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### APPENDIX **A :**  **VERIFICA TION CODES**  **A1.0 MODFLOW2000**  The MODF LOW ground water software has been developed by the USGS and has been continuously

upgraded since the first version, MODFLOW88 was released in 1988 (McDonald and Harbaugh 2003) . MODFLOW - 2005 is the newes t version currentl y available . Together, the different versions of MODFLOW have an international user base of over 1 , 000 users . As a ground water flow and transport simulator, the MODFLOW and related s oftware is suited to the simulation of a wide variety o f saturated zon e flow and transport problems. As part of EPA’s regulatory oversight of the Waste Isolation Pilot Plant (WIPP), located in southeastern New Mexico , the U.S. Department of Energy (the Department or DOE) that operates the WIPP repository must continue to meet the certification requirements of the EPA and , in part , must demonstrate on an ongoing basis that P erformance Assessment computer software is in compliance with regulations outlined in Section § 194.23

– Models and Computer Codes . T his sec tion presents DOE’s verification and validation of MODFLOW2000. **A1.1 INTRODUCTION**  MODFLOW is a computer program that numerically solv es the three - dimensional ground water flow equation for a porous medium by using a finite - difference method . MODFLOW is design ed to be modular , in that different functionalitie s, such as wells, rivers, evapo transpiration, etc., can be added as modules to the basic ground water flow solutions . Although MODFLOW was designed to be easil y enhanced, the design was oriented toward ad di tions to the ground water flow equation . Frequently , there is a need to solve additional equations; for example, transport equations and equations for estimating parameter values that produce the closest match between model - calculated heads and flows and m easured values . The version of MODFLOW used b y DOE, MODFLOW2000 (MF2K) is designed to simulate more complex boundary conditions (WIPP 2002; Donald and Harbaugh 1988; Harbaugh et al. 2000; MODFLOW 2 000) . The user’s manual for MODFLOW 2000 (Harbaugh et al. 2 000) contains an overview of the old and added design concepts, documents one new package, and contains input instructions for usin g the model to solve the ground water flow equation . For transient and ste ady - state, single - phase, ground water flow problems , the MODFLOW2000 software is executed with the prescribed boundary and initial conditions . MODFLOW was not used for the CCA . Software Requirements (SNLNP 19 - 1) requires that the following seven primary documents be developed, reviewed, and mainta ined fo r the MODFLOW software: Software Q uality A ssurance (QA) Plan Requirements Document (RD) Verific ation and Validation Plan (VV P) User ’ s Manual (UM) Design Document (DD) Implementation Document (ID) Validation Document (VD)A - 2

DOE reviewed the pre - existing documentation available for MODFLOW2000 from the USGS and found it to provide the necessary information that is usually within the RD, DD, UM, and VVP . Therefore, the onl y additional documents that were produced b y DOE are the Software QA Plan (WIPP PA 2003c) , the ID (WIPP PA 2003b) , VD (WIPP PA 2003a) , and the Installation and Check Out forms (WIPP PA 2003d) . DOE notes that documentation f or Version 1.6 will remain as the base document for an y future versions of the software, with addenda for each of the docum ents defining the additional scope of the revised software . Configuration control is maintained through completion of Installation & Checkout (I&C) documentation for all changes made to MODFLOW2000 and sy stem software and/or sy stem hardware . In addition, C hange Control (CC) and Software Problem Report (SPR) documents are completed, as appropriate. The construction of newer clusters of Linux - based computers has required the testing of certain codes that have been previously qualified on older hardware. In 2003, MODFLOW2000 Version 1.6 was qualified for use on the PC - based L inux cluster (WIPP PA 2003a) . The Agency reviewed DOE’s qualification and accepted the verification of MODFLOW2000 Version 1.6 on the L inux platform (EPA 2004) . DOE used these EPA approv ed software and hardware configurations to support CRA - 2004 and PABC - 2004. The L inux - based cluster was upgraded in 2006 (new processors and other hardware) and is now called the “Geo - Hydro Linux Cluster” (WIPP PA 2008) . This cluster is comprised of three different hardware groups, each with a group name : (1) e leionomae, (2) pegaeae, and (3) crinaeae . The computers are connected to a job control server, “teth ys .sandia.gov , ” which is not used for execution of codes . Because the hardware is new, but the software codes are unchanged and are not going to be recompiled, DOE only conducted regression testing to validate that the codes perform correctl y on the new sy stems . For both CRA - 2009 and PABC 2009, DOE used MODFLOW 1.6 in conjunction with the three hardware groups associated with the “Geo - Hydro Linux Cluster” mentioned above . The approach, results and Agency findings pertaining to this upgraded hardware are discussed below. **A1.2 TEST METHODOLOGY**  The DOE designed eight test cases to verify the functional require ments necessary for the verification/validation of the computer code for WIPP . The input files and corresponding output files are provided with the installation package . Li stings of these files are included in Appendix A to the VD corresponding to the test number and test name . Validation testing consisted of running all test cases and checking resulting output for consistency with documented results . The test cases were run with the production executable (e.g., the executable version used for PA compliance calculations) for MF2K . The production executable was created on the target platform b y the code sponsor and stored using CVS (e.g., Concurrent Versions Sy stem) version control on the target platform (CVSROOT - /h/WIPPcvs, repository - src/mf2k) . The exec utable, source code and test problems were also stored in SCMS on the WIPP Compaq Alpha cluster (Library - MF2K, cla ss - VER_0160). The MF2K production executable and input and output test files were obtained from c onfiguration management and placed in the test directories on the target platform . All of theA - 3

