Chapter 2 Getting Started
Contents
1. 13 4 Modify the the water level amplitude from 0 8 to 1 0 m 2 4 MODIFYING MODEL SETUP 45 ud2obu_amp 14 00714 0 000000 zetobu_amp 1 000000 0 000000 Note that the amplitude of the depth integrated velocity is proportional to the water level amplitude in the river test case and needs therefore be divided by 0 8 5 Save the file under the new name riverTnew 2uvobcl1A 6 Run the model with the new boundary definitions Run 2 4 2 Adapting model set up via the Usrdef_ files We are now going to repeate the model setup changes by adapting the FOR TRAN code in the Usrdef_ files 2 4 2 1 installing and running the example test We re install compile and run the tutorial version of river test again now without making use of the CIF The steps are similar to ones shown in the previous section but repeated here for clarity 1 Select a working directory e g cd home coherens rivertest 2 Create a link with the COHERENS root directory a path name can be defined instead of V2 5 e g In s V2 5 COHERENS 3 Install the tutorial version of the river test case COHERENS install_test t tutorial river 4 Adapt your settings by changing coherensflags cmp 5 Compile e g for Intel Fortran make linux iforts 6 Run the test case Run 46 CHAPTER 2 GETTING STARTED 2 4 2 2 changing model setup through the Usrdef_ files The modifications in the model setup discussed with the CIF method in the previous section can equa2. 4 MODIFYING MODEL SETUP 35 editing the Usrdef FORTRAN files The two methods are described in the subsections below 2 4 1 Modifying model setup via CIF 2 4 1 1 short CIF introduction The central input file CIF is a functionality introduced in COHERENS V2 1 aimed to define or re define parameters for model setup without having to do a recompilation More information on the format of the CIF file can be found in the User Documentation In addition all forcing data can be provided in a standard COHERENS format These formats can be read by the program without the need to change the model setup code and recompile the program in the Usrdef files 2 4 1 2 tutorial river test case The following procedure needs to be used to install the tutorial version of the river test case 1 Select a working directory e g cd home coherens riverCIF 2 Create a link with the COHERENS root directory a path name can be defined instead of V2 5 e g ln s V2 5 COHERENS 3 Install the tutorial version of the river test case COHERENS install_test t tutorial river 4 Adapt your settings by changing coherensflags cmp 5 Compile e g for Intel Fortran make linux iforts The following procedure is recommended to run the river test case with the CIF functionality 1 Open the file defruns 36 CHAPTER 2 GETTING STARTED riverOT riveriT which shows that no CIF will be read or produced Run the test case Run T
3. IDL or Matlab as long as they can read the netCDF format Some other external libraries which you can use with COHERENS such as MPI will not be used in this introduction The used software and libraries can be found at e MPI nttp www ncs anl gov research projects apich2 netCDF hnttp aww unidata ucar edu software netcd NcView Ferret Octave 2 1 2 Short Linux introduction This section will make you familiar with working under Linux If you are already familiar with Linux you can skip this section without problem The first thing to do is to open a terminal in which we can execute the commands we need Before we continue there are three important things to know when working on the Linux command line 1 Linux commands and file names are case sensitive Thus Run is not the same as run 2 Linux can help you finish commands especially file names and directo ries when you press on the tab key Try using this as often as possible 3 In Linux files and folders are separated by a forward slash not a backslash that is used in Windows Using the wrong slash can give very unexpected results The following commands are very useful when working with Linux 2 1 INTRODUCTION 17 2 1 2 1 getting help If you do not know which command to use use apropos It will tell you which commands to use For example if you want to know how to copy a file type apropos copy This gives you many results in
4. e Change the number of cells X001 280 e Change the bathymetry by copying all values 20 after depmean glb such that are now 280 numbers depmeanglb 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 e Change the grid index location of the open boundary to make it compliant with the new grid iobu 1 281 e Convert the text file back to a netCDF file using ncgen look up how it works using man ncgen ncgen b riverTmodgrd txt o riverTnew modgrdN 8 The new grid file can also be created alternatively through the CIF 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 2
5. the run Define grid IOPT_GRID_NODIM 3 50 CHAPTER 2 GETTING STARTED Use open boundary conditions IOPT_OBC_2D 1 Switching on simulation of baroclinic currents IOPT_DENS 1 IOPT_DENS_GRAD 1 Calculate salinity IOPT_SAL 2 Turbulence switch for limiting conditions IOPT_TURB_IWLIM 1 Set up model grid Note that you always define an extra dummy cell on the edges NC 141 NR 2 NZ 20 Define number of sea boundary conditions NOSBU 2 NOSBV 0 Define number of river boundary conditions NRVBU 0 NRVBV 0 Define number of tidal constituents at the boundary NCONOBC 1 Define type of constituent S2 51 INDEX_OBC 51 Set start and endtime amd Time step CSTARTDATETIME 2003 01 03 00 00 00 000 CENDDATETIME 2003 01 06 00 00 00 000 DELT2D 30 IC3D 10 Select constant water depth DEPMEAN_CST 20 2 5 FORMAT AND SPECIFIC SYNTAX OF A CIF 5l Accelaration of gravity GACC_REF 9 81 Bottom friction coefficient ZROUGH_CST 0 6E 02 Define restart files NORESTARTS 0 define runtitle INTITLE riverT OUTTITLE riverT Define number of outputs for time series NOSETSTSR 1 NOVARSTSR 6 Model files LCR RRR IRR k k k kk kk GK kkk kkk kk The format is file descriptor file number input 1 output 2 format A ascii N netcdf U binary status R read W write N usrdef filename tlimi tlim2 tlim3 endfile info time_regular pat
6. to the erroneous value of 4 in routine usrdef_mod_params preferentially in section Switches within the file Usrdef_Model f90 SUBROUTINE usrdef_mod_params lopt_grid_nodim 4 END SUBROUTINE usrdef_mod_params 9 Compile and run The same error message as in the CIF example is issued Form of the output file The instructions for modifying the format of an output file are as follows 1 Edit the file Usrdef_Time_Series f90 gedit Usrdef_Time_Series f 90 2 Change the output format by adding the two lines 48 CHAPTER 2 GETTING STARTED SUBROUTINE usrdef_tsr_params tsr2d 1 form 7A tsr2d 2 filename riverT txt END SUBROUTINE usrdef_tsr_params in routine usrdef_tsr_params The second line changes the name of the output file as well 3 Compile and run Grid resolution Halving the grid size in the X direction is easily per formed by modifying the following lines in Usrdef_Model f90 SUBROUTINE usrdef_mod_params nc 281 nr 2 nz 20 500 0 500 0 surfacegrids igrd_model 1 delxdat surfacegrids igrd_model 1 delydat END SUBROUTINE usrdef_mod_params Contrary to the CIF case the output grid the grid index of the open boun dary locations and the bathymetry are automatically adapted by the code to the new grid Modification of open boundaries The upstream open boundary con dition is reset from the characteristic 11 to the Flather 8 method and the tidal amplitude of the water level is
