents to observations, composite 

scaled sensitivities, and prediction scaled sensitivities. Parameter-estimation mode will produce optimal parameter values for the 

observation weights if convergence is achieved. When the PES Process is activated in the name file, the method of running this 

mode for all parameters or for a set of parameters is the same as previously described for the parameter-sensitivity mode.

Output produced only in the parameter-estimation mode, including the dvr. pa and dvr._pc files, contains information 

about parameter estimation by iteration and only final parameter estimates, respectively. With an active PES Process, additional 

statistics, such as estimated parameter values, standard deviations, coefficients of variation, and 95 percent linear confidence 

intervals, are written to the GLOBAL file (table 7) (Hill, 1998). 

Typical Uses of the DVRFS Model

Since publication of the DVRFS model, the authors have responded to model users regarding questions about predictive 

pumping scenarios and conversion of the model from a transient to a steady-state simulation. Both of these scenarios are 

addressed in following sections which pertains to editing the model archive files. The required editing of model inputs to achieve 

these model modifications for execution in forward model mode with observations and parameter-value substitution (Hill and 

others, 2000, p. 12) is described. The observation packages (CHOB, DROB, and HOB) are not required to conduct model 

simulations in forward mode when the OBS Process is inactive. However, conducting model simulations in the forward mode 

with the OBS Process active produces additional output that aids model evaluation. If a user is not utilizing the OBS Process, 

inactivate the OBS Process and the CHOB, DROB, and HOB Packages in the name file and disregard editing instructions for 

these files.

Predictive Pumping Scenarios

To simulate predictive pumping scenarios, or pumping that extends beyond the last stress period of the DVRFS model, the 

DIS file and the WEL1 Package (or the MNW1 Package) are the primary two files that require editing. The total length of the 

model simulation may be changed by adding additional stress periods in the DIS file. Any pumping that occurs during these 

additional stress periods can be included in the WEL1/MNW1 Package by specifying pumping rates, well locations, and time 

of pumping. All other packages which contain parameter information by stress period (CHD, HFB6, DRN, and RCH Packages) 

also need to reflect an increase in the total number of stress periods. Parameter definitions from the previous time step may be 

repeated for each of the new stress periods. 

In the DIS file, extend the number of stress periods by adding a line, at the end of the file, for each additional stress period, 

and increase the total number of stress periods (variable NPER).

• For example, in the first data row of the DIS file (DIS_WT_CONFINED.txt), increase the total number of stress periods 

from 87 to 90 as indicated by the gray highlighting of the variable NPER:

# DIS Package Line 0: Text

16 194 160 90 4 2 Line 1: NLAY NROW NCOL NPER ITMUNI LENUNI

Next, specify the length of each of the three additional stress periods (variable PERLEN), the number of time steps 

(variable NSTP), the time step multiplier (variable TSMULT), and identify the additional stress period as transient (TR). 

• For example, at the end of the DIS file, add three new transient stress periods, each 4 years in length with 3 time-steps 

and a time step multiplier of 1, for a total of 90 stress periods:

1462 3 1 TR Line 7: PERLEN NSTP TSMULT (stress period 88)

1462 3 1 TR Line 7: PERLEN NSTP TSMULT (stress period 89)

1462 3 1 TR Line 7: PERLEN NSTP TSMULT (stress period 90).

Typical Uses of the DVRFS Model 19
Well locations are identified by model layer, row, and column. Approximate well locations by row and column can be 

calculated from Universal Transverse Mercator (UTM) coordinates using the following equations:

Column = INT((easting - 437,000)/1500) + 1 , (1)

Row = INT((4,219,000 - northing)/1500) + 1, (2)

where 

INT is a function which converts a real number to an integer by truncating values after the decimal point, and the easting 

and northing coordinates are UTM zone 11.

To add additional pumping or well injection during the three new stress periods, add to the end of the WEL1 Package the 

number of non-parameter wells read for the current stress period (variable ITMP), and the layer, row, and column of the well 

followed by the pumping rate (variables Layer, Row, Column, and Q) for each stress period. A negative pumping rate indicates 

discharge from the ground-water system. For example, to add a pumping well (model layer 1, row 141, column 100) and another 

pumping well (model layer 1, row 147 and column 104) that each pump at a rate of 2.36 m3/d in each of the three additional 

stress periods, the following lines would be added to the end of the WEL1 Package:

2

1 141 100 -2.36

1 147 104 -2.36

2

1 141 100 -2.36

1 147 104 -2.36

2

1 141 100 -2.36

1 147 104 -2.36

After editing files, execute MODFLOW-2000 in the forward mode with observations and parameter-value substitution.

