-
Notifications
You must be signed in to change notification settings - Fork 1
usgs-coupled/webmod
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
README.TXT Current versions of this file and the software are available at https://doi.org/10.5066/F7P26W9K Water, Energy, and Biogeochemical Model (WEBMOD) This file describes three batch versions of WEBMOD for Windows and Linux: (1) A Windows version with a compiled executable, (2) A Linux version with a compiled executable, and (3) Source code that can be compiled by a Makefile generated by configure or CMake. All distributions contain a compiled Java jar executable that can be used as a graphical user interface to WEBMOD. The interface is a modified version of the MMS Tool which has a feature called the Parameter Tool as described in the following: Markstrom, S.L., and Koczot, K.M., 2008, User’s manual for the object user interface (OUI)—An environmental resource modeling framework: U.S. Geological Survey Open File Report 2008–1120, 39 p. [Also available at http://pubs.usgs.gov/of/2008/1120/.] Input files are all ASCII files that can be edited with a text editor such as Notepad or Notepad++. The Notepad++ interface has the additional advantage of syntax highlighting for PHREEQC input files such as webmod.pqi. Notepad++ is available at http://www.hydrochemistry.eu/downl.html. Alternatively, input for two projects, Andrews Creek and DR2 Drain, are included in the project directories as macro-enabled Microsoft workbooks, Andrews.xlsm and dr2.xlsm, and can be written to ASCII using the included macro ExportText. TABLE OF CONTENTS A. Distribution files B. Documentation C. Installing the Windows batch version of WEBMOD with executable D. Compiling and installing the Windows batch version of WEBMOD without executable E. Compiling and installing the Linux batch version of WEBMOD F. Running WEBMOD G. Description of three projects H. Contacts ----------------------------------------------------------------------------------- A. Distribution files ----------------------------------------------------------------------------------- The following distribution packages of the batch version of WEBMOD are available for Windows and Linux: webmod-@VERSION@-@[email protected] Windows GUI and CLI for running WEBMOD models. 64-bit executable compiled using Microsoft Visual C++ 2012 and Intel Visual Fortran 2013. webmod-@VERSION@-@[email protected] Linux GUI and CLI for running WEBMOD models. 64-bit executable compiled using GNU g++ and gfortran 4.8.4. webmod-@VERSION@-@[email protected] WEBMOD source code. Requires compilation using configure or CMake. ----------------------------------------------------------------------------------- B. Documentation ----------------------------------------------------------------------------------- Citation for the WEBMOD User's Manual: Webb, R.M.T., and Parkhurst, D.L., 2017, Water, Energy, and Biogeochemical Model (WEBMOD), user’s manual, version 1: U.S. Geological Survey Techniques and Methods, book 6, chap. B35, 171 p., https://doi.org/10.3133/tm6B35. The Users Manual will be located in .\Distribution\doc\ tm6b35.pdf Before attempting to simulate chemical reactions in WEBMOD, the chemistry input file webmod.pqi must run successfully in PHREEQC using the database phreeqc_web_lite.dat. Therefore the following citations of PHREEQC will aid the uninitiated: Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples for PHREEQC version 3--A computer program for speciation, batch-reaction, one- dimensional transport, and inverse geochemical calculations: U.S. Geological Survey Techniques and Methods, book 6, chap. A43, 497 p. http://pubs.usgs.gov/tm/06/a43/. Parkhurst, D.L., and Appelo, C.A.J., 1999, User's guide to PHREEQC (Version 2)-- A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations: U.S. Geological Survey Water-Resources Investigations Report 99-4259, 312 p. http://pubs.er.usgs.gov/publication/wri994259. Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface to the geochemical model PHREEQC: U.S. Geological Survey Fact Sheet FS-031-02, 2 p. ----------------------------------------------------------------------------------- C. Installing the Windows batch version of WEBMOD with executable ----------------------------------------------------------------------------------- Installing consists of extracting the distribution from the webmod-@VERSION@-@[email protected] file using 7-Zip or Windows built-in "Extract-All..." tool. The "Extract-All..." tool can be accessed by right-clicking on the zip file. 7-Zip is available at http://www.7-zip.org. The zip file contains a top-level directory (webmod-@VERSION@-@REVISION@-x64) which includes the following subdirectories: bin\ doc\ lib\ projects\ ----------------------------------------------------------------------------------- D. Compiling and installing the Windows batch version of WEBMOD without executable ----------------------------------------------------------------------------------- In general, to compile WEBMOD, you will need: (a) CMake (build process