MODEL ARCHIVE Created November 7, 2016. # Reference to the model documentation report with doi. Garcia, C.A., Jackson, T.R., Halford, K.J., Sweetkind, D.S., Damar, N.A., Fenelon, J.M., and Reiner, S.R., 2017, Hydraulic Characterization of Volcanic Rocks in Pahute Mesa Using an Integrated Analysis of 16 Multiple-Well Aquifer Tests, Nevada National Security Site, 2009-2014, U.S. Geological Survey Scientific Investigations Report 2016-5151, 64 p, http://dx.doi.org/10.3133/sir20165151. # Reference to the model data release with doi. Jackson, T.R., Halford, K.J., and Garcia, C.A., 2017, MODFLOW-2005 and PEST models used to simulate multiple-well aquifer tests and characterize hydraulic properties of volcanic rocks in Pahute Mesa, Nevada: U.S. Geological Survey data release, http://dx.doi.org/10.5066/F76H4FJQ. The integrated groundwater-flow model is composed of 11 MODFLOW models, which simulated drawdowns from pumping one to three wells at a well site. Each of these 11 groundwater-flow models are referred to as a “well-site model.” Aquifer test results were integrated by simultaneously interpreting observed drawdowns from all aquifer tests with multiple groundwater-flow models. The integrated analysis ensured that hydraulic properties of volcanic rocks underlying Pahute Mesa were consistent with observed hydraulic connections among wells and across structural features for all aquifer tests. Integration of multiple groundwater-flow models allows for the simultaneous calibration and interpretation of the 16 multiple-well aquifer tests. Multiple groundwater-flow models allowed grid refinement near each pumping well and different pumping schedules specific to each aquifer test. Multiple groundwater-flow models also facilitated independent aquifer-test assessments and provided assurance that simulated drawdowns and sensitivities were computed and extracted correctly. The integrated analysis of multiple groundwater-flow models ensured that a single, consistent set of hydraulic properties was estimated for the study area. Inconsistent hydraulic-property distributions would be estimated if each aquifer test was interpreted individually because drawdown responses from multiple aquifer tests traverse similar volumes of rock. An integrated analysis of multiple aquifer tests also reduced hydraulic-property estimate uncertainty along the periphery of drawdown detection, which was limited spatially by existing wells during early aquifer testing (2009–10). The underlying directories contain batch files, model input and output files, PEST input and output files, Excel workbooks, and supporting utilities used for the simulations described in the report. Descriptions of the data in each subdirectory are given to facilitate understanding of this data release. File descriptions are provided for select files to provide additional information that may be of use for understanding this data release. The model simulations were run with MODFLOW-2005 version 1.11.00 and PEST version 12.1.0. Support is provided for correcting errors in the data release and clarification of the modeling conducted by the U.S. Geological Survey. Users are encouraged to review the model documentation report (http://dx.doi.org/10.3133/sir20165151) to understand the purpose, construction, and limitations of this model. Reconstructing the data release from the online data release : ------------------------------------------------------------- This data release is available from: http://dx.doi.org/10.5066/F76H4FJQ The models, along with post-processing tools, will run successfully only if the original directory structure is correctly restored. The data release is divided into several pieces to reduce the likelihood of download timeouts. Small files (readme.txt and modelgeoref.txt) are available as uncompressed files. All other files are zipped at the subdirectory level. For example, the files in the "georef" subdirectory are zipped into a zip file named "georef.zip". All zip files should be unzipped into a directory with the same name as the zip file name without the .zip extension. The highest-level directory structure of the original data release is: SIR2016-5151/ ancillary/ bin/ georef/ model/ output/ source/ The full directory structure of the data release and the zip files associated with each subdirectory are listed below. The model was run on a Windows 7 64-bit operating system. Windows is a requirement for performing actions outside of running the