Download CrunchTope.

Transcription

1 Download CrunchTope

2 Installing: Windows ~7 1. Download zip file and place in user directory. 2. Unzip folder. Should be an executable inside labeled CrunchTope-64bit.exe 3. In order to run the exectuable from any window you need to set the path to your executable: 1. Go to: Control Panel > System>Advanced System Settings (left hand side in windows 6) 2. Then: > Environment Variables (at bottom) > System Variables If this is blocked go to user variables for Whoever 3. Find the path to executable by going to the directory where the executable is set, here in StanfordJoe\CrunchTopeExecutable, then click and right click to copy the full address. 4. Add the full address of the Windows folder AT THE END of PATH (DO NOT DELETE WHAT COMES BEFORE), instead append to the end of the path So, for example you would add the bold red text below: C:\Program Files (x86)\tecplot\tec360\bin;c:\program Files (x86)\intel\composer XE 2011 SP1\redist\ia32\tbb\vc10;C:\Program Files (x86)\intel\composer XE 2011 SP1\redist\intel64\tbb\vc10;C:\Program Files (x86)\intel\composer XE 2011 SP1\redist\intel64\ipp;C:\Program Files (x86)\intel\composer XE 2011 SP1\redist\ia32\ipp;C:\Users\StanfordJoe\CrunchTopeExecutable

3 Installing: Windows ~7 4. Then move to new CrunchFlow directory: $ cd CrunchTope 5. To run the code type name of executable, from the directory containing the input file and database you would like to run: $ CrunchTope (or CrunchTope-64bit.exe) 7. It should prompt you for an input file name. If it does not do this, let us know.

4 Installing: Mac OS X.i 1. Download zip file and place in user directory. The folder and the executable do not need to have the same name. 2. Find downloaded file CrunchTope-Mac and change permissions to executable 3. Open terminal, which can be found in Utilities (bash shell by default) If you need to determine the path to your directory, type pwd into the terminal window:

5 Installing: Mac OS X.i 4. Open your bash file in vi: $ vi.bashrc The file may be blank if you do not have a pre-existing bash file. Type i (you should be able to insert text now) Modify it to read (replace red text with your directory information): CrunchTope_Dir=/Users/katemaher/CrunchTopeMac PATH=$PATH:${CrunchTope_Dir} Make absolutely sure that the $ in PATH=$PATH:$... are correct or you will erase your System Definition of PATH and the OS will only look in CrunchTope_Dir. When done type: esc then : then wq or just zz

6 Installing: Mac OS X.i 5. Now source your bash file in terminal window: $ source.bashrc 6. You will need to re-course the.bashrc each time you open a new terminal. 7. Then move to new CrunchFlow directory: $ cd CrunchTope 7. To run the code type name of executable, from the directory containing the input file and database you would like to run: $ CrunchTope-Mac 8. It should prompt you for an input file name. If it does not do this, let us know. Hit enter and you will return to command line. (Remember to type exit before you close the terminal window.)

7 Code Structure: Input file formats NEVER USE THE TAB KEY, EVER! The input for CrunchFlow is keyword based, so the order in which various input blocks and parameters are specified is unimportant. There are two broad hierarchical divisions of inputs: at the highest level are keyword blocks, which contain a series of keyword parameters. All keyword blocks terminate with END The possible keyword blocks include the following: Example AQUEOUS_KINETICS BOUNDARY_CONDITIONS CONDITION DISCRETIZATION FLOW GASES INITIAL_CONDITIONS ION_EXCHANGE MINERALS OUTPUT POROSITY PRIMARY_SPECIES RUNTIME SECONDARY_SPECIES SURFACE_COMPLEXATION TEMPERATURE TITLE TRANSPORT

8 Code Structure: Database and Results In addition to an input file for every run of CrunchFlow (the name of which is specified by the user), the code will also look for a database file. The default database file is datacom.dbs, a reformatted version of the EQ3/EQ6 database which has been augmented with some surface complexation and ion exchange data, along with sections for both mineral and aqueous kinetics. [see next slides] CrunchFlow will generate an output file with the extension out, preceded by the name specified as the input file name. This file contains the stoichiometric reaction matrix and speciation of geochemical conditions (i.e., initial and boundary conditions). CrunchFlow will also generate additional results files containing information about total concentrations, activities, aqueous and mineral reaction rates, mineral saturation states, etc. all ending in out.

