Publication Stewart, A.M., 2017, Hydrologic Assessment and Numerical Simulation of Groundwater Flow, San Juan Mine, San Juan County, New Mexico, 2010–13: U.S. Geological Survey Scientific Investigations Report 2017-5155, 90 p. https://doi.org/10.3133/sir20175155 Data release Stewart, A.M., 2017, MODFLOW-NWT and MODPATH5 models used to identify potential flow paths from San Juan Mine to hydrologic receptors, San Juan County, New Mexico: U.S. Geological Survey data release https://doi.org/10.5066/F75719JV MODEL ARCHIVE ------------- Archive created: 2017-11-15 SIR2017-5155/ Description: ----------- The underlying directories contain all of the input and output files for the simulations described in the report, as well as MODFLOW-NWT (Version 1.0.9 07/01/2014) and Mpathr5_0.exe (version 5) source codes. Descriptions of the data in each subdirectory are given to facilitate understanding of this model archive. Files descriptions are provided for select files to provide additional information that may be of use for understanding this model archive. The model described herein was run on a 64 bit Dell Computer with a Windows 7 Enterprise SP1 operating system. 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 complete model report (https://doi.org/10.3133/SIR2017-5155) to understand the purpose, documentation report construction, and limitations of this model. Reconstructing the model archive from the online data release: -------------------------------------------------------------- The model archive is available as a data release from: https://doi.org/10.5066/F75719JV The models will run successfully only if the correct directory structure is correctly restored. The model archive is broken 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 model archive is: SIR2017-5155/ bin/ georef/ model/ output/ source/ The full directory structure of the model archive and the files within each subdirectory are listed below. Running the model(s): -------------------- Seven different model simulations and two particle-tracking analysis runs are included in this archive. The models were run in a specific order with the previous model simulation providing the starting heads for the next simulation. (See below) MODFLOW-NWT ----------- Each simulation has a name, listed below, which has an associated name file used to run the corresponding simulation. When MODFLOW-NWT is executed, a single prompt is issued for the name file that specifies the input files to be used in the simulation, as well as, the output files that are created. Responding to this prompt with the name file listed below will initiate the corresponding simulation. The simulations that are documented can be run by opening a command line/terminal in the model subdirectory and typing: ..\..\bin\MODFLOW-NWT_64.exe .nam or each simulation directory contains a Windows batch file that can be used to run the MODFLOW simulation in that folder. The batch file can be executed either by double clicking the file name or by opening a Command Prompt window, navigating to this folder, and typing in the name of the batch file then entering the name file name - .nam RunModflow.bat Note: Output will be printed in the model input directory. Previously generated output is provided in the output folder so users can verify their model output results. MODPATH5 -------- Two particle-tracking anaylses are included in the model archive. Each particle tracking run has a MODPATH response input file. This file contains input responses of the user that were recorded during a previous execution of MODPATH. When MODPATH is executed, a single prompt is issued for the response file that specifies the input files to be used in the analysis, as well as, the output files that are created. The particle-tracking analysis that are documented can be run by opening a command line/terminal in the model subdirectory and typing: ..\..\bin\MPathr5_0.exe .rsp or each simulation directory contains a Windows batch file that can be used to run the MODPATH anaysis in that folder. The batch file can be executed either by double clicking the file name or by opening a Command Prompt window, navigating to this folder, and typing in the name of the batch file then entering the response file name - MP-case1.rsp or MP-case2.rsp RunModpath.bat Summary of the simulations --------------------------- MODEL SIMULATION SIMULATION DESCRIPTION OF SUBDIRECTORY NAME SIMULATION ---------------- ---------- -------------- steadystate1_ForInitHds ss1_ini_for_dd1.nam Predevelopment conditions. Writes out initial heads for the transientdd1 simulation. Transientdd1 trdd1.nam Simulates mine dewatering and oil and gas groundwater extraction. Transientdd1_ForInitHds trdd1_ini_for_dd2.nam Same as transientdd1 simulation but writes out initial heads for transientdd2 simulation. Transientdd2 trdd2.nam Simulates mine dewatering and oil and gas groundwater extraction of Transientdd1 run but with subsurface subsidence effects and hydraulic property changes resulting from surface mining. Transientdd2_ForInitHds trdd2_for_recovery_inihds.nam Same as transientdd2 simulation but writes out initial heads for recoveryCase1 and recoveryCase2 simulations. recoveyCase1 