model and viewing model results. Microsoft Excel workbooks were used to pre-process aquifer test data and generate all MODFLOW and PEST files for the integrated groundwater-flow model. Microsoft Excel workbooks also were used to post-process model results for generating report figures and tables. Running the model: The integrated groundwater-flow model can be run from a batch file. In the model\IntegratedGroundwaterFlowModel\MASTER directory, the batch file 00_PEST_PM.bat does the following tasks: 1. runs the 11 well site models sequentially the batch file calls 01_MF_Build-Call-Extract.bat in each well site model directory MF_* The batch file, 01_MF_Build-Call-Extract.bat: (a) transfers pilot point files from the MASTER directory to the local directory (MF*\Arrays); (b) creates 2D arrays of hydraulic conductivity, which are distributed by hydrostratigraphic unit extent (Array.HSU-HydK_*.txt) and model layer (Array.MF-HydK_*.txt); (c) creates 2D arrays of specific storage, which are distributed by hydrostratigraphic unit extent (Array.HSU-Ss_*.txt) and model layer (Array.MF-Ss_*.txt); (d) runs the MODFLOW model using MODFLOW-2005; (e) calls the PEST groundwater utility MOD2OBS to extract simulated drawdowns at the same times as observed drawdowns; and (f) calls a FORTRAN utility TrimSIMp.exe that corrects water-level change at pumping wells for wellbore storage effects. 2. Runs post-processing routines in the ancillary\PS_ViewK+DD subdirectory Batch file, 00_PostProcess.bat, calls 4 batch files: (a) 01_Sub.BuildArrays.bat calls routines from the PS_ViewK+DD\00_MVsee_DD subdirectory 01_Sub.BuildArrays.bat calls batch file 01_ManyDD.bat and uses the FORTRAN utility mm_compare.exe to process the results of all 11 MODFLOW models in order to generate a 2D transmissivity array (Array.2D-TRAN.txt) and a 2D array of maximum drawdown extent (Array.2D-DDmax.txt). The 2D arrays are copied to the output directory. (b) 01_Sub.BuildPSparts.bat calls routines from the PS_ViewK+DD\00_DrawPatch subdirectory 01_Sub.BuildPSparts.bat calls batch file 01_GO_PLOT.bat to generate text files that are used to plot 2D distributions of hydraulic conductivity, specific storage, specific yield, transmissivity, and maximum drawdown extent in post script files (*.ps). (c) 01_Sub.CreatePS_HydK.bat calls routines from the PS_ViewK+DD\00_Map-PS subdirectory 01_Sub.CreatePS_HydK.bat calls batch file 00_PSnow.bat, which generates post-script files containing 2D distributions of transmissivity and maximum drawdown extent, and 2D distributions of hydraulic conductivity by hydrostratigraphic unit. Fault traces, well locations, pilot point locations and estimated values, and Nevada National Security Site boundary also are shown in post-script files. All post script files are copied to the output directory. (d) 01_Sub.CreatePS_Ss.bat calls routines from the PS_ViewK+DD\00_Map-PS subdirectory 01_Sub.CreatePS_Ss.bat calls batch file 00_PSnowSs.bat, which generates post-script files containing a 2D distribution of specific yield, and 2D distributions of specific storage by hydrostratigraphic unit. Fault traces, well locations, pilot point locations and estimated values, and Nevada National Security Site boundary also are shown in post-script files. All post script files are copied to the output directory. readme.txt This ASCII text file describes the organization of the model archive structure, batch files, MODFLOW and PEST input and output files, and Microsoft Excel workbooks used for pre-processing aquifer test data and model inputs and post-processing model results. modelgeoref.txt This ASCII text file defines the four corners of the model domain in decimal degrees. ancillary directory: This directory contains model pre- and post-processing utilities, drawdown estimates, and pumping data. The ancillary directory contains three subdirectories: 1. ModelGenerator: contains model generation files and utilities 2. PS_ViewK+DD: contains model post-processing utilities for viewing model results 3. Figures+Tables contains post-processing utilities for creating report figures and tables The ModelGenerator directory contains 3 subdirectories and 2 files: 1. DD_Processed: Microsoft Excel workbooks of estimated drawdowns for each multiple-well aquifer test and weights assigned to estimated drawdowns. 