input files were used unmodified from the source code package, except for the *.nam file, where the file pathnames were modified to reflect the different syntax between the Windows and L inux operating s ys tems . The MF2K output listing files, *.lst , created during testing were compared to the output listing files obtained from the MF2K installation package, and differences were noted and addressed . The listing file is the primary ASCII text file created b y M F2K and contains an input echo, solver performance information, calculated head and a budget summary . This same procedure was used for all the tests, with the exception of Test Case 8, the algebraic multi - grid (AMG) test . The intent of Test Case 8 is to ve rify the L inked algebraic Multi - Grid solver (LMG) package that was not included in the MODFLOW2000 test suite . A test identical to Test Case 1, BCF2SS, was chosen, except that the solver has been switched from the Strongl y Implicit Procedure (SIP) to the L MG or linked algebraic Multi - Grid solver . The results of Test Case 8 were compared to the results of Test Case 1. After the code was verified, it was regression tested against the verification results (WIPP PA 2009a, 2009b, and 2009c) . The run - control for these tests was done using the csh script RunReadScript and the Python programs ReadScript.py and Format.p y . RunReadScript was used to run ReadScript.py

(for processing the list of files to be checked out, checked in, executed and compared), run Fomat.py (for formatting the output of ReadScript.py into an Word file), and then check the log and Word files into the repository . The specific input script and the locations within the CVS repository where the input script and log file can be found are presented in the regression test documentation (WIPP PA 2009a, 2009b, and 2009c) . The UNIX diff (e.g., difference) command was used to compare the output to original data . The diff command does a character - by - character comparison of two ASCII files (binary files cannot be compared) . An y differences are reported b y listing the line number in the first file, the type of change ( “ a ” for addition, “ c ” for change, “ d ” for deletion), and then the line numbers in the second file. The test was considered successful if the MODFLOW2000 output listing file was the same as the documented listing file within reasonable accuracy , and accounting for date and filename changes . Reasonable accuracy was defined as numericall y equal, except in the last printed digit for numbers printed with 6 or less digits, or in the digits greater than the 6 th for numbers printed with greater than 6 digits . Original output files are listed in the appendix, while the output files generated during testing were stored in CVS on the target platform and in SCMS accessible from the WIPP VMS Alpha cluster . The same criteria were used for all the test cases. **A1.3 TEST RESULTS**  The regression testing performed on the “eleiono mae” cluster shows that MODFLOW 2000 V ersion 1.6 is working in the same manner as the software performed on the original test platform. **A1.4 THE AGENCY’S CONCLUS**  **IONS** All test results met the acceptance criteria specified in Section 5.2 of the VD (WIPP PA 2003a) . Those differences that were present were character differences , due to the addition of the buildA - 4

date to the listing header , and in sy ntax differences between Windows and Linux pathnames, or were floating - point differences in insignificant digits . The AMG/LMG test produced very different output listings due to solver - specific output, but the head results and ground water budgets were the same as the PCG (Test Case 1, BCF2SS) results to within the acceptance criteria . Therefore, the Agency concludes that MO DFLOW 2000 Version 1.6 can be considered verified for use on the “eleionomae, pegaeae, and crinaeae” cluster of machines. 