Converting from a Transient to Steady-State Simulation

For users who wish to compare DVFRS hydraulic properties with an existing model, it may be an advantage to run the 

model with steady-state conditions, instead of transient conditions, for faster sensitivity analysis computations. Oftentimes in 

ground-water modeling, a steady-state solution is approximated with a long transient stress period. Significant drawdown occurs 

at some locations in the DVRFS model and adding a long final transient stress period to the existing model would require rewetting if pumping was turned off during a long final stress period. As rewetting may result in numerical instabilities (Harbaugh 

and others, 2000), a different approach is proposed.

To convert the DVRFS model from a transient to a steady-state simulation, some transient information must be removed. To 

simulate only a single initial steady-state stress period, change the total number of stress periods to 1. In this case, model stresses

during the existing transient stress periods do not need to be removed as they are effectively turned off leaving only a single 

steady-state stress period. The observation files, the DIS file which specifies time discretization, and storage parameters in the 

HUF2 Package and SEN Process require editing. The OC Option also requires editing so that printing and saving does not occur 

from the transient stress periods that have been removed from the model simulation. Additionally, all observation packages 

(CHOB, DROB, and HOB) must be edited so that no observations are specified in times that extend beyond the period of the 

steady-state simulation. 

20 A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
 To convert the transient simulation to a steady-state simulation, specify a single steady-state stress period in the DIS file. If 

a single steady-state stress period is specified, the additional transient stress periods, which are specified on subsequent lines in 

the file, will not be read.

• In the DIS file (DIS_WT_CONFINED.txt), change the variable NPER to 1 to reflect a single steady-state stress period.

For example, replace the 87 stress periods in DIS file:

# DIS Package Line 0: Text

16 194 160 87 4 2 Line 1: NLAY NROW NCOL NPER ITMUNI LENUNI 

with a single steady state stress period as indicated by the gray highlighting:

# DIS Package Line 0: Text

16 194 160 1 4 2 Line 1: NLAY NROW NCOL NPER ITMUNI LENUNI.

To convert from a transient to a steady-state simulation, specific storage parameters (parameter types SS and SYTP) must 

be removed from the HUF2 Package (HUF2_CONFINED.txt) and the SEN Process (SENSITIVITY.txt) files. The removal 

of these parameters also must be reflected in the total number of HUF2 Package parameters (variable NPHUF) and the total 

number of parameters in the SEN Process (variables NPLIST and MXSEN). If the seven storage parameters (STOR_12, 

STOR_34, STOR_4VUP, STOR_4C, SY_OTHER, SY_PAH, and SY_PUMP) are removed from the HUF2 Package (lines 246 

to 283) and the SEN Process (lines 97 to 103), the variable NPHUF, which specifies the total number of parameters in the HUF2 

Package (HUF2_CONFINED.txt), also must decrease by seven (from 69 to 62) as indicated by the gray shading in the first data 

row in the HUF2 Package:

# HUF2 Package

#

36 -9999 27 62 0 IHUFCB HDRY NHUF NPHUF IOHUF.

Additionally, the total number of parameters in the SEN Process must be decreased from 100 to 93 as indicated by the gray 

shading in the first data row.

# SEN Package Line 0: Text (Line 3: PARNAM ISENS LN B BL BU BSCAL)

93 -1 0 93 Line 1: NPLIST ISENALL IUHEAD MXSEN

As steady-state conditions were defined as pre-development conditions with no pumping, the MNW Package should be 

deactivated in the name file.

In the OC Option, remove all references to stress periods after stress period 1. 

• For example, in the OC Option (OC.txt) remove lines 14 to 27.

After the above editing is complete, model simulations will be executed with steady-state conditions if the OBS Process is 

deactivated in the name file. To run the model with steady-state conditions and an active OBS Process, edit the DROB and HOB 

Packages. The CHOB Package does not require editing because all observations occur during the steady-state stress period.