rec1.nam Simulates groundwater recovery from mining and oil and gas well dewatering. Incorporates all hydrologic parameters and grid cell changes from transientdd1 and transientdd2 runs. Varied hydraulic conductivity and porosity values. recoveyCase2 rec2.nam Simulates groundwater recovery from mining and oil and gas well dewatering. Incorporates all hydrologic parameters and grid cell changes from transientdd1 and transientdd2 runs. Varied hydraulic conductivity and porosity values. Files: ----- readme.txt: This file documents the structure of the model archive. modelgeoref.txt: ASCII file with the four corners of the model domain. Model data files are provided as decimal degrees in NAD 1983 projection. bin/ Description: ----------- This directory contains the 64-bit executables used to do the analysis documented in the report https://doi.org/10.3133/SIR20175155 Files: ----- MODFLOW-NWT_64.exe - 64 bit MODFLOW-NWT executable Mpathr5_0.exe - MODPATH version 5.0 executable georef/ Description: ----------- This directory contains a shapefile defining the active and inactive areas of the model documented in the report, https://doi.org/10.3133/SIR20175155 Files: ----- SIR2017_5155.dbf: part of the SIR2017_5155.shp shapefile SIR2017_5155.prj: part of the SIR2017_5155.shp shapefile SIR2017_5155.shp: part of the SIR2017_5155.shp shapefile SIR2017_5155.shx: part of the SIR2017_5155.shp shapefile SIR2017_5155.sbx: part of the SIR2017_5155.shp shapefile SIR2017_5155.cpg: part of the SIR2017_5155.shp shapefile SIR2017_5155.sbn: part of the SIR2017_5155.shp shapefile SIR2017_5155.shp.xml: part of the SIR2017_5155.shp shapefile model/ Description: ----------- This directory contains all of the input files for the model simulations and particle-tracking analysis documented in the report, https://doi.org/10.3133/SIR20175155 Files: ----- None steadystate1_ForInitHds/ Description: ----------- This directory contains the name file and all of the input files used to run a steady-state simulation documented in the report. This simulation: -represents conditions prior to oil and gas development and mining activities. -represents hydraulic parameters and stresses that minimized the least-sum-of-squares objective function for 14 measured or inferred groundwater elevations. -was calibrated for hydraulic conductivity parameters and for recharge and evapotranspirational stresses. Details can be found in the associated Scientific Investigation Report https://doi.org/10.3133/sir2017-5155. Files: ----- ss1.bas - MODFLOW 2005 basic package input file. The Basic package is used to specify data including locations of active, inactive, and specified head cells; the head stored in inactive cells; and the initial heads in all cells. ss1.dis - MODFLOW discretization input file. The Discret- ization file is used to specify data including the number of rows, columns, and layers; cell sizes; and time discretization. ss1.evt - MODFLOW evapotranspiration package input file. The Evapotranspiration package is used to simulate a head-dependent flux out of the model distributed over the top of the model. ss1.ghb - MODFLOW general head boundary package input file. The General-Head Boundary package is used to simulate head-dependent flux boundaries. ss1.hob - MODFLOW hydrologic observations input file. The Head-Observation input file is used to specify observations of head for use in the observation process. ss1.nwt - MODFLOW Newton solver input file. The Newton solver files specifies parameters to be used to solve the finite-difference equations in each step of a MODFLOW-NWT stress period. ss1.oc - MODFLOW output control input file. The Output Control Option is used to specify which head, drawdown, or budget data should be printed or saved. ss1.rch - MODFLOW recharge package input file. The Recharge package is used to simulate a specified flux distributed over the top of the model. ss1.sfr - MODFLOW streamflow routing package input file. The Streamflow-Routing package is used to simulate streams in a model. ss1.upw - MODFLOW upstream weighting package input file. The Upstream Weighting package is used to specify properties controlling flow between cells in MODFLOW-NWT. ss1.zone - MODFLOW zone definition input file. The Zone File is used to specify zone arrays which can be used to specify the cells in a layer variable that are associated with a parameter. ss1_ini_for_dd1.nam - MODFLOW name input file for this steady-state simulation. The Name file specifies the names of the input and output files, associates each file name with a fortran unit number and identifies the packages that will be used in the model. usgs.model.reference - file containing data needed to register the model in space and time. transientdd1/ Description: ----------- This directory contains the name file and all of the input files used to run the first transient simulation documented in the report. This simulation produces trdd1.hds--potentiometric results for all 45 stress periods. This simulation: - incorporates transient drawdown from local and regional dewatering and includes ini_for_dd1.hds generated by the steadystate1_ForInitHds simulation. - is entitled "transient" but