7. version executes much faster up to 5 times faster Therefore for real simulations one should always use this optimization If you are using the gfortran compiler you can switch of the optimization by setting take care with the difference between the capital O and the number 0 FCOPTS 00 For the Intel Fortran compiler you can disable the optimization by setting FCDEBUG 00 In order to compile the code close gedit and type for gfortran make linux gfort In order to compile the model using the Intel Compiler type 22 CHAPTER 2 GETTING STARTED make linux iforts This command will print some information on the screen mainly showing which files were compiled It may also show some warnings or errors In case the compilation was successful the last output line should be something like make 1 Leaving directory home coherens rivertest The compilation generated many additional files Use the command 1s in order to examine the files that are present in the working directory We are now ready to run the simulation 2 2 3 Running COHERENS In COHERENS the different runs that are done during a simulation are de fined in the file defruns which is located in the working directory Open this file in gedit in order to examine the runs that are being performed gedit defruns In this file all the runs are defined with the following syntax Run name CIF options CIF file name Note that the last two inputs CIF o
8. 0 20 20 20 20 20 20 20 20 20 20 20 20 20 20 AN ASN NA NA NA NA 44 CHAPTER 2 GETTING STARTED e Edit the defruns file and disable the second run river0OT R riverOT CifModA river1T R riveriT CifModA e In riverOT CifModA change the line MODFILES modgrd 1 1 N R riverT modgrdN 0 0 0 0 F F into MODFILES modgrd 1 1 N W riverTnew modgrdN 0 0 0 0 F F e Run the test case and replace the W again to R on the same line in the riverOT CifModA The new grid file has now been generated automatically 9 Run the model now with the new grid resolution Run Note that for this exercise it is necessary to run both simulations riverOT and river1 T because the initial conditions that are generated in run riverOT are changed with the new grid resolution and need to be provided for river1 T Modification of open boundaries This exercise is focused on the modifi cation of the definitions of the open boundaries by editing the open boundary file The instructions are given below 1 Edit both CIFs files in order to use a new file with boundary conditions MODFILES 2uvobc 1 1 A R riverTnew 2uvobc1A 0 0 0 0 F F 2 Open and edit the riverT 2uvobc1A file generated previously which contains the open boundaries in COHERENS ASCII format gedit riverT 2uvobciA 3 Modify the type of the upstream open boundary condition from the characteristic method 11 to the method of Flather 8 ityp2dobu 8
9. 00 into CENDDATETIME 2003 01 04 00 00 00 000 The previous re setting can also be made by inserting the comment character in the first column of the line with the old definition CENDDATETIME 2003 01 06 00 00 00 000 CENDDATETIME 2003 01 04 00 00 00 000 3 Run the model with the new simulation time Run Note that the time steps for the output data are adapted automatically This is seen by opening the warlog file gedit riveriT warlogA This will show a warning that the last time step for output is equal to the last time step in the model However if you would have increased the calculation time you would have had to adapt the number of time steps that is outputted manually 38 CHAPTER 2 GETTING STARTED WARNING value of integer component tlims 2 and element 1 of array tsrgpars is set from 8640 to 2880 Check in the output data that you now have indeed only one day of output data You can do this easily using ncdump by typing use man ncdump to look up what v means ncdump v time riverT_1 tsout2N less Modification of the time step This exercise is focused on the modifi cation of the time step by editing the CIF file the instructions are given below 1 Open and edit the CIF gedit river1T CifModA 2 Set the 2 D time step to 15 seconds COHERENS also has a 3 D time step for barotropic calculations which is given as the number of 2 D time steps that pass before a 3 D step is done This is given by th
10. Chapter 2 Getting Started 2 1 Introduction In this tutorial manual an introduction is given how to work with COHE RENS We present two COHERENS test cases river and bohai and show how to compile the code run the test case view the results with various free software visiualisation tools and show how model setup is arranged and can be modified The objective of this chapter is to give a first introduction to COHERENS for a beginning user A more extended description with more technical de tails about installation and compilation of the code are found in the User Documentation 2 1 1 General requirements We will make the following assumptions on your system and the installation of COHERENS e You use COHERENS V2 4 or higher Older versions of COHERENS have a slightly different syntax e You have managed to install COHERENS correctly and to set the com piler options correctly in compilers cmp see below e You have a working installation of netCDF on your computer or work station Note that if you install a compiler you have to do this before you install netCDF Otherwise the netCDF installation will not generate the correct binary files for your compiler 15 16 CHAPTER 2 GETTING STARTED e You have some software for doing post processing In this manual we will use the free software packages NcView Ferret and Octave However it is very well possible to use other free or commercial post processing software such as