2. HSU-PP_Extents: contains 2 directories of files used to generate pilot point distributions by hydrostratigraphic unit (a) PilotPointGenerator directory Microsoft Excel workbook GeologyExtents+PP.xlsm is used to generate pilot points based on user-specified pilot point locations Microsoft Excel workbook GeologyExtentsPAD+PP.xlsm is used to generate pilot points based on user-specified pilot point locations and zones where a user wants a greater concentration of pilot points Microsoft Excel workbooks DenseZONES.xlsm and ConvexHull.xlsm are used to generate zones/polygons where a user wants a greater concentration of pilot points (b) TransferPP_OLDtoNEWsoln directory 00_Instruction.txt provide a set of instructions for using Microsoft Excel workbooks to transfer hydraulic conductivity, specific yield, and specific storage values from an old set of pilot points to a new set of pilot points. Matlab subdirectory contains files for performing the same actions as Microsoft Excel workbooks, except in a Matlab environment. 3. Templates_MF+PEST_Spec: template files used to build integrated groundwater-flow model 4. 00_Grid+Layer-PM2_UTM.xlsm: Microsoft Excel workbook with macros used to generate MODFLOW and PEST input files. Macros open and write data to template files in the Templates_MF+PEST_Spec directory. 5. ModelRunInstructions.txt: A set of step-by-step instructions for building the integrated groundwater-flow model The PS_ViewK+DD directory contains 4 subdirectories and 5 batch files: 1. 00_ExecPS: contains FORTRAN executables for post-processing model output files to generate consolidated model results. 2. 00_MVsee_DD: contains batch files and scripts for generating 2D arrays of transmissivity and maximum drawdown extent. To generate transmissivity field: batch files import model discretization (INPUT_*.DIS.txt) and hydraulic conductivity by model layer (Array.HSU-HYDK_*.txt) for each MODFLOW model mm_compare.exe interpolates hydraulic conductivity field from MODFLOW model discretization to a user-specified discretization and collapses 3D hydraulic conductivity field to a 2D array batch files also import model discretization (INPUT_*.DIS.txt) and unformatted drawdown (OUTPUT_*.ufh) results for each MODFLOW model mm_compare.exe interpolates drawdowns from MODFLOW model discretization to a user-specified discretization, makes the maximum drawdown for each cell, and generated a 2D array of maximum drawdowns 3. 00_DrawPatch: contains batch files and scripts for generating 2D arrays of hydraulic conductivity, specific yield, and specific storage by hydrostratigraphic unit, and input files for building post-script files. 4. 0_Map-PS: contains batch files and scripts for generating post-script map files showing hydraulic conductivity, specific yield, and specific storage fields by hydrostratigraphic unit. Post-script files also show fault traces, pumping and observation wells, pilot point locations and estimated values, and Nevada National Security Site boundary. There are 5 subdirectories: (a) BaseMap: contains text files of line data used to draw fault traces, base map area, and other spatial line data. (b) Plot_It: contains text files generated by batch files in the 00_DrawPatch directory. Line data in this directory includes transmissivity, hydraulic conductivity, specific yield, specific storage, and maximum drawdown contour data, and pilot point locations and values. (c) ps_out: contains post script map files (*.ps) that are generated by 00_PSnow.bat and 00_PSnowSs.bat post script files are 2D distributions of transmissivity, hydraulic conductivity, specific yield, specific storage, and maximum drawdown extent. (d) PSdefine: contains color and style definitions for plotting model output results (e) XY-ASCII: contains text files used to define explanations (legends) used in post script files. 5. 00_PostProcess.bat: batch file called by model run batch file (00_PEST_PM.bat). 00_PostProcess.bat batch file calls subroutines (01_Sub.