Most observations in the DROB Package are specified during stress period 86. Because only two discharge locations 

have flows that diminish with time, the observation flows in stress period 86 also reflect steady-state conditions, and only the 

observation time requires editing. 

• In the DROB Package (drob_tr.txt), the observation flow and associated observation weight does not need to be changed; 

however, the time associated with each observation should be switched from stress period 86 to stress period 1 by 

changing the variable for the reference stress period (IREFSP) from 86 to 1.

Typical Uses of the DVRFS Model  21
 For example, for the drain observation at Furnace Creek Wash springs in Death Valley (OBS-DV-FRNFN) highlighted 

below in gray, the change is from stress period 86:

1 9

OBS-DV-FRNFN 1 86 -11522. 0.280 2 3

1 122 50 1.00

1 123 49 1.00

1 123 50 1.00

1 124 49 1.00

1 124 50 1.00

1 125 49 1.00

1 125 50 1.00

1 126 50 1.00

1 126 51 1.00

to stress period 1:

1 9

OBS-DV-FRNFN 1 1 -11522. 0.280 2 3

1 122 50 1.00

1 123 49 1.00

1 123 50 1.00

1 124 49 1.00

1 124 50 1.00

1 125 49 1.00

1 125 50 1.00

1 126 50 1.00

1 126 51 1.00

Four drain observations at two locations (Manse and Bennetts Springs in Pahrump Valley), which reflect decreasing flows 

over time, must be removed as they do not reflect steady-state conditions: OB-PAH-BENT (stress period 48), O-PAH-BENT 

(stress period 87), OB-PAH-MANS (stress period 48), and O-PAH-MANS (stress period 87). The change in the total number of 

observations (from 49 to 45) must be reflected in the first data row of DROB Package.

• In the DROB Package (drob_tr.txt), remove observations O-PAH-BENT (lines 809-846), OB-PAH-BENT (lines 771-

808), OB-PAH-MANS (lines 861-874) and O-PAH-MANS (lines 875-888).

• In the DROB Package (drob_tr.txt), edit the total number of observations (variables NQDR and NQTDR) from 49 to 45. 

Thus the first data row of the file changes from:

#Observations in the 1997=86 stress period and stress period 1. 

49 769 49

 to: 

#Observations in the 1997=86 stress period and stress period 1. 

45 769 45

as indicated by the gray highlighting.

In the HOB Package, remove observations that do not reflect steady-state conditions. This can be accomplished by 

removing hydraulic head observations with PLOT-SYMBOL values of 2 or 3 (so that just PLOT-SYMBOL values of 0 and 1 

remain) or by deleting entries that occur at times other than during the steady-state stress period. Update the change in the total 

number of head and head change observations (variable NH) in the first data row of the HOB Package.

• In the HOB Package (HOBs_sstr.txt), remove observations that occur during the transient stress periods.

• In the HOB Package, update variable NH, the total number of head and head change observations.

After editing, execute MODFLOW-2000 in the forward mode with observations and parameter-value substitution (table 7).

22  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Summary

This guide informs the user about the files, structures, 

and parameters provided in the electronic resources of the 

transient DVRFS model. Input, output, and model simulation 

modes with MODFLOW-2000 of likely utility to the user are 

described. Input includes observation packages that contain 

observations of hydraulic head and head change, flows, and 

flows associated with groups of constant head cells along 

portions of the model boundary. The source of information and 

assumptions on which the observation values and weights are 

based is discussed. These observations provide model users 

a tool to evaluate model fit that is critical to analyzing any 

application of the DVRFS model. In addition to characterizing 

the input and output of the DVRFS model, the mechanics of 

creating such output is explored for several types of model 

modes: forward, parameter-sensitivity, and parameterestimation. For typical users of the DVRSF model, two 

common modifications of the model arise: predictive pumping 

scenarios and conversion of the model from a transient to a 

steady-state simulation. Editing of the model archive files to 

achieve both of these model modifications is outlined with 

examples. 

References Cited

Anderman, E.R., and Hill, M.C., 2000, MODFLOW-2000, 

The U.S. Geological Survey modular ground-water flow 

model—Documentation of the hydrogeologic-unit flow 

(HUF) package: U.S. Geological Survey Open-File Report 

00–342, 89 p.