11. View you always must give the filename of the data that is plotted in the command to start the graphical user interface An example of the user interface in NcView is given in Figure 2 1 The first thing to do when working with NcView is selecting the variable to plot This can be done by clicking on the name of the variable you want to select We start by plotting the sea surface elevation In order to do so click on the button with zeta which is the name used on COHERENS for the sea surface elevation In order to get more information on a variable click on the button with the question mark You should now see a plot of the sea surface elevation as function of the x location on the x axis and time on the y axis We can change this by clicking on the Axes button If you do so a dialog box will appear that lets you select the axes to plot In this case there are only two possible options the time and the x dimension Hence it is not necessary to change the axes Close the dialog box by clicking on cancel To make the plot larger click on the button that says M xn where n is the magnification scale As you can see the image is magnified and the name of this button is changed to the new magnification Press this button again to make the plot even larger When can change the colors in the graph by clicking the leftmost button its name is one of the color maps probably 3gauss Click this button and see how the colors change Try out the d
12. and contours together we must add the overlay option vector overlay uvel t 20 wphys t 20 Once again we can plot time series or profiles but now we need to provide two axis locations between brackets plot sal z 1 t 20 Finally we make an animation using the repeat statement of the first 50 time steps For the animation of the salinity contours type repeat t 1 50 animate loop 1 contour sal For the animation of the flow vectors type repeat t 1 50 animate loop 1 vector uvel wphys 2 3 3 visualising with Octave and Matlab Now we are going to run a second test case which is called bohai This test case is a simulation of the tides in the Bohai Sea northern part of the Yellow Sea see Figure 2 3 The commands are the same as for the previous river test Take care of the following 32 CHAPTER 2 GETTING STARTED CHINA nutes tere NORTH Berns es EA Den engte Tone Korea oP yorurere a Bona i Bay everee on Sea ae an dl s i Leros tan 3 cans wee Figure 2 3 Map of the Bohai sea e Edit the defruns file by commenting all lines i e inserting a in the first column except the first one such that only the first run is made The name of this run is bohatA Note that contrary to the river there is no spin up run e The date of the simulation which you need to check the advance of the calculations is in the year 1999 look this up in the file Usr def_Model f90 Note that running thi
13. arrays xout yout and the elevation data zeta In Matlab R2008a and higher you can load variables from the netCDF file using the ncread function locallat ncread bohaiA_1 1amp1t2N xout locallon ncread bohaiA_1 1amp1t2N yout localzeta ncread bohaiA_1 1amp1t2N zeta To let your graphs appear in a workable screen format set the display to the correct environment only for Octave setenv GNUTERM wxt Now you can make your first graph zetafig localzeta 1 contourf localxout localyout zetafig Add a colorbar by typing colorbar Put a title and axis legends title M2 amplitude fontsize 20 fontname Arial_black xlabel longitude fontsize 12 fontname Arial ylabel latitude fontsize 12 fontname Arial 34 CHAPTER 2 GETTING STARTED M2 amplitude 41 40 5 H m N oO latitude S oO D 38 5 oO gt 37 5 118 119 120 121 122 123 124 125 longitude Figure 2 4 Example figure generated with Octave 9 To export the file print dpng bohai_M2amp png The result is shown in Figure 10 To improve pixel size print dpng S800 800 bohai_M2amp png 11 For more information on atopic type help topic for example help print 2 4 Modifying model setup Two methods are available to adapt the model settings In the first one the model parameters are changed in the CIF The second one consists in 2
14. at the test runs with half the current grid size Firstly change the number of columns of the compu tational grid from nc 141 to nc 281 NC 281 NR 2 Secondly change the grid size from 1000 to 500 m Change the fifth and sixth fields in the line SURFACEGRIDS 1 1 0 0 1000 1000 0 0 in both CIFs to SURFACEGRIDS 1 1 0 0 500 500 0 0 Use a new file to called riverT new modgrdN for the bathymetry We will generate this file in a moment MODFILES modgrd 1 1 N R riverTnew modgrdN 0 0 0 0 F F Also change the eleventh field for the time series output grid parameter TSRGPARS in river1T CifModA only from 140 to 280 TSRGPARS 1 7 F F 1 2003 01703 00 00 007000 3 0 0 1 280 1 1 1 1 1 20 Now save the files We will continue by making a new bathymetry file Generate the new bathymetry file Convert the COHERENS netCDFfile an ASCII text file that can easily be edited using ncdump ncdump riverT modgrdN gt riverTmodgrd txt 4The actual number of active in the X direction is given by nc 1 Halving the grid size means then that nc is reset to 2 nc 1 1 281 2 4 MODIFYING MODEL SETUP 43 In this command the gt sign is used to send output from one program in this case ncdump to a file riverT modgrd txt Edit the river Tmod grd txt file generated for a new grid resolution gedit riverTmodgrd txt The changes that you have to make are e Change the file name netcdf riverTnew
15. b In order to visualize the data we must first start Ferret by typing ferret Now we are inside Ferret We can see this because the command prompt has changed in yes The first thing to do is load the data with the use command Type use riverA_1 tsout2N This will load the file riverT_1 tsout2N with the two dimensional data Now we inspect the variables that are in that file by typing show data You should now see a list with the variables that were saved in the file riverA_1 tsout2N We can make contour plots of these data x and time axis by typing contour zeta contour umvel We can also make a graph of the velocity at one location or at one moment in time by typing respectively plot umvel x 50 plot umvel t 200 In this command the part between the square brackets is used to tell Ferret which data has to be plotted It is also possible to plot various of these data together by typing 30 CHAPTER 2 GETTING STARTED plot umvel x 50 zeta x 50 plot umvel x 50 umvel x 100 Saving files is somewhat cumbersome in Ferret The first thing you need to do is tell Ferret to save every graph it makes as a meta file which is special a text file containing the data of the plot You can do this by typing set mode metafile Now make the same contour plots as you did before When you do not want to plot any more files you can type cancel mode metafile Now close Ferret by typing exit The metafiles that are mad
16. ber stations start x end x stepx start y end y step y start z end z step z start time end time timestep note that the end time may have to change if you change the time step or time interval of the simulation TSRGPARS 1 T F F T 2003 01 03 00 00 00 000 3 0 0 1 140 1 1 1 1 1 20 1 0 8640 180 2 5 FORMAT AND SPECIFIC SYNTAX OF A CIF 53 Vk ak ak 2K gt K OK OK OK KK FK K FK FK 2K K K FK FK FK K KK FK KK K 2K 2K K FK 2K 2K OK OK Do not remove the above Parameters for time averaged output L akk ak OK OK 2K gt K KO 2K K FK FK KK K FK 2K FK K KK FK KK FK FK 2K K FK 2K 2K OK OK Do not remove the above Parameters for harmonic analysis T akk ak akk OK OK OK FK FK 2 KK K KK FK KK FK 2K K FK 2K 2K OK OK Do not remove the above l Parameters for harmonic output 54 CHAPTER 2 GETTING STARTED