*.bat) in PS_ViewK+DD directory, which call batch files in the 00_MVsee_DD, 00_DrawPatch, and 00_Map-PS directories. The Figures+Tables directory contains 5 subdirectories, 1 batch file, and 1 file: 1. Figure24: PM_AQ1: text file of 1D array of mean hydraulic conductivity values from all MODFLOW models PM_AQ4: text file of 1D array of maximum drawdown from all MODFLOW models HydK_BoxPlot: Microsoft Excel workbook used to generate hydraulic conductivity box plots 2. Figure25: Fig01_T_DD.ps: post-script file showing transmissivity, maximum drawdown extent, pumping and observation wells, and fault traces 3. Figure26_Table12: 04_Sample_K-T_ExtractT.xlsm: Microsoft Excel macro workbook with Visual Basic for Applications (VBA) macros used to generate transmissivity distributions for all pumping and observation wells in the model domain Fig26+Table12-ExtractT-500ft.xlsx: Microsoft Excel workbook used to generate Figure 26 and Table 12 4. Table10: PM_AQ1: text file of 1D array of mean hydraulic conductivity values from all MODFLOW models PM_AQ4: text file of 1D array of maximum drawdown from all MODFLOW models Table10: Microsoft Excel workbook used to generate hydraulic conductivity and investigated volumes for Table 10 5. Table11: INPUTS: 2D arrays from integrated groundwater-flow model: specific yield (Array.HSU-Ss_0069.txt), specific storage (Array.HSU-Ss-M_*.txt), and maximum drawdown (Array.2D-DDmax.txt) Microsoft Excel workbooks: model discretization (ER-20-11_DIS.xlsx), hydrostratigraphic unit ibound arrays (HSUIbound.xlsx), and observation well locations in Universal Transverse Mercator projection zone 11 (Wells.xlsx) Table11.xlsx: Microsoft Excel workbook generated by ComputeStorage.exe, which generates storage values for Table 11 MyAppInstaller_web.exe - A Matlab application that must be run if Matlab is not installed on your machine. If the user does not have a Matlab license installed, run the executable, which will download Matlab libraries to your machine in order to run the executable ComputeStorage.exe 6. GetModelResults.bat Batch file copies model output to appropriate figure and table folders for creating report figures and tables 7. GenerateFigures+TablesDirections.docx Lists step-by-step instructions for generating figures and tables in each subdirectory bin directory: This directory contains FORTRAN compiled code used in the study. Directory contains the compiled executables for MODFLOW, PEST, PEST groundwater utilities, and user-developed utility programs that process the model output files to generate 2D hydraulic property arrays. MODFLOW EXECUTABLES mk2k.exe - USGS MODFLOW-2005 executable PEST EXECUTABLES beopest64.exe - PEST executable to run model in parallel ppest.exe - PEST executable to run model in parallel pest.exe - PEST executable to run model in series pestchek.exe - PEST utility to check for PEST input errors GROUNDWATER UTILITIES ppk2fac.exe - Groundwater utility used to generate pilot point factor files fac2real.exe - Groundwater utility carries out spatial interpolation based on interpolation factors calculated by PPK2FAC and pilot point values contained in a pilot points file. - Program generates 2D arrays of hydraulic properties defined by hydrostratigraphic unit twoarray.exe - Groundwater utility used to add/subtract/multiple/divide one array by another array mod2obs.exe - Groundwater utility used to extract simulated head/drawdown at same times as observed head/drawdown for model comparison. USER-GENERATED FORTRAN UTILITIES NoComment.exe - FORTRAN utility to remove comments from PEST control file before running PEST File2MV.exe - Generates MODFLOW input and output for viewing hydrostratigraphic framework model geocodes in ModelViewer - MODFLOW files are generated based on 1D array of geocodes in *1 and *2 text files Fill3D_by_HSU.exe - FORTRAN utility used to convert 2D arrays of hydraulic properties defined by hydrostratigraphic unit to 2D arrays of hydraulic properties defined by MODFLOW model layer - Converts Array.HSU-*.txt to Array.MF-*.txt GEO2HSU.exe - Generates 2D ibound arrays showing the maximum spatial extent of geology codes mm_compare.exe - Computes the integrated transmissivity and maximum drawdown extent for all groundwater-flow models ReformARRAY.exe - Converts 1D array output from fac2real.exe to a 2D array so that 1 row on each line and MODFLOW can read array output TrimSIMp.exe - Used to correct water-level declines at pumping well location for wellbore storage effects georef directory: This directory contains a polygon shapefile showing the maximum extent of the study area, where the polygon represents the active model domain. model directory: This directory contains the integrated groundwater-flow model. The integrated groundwater-flow model is composed of 11 MODFLOW models, which simulated drawdowns from pumping one to three wells at a well site. The IntegratedGroundwaterFlowModel directory contains a MASTER subdirectory. The MASTER subdirectory contains all PEST and other supporting files for global optimization of all aquifer-tests. 00_PEST_PM.bat in the .