Anderman, E.R., and Hill, M.C., 2003, MODFLOW-2000, 

The U.S. Geological Survey modular ground-water flow 

model—Three additions to the hydrogeologic-unit flow 

(HUF) package—Alternative storage for the uppermost 

active cells (STYP parameter type), flows in hydrogeologic 

units, and the hydraulic conductivity depth-dependence 

(KDEP) capability: U.S. Geological Survey OpenFile Report 03–347, 36 p. Accessed April 14, 2004 at 

http://water.usgs.gov/nrp/gwsoftware/modflow2000/

modflow2000.html.

Bedinger, M.S., and Harrill, J.R., 2004a, Appendix 1. 

Regional potential for interbasin flow of ground water, in 

Belcher, W.R., ed., Death Valley regional ground-water flow 

system, Nevada and California—Hydrogeologic framework 

and transient ground-water flow model: U.S. Geological 

Survey Scientific Investigations Report 2004-5205, p. 

357-374. Accessed June 8, 2004 at http://pubs.water.usgs.

gov/sir20045205/.

Bedinger, M.S., and Harrill, J.R., 2004b, Plate 1. Regional 

potential for interbasin flow of ground water in the Death 

Valley regional ground-water flow system area, Nevada 

and California, in Belcher, W.R., ed., Death Valley regional 

ground-water flow system, Nevada and California—

Hydrogeologic framework and transient ground-water flow 

model: U.S. Geological Survey Scientific Investigations 

Report 2004-5205.

Belcher, W.R., D’Agnese, F.A., and O’Brien, G. M., 2004, 

Chapter A. Introduction, in Belcher, W.R., ed., Death 

Valley regional ground-water flow system, Nevada and 

California—Hydrogeologic framework and transient 

ground-water flow model: U.S. Geological Survey Scientific 

Investigations Report 2004-5205, p. 7-19. Accessed April 

13, 2004 at http://pubs.water.usgs.gov/sir20045205/.

D’Agnese, F.A., Faunt, C.C., Turner, A.K., and Hill, M.C., 

1997, Hydrogeologic evaluation and numerical simulation 

of the Death Valley regional ground-water flow system, 

Nevada and California: U.S. Geological Survey WaterResources Investigations Report 96–4300, 124 p.

D’Agnese, F.A., O’Brien, G.M., Faunt, C.C., Belcher, W.R., 

and San Juan, C., 2002, A three-dimensional numerical 

model of predevelopment conditions in the Death Valley 

regional ground-water flow system, Nevada and California: 

U.S. Geological Survey Water-Resources Investigations 

Report 02–4102, 114 p.

Faunt, C.C., D’Agnese, F.A., and O’Brien G.M., 2004a, 

Chapter D. Hydrology, in Belcher, W.R., ed., Death 

Valley regional ground-water flow system, Nevada and 

California—Hydrogeologic framework and transient 

ground-water flow model: U.S. Geological Survey Scientific 

Investigations Report 2004-5205, p. 137-164. Accessed 

April 13, 2004 at http://pubs.water.usgs.gov/sir20045205/.

Faunt, C.C., Blainey, J.B., Hill, M.C., D’Agnese, F.A., and 

O’Brien, G.M., 2004b, Chapter F. Transient Numerical 

Model, in Belcher, W.R., ed., Death Valley regional groundwater flow system, Nevada and California—Hydrogeologic 

framework and transient ground-water flow model: U.S. 

Geological Survey Scientific Investigations Report 2004-

5205, p. 257-352. Accessed April 13, 2004 at http://pubs.

water.usgs.gov/sir20045205/.

Halford, K.J., and Hanson, R.T., 2002, User guide for the 

drawdown-limited, multi-node well (MNW) package for the 

U.S. Geological Survey’s modular three-dimensional finitedifference ground-water flow model, versions MODFLOW96 and MODFLOW-2000: U.S. Geological Survey OpenFile Report 02–293, 33 p.

References Cited  23
Hanson, R.T., and Leake, S.A., 1999, Documentation of 

HYDMOD, a program for extracting and processing timeseries data from the U.S. Geological Survey’s modular 

three-dimensional finite-difference ground-water flow 

model: U.S. Geological Survey Open-File Report 98–564, 

57 p.

Harbaugh, A.W., 1990, A computer program for calculating 

subregional water budgets using results from the U.S. 