the first stress period is steady- state with an assumed length of 1 year, and the following 44 stress periods are transient with lengths of 1 year each. The first stress period is run to steady-state to improve the representation of drawdown imposed by long-term regional de- watering for oil and gas development, i.e., dewatering for oil and gas is simulated with the well package during stress period 1 at half the rate of the 2nd through 45th stress periods. - represents grid alterations to represent changes to the Shumway Arroyo during the early years of mining, necessarily imposed for all stress periods. - represents process pond recharge for 3 grid cells is included in the 1st through 45th stress periods. -represents dewatering for surface mining from 1973 through 2000, a hiatus from mine dewatering during 2001, dewatering for underground mining from 2002 through 2016 (excluding 2012), and ongoing regional dewatering for oil and gas extraction during all transient stress periods. -transientdd1 model grid differs from the steadystate1 model grid for grid cells representing changes to Shumway Arroyo as follows: associated changes are made to dis, upw, rch, and etv input files. Details can be found in the associated Scientific Investigation Report https://doi.org/10.3133/sir2017-5155. Files: ----- See steadystate1_ForInitHds for full file descriptions. trdd1.nam: MODFLOW name file that contains input and output files for the simulation trdd1.oc: MODFLOW output control input file transientdd1_ForInitHds/ Description: ----------- This directory contains the name file and all of the input files used to run the first transient simulation which produces ini_for_dd2.hds--the initial conditions needed for the 2nd transient drawdown model. Files: ----- trdd1_ini_for_dd2.nam: MODFLOW name file that contains input and output files for the simulation trdd1_for_dd2_inihds.oc: MODFLOW output control input file used to output an initial heads file for the transientdd2 simulation. usgs.model.reference: File to register model in time and space transientdd2/ Description: ----------- This directory contains the name file and all of the input files used to run the second transient simulation documented in the report. This is the 4th simulation to be run which produces trdd2.hds--potentiometric results for all 18 stress periods. This simulation: -requires ini_for_dd2.hds input -represents a model grid that differs from the trandientdd1 grid as follows: model grid cells that represent surface-mined and some underground-mined areas have been assigned revised hydraulic conductivity parameters representative of mine spoil. -has bottom elevation of Layer 2 cells above Layer 3 cells representing mined coal were raised by 42.75 meters so as to represent Layer 3 conversion to subsided overburden with a total thickness of 47.75 meters. Associated changes are made in the trdd2.dis and trdd2.upw input files to represent these revised conditions. -incorporates the continuation of dewatering of the underground mine and of regional oil and gas dewatering for 18 additional transient stress periods, through the end of underground mining. -includes additional recharge added to 3 grid cells to represent pond leakage is continued throughout this simulation. Details can be found in the associated Scientific Investigation Report https://doi.org/10.3133/sir2017-5155. Files: ----- See steadystate1_ForInitHds for full file description. trdd2.nam: MODFLOW name file that contains input and output files for the simulation trdd2.oc: MODFLOW output control input file transientdd2_ForInitHds/ Description: ----------- This directory contains the name file and all of the input files used to run the second transient simulation which produces trdd2_recovery_ini.hds, the initial conditions for the groundwater recovery model (both cases) Files: ----- trdd2_for_recovery_inihds.nam: MODFLOW name file that contains input and output files for the simulation trdd2_for_recovery_inihds.oc: MODFLOW output control input file used to output an initial heads file for the two recovery simulations. usgs.model.reference: File to register model in time and space recoveryCase1/ Description: ----------- This directory contains the name file and all of the input files used to run the first recovery simulation documented in the report. This simulation: - applies literature values for mine-spoil hydraulic conductivity and porosity to those grid cells representing mine reclamation and similarly adjusts grid cells representing subsided overburden in layer 3, representing the mined-out coal seam. - includes trdd2_recovery_ini.hds - has a model grid that differs from the transientdd2 grid at grid cells representing some underground-mined areas simulated with the transientdd2 model, including changes to upw. Rch input file is adjusted to remove process pond leakage from 3 cells, under the assumption that mining and power production activities at the generating station have ceased. - applies literature values for storage parameters and porosity estimates variously for mine spoil in the upw input files. Large porosity values are assumed in cells representing the subsided overburden of the underground