### A2.0 **MT3D** MT3D ( Modular 3D Solute Transport Model) is a comprehensive three - dimensional numerical model for simulating solute transport in complex hydrogeologic settings . MT3D has a modular design that permits simulation of transport processes independentl y or jointly . MT3D is capable of modeling advection in complex steady - state and transient flow fields, anisotropic dispersion, first - order decay

and production reactions, and linear and nonlinear sorption . Itcan also handle bi oplume - ty

pe reactions, monad reactions, and daughter products . This enables MT3D to do multi - species reactions and simulate or assess natural attenuation within a contaminant plume . MT3D is linked with the USGS ground water flow simulator, MODFLOW, and is designed speci ficall y to handle advectivel y dominated transport problems without the need to construct refined models specifically for solute tr ansport . MT3D was developed by the University of Alabama’s Hydrogeology Group and the verification of MT3D is provided in Zheng (2006) and Zheng and Wang (1999). 

### A3.0 **REFERENCES** Donald, M.G., and A.W. Harbaugh, A.W., 1988 . A Modular Three -Dimensional Finite Difference Ground

- water Flow Model , TWI6 - A1, 588 p . U.S. Geologic Survey , Reston, Virginia . ERMS #522202. EP A 2004 . “Review of WIPP Performance Assessment Computer Code Migration, March 31, 2004.” Environmental Protection Agency . Harbaugh, A.W., E.R. Banta, M.C. Hill, and M.G. McDonald, 2000 . MODFLOW - 2000, The U.S. Geological Survey Modular Ground - Wa ter Model

– User Guide To Modularization Concepts And The Ground

- Water Flow Process , U.S. Geological Survey Open - File Report 00 - 92 . ERMS #522197. MODFLOW 2000 . The U.S. Geological Survey Modular Ground - Water Model

– User Guide to the LINK - AMG (LMG) Package for Solv ing MATRIX Equations Using an Algebraic Multigrid Solver , MODFLOW - 2000 . U.S. Geological Survey Open - File Report 00 - 92 . ERMS #52220. WIPP PA 2002 . Code Classification and Review of Pre - Existing Documentation for MODFLOW . Memo from Sean McKenna to Mario Chavez, Sept. 30, 2002, Sandia National Laboratories, Albuquerque, New Mexico . ERMS #523942.A - 5

WIPP PA 2003a . “Validation Document for MODFLOW - 2000 Version 1.6 dated March 2003.” Sandia WIPP Central Files . ERMS#523867 WIPP PA 2003b . “Implementation Document for MODFLOW - 2000 Version 1.6 dated March 2003.” Sandia WIPP Central Files . ERMS#523868. WIPP PA 2003a . “QA Plan for MODFLOW - 2000 Version 1.6 dated March 2003.” Sandia WIPP Central Files . ERMS#523869. WIPP PA 2003d . “Installation and Checkout for MODFLO W - 2000 Version 1.6 dated March 5, 2003.” WIPP PA (Performance Assessment) 2008 . “Change Control Form for MODFLOW 2000, Version 1.6.” Sandia National L aboratories . Sandia WIPP Central Files WPO . ERMS #550152. WIPP PA 2009a . “Regression Testing Document f or MODFLOW - 2000 Version 1.6 on the “eleionomae” subset of the GeoHydro cluster dated February 25, 2009.” Sandia National Laboratories . Sandia WIPP Central Files . ERMS #550911. WIPP PA 2009b . “Regression Testing Document for MODFLOW - 2000 Version 1.6 on th e “pegaeae” subset of the GeoHydro cluster dated February 25, 2009.” Sandia National Laboratories . Sandia WIPP Central Files . ERMS #550915. WIPP PA 2009c . “Regression Testing Document for MODFLOW - 2000 Version 1.6 on the “crinaeae” subset of the GeoHydro cluster dated February 25, 2009.” Sandia National Laboratories . Sandia WIPP Central Files . ERMS #550916. Zheng, C . , 2006 . MT3DMS v5.2 A Modular Three -Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion and Chemical Reactions of Contaminants in Groundwater Systems Supplemental User's Guide, University of Alabama, Tucsaloosa, Alabama. Zheng, C . and P. Wang, 1999 . MT3DMS: A Modular Three -Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion, and Chemic al Reactions of Contaminants in Groundwater Systems; Documentation and User's Guide, SERDP - 99 - 1, University of Alabama, Tuscaloosa, Alabama.