\MASTER directory analyzes all aquifer test results with PEST. 01_MF_ALL.bat is the "model" called by PEST that sequentially calls the 01_MF_Build-Call-Extract.bat batch file under each .\MF_* directory. Instructions for reading observation, template, and instruction files under each .\MF directory are documented in the commented PEST control file, pest_pm-all.pst_commented.txt. The files 01_TransferK-PP.xlsm and 02_TransferSs-PP.xlsm create PEST template files, import pilot-point values, create Tikhonov regularization observations, and write all parameter information and prior information for the PEST control file. PEST template files are in the MASTER folder and have the prefix TPL-*. Files containing pilot point names, (X,Y) locations, pilot point values, and modified HSU numbers are in the MASTER folder and have the prefix PP_*. Tikhonov regularization observations are prior information in the PEST control file and is written in the PEST_PriorInfo2Regular* text files in the MASTER folder. Parameter information is written in the PEST_Parameters* text files and tied parameter information is written in the PEST_TIED-Parameters* text files. The PEST control file and global optimization results are written to text files with the prefix pest_pm-all*. Batch file 04_PESTcheck.bat runs the PESTchek utility that checks PEST input files for errors. 03_CollectHydros.bat copies all hydrograph *.gif files from the MF*\Hydros directories and pastes them into a new directory in MASTER\Hydros. The integrated groundwater-flow model is composed of 11 groundwater-flow models: 1 . MF_ER-20-4D 2. MF_ER-20-7 3. MF_ER-20-8#2m 4. MF_ER-20-8mID 5. MF_ER-20-11 6. MF_ER-EC-11m 7. MF_ER-EC-12mSI 8. MF_ER-EC-13mLZ 9. MF_ER-EC-13mUZ 10. MF-ER-EC-14mSD 11. MF_ER-EC-15mSID Each .\MF* directory contains MODFLOW, PEST, and groundwater utility input and output files, batch files, Model Viewer files, and hydrographs. MODFLOW input and output files have the prefixes INPUT and OUTPUT, respectively. PEST and MOD2OBS—a groundwater utility for extracting simulated drawdowns at well locations—have input and output files with the prefix Pcomp. The *_spc.txt files are grid specification files used to define the model grid discretization for PEST and other groundwater utilities. Each .*MF directory has 5 batch files: 1. 01_MF_Build-Call-Extract.bat runs the MODFLOW model in the currect directory and calls the 4 batch files (01_Sub.*.bat) 2. 01_Sub.ArrayBuild-K.bat - creates 2D arrays of hydraulic conductivity for each MODFLOW layer (Array.MF-HydK*.txt) and by hydrostratigraphic unit (Array.HSU-HydK_*.txt), which are in the \Arrays subdirectory 3. 01_Sub.ArrayBuild-Ss.bat - creates 2D arrays of specific yield and specific storage for each MODFLOW layer (Array.MF-Ss*.txt) and by hydrostratigraphic unit (Array.HSU-Ss_*.txt), which are in the \Arrays subdirectory 4. 01_Sub.Mod2OBS.bat - extracts simulated drawdowns at the same times as observed drawdowns for each observation well location - generates output file Pcomp_*.WLsimulated.txt 5. 01_Sub.TRIMadjust.bat - corrects simulated water levels in pumping well for wellbore storage - provides a correction to output file Pcomp_*.WLsimulated.txt Each .*MF directory has 2 Microsoft Excel macro workbooks: 1. 03_PEST-Hydros_ER-20-4D.xlsm - Generates hydrographs for each aquifer test MODFLOW model - on the SEE tab, the "GET" button reads in measured and simulated water levels and observation weights - on the SEE tab, the "BURP" button makes a Hydros directory and generates *.gif hydrograph files with computed statistics of unweighted and weighted sum-of-squares errors and root-mean-square errors. 2. 04_Sample_K-T_ER-20-4D.xlsm - Workbook used to view vertical distribution of hydraulic conductivity, transmissivity, and hydrostratigraphic units at each pumping and observation well location. - on the SEE tab, the "GET" button reads in grid specification file, hydraulic conductivity arrays by MODFLOW layer, geocode arrays, and observation well locations - the drop-down menu in cell B26 is used to view the vertical distribution of hydraulic conductivity, hydrostratigraphic units, well screens and observation points in the model domain. Each directory has two subdirectories: Arrays and GeoMV. The Arrays subdirectory contains pilot point files, arrays, and array creating routines. Batch file 00_CreateFACfileK+Ss.bat calls subroutine batch files 01_Sub.CreateFACfileK.bat and 01_Sub.CreateFACfileSs, which are