mine area. - includes grid cells representing the underground mine area that were not changed from the steadystate1 grid configuration. This grid cell configuration was intended to represent columns and long spans of where coal was not mined. - estimates groundwater recovery potentiometric configurations for 20,000 years (500 40-year stress periods) after the cessation of mining. Details can be found in the associated Scientific Investigation Report https://doi.org/10.3133/sir2017-5155. Files: ----- See steadystate1_ForInitHds for full file description. rec1.nam: MODFLOW name file that contains input and output files for the simulation rec1.upw: MODFLOW upstream weighting package input file. The Upstream Weighting package is used to specify properties controlling flow between cells in MODFLOW-NWT. recoveryCase2/ Description: ----------- This directory contains the name file and all of the input files used to run the second recovery simulation documented in the report. This simulation: - second groundwater recovery, where Case 2 applies reduced values for mine-spoil hydraulic conductivity and porosity, with some values foundin the literature review, to assess effects to results of the large fraction of swelling clay reported in mine spoil - inlcudes trdd2_recovery_ini.hds - has a model grid that differs from the transientdd2 grid at grid cells representing some underground-mined areas simulated with the transientdd2 model, including changes to upw. Rch input is adjusted to remove process pond leakage from 3 cells, under the assumption that mining and power production activities at the generating station have ceased. - differ from Case1 only by changes made to storage parameters and porosity estimates for mine spoil in the upw input files. - has grid cells representing the underground mine area that were not changed from the steadystate1 grid configuration. This grid cell configuration was intended to represent columns and long spans of where coal was not mined. - estimates groundwater recovery potentiometric configurations for 20,000 years (500 40-year stress periods) after the cessation of mining. Details can be found in the associated Scientific Investigation Report https://doi.org/10.3133/sir2017-5155. Files: ----- rec2.nam: MODFLOW name file that contains input and output files for the simulation rec2.upw: MODFLOW upstream weighting package input file. The Upstream Weighting package is used to specify properties controlling flow between cells in MODFLOW-NWT. particle_trackCase1/ Description: ----------- This directory contains the name file and all of the input files used to run the particle-tracking analysis using the output from the first recovery simulation documented in the report. Files: ----- MP-case1.dat - MODPATH input file containing names of MODPATH input and output files. MP-case1.rsp - MODPATH response input file. RunModpath.bat - Windows batch file used to run the MODPATH particle-tracking simulation in this folder. case1.dat - MODPATH main data input file. The main data file is used by MODPATH and MODPATH-PLOT to define most of the basic elements of the MODPATH simulation. case1.ptr - MODPATH input file containing initial particle locations. particle_trackCase2/ Description: ----------- This directory contains the name file and all of the input files used to run the particle-tracking analysis using the output from the second recovery simulation documented in the report. Files: ----- MP-case2.dat - MODPATH input file containing names of MODPATH input and output files. MP-case2.rsp - MODPATH response input file. RunModpath.bat - Windows batch file used to run the MODPATH particle-tracking simulation in this folder. case2.dat - MODPATH main data input file. The main data file is used by MODPATH and MODPATH-PLOT to define most of the basic elements of the MODPATH simulation. case2.ptr - MODPATH input file containing initial particle locations. output/ output.steadystate1_ForInitHds/ Description: ----------- This directory contains the output files from the steady-state simulation documented in the report. Files: ----- ini_for_dd1.hds - MODFLOW binary (unformatted) head output file to be used as initial heads for the transientdd1 simulation. This file generated using the ss1_ini_for_dd1.nam name file. HobData.txt - MODFLOW output file with observed and simulated water levels at observation wells. ss1.lst - MODFLOW output file listing the results of the simulation. ss1.cbb - Cel-by-cell flow from simulation. ss1_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.transientdd1/ Description: ----------- This directory contains the output files from the first transient simulation documented in the report. Files: ----- trdd1.hds - MODFLOW binary (unformatted) head output file generated using the trdd1.nam name file. Model heads for all stress periods are included in this file. trdd1.lst - MODFLOW output file listing the results of the simulation. trdd1.cbb - MODFLOW cell-by-cell flows. trdd1_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.transientdd1_ForInitHds/ Description: ----------- This directory contains the output files from the first transient simulation which produces ini_for_dd2.hds--the