Geological Survey modular three-dimensional ground-water 

flow model: U.S. Geological Survey Open-File Report 

90-392, 46 p. Accessed June 1, 2005 at http://water.usgs.

gov/nrp/gwsoftware/zonebud2/zonebudget2.html.

Harbaugh, A.W., 1995, Direct solution package based on 

alternating diagonal ordering for the U.S. Geological Survey 

modular finite-difference ground-water flow model: U.S. 

Geological Survey Open-File Report 95-288, 46 p.

Harbaugh, A.W., and McDonald, M.G., 1996, User’s 

documentation for MODFLOW-96, an update to the U.S. 

Geological Survey modular finite-difference ground-water 

flow model: U.S. Geological Survey Open-File Report 

96-485, 56 p. Accessed June 1, 2005 at http://water.usgs.

gov/software/modflow-96.html.

Harbaugh, A.W., Banta, E.R., Hill, M.C., and McDonald, 

M.G., 2000, MODFLOW-2000, The U.S. Geological 

Survey modular ground-water model – User guide to 

modularization concepts and the ground-water flow process: 

U.S. Geological Survey Open-File Report 00-92, 121 p.

Harrill, J.R., and Bedinger, M.S., 2004, Appendix 2. Estimated 

boundary flows, in Belcher, W.R., ed., Death Valley regional 

ground-water flow system, Nevada and California—

Hydrogeologic framework and transient ground-water flow 

model: U.S. Geological Survey Scientific Investigations 

Report 2004-5205, p. 375-408. Accessed April 13, 2004 at 

http://pubs.water.usgs.gov/sir20045205/.

Hevesi, J.A., Flint, A.L., and Flint, L.E., 2003, Simulation of 

net infiltration and potential recharge using a distributed 

parameter watershed model of the Death Valley region, 

Nevada and California: U.S. Geological Survey Water 

Resources Investigations Report 03-4090, 91 p.

Hill, M.C., 1990, Preconditioned conjugate-gradient 2 

(PCG2), a computer program for solving ground-water 

flow equations: U.S. Geological Survey Water-Resources 

Investigations Report 90-4048, 43 p.

Hill, M.C., 1998, Methods and guidelines for effective model 

calibration: U.S. Geological Survey Water-Resources 

Investigations Report 98-4005, 90 p.

Hill, M.C., Banta, E.R., Harbaugh, A.W., and Anderman, 

E.R., 2000, MODFLOW-2000, The U.S. Geological 

Survey’s modular ground-water flow model—User guide 

to the observation, sensitivity, and parameter-estimation 

procedures and three post-processing programs: U.S. 

Geological Survey Open-File Report 00–184, 209 p.

Hsieh, P.A., and Freckleton, J.R., 1993, Documentation of a 

computer program to simulate horizontal-flow barriers using 

the U.S. Geological Survey modular three-dimensional 

finite difference ground-water flow model: U.S. Geological 

Survey Open-File Report 92–477, 32 p.

IT Corporation, 1996, Underground test area subproject, Phase 

I, Data analysis task, volume VI—Groundwater flow model 

data documentation package: Las Vegas, Nev., Report 

ITLV/10972–181 prepared for the U.S. Department of 

Energy, 8 volumes, various pagination.

Laczniak, R.J., Smith, J.L., Elliott, P.E., DeMeo, G.A., 

Chatigyn, M.A., and Roemer, G.J., 2001, Ground-water 

discharge determined from estimates of evapotranspiration, 

Death Valley regional flow system, Nevada and California: 

U.S. Geological Survey Water-Resources Investigations 

Report 01–4195, 51 p.

McDonald, M.G., and Harbaugh, A.W., 1984, A modular 

three-dimensional finite difference ground-water flow 

model: U.S. Geological Survey Open-File Report 83-875, 

528 p.

McDonald, M.G., and Harbaugh, A.W., 1988, A modular 

three-dimensional finite difference ground-water flow 

model: U.S. Geological Survey Techniques of Water 

Resources Investigations, Book 6, Chapter A1, 586 p.

Mehl, S.E., and Hill, M.C., 2001, MODFLOW-2000, the U.S. 

Geological Survey modular ground-water model —User 

guide to the LINK-AMG (LMG) Package for solving 

matrix equations using an algebraic multigrid solver: U.S. 