manager) (b) a C++ compiler, (c) a Fortran compiler, (d) familiarity with the compiler and the Windows operating system. D.1. Download and install CMake CMake can be downloaded from http://www.cmake.org/. If you download the executable, CMake is installed when you execute it. D.2. Extract the distribution file webmod-@VERSION@-@[email protected] The directory webmod-@VERSION@-@REVISION@ is created when the files are extracted; if this directory already exists, you may want to delete or rename it before extracting the files. The following directory structure is created (the contents of each directory are shown to the right): webmod-@VERSION@-@REVISION@ Files related to CMake `--config Files used by configure on linux systems `--Distribution Examples from user's guide--limited version of Andrews used in verification test `--doc Documentation files `--IPhreeqcMMS IPhreeqc source code `--lib Java classes for MMS Tool and Parameter Tool GUIs `--m4 m4 source code used by autoconf `--mmf_c MMF source code `--webmod.d WEBMOD Source code `--Tests Files used to test the compilation D.3. Generate a Visual Studio solution CMake has many options other than Visual Studio, but here we assume that you are using some version of Visual Studio. On the first use of CMake, it may be necessary to close all Visual Studio instances. Open CMake. Fill in the top two lines: Where is the source code: The top level directory (ie c:/webmod-@VERSION@-@REVISION@). Where to build the binaries: A new directory. It is suggested that the name of the directory include the characteristics of the library that is built, including the VS version, and 32/64 bit, such as VS2012_x64. Click Configure. From the pulldown menu of the cmake-gui popup, select the 64-bit version for your Visual Studio. Normally, the default radio button should be sufficient. Click Finish. Options in the top panel: (1) CMAKE_INSTALL_PREFIX--Sets the the install directory where the compiled program and example input files will be saved. It is suggested that an INSTALL directory be defined inside the directory chosen for the binaries. Click Configure until the screen is not red. If the screen remains red, you will have to deal with the CMake error messages. Click Generate. You should now have a Visual Studio solution file (.sln) in the directory chosen for the binaries (second line of CMake screen). At any point, you can delete the contents of the directory and start over. You can make solutions for different Visual Studios, or different options in other directories. D.4. Compile and install WEBMOD Open the Visual Studio solution in the build directory defined in CMake. The default configuration is "Debug". If you want a release version change the configuration to "Release". Build ALL_BUILD. IPhreeqc is compiled. mmf is compiled. webmod is compiled. all modules and libraries are linked and webmod executable created. Build RUN_TESTS. Programs that test webmod are compiled and run. Build INSTALL. The executables, WEBMOD database files, and documentation are installed in the install directory selected in CMake (denoted "install" in the following descriptions). Install: README.txt this readme file NOTICE.txt User rights notice Install\bin directory: Subdirectories with executables Install\lib files: Java archive files used to run the GUI Install\doc files: Manual for WEBMOD version 1 Install\projects directory: Example input files from the user's manual ----------------------------------------------------------------------------------- E. Compiling and installing the Linux batch version of WEBMOD ----------------------------------------------------------------------------------- No support beyond this README file is provided for users compiling their own versions of the software. In general, to compile the software, you will need: (a) a C++ compiler, and (b) a Fortran compiler, and (c) a minimal level of knowledge of configure, Make, the compiler, and the Linux operating system. A Makefile can be generated by configure, and the Makefile can be used to compile, test, and install the software. E.1. Extracting the files Follow the steps below to extract the files from a distribution tar file. Steps in extracting files Explanation ---------------------------------------- ----------------------------------- gunzip webmod-@VERSION@-@[email protected] Uncompress the tar.gz file. tar -xvpof webmod-@VERSION@-@[email protected] Extract files from the tar file. The directory webmod-@VERSION@-@REVISION@ is created when the files are extracted; if this directory already exists, you may want to delete or rename it before extracting the files. The following directory structure is created (the contents of each directory are shown to the right): webmod-@VERSION@-@REVISION@ Files related to configure `--config More configure files `--Distribution Examples from user's guide--limited version of Andrews used in verification test `--doc Documentation files `--IPhreeqcMMS IPhreeqc source code `--m4 m4 source code used by autoconf `--mmf_c MMF source code `--webmod.d WEBMOD Source code `--Tests