17. cluding the one you need which is cp In order to understand how to use this command use man Type man cp 2 1 2 2 working with files To see which files are in a directory use 1s or 1s 1f The latter gives more information Try them both ls ls 1 Aliases for some commands may be defined on your computer A common alias is 11 which is the same as 1s 1 The command for copying a file is cp sourcefile destination The command for moving a file mv sourcefile destination The command for deleting a file is rm filetodelete In case you want to use any of these commands on directories you must add r rm r directorytodelete In order to know how much free space there is on the hard disk type df h Finally it is important to know that you can use the symbol to send out put from one program to another program For example you can use the command less to view the output of the previous command df h less Exit less by typing the letter q Tnote that 1 is the letter 1 and not the number 1 18 CHAPTER 2 GETTING STARTED 2 2 Running a test case 2 2 1 Installing a COHERENS test case First you will need to go to the directory where the COHERENS source files are installed We will assume here that we have them installed on the directory V2 5 where stands for your home directory When installing a COHERENS test case such as the river test we always start by making a new folder in which the results are p
18. e variable IC3D In order to leave the 3 D time step unchanged we modify this value as well by changing DELT2D 30 IC3D 10 into DELT2D 15 IC3D 20 3 Run the model with the new time step Run Visualize the results 2 4 MODIFYING MODEL SETUP 39 Checking of errors in the CIF This exercise we will make some errors in the CIF file such that an error message is generated by COHERENS In this way you learn to find the error messages and solve them 1 Open and edit the CIF gedit river1iT CIF 2 Create an error in the CIF by re editing the line IOPT_GRID_NODIM 3 to IOPT_GRID_NODIM 3 Save the file and run the model Run An error message will be generated in the river1T errlogA file Open this file and verify the error message It will look like this Error occurred on line 29 of CIF file river1iT CifModA Variable name is not defined A total of 1 errors occurred in read_cif_params Error type 7 Invalid initial values for model parameters or arrays PROGRAM TERMINATED ABNORMALLY This message tells you that the syntax in the CIF is not correct Now we try to correct this message but make another mistake Edit the CIF and type IOPT_GRID_NODIM 4 This is obviously an error because the maximum number of dimensions in COHERENS is 3 When you inspect the file river T errlogA you will see the following Invalid value for integer parameter iopt_grid_nodim 4 Must be between 1 and 3 A total of 1
19. e by Ferret are text files with the name metafile plt nr in which nr is the number of the file In order to transform them to graphical files which you can use in reports you have to use the command Fprint Fprint o outputfile0O ps p portrait metafile plt Fprint o outputfileOl ps p portrait metafile plt 017 Note that we used an asterisk in this command because Fprint changes the filename every time it is invoked Note that Fprint prints to a file so in order to use it a default printer must be selected Open Ferret again to visualize the three dimensional data ferret We first load the three dimensional datafile and see which data it contains use riverA_1 tsout3N show data In this file we can make a vector plot of the velocity field at time step 20 using an example is given in Figure vector uvel t 20 wphys t 20 We can also make a contour plot of the salinity at this moment in time contour sal t 20 2 3 POST PROCESSING THE RESULTS 31 ludunits 3 Couldn t open units database hone pierce 1ib udunits1 ete udua Note Udunits units file not found no units conversion will be attep i FERRET 1 21 Apr 11 10 09 put path of units file in environmental variable UDUNITS PATH Note no Ncview app defaults fite found using internat defaults calculating min and maxes for uvet vit calculating min and maxes for vvet Tit DATA SET riverA_1 tsout3N calculating min and maxes for vv
20. e command top Type top This will show a list of the processes that are occurring on the computer and how much processor time they are using You can close this program by typing the letter q from quit We can also examine how far the run has advanced using the command grep which searches a text file for the occurrence of a word given by the user We apply it here to the runlog file which is a text file COHERENS produces and in which the time step is written We can search for these time steps in the file and then send it to another program called tail which returns only the last lines of data For sending information from one program to the next this is called a pipe we use the vertical line Thus in order to find the last occurrence of the string 2003 the calculations in this file have a start date and end date in 2003 in the runlog file we use the command grep 2003 riverOA runlogA tail 1 You can also use this command without tail in order to get all occurrences of the string 2003 grep 2003 riverOA runlogA After the model has finished something like this will be written to the terminal Main program terminated real 0m19 678s user 0m18 490s sys Om1 154s 24 CHAPTER 2 GETTING STARTED Let s have a look at the files that are generated by COHERENS All these files have a name that is generated from the name of the run defined in the file defruns ls river This should give the following resu
21. errors occurred in check_mod_filepars Error type 7 Invalid initial values for model parameters or arrays PROGRAM TERMINATED ABNORMALLY Here COHERENS tells you that the number of grid dimensions should be between 1 and 3 and thus the value of 4 is not allowed Try to perform additional changes in the CIF file to generate some other error messages Fix the errors and move on to the next exercise 40 CHAPTER 2 GETTING STARTED Form of the output file In this exercise we modify the format of the output file by editing the CIF The instructions are given below 1 Open and edit the CIF gedit river1T CifModA 2 Change the format of the output file from netCDF to ASCII Change the third character of the string TSR2D 1 T N riverT_1 tsout2N T 2 from N to A TSR2D 1 T A riverT_1 tsout2N T 2 3 Run the model with the new output format Run Now you have a new file called riverT_1 tsout2N containing ASCII output data Open the file in gedit to inspect the data 4 Change the current default filename for easy management on the same input line TSR2D 1 T A riverT txt T 2 5 Run the model with the new output filename Run We strongly recommend you to use the netCDF format for your output Therefore undo the changes done during this exercise and continue to the next one 2 4 MODIFYING MODEL SETUP 41 Modification of model settings This exercise is focused on the modifi cation of some settings of the model s