Geological Survey Open-File Report 01-177, 33 p.

Moreo, M.T., Halford, K.J., La Camera, R.J., and Laczniak, 

R.J., 2003, Estimated ground-water withdrawals from the 

Death Valley regional flow system, 1913–1998, Nevada 

and California: U.S. Geological Survey Water-Resources 

Investigations Report 03–4245, 28 p.

Poeter, E.P., and Hill, M.C., 1997, Inverse models: a necessary 

next step in ground-water modeling, Ground Water, v. 35, 

no. 2, p. 250-260.

San Juan, C.A., Belcher, W.R., Laczniak, R.J., and Putnam, 

H.M., 2004, Chapter C. Hydrologic components for model 

development, in Belcher, W.R., ed., Death Valley regional 

ground-water flow system, Nevada and California—

Hydrogeologic framework and transient ground-water flow 

model: U.S. Geological Survey Scientific Investigations 

Report 2004-5205, p. 99-136. Accessed April 13, 2004 at 

http://pubs.water.usgs.gov/sir20045205/.

Wilson, J.D., and Naff, R.L., 2004, The U.S. Geological 

Survey modular ground-water model — GMG linear 

equation solver package documentation: U.S. Geological 

Survey Open-File Report 2004-1261, 47 p. Accessed 

June 1, 2005 at http://water.usgs.gov/nrp/gwsoftware/

modflow2000/modflow2000.html.

Winston, R.B., 2000, Graphical user interface for MODFLOW, 

version 4: U.S. Geological Survey Open-File Report 

00-315, 27 p. Accessed June 1, 2005 at http://water.usgs.

gov/nrp/gwsoftware/GW_Chart/GW_Chart.html.

24  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
Input files:

BAS_active.txt - basic package 

CHOB_15reg.txt - constant head observations

CHD_15reg_tr.txt - constant heads 

DIS_WT_CONFINED.txt - discretization 

DRN_tr.txt - drains (DRN package)

DROB_tr.txt - drain observations

HFB_final_tr.txt - horizontal-flow barriers 

HOBs_sstr.txt - head observations

HUF2_CONFINED.txt - hydrogeologic unit flow 

HOBS_sstr.hyd - hydmod

KDEP.txt - depth decay

MNW_withdrawal_1_7_20.txt - multinode well

MULT.txt - multiplier

NAME.txt - names of input and output files

OBS.txt - observation process

OC.txt - output control

PCG.txt - pcg solver

PES.txt - parameter estimation settings

RCH_tr.txt - recharge

SENSITIVITY.txt - sensitivity process (actually contains parameter 

values)

ZONE.txt - zones

ibound1.asc - ibound array layer 1 (BAS6 package)

ibound2.asc - ibound array layer 2 (BAS6 package)

ibound3.asc - ibound array layer 3 (BAS6 package)

ibound4.asc - ibound array layer 4 (BAS6 package)

ibound5.asc - ibound array layer 5 (BAS6 package)

ibound6.asc - ibound array layer 6 (BAS6 package)

ibound7.asc - ibound array layer 7 (BAS6 package)

ibound8.asc - ibound array layer 8 (BAS6 package)

ibound9.asc - ibound array layer 9 (BAS6 package)

ibound10.asc - ibound array layer 10 (BAS6 package)

ibound11.asc - ibound array layer 11 (BAS6 package)

ibound12.asc - ibound array layer 12 (BAS6 package)

ibound13.asc - ibound array layer 13 (BAS6 package)

ibound14.asc - ibound array layer 14 (BAS6 package)

ibound15.asc - ibound array layer 15 (BAS6 package)

ibound16.asc - ibound array layer 16 (BAS6 package)

hd_lay1.asc - starting heads layer 1 (BAS6 package)

hd_lay2.asc - starting heads layer 2 (BAS6 package)

hd_lay3.asc - starting heads layer 3 (BAS6 package)

hd_lay4.asc - starting heads layer 4 (BAS6 package)

hd_lay5.asc - starting heads layer 5 (BAS6 package)

hd_lay6.asc - starting heads layer 6 (BAS6 package)

hd_lay7.asc - starting heads layer 7 (BAS6 package)

hd_lay8.asc - starting heads layer 8 (BAS6 package)