initial conditions needed for the 2nd transient drawdown model. Files: ----- ini_for_dd2.hds - MODFLOW binary (unformatted) head output file to be used as initial heads for the transientdd2 simulation. This file generated using the trdd1_ini_for_dd2.nam name file. This head file contains only the heads from the last time step of the last stress period of the simulation. trdd1_inihds.lst - MODFLOW output file listing the results of the simulation. trdd_inihds.cbb - MODFLOW cell-by-cell flows. trdd1_inihds_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.transientdd2/ Description: ----------- This directory contains the output files from the second transient simulation documented in the report. Files: ----- trdd2.hds - MODFLOW binary (unformatted) head output file generated using the trdd2.nam name file. Model heads for all stress periods are included in this file. trdd2.lst - MODFLOW output file listing the results of the simulation. trdd2.cbb - MODFLOW cell-by-cell flows. trdd2_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.transientdd2_ForInitHds/ Description: ----------- This directory contains the output files from the second transient simulation which produces trdd2_recovery_ini.hds, the initial conditions for the groundwater recovery model (both cases) Files: ----- trdd2_recovery_ini.hds - MODFLOW binary (unformatted) head output file to be used as initial heads for the recoveryCase1 and recoveryCase2 simulations. This file generated using the trdd2_for_recovery_inihds.nam name file. This head file contains only the heads from the last time step of the last stress period of the simulation. trdd2_inihds.lst - MODFLOW output file listing the results of the simulation. trdd2_inihds.cbb - MODFLOW cell-by-cell flows. trdd2_inihds_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.recoveryCase1/ Description: ----------- This directory contains the output files from the first recovery simulation documented in the report. Files: ----- rec1.cbb - MODFLOW binary (unformatted) output file with cell by cell inflow and outflow data for each stress period of the model simulation. rec1.hds - MODFLOW binary (unformatted) head output file generated using the rec1.nam name file. Model heads for all stress periods are included in this file. rec1.lst - MODFLOW output file listing the results of the simulation. rec1_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.recoveryCase2/ Description: ----------- This directory contains the output files from the second recovery simulation documented in the report. Files: ----- rec2.cbb - MODFLOW binary (unformatted) output file with cell by cell inflow and outflow data for each stress period of the model simulation. rec2.hds - MODFLOW binary (unformatted) head output file generated using the rec2.nam name file. Model heads for all stress periods are included in this file. rec2.lst - MODFLOW output file listing the results of the simulation. rec2_streamflow.dat - MODFLOW output file listing simulated streamflow into or out of modeled stream reaches and into or out of the aquifer. output.particle_trackCase1/ Description: ----------- This directory contains the output files from the particle- tracking analysis using the output from the first recovery simulation documented in the report. Files: ----- case1_endpoint - MODPATH output file with particle endpoint coordinates. case1_pathline - MODPATH output file with the coordinates of particle track lines. case1.cbf - MODPATH binary (unformatted) composite budget output file containing cell by cell flow budgets. summary.pth - MODPATH output listing file showing the results of the MODPATH simulation. output.particle_trackCase2/ Description: ----------- This directory contains the output files from the particle- tracking analysis using the output from the second recovery simulation documented in the report. Files: ----- case2_endpoint - MODPATH output file with particle endpoint coordinates. case2_pathline - MODPATH output file with the coordinates of particle track lines. case2.cbf - MODPATH binary (unformatted) composite budget output file containing cell by cell flow budgets. summary.pth - MODPATH output listing file showing the results of the MODPATH simulation. source/ Description: ----------- This directory contains the source files for the standard code version of MODFLOW-NWT (version 1.0.9) used to run model simulations included in this data release. The source code for MODPATH (version 5) was used for the particle-tracking analysis also is included. Files: ----- None MODFLOW-NWT/ Subfolder containing fortran source files for MODFLOW-NWT. Files in this folder can be compiled into a MODFLOW-NWT executable using a fortran compiler. MODFLOW-NWT documentation is available at: https://water.usgs.gov/ogw/modflow-nwt/. MPATH/ Subfolder containing fortran source files for MODPATH version 5.0. Files in this folder can be compiled into a MODPATH executable using a fortran compiler. Documentation for the current version of MODPATH is available at: https://water.usgs.gov/ogw/modpath/. Documentation for MODPATH 5.0 is available at: https://pubs.er.usgs.gov/publication/ofr94464 and https://pubs.er.usgs.gov/publication/ofr94463.