22. et calculating min and maxes for sat X connection to 0 0 broken explicit kitt or server shutdown labr indc abr 3 rivertest ferret NOAA PMEL THAP FERRET v6 7 Linux gfortran 2 6 18 238 1 1 e15 04 04 11 wr 21 Apr 11 10 09 ah yes use rivera 1 tsout3n yes Usit ERROR unknown command Usit oe a yes list ERROR invalid command no data specified yes list vars ERROR variable unknown or not in data set VARS yes show data N currently SET data sets er 1 gt riverA_1 tsout3N defautt name titte I 3 K ll XOUT x coorainate rme ni YOUT Y coordinate me 11 3 zout Z coorainate rme 1 1 20 e4 DEPOUT Mean water depth i140 1 1 5 TIME Tine ZETOUT Surface elevation ie 1 1 ai UVEL X component_of_current i10 1 1 1 20 ai a a WEL Y component_of_current ie 1 1 1 20 WPHYS Physical_vertical velocity 1 140 1 1 1 20 2 E pe SAL Satinity bo 11 1 20 a ot L L yes define grid x xout y yout mygrid 10 30 s 70 90 no 130 yes show grid x Default grid for DEFINE VARIABLE is ABSTRACT Last successful data access was on grid GOEL X component_of_current m s Physical_vertical_velocity m s GRIO GOEL nane axis pts start ena raaa XOIN x mor a 140 YOIM Y leo 1 normal Z normal T yes contour sal yes contour uvel yes vector uvel wphys Using every 4th vector in the X direction yes vector uvel wphys Using every dth vector in the X direction Figure 2 2 Screenshot of using Ferret If we want to plot the vectors
23. etup by editing the CIF in the present exercise we will modify the roughness height the instructions are given be low 1 Open and edit the CIF gedit river1T CifModA 2 Set the roughness to 0 3E 02 m ZROUGH_CST 0 3E 02 3 Run the model with the new roughness Run Visualize the results and see what the effects is of the changed bed roughness You can modify many things in COHERENS including the numerical scheme the turbulence model and many physical parameters Try to modify some other settings by looking them up in the user manual and seeing what they do Interesting settings to change are e The numerical scheme for advection using IOPT_ADV_SCAL lOPT_ADV_2D and IOPT_ADV_3D e Horizontal viscosities using IOPT_HDIV_2D IOPT_HDIV_3D HDIFMOM_CST and HDIFSCAL_CST e Vertical turbulence model using IOPT_VDIF_COEF and the various tur bulence switches IOPT_TURB_ Grid resolution This exercise is focused on the modification of the grid resolution by editing the CIF as well as the input files In this way you get already a first idea how to set up a new model application The instructions are given below 1 Adapt the defruns file in oder to make sure that both simulations are run i e remove the on the first line river0OT R riverOT CifModA river1T R riveriT CifModA 42 CHAPTER 2 GETTING STARTED Open and edit both CIFs gedit riverOT CifModA gedit river1T CifModA We are now resetting the setup so th
24. h Grid input MODFILES modgrd 1 1 N R riverT modgrdN 0 0 0 0 F F Open boundary conditions input MODFILES 2uvobc 1 1 A R riverT 2uvobciA 0 0 0 0 F F Initial conditions input restart file from simulation 0 MODFILES inicon 1 1 N N riverT phsfinN 0 0 0 0 F F Horizontal coordinates SURFACEGRIDS 1 1 0 0 1000 1000 0 0 T akak GO KO KO OK FK FK FK KK K FK KK K KK 2K KK FK FK 2K K FK 2K 2K OK OK Do not remove the above 52 CHAPTER 2 GETTING STARTED Parameters for time series output Definition of the output variables The format is number output key id dimension 0 2 3 oopt klev dep node fortran name long name unit Only the first 3 are required Surface elevation 92 TSRVARS 1 92 2 5 553 Depth avg U velocity 104 TSRVARS 2 107 2 U velocity TSRVARS 3 109 3 3 3335 gt 9 V velocity TSRVARS 4 121 3 Vertical velocity TSRVARS 5 123 3 Salinity TSRVARS 6 128 3 Matching the variables to sets Format iset ivari ivar2 etc IVARSTSR 1 2 3 4 5 6 Definition of the output files Format set number defined T F format A ascii N netCDF U binary filename info T F path header_type TSR2D 1 T N riverT_1 tsout2N T 2 TSR3D 1 T N riverT_1 tsout3N T 2 Definition of output grid Format set number gridded T F gridfile T F land_mask T F timegrid T F ref_date number dimensions num
25. he simulation has now created the following input files in standard COHERENS format e riverT modgrdN model grid arrays e riverT 2uvobc1A open boundary conditions e riverT phsfinN initial conditions produced by the initialisation run for the final one Run the test case again now using the CIF functionality cp cifruns defruns Open the file defruns river0OT R riverOT CifModA river1T R river1iT CifModA You may open the CIF files to see how information is passed to COHE RENS 2 4 1 3 changing model setup through the CIF Now we are going to change the model by adapting the CIF file and the forcing files We will do the following 1 2 3 4 On Change the simulation time Adjust the time step Modify settings e g roughness length Change the form of the output file e g from netCDF to ASCII Modify the grid resolution number of rows and columns grid size Modify the open boundary conditions 2 4 MODIFYING MODEL SETUP 37 Changing simulation time The first modification is the modification of the simulation time by editing the CIF file 1 Change the defruns file gedit defruns We will switch off the first of the two simulations for the moment and only do changes in the second file riverOT R riverOT CifModA river1iT R river1T CifModA 2 Open and edit the CIF gedit river1T CifModA Set the simulation time to 1 day by changing the line CENDDATETIME 2003 01 06 00 00 00 0
26. ifferent colormaps and select one you find useful to work with A useful selection may be ssec The ranges of the colorbar are set by the button with Range Click on it in order to get a dialog box in which you can set the limits of the colorbar You can also choose to highlight some special ranges by clicking on the button linear The name of the button will change in low and the resolution in the color bar will increase for low values of the water level By clicking it again it will say Hi and have more resolution for high values of the water level The button which says Bi lin will influence the way in which the colors are interpolated default is bi linear interpolation By clicking it it will say Repl which gives nearest neighbor interpolation The latter is less visually appealing but is 28 CHAPTER 2 GETTING STARTED Neview 1 93 no variable selected Neview 1 93h David W Pierce 13 April 2009 SELECT A VARIABLE TO START Current x 29 3592 y 0 560638 Quit SEKEN i gt b gt Edit AE 3gauss InvP InvC MagXt Linear Axes Range Bilin Print Var Dim Name Current Current Figure 2 1 Screenshot of using NcView is sometimes useful near the edges Finally we are going to make some files of the data This can be done by clinking on the button Print A dialog box will appear Click on the button File in order to make a file with the data and click on OK Use nautilus or konqueror the Linux program