hd_lay9.asc - starting heads layer 9 (BAS6 package)

hd_lay10.asc - starting heads layer 10 (BAS6 package)

hd_lay11.asc - starting heads layer 11 (BAS6 package)

hd_lay12.asc - starting heads layer 12 (BAS6 package)

hd_lay13.asc - starting heads layer 13 (BAS6 package)

hd_lay14.asc - starting heads layer 14 (BAS6 package)

hd_lay15.asc - starting heads layer 15 (BAS6 package)

hd_lay16.asc - starting heads layer 16 (BAS6 package)

delr.txt - row spacing (DIS package)

delc.txt - column spacing (DIS package)

lay1_wt_sim.asc - top of layer 1 (DIS package)

lay2_top.asc - top of layer 2 (DIS package)

lay3_top.asc - top of layer 3 (DIS package)

lay4_top.asc - top of layer 4 (DIS package)

lay5_top.asc - top of layer 5 (DIS package)

lay6_top.asc - top of layer 6 (DIS package)

lay7_top.asc - top of layer 7 (DIS package)

lay8_top.asc - top of layer 8 (DIS package)

lay9_top.asc - top of layer 9 (DIS package)

lay10_top.asc - top of layer 10 (DIS package)

lay11_top.asc - top of layer 11 (DIS package)

lay12_top.asc - top of layer 12 (DIS package)

lay13_top.asc - top of layer 13 (DIS package)

lay14_top.asc - top of layer 14 (DIS package)

lay15_top.asc - top of layer 15 (DIS package)

lay16_top.asc - top of layer 16 (DIS package)

lay16_bot.asc - bottom of layer 16 (DIS package)

rch1_modmd.asc - multiplier array used to represent initial recharge 

(MULT package)

land_surface.asc - land surface (used for depth decay) (KDEP file)

lca_zone.asc - zone array (ZONE package)

lccu_zone.asc - zone array (ZONE package)

vsu_zone.asc - zone array (ZONE package)

cald_zone.asc - zone array (ZONE package)

ovu_zone.asc - zone array (ZONE package)

infil_zone_9.asc - zone array (ZONE package)

tmva_zone.asc - zone array (ZONE package)

vsu_up_zone.asc - zone array (ZONE package) 

xcu_zone.asc - zone array (ZONE package)

chvu_zone.asc - zone array (ZONE package)

cfbcu_zone.asc - zone array (ZONE package) 

bru_zone.asc - zone array (ZONE package)

sy_zone.asc - zone array (ZONE package)

pva_zone.asc - zone array (ZONE package)

lca_modt.asc hydrogeologic unit top (HUF2 package)

lca_thickt.asc hydrogeologic unit thickness (HUF2 package)

lca_t1_modt.asc hydrogeologic unit top (HUF2 package)

lca_t1_thickt.asc hydrogeologic unit thickness (HUF2 package)

lccu_modt.asc hydrogeologic unit top (HUF2 package)

lccu_thickt.asc hydrogeologic unit thickness (HUF2 package)

lccu_t1_modt.asc hydrogeologic unit top (HUF2 package)

lccu_t1_thickt.asc hydrogeologic unit thickness (HUF2 package)

lfu_modt.asc hydrogeologic unit top (HUF2 package)

lfu_thickt.asc hydrogeologic unit thickness (HUF2 package)

ovu_modt.asc hydrogeologic unit top (HUF2 package)

ovu_thickt.asc hydrogeologic unit thickness (HUF2 package)

pva_modt.asc hydrogeologic unit top (HUF2 package)

pva_thickt.asc hydrogeologic unit thickness (HUF2 package)

oacu_modt.asc hydrogeologic unit top (HUF2 package)

Appendix A: File Archive Documentation

The model files described below can be obtained from http://pubs.water.usgs.gov/sir20045205/ and clicking on the link 

“Model Archive.” Brief descriptions of the input and output files follow. Input files are identified separately from output files.