used to generate pilot point factor files for hydraulic conductivity and specific yield/storage pilot points, respectively. Pilot point factor files are generating when 01_Sub.CreateFACfileK.bat and 01_Sub.CreateFACfileSs call the subroutine 01_Sub.FACfileCreate1.bat. 00_Sub.PP2HSU.bat and 02_Sub.ReformARRAY.bat are batch-file subroutines that translate pilot point values to an HSU array (Array.HSU-*.txt) and reformat arrays, respectively. MODFLOW hydraulic conductivity and specific storage arrays (Array.MF-*.txt) are created by batch as PEST calls the local file 01_MF_Build-Call-Extract.bat. The *1 and *2 files are 1D arrays of geocodes for the hydraulic conductivity field and specific yield/storage fields, respectively. The GeoMV subdirectory contains hydrogeologic frameworks as mapped to an aquifer-test model. The hydrogeologic framework as mapped to an aquifer-test model was visualized with Model Viewer (Hsieh and Winston, 2002) by assigning codes to each of the HSUs and warping these codes into a bogus MODFLOW model. Simulated displacements and juxtaposition of units along the principal fault structures was checked with the Model Viewer files. The batch file 01_CreateGeoMV.bat first creates the Array.HSU-IBND*.txt files, which are IBOUND arrays showing the maximum 2D extent of each hydrostratigraphic unit. Then, the batch file generates all MODFLOW files in the GeoMV subdirectory based on the 1D array of geocodes in the *1 and *2 text files. The *.mv file is a ModelViewer file for viewing the hydrogeologic framework for the aquifer-test model. output directory: This directory contains consolidated model output results. Model output results include: 1. Array.2D-TRAN.txt - 2D array of transmissivity 2. Array.2D-DDmax.txt - 2D array of maximum drawdown extent 3. Array.HSU-HydK-M_*.txt - 2D arrays of hydraulic conductivity by hydrostratigraphic unit 4. Array.HSU-Ss-M_*.txt - 2D arrays of specific storage by hydrostratigraphic unit 5. Fig01_T_DD.ps - post-script map file showing transmissivity and maximum drawdown extent. 6. Fig*_HSU_K.ps - post-script map files showing hydraulic conductivity fields by hydrostratigraphic unit. 7. Fig*_HSU_Ss.ps - post-script map files showing specific storage fields by hydrostratigraphic unit. source directory: This directory contains the source code that was developed as part of the project to facilitate post-processing model output files to consolidated aquifer-test results. MODFLOW EXECUTABLES MF2005.1_11 - USGS MODFLOW-2005 version 1.11.00 source code USER-GENERATED UTILITIES NoComment - FORTRAN source code to remove comments from PEST control file beforing running PEST File2MV - FORTRAN source code to generate MODFLOW input and output for viewing hydrostratigraphic framework model geocodes in ModelViewer Fill3D_by_HSU - FORTRAN source code used to convert 2D arrays of hydraulic properties defined by hydrostratigraphic unit to 2D arrays of hydraulic properties defined by MODFLOW model layer GEO2HSU - FORTRAN source code used to generate 2D ibound arrays showing the maximum spatial extent of geology codes mm_compare - FORTRAN source code computes the integrated transmissivity and maximum drawdown extent for all groundwater-flow models ReformARRAY - FORTRAN source code converts 1D array output from fac2real.exe to a 2D array so that 1 row is on each line and MODFLOW can read array output TrimSIMp - FORTRAN source code used to correct water-level declines at pumping well location for wellbore storage effects ComputeStorage - MATLAB source code used to compute geometric mean of specific yield and specific storage of integrated groundwater-flow model NOTE: THE FOLLOWING PEST AND GROUNDWATER UTILITIES CAN BE OBTAINED AT THE FOLLOWING WEBSITE: http://www.pesthomepage.org/ beopest64.exe - PEST executable to run model in parallel ppest.exe - PEST executable to run model in parallel pest.exe - PEST executable to run model in series pestchek.exe - PEST utility to check for PEST input errors ppk2fac.exe - Groundwater utility used to generate pilot point factor files fac2real.exe - Groundwater utility carries out spatial interpolation based on interpolation factors calculated by PPK2FAC and pilot point values contained in a pilot points file. twoarray.exe - Groundwater utility used to add/subtract/multiple/divide one array by another array mod2obs.exe - Groundwater utility used to extract simulated head/drawdown at same times as observed head/drawdown for model comparison.