27. ith other versions of COHERENS as long as they are not older than 2 4 3The t option is new from COHERENS V2 4 on In older versions this option must not be used 2 2 RUNNING A TEST CASE 19 ls Now you should see the following output BCOMPS deffigs txt postparsD SETUP BSOURCE defposts river txt SOURCE cifruns defruns Run SSOURCE COHERENS files vis Run_hpd_par Usrdef_Harmonic_Analysis f90 coherensflags cmp Makefile Run_hpd_ser Usrdef_Model 90 COMPS postparsA Run_vic Usrdef_Output 90 con_sub_river postparsB SCOMPS Usrdef_Time_Series f90 DATA postparsC SCR The files have different meanings They are not all necessary for our purposes We will now examine the most important of these files The names in capitals are symbolic links to important locations for CO HERENS For example the link SOURCE points to the FORTRAN source files of the model The link COMPS points to the files needed for the compi lation The model setup is given in the four files whose name starts with Usr def For our purposes the two most important ones are Usrdef_Model f90 which contains the model input and Usrdef_Time_Series f90 which contains information on the data that should be exported as time series We will discuss this later in the tutorial After installing the test case we are now ready to compile the model This will be explained in the next section 2 2 2 Compiling COHERENS Before we compile the model we have a look at the fi
28. laced In order to do so type the following commands cd mkdir river cd river We follow by making a link to the COHERENS directory in which the source code and installation scripts are placed The name of the link must be COHERENS We can make the link by typing the following command In s V2 5 COHERENS Here the two arguments are first the location to which the link points and secondly the name of the link In this command the two dots are used to refer to the directory that is above the current directory In case the COHERENS source files are located in another directory you must adapt the first argument V2 5 such that it is the location of the directory containing your COHERENS files The first test case that we are going to do is called river It describes the evolution of an estuarine salinity front advected by a tidal current and the cor responding estuarine circulation in an open non rotating channel as descri bed in the User Documentation We run the installation script install_test in the COHERENS directory which copies the necessary files to our direc tory COHERENS install_test t river In this command the argument of the script is the name of the test cased There are many test cases delivered with COHERENS Their model setups can be found in the directory COHERENS setup In order to examine the files that are generated we use the command 1s Type The examples below can be run in the same way w
29. le no need to change this file We will use here 2 2 RUNNING A TEST CASE 21 the Intel Fortran compiler ifort or the GNU Fortran compiler gfortran We will look up the settings for this compiler in compilers cmp In this file you should see the following statements they may be different because of local settings on your computer Linux gfortran GNU Fortran linux gfort MAKE EXEFILE FC gfortran FCOPTS 03 FCDEFS FCDEBUG CPP CPPF cpp CPPOPTS traditional cpp CPPDEFS CPPDFLAGS Intel fortran compiler v 9 without MPI dynamically linked linux iforts MAKE EXEFILE FC ifort FCOPTS cpp1 i dynamic FCDEFS CPPDFLAGS FCDEBUG FCIFLAGS_COMP W1 rpath usr local intel lib CPP _ CPPF cp CPPOPTS _ CPPDEFS The first word before the colon e g linux iforts is the name of the compiler setting also called the target There are two settings for the Intel com piler in this file linux iforts is the normal option for using the Intel Fortran Compiler This is the recommended setting when performing simulations In this tutorial we will make a few changes in this file in order to speed up the compilation process This is done by disabling the optimization that is performed by the compiler This optimization takes a lot of time On our machine the compilation with optimization takes about 25 minutes With out optimization it takes only one minute However the optimized
30. les that determine the compilation process There are three First there is Makefile which contains instructions about the order in which the model is compiled Second there is the file coherensflags cmp This file contains some statements which determine which options are used in the compilation of the model Thus you can make the program a little bit different by changing the options in this file We will edit this file An easy to use text editor with a graphical user interface in Linux is called gedit Open the file by typing gedit coherensflags cmp Note that if gedit is not installed on your system or if you prefer other text editors such as vi nano or emacs you can of course use these instead of gedit Now we are going to add two options Change the line that starts with CPPDFLAGS into the following 20 CHAPTER 2 GETTING STARTED CPPDFLAGS DALLOC DCDF The meaning of these two switches is the following The first one DALLOC changes the location in the memory that is used in COHERENS more varia bles are placed on the heap instead of on the stack The first advantage of using this option is that there is a much lower risk that the model crashes because the amount of memory is too low The reason is that there is much more memory available on the heap than on the stack The second advantage is that less CPU memory is used by the model The eventual disadvantage of using this option is that the model might become slightl