Appendix A  25
Input Files—Continued

oacu_thickt.asc hydrogeologic unit thickness (HUF2 package)

tmva_modt.asc hydrogeologic unit top (HUF2 package)

tmva_thickt.asc hydrogeologic unit thickness (HUF2 package)

chvu_modt.asc hydrogeologic unit top (HUF2 package)

chvu_thickt.asc hydrogeologic unit thickness (HUF2 package)

cfta_modt.asc hydrogeologic unit top (HUF2 package)

cfta_thickt.asc hydrogeologic unit thickness (HUF2 package)

cfbcu_modt.asc hydrogeologic unit top (HUF2 package)

cfbcu_thickt.asc hydrogeologic unit thickness (HUF2 package)

cfppa_modt.asc hydrogeologic unit top (HUF2 package)

cfppa_thickt.asc hydrogeologic unit thickness (HUF2 package)

yvu_modt.asc hydrogeologic unit top (HUF2 package)

yvu_thickt.asc hydrogeologic unit thickness (HUF2 package)

yacu_modt.asc hydrogeologic unit top (HUF2 package)

yacu_thickt.asc hydrogeologic unit thickness (HUF2 package)

uca_modt.asc hydrogeologic unit top (HUF2 package)

uca_thickt.asc hydrogeologic unit thickness (HUF2 package)

uccu_modt.asc hydrogeologic unit top (HUF2 package)

uccu_thickt.asc hydrogeologic unit thickness (HUF2 package)

yaa_modt.asc hydrogeologic unit top (HUF2 package)

yaa_thickt.asc hydrogeologic unit thickness (HUF2 package)

xcu_modt.asc hydrogeologic unit top (HUF2 package)

xcu_thickt.asc hydrogeologic unit thickness (HUF2 package)

wvu_modt.asc hydrogeologic unit top (HUF2 package)

wvu_thickt.asc hydrogeologic unit thickness (HUF2 package)

la_modt.asc hydrogeologic unit top (HUF2 package)

la_thickt.asc hydrogeologic unit thickness (HUF2 package)

oaa_modt.asc hydrogeologic unit top (HUF2 package)

oaa_thickt.asc hydrogeologic unit thickness (HUF2 package)

vsu_low_modt.asc hydrogeologic unit top (HUF2 package)

vsu_low_thickt.asc hydrogeologic unit thickness (HUF2 package)

scu_modt.asc hydrogeologic unit top (HUF2 package)

scu_thickt.asc hydrogeologic unit thickness (HUF2 package)

bru_modt.asc hydrogeologic unit top (HUF2 package)

bru_thickt.asc hydrogeologic unit thickness (HUF2 package)

vsu_up_modt.asc hydrogeologic unit top (HUF2 package)

vsu_up_thickt.asc hydrogeologic unit thickness (HUF2 package)

icu_modt.asc hydrogeologic unit top (HUF2 package)

icu_thickt.asc hydrogeologic unit thickness (HUF2 package) 

Output files:

GLOBAL.txt - MF2K output file that contains information that 

applies to the model simulation as a whole

LIST.txt - MF2K output file that contains output from the procedures 

of the flow process (such as model results - hydraulic head, 

drawdown, and volumetric budget)

WELL_PACKAGE.wl1 - well package generated given current 

model parameters based on multi-node well process

CBCF.bin - binary cell by cell flow values (values written depend on 

flags in other files)

HEADSOUT.txt - simulated heads by layer and time specified in 

output control file

DRAWDOUT.txt - simulated drawdown by layer and time specified 

in output control file

HYDROGRAPHS.sav - binary output for hydrographs (used by 

HYDMOD)

dvr._b - output derived from observation process (output depends on 

flags in PES file)

dvr._nm - output derived from observation process (weighted 

residuals and probability plotting)

dvr._os - output derived from observation process (unweighted 

simulated equivalents and observations)

dvr._r - output derived from observation process (unweighted 

residuals)

dvr._w - output derived from observation process (weighted 

residuals)

dvr._ws - output derived from observation process (weighted 

simulated equivalents and residuals)

dvr._ww - output derived from observation process (weighted 

simulated equivalents and observations)

26  A Guide for Using the Transient Ground-Water Flow Model of the DVRFS, Nevada and California
For more information concerning the research in this report, contact 

Director, Nevada Water Science Center

U.S. Geological Survey

2730 N. Deer Run Road

Carson City, Nevada 89701

http://nevada.usgs.gov/
OFR 2006–1104 Blainey and others

A Guide for Using the Transient Ground-Water Flow Model of the Death Valley 

Regional Ground-Water Flow System, Nevada and California