Files used to test the compilation Notes: (a) A compiled executable is not included in the source distribution. (b) It is recommended that no user files be kept in the WEBMOD directory structure. E.2. Change directory to the directory that was extracted from the tar file. cd webmod-@VERSION@-@REVISION@ E.3. Make a directory, for example, Release. mkdir Release E.4. Change directory to Release. cd Release E.5. Run configure Many of the options for configure can be seen by typing: ../configure --help The most common option: --prefix=dir specifies the directory for installation of the library. Default is /usr/local, $HOME would install to your home directory. Run configure as follows: ../configure [options] E.6. Compile the program make [-j n] Optionally, use -j n--where n is the number of compilations make runs in parallel. E.7. Check that compiled version runs the test cases. Check may take several minutes. make check Results of running the test cases are stored in the directory Release/test E.8. Install the program. By default the program is installed in /usr/local/bin and /usr/local/share/doc/webmod. You can specify an installation prefix other than "/usr/local" by using the prefix option, --prefix=$HOME for example. make install The locations of various files are given below, where "install" is the installation directory, /usr/local by default, or the value given by the --prefix option to configure. Executable: install/bin/webmod Documentation: install/share/doc/webmod tm6b35.pdf Manual for WEBMOD version 1.0 README.TXT this readme file Three project directories: install/share/doc/webmod/projects Input files for 3 examples documented in the manual ----------------------------------------------------------------------------------- F. Running WEBMOD ----------------------------------------------------------------------------------- The WEBMOD executable is installed in the .\bin\ directory. if .\bin\ is in the PATH, then WEBMOD can be executed in a command window from a selected .\projects directory such as .\projects\Andrews\ with the following command webmod -C.\control\webmod.control The WEBMOD simulation will then be run using inputs and outputs specified in the control file .\projects\Andrews\control\webmod.control Alternatively, WEBMOD can be run by a script on Linux (*.sh) or a batch file on Windows (*.bat). The scripts and batch files are run in the selected \projects\ directory. ie. .\projects\Andrews. command explanation ----------------------------- ----------------------------------------- webmod.bat or Prints model self-documentation to \control\ webmod.sh directory then runs WEBMOD simulation as instructed in \control\webmod.control. webmod_gui.bat or Prints model self-documentation to \control\ webmod_gui.sh directory then begins an interactive session of WEBMOD simulation using the MMS Tool GUI. webmod.paramtool.bat or Prints model self-documentation to \control\ webmod.paramtool.sh directory then begins an interactive session to review and modify WEBMOD parameters using the Param Tool GUI. webmod_print.bat or Prints self-documentation files in \control\ webmod_print.sh directory ----------------------------------------------------------------------------------- G. Description of .\projects\ ----------------------------------------------------------------------------------- Three projects are included with the Distribution. Andrews, DR2, and Andrews_tutorial. As described in WEBMOD manual. Andrews\ simulates hydrology and geochemisty for the Andrews Creek watershed in Rocky Mountain National Park in Colorado. Input chemistry varies as described by biweekly sampling by the National Atmospheric Deposition Program. DR2\ simulates hydrology and specific conductivity using chloride as a proxy for specific conductivity. Precipitation, canal irrigation, and upgradient groundwater are all assigned constant concentrations as described in .\input\webmod.pqi Andrews_tutorial\ The project Andrews_tutorial is a deliberately miscalibrated version of Andrews. As detailed in the User’s Manual in the section “Quick Start Guide > Andrews Creek simulation and calibration”, the user is instructed to modify two hydrologic parameters in Andrews_tutorial\input\webmod.params, rain_adj and snow_adj, to better match observed streamflow, turn on geochemical simulations(chem_sim=1), then modify the surface to volume ratios in Andrews_tutorial\input\webmod.pqi that determines the weathering rate of of oligoclase. Upon completion of the 45 steps, the output files in Andrews_tutorial\output\ will be identical to those in Andrew\output\ after execution of the WEBMOD simulation in that project directory. ----------------------------------------------------------------------------------- H. Contacts ----------------------------------------------------------------------------------- Inquiries about this software distribution should be directed to: e-mail: [email protected] or [email protected]
About
No description, website, or topics provided.
Resources
Stars
Watchers
Forks
Packages 0
No packages published