31. lly well be performed by modifying the setups defined in the Usrdef_ files Main difference is that you need to recompile the code each time a Usrdef_ file has been changed This recompilation only takes a few seconds of time Changing model setup parameters As before switch off the first of the two simulations in defruns riverOT riveriT 1 Edit the file Usrdef_Model f90 gedit Usrdef_Model 90 2 To change the simulation time modify the following line in routine usrdef_mode_params from CendDateTime 2003 01 06 00 00 00 000 into CEndDateTime 2003 01 04 00 00 00 000 3 Note that lower case characters are used preferentially for variable names contrary to the CIF where all parameter names are given in upper case 4 Since the comment character has the same meaning in FORTRAN as for the CIF you may also comment the old definition CEndDateTime 2003 01 06 00 00 00 000 CEndDateTime 2003 01 04 00 00 00 000 5 Recompile and run the modified test make linux iforts Run 2 4 MODIFYING MODEL SETUP 47 6 A new time step is taken by changing the following lines in Usrdef Model f90 routine usrdef_mod_params from delt2d 30 0 ic3d 10 to delt2d 15 0 ic3d 20 7 The roughness length parameter zrough_cst can be changed in the same routine 8 The switch iopt_grid_nodim is not defined in Usrdef_Model f90 COHE RENS will therefore take the default value which is 3 You can reset this value
32. lt riverOA cifmodA river0A inilogA river0A runlogA river0A timingA river0A warlogA riveriA cifmodA riveriA inilogA riveriA runlogA riveriA timingA riveriA warlogA riverA_1 resid3I riverA_1 resid3N riverA_1 tsout2I riverA_1 tsout2N riverA_1 tsout3I riverA_1 tsout3N riverA_2 tsoutOA riverA_2 tsoutOlI riverA 2uvobc1U riverA modgrdU riverA phsicsU river txt These files have the following meanings e Files ending at inilogA are the initialization log files The name of each subroutine that is called during the initialization is written to this file It is mainly important for debugging of a model setup and code developers e Files with suffix runlogA are log files writing information during the actual run of the model This files may become quite large for long runs We have already seen it before when we used this file to examine the progress of the simulations Otherwise it is also more important 2 2 RUNNING A TEST CASE 25 for code developers than for model users However it sometimes oc curs that an error is written to a log file in addition to the errlog file discussed below e The files ending with timingA contain information on the time it took for the model to run Open the file riverOA timingA in gedit and examine the results This file shows how long the simulation took and it also shows the percentages of the time that different parts of the calculation took such as 2D calculation 3D calculation input and
33. output e Files ending at warlogA are files with warnings about settings that were automatically changed by COHERENS Before the start of the si mulations COHERENS checks whether some parameters in the model have appropriate values and if not COHERENS resets them automat ically When COHERENS changes these values it writes a warning in this file It may be useful after each simulation to inspect the warlogA files They can give information on some model settings that were not intended by the user and they may explain unexpected results in the si mulations Open riverOA warlogA in gedit and examine the warnings In this case there are no important changes made to the model e A file that should not be present is the errlogA file In this file error messages are written and the execution of the program stops Examples of this are incompatible options which can not be automatically reset At the end of the simulation COHERENS automatically removes this file This means that you know for certain that something went wrong with the simulations if this file is present at the end of the simulation You should then examine this file and fix the problem Make sure that there is no errlog file by typing ls errlogA If an error log file exists but is empty you must check the runlog or inilog files to see firstly whether some error message was written to one of these files If no error message has been written the program crashed by a
34. ption and CIF file name are optional which means that you can leave them empty However you must always put the two commas on this line Otherwise COHERENS will generate an error Comments can be set in the defruns file by adding an exclamation mark There are two options for CIF files In order to read a CIF file one must add the letter R note that this option is case sensitive In order to write a CIF file one must add the letter W We will change the defruns file We do so by adding W after the first comma on the first two lines and inserting an exclamation mark at the beginning of the next lines The result looks like riverOA W riveriA W riverOB river1B river0C river1C riverOD river1D 2 2 RUNNING A TEST CASE 23 Note that in the test case river each run actually exists of two different runs with the numbers 0 and 1 In the run with number zero a spin up calculation is done without salinity in order to determine the initial conditions for the actual run In the run with number one the calculation of the estuarine circulation is performed After closing gedit we can run the model with the command Run amp This command will run the model The ampersand amp makes the model run in the background which means that we can keep working on the command line We can for example use the command 1s to see which files are being made by COHERENS We can check whether COHERENS is still running with th
35. reset from 0 8 to 1 0 m in Usr def Model f90 SUBROUTINE usrdef_2dobc_spec ityp2dobu 1 8 ityp2dobu 2 13 amp 1 0 phase halfpi END SUBROUTINE usrdef_2dobc_spec 2 5 FORMAT AND SPECIFIC SYNTAX OF A CIF 49 Note that only the parameter amp needs to be changed The amplitudes of the water elevation and depth integrated current are automatically adapted by the code in routine usrdef_2dobc_spec 2 5 Format and specific syntax of a CIF Example of a CIF file for the test case River The CIF used in this tutorial is shown here as an example what the CIF looks like LCR AAA RI I OKA ARAKI I I A A 2k KK kkk kkk kkk kk kkk k kk This is an example CIF file for running the test case river It is the second of two files which runs the simulation of a density current This file uses the tutorial settings Written by Alexander Breugem April 2012 LCA AAR RI I I I ICI AK AK CA ACA A A 1K KK KK CA A kkk kk kkk k kk Monitoring parameters LCA A ARR I I I OKI AAR ACA A A A kK KK KEK CA A A A A kkk kkk kk In this part parameters are defined that determine the parameters tha are written to the logfiles Get resonable amount of logdata Increase the number to obtain more data LEVPROCS_INI 7 LEVPROCS_RUN 3 Generate a detailed timing file LEVTIMER 3 DoE EEEE EEE o kk kk kkk kkk kkk kkk kkk kkk kkk Switches and parameters Do not remove the above l In this part parameters are set for