9 Modifying files in Notepad/TextEdit The database may be modified the usual safe practice is to rename the database file for custom applications and to insert this name into the appropriate field in the input file. In modifying and saving input files, it is best not to use such word processing programs as WORD, since these programs tend to produce formatted output that may not be interpreted properly by CrunchFlow. Best is to use NOTEPAD or other similar programs (e.g., TEXTEDIT) as a simple text editor. In Windows XP, one can associate files with the extension.in, for example, with the program NOTEPAD, so that this program is used automatically to open the file in question. It is also customary to associate the standard output files ending in.out or.dat with NOTEPAD. Finally, it is important not to use tabs of any kind in the input file the tabs may not work, since CrunchFlow will be looking for space-delimited inputs and the tabs may or may not be recognized. In addition, the tabs often don t carry over to other computer architectures like LINUX or UNIX.

10 Database format: Open the Database (.dbs): # of and temperatures for log K eq Stuff related to activity coefficient models Primary species listed at top, along with size, charge, and molecular weight. These are the components you can use to define your system

11 Database format: Scrolling down you will find the secondary species Reactions written in terms of basis species Secondary species

12 Minerals gases

13 Mineral kinetics aq. kinetics Unlike thermo, mineral kinetics are not fixed. Must be pulled from literature under relevant conditions. Use any number with caution!!!!

14 Setting up input files: speciation only Runtime section tells the code what you want it to do and how you want it done (solvers, etc.) Specify primary species (secondary in separate keyword block ) Conditions contain specified chemical conditions! means don t read CrunchFlow will skip text with!

15 Setting up input files: speciation only 2

16 Setting up reactive transport problems 1. Establish flow and transport conditions in *.in file 1. Discretization 2. Time (run time and time intervals for printing) 3. Diffusion, dispersion, constant flow or permeability and pressure heads 2. Establish boundary and initial conditions with single component ( tracer ) 3. Run tracer tests on domain, check mass balance, divergence in flow field, etc. 4. Build up chemical system by determining overall reaction network on paper. 5. Add relevant primary species and perform a database sweep to find secondary species, then add these to *.in file. 6. Bring in the reactions one at a time and examine results. If complex flow field, then use a simple 1-D system to diagnose chemical reactions. 7. Even if you know the reaction rates you want to use, start off with slower reaction rates, either by decreasing the surface area of solid phases, or decreasing the rate constant for the aqueous reactions.

17 Y-dir (nx) Ghost cells and Boundary conditions Formatting of VELOCITY fields for crunch X0, Y X0,Y X0,Y X0,Y X1,Y0 X2,Y0 X3,Y0 X4,Y0 X dir (nx) X vel X0,Y1 X1,Y1 X2,Y1 X3,Y1 X4,Y1 X0,Y2 X1,Y2 X2,Y2 X3,Y2 X4,Y2 X0,Y3 X1,Y3 X2,Y3 X3,Y3 X4,Y3 X0,Y4 X1,Y4 X2,Y4 X3,Y4 X4,Y4 Y vel X1,Y0 X2,Y0 X3,Y0 X4,Y0 X1,Y1 X2,Y1 X3,Y1 X4,Y1 X1,Y2 X2,Y2 X3,Y2 X4,Y2 X1,Y3 X2,Y3 X3,Y3 X4,Y3 X1,Y4 X2,Y4 X3,Y4 X4,Y4

18 Y-dir (nx) Ghost cells and Boundary conditions Formatting of PERMEABILITY fields for crunch X1,Y5 X2,Y5 X3,Y5 X4,Y5 X0, Y X5,Y4 X0,Y X5,Y3 X0,Y X5,Y2 X0,Y X5,Y1 X1,Y0 X2,Y0 X3,Y0 X4,Y0 X dir (nx) X vel X0,Y1 X1,Y1 X2,Y1 X3,Y1 X4,Y1 X5,Y1 X0,Y2 X1,Y2 X2,Y2 X3,Y2 X4,Y2 X5,Y2 X0,Y3 X1,Y3 X2,Y3 X3,Y3 X4,Y3 X5,Y3 X0,Y4 X1,Y4 X2,Y4 X3,Y4 X4,Y4 X5,Y4 Y vel X1,Y0 X2,Y0 X3,Y0 X4,Y0 X1,Y1 X2,Y1 X3,Y1 X4,Y1 X1,Y2 X2,Y2 X3,Y2 X4,Y2 X1,Y3 X2,Y3 X3,Y3 X4,Y3 X1,Y4 X2,Y4 X3,Y4 X4,Y4 X1,Y5 X2,Y5 Etc.