36. s test takes about 10 15 minutes depending on the capacity of your machine e When visualizing the data with Ferret you must define the x and y data to make time series Because this case is two dimensional there is only a tsout2N file We are using the file bohai_l lamplt2N with the harmonically analysed surface M gt amplitudes as example for making visualisation with Octave or Matlab 1 Download the octcdf package for Ubuntu this is rather straightforward using sudo apt get install octave octcdf For other platforms such as Windows a useful wiki might be http modb oce ulg ac be mediawiki index php NetCDF_toolbox_for_Octave 2 In this package the ncdump function is included which provides infor mation about all the contents of the netCDF file In our example file 2 3 POST PROCESSING THE RESULTS 33 we see that there are 3 dimensions and 7 variables The variable we are interested in is zeta we are also interested in the dimensions xdim longitude ydim latitude and time depth is constant in this example so we disregard it To load a variable to the Octave environment firstly check whether the file ncparsen m has been copied from the scr to your working directory and type in the qtOctave terminal locallat ncparsen bohaiA_1 lamp1t2N xout locallon ncparsen bohaiA_1 lamp1t2N yout localzeta ncparsen bohaiA_1 1amp1t2N zeta to load the spatial coordinate
37. s that do the same as windows explorer to look up the file Click on it to see it Now click on umvel to visualize the depth averaged velocities in the x direction and also make an output file with these data Finally close NcView by clicking on Quit We continue by visualizing the 3 D data In order to open the 3 D file type nceview riverA_1 tsout3N In this file three dimensional data are stored In fact because the river test case is two dimensional there is no information in the y direction only the data in the x z direction can be displayed We will start by visualizing the salinity Click on sal to visualize the salinity Now you will see the initial 2 3 POST PROCESSING THE RESULTS 29 salinity profile in the x z plane We can go to a different moment in time by clicking the arrow to the right By clicking the two arrows to the right an animation is shown You can change the speed of the animation by sliding the slider to the right of the text delay Watch the animation and observe how the salinity intrusion develops Close NcView We will now continue to make visualizations in Ferret 2 3 2 visualising with Ferret Ferret is a more advanced tool for displaying graphics which has much more possibilities than NcView However it is somewhat more difficult to use than NcView since options are given through the command line Nevertheless no real program is necessary to view output which is different from for example Matla
38. type of error not detected by COHERENS e The file with suffix cifmodA contains an automatically generated cen tral input file CIF Open the file river1A cifmodA in gedit It con tains some lists of the different parameters in the model Each of these lists is separated from the others with a hash sign Comments can 26 CHAPTER 2 GETTING STARTED be given with an exclamation mark The CIF file while be discussed in more detail in the next chapter e There are files with the results of the simulation Files whose names contain the string tsout and end with the letter N contain time se ries of some variables For this simulation there are three of them riverA_1 tsout2N riverA_1 tsout3N and riverA_2 tsout0A The number after tsout indicates the dimension which can be 0 1 or 2 As an exam ple riverA_1 tsout3N contains three dimensional data The last letter of the extension indicates the type of data The letter N stands for netCDF Other possibilities are A for ASCII and U for binary Files ending at are ASCII files contain information about the output data but do not contain the data themselves Files with the string resid in their name have been generated for harmonic analysis Their meaning is similar to the tsout files discussed above e The file whose names contain the string 2uvobc modgrd and phsics are created by COHERENS for internal use only and are of no interest for the present discussion e Finally the file
39. with the suffix txt is a small ASCII file describing the setups of the different experiments which can be conducted with the test case river Because the netCDF output contains binary files we need a special tool for examining the data It is called ncdump In order to examine the results use the following command ncdump riverT_1 tsout2N less Here the command less is used as a viewer You can close this program by typing q Using ncdump you can see which variables are in the file and which values they have However it is normally more instructive to visualize the data We will do that in the next sections An alternative of the less command is to send the ASCII output to an other data file For example the three dimensional output can be examined by typing ncdump riverT_1 tsout3N gt gt outdat gedit outdat Compare the variables that are in this file with those in the two dimensional file What are the differences in the dimensions and the variables Also notice the meaning of the different variables by observing the long_name and units attributes 2 3 POST PROCESSING THE RESULTS 27 2 3 Post processing the results 2 3 1 Visualising with Ncview Ncview is a tool for visualizing netCDF data files It is very easy to use because of its graphical user interface However its possibilities are limited In order to start this program for a certain data file type the following command ncview riverA_1 tsout2N When using Nc
40. y slower The second option DCDF enables the netCDF module in COHERENS Without this option it is not possible to use netCDF input and output If you do not set this option and you are trying to generate netCDF output COHERENS will run normally but the files are not generated Another option that can be set in this way and which will not further discussed in this tutorial is the enabling of parallel computations by setting the switch DMPI Further you need to select the paths of the netCDF installation usually this is in usr local You can do this by removing the comments indicated by a hash in the lines related to netCDF and changing if necessary the location of your netCDF files The result should look something like this netCDF directory path NETCDF_PATH usr local netCDF library file NETCDF_LIB_FILE netcdf netCDF include options FCIFLAGS_NETCDF I NETCDF_PATH include netCDF library options FLIBS_NETCDF L NETCDF_PATH lib 1 NETCDF_LIB_FILE Now save and close the file The third file that is important for the course is compilers cmp which is located in the folder COHERENS code physics comps given by the symbolic link COMPS We will open this file in gedit to see its contents gedit COMPS compilers cmp In this file there is a list of targets Each target defines a set of options for different compilers If one these compilers has been installed on your machine there is in princip
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