GENIE BiogemTutorial - Revision history

Genie-user: GENIE:BiogemTutorial moved to GENIE BiogemTutorial: make public

2008-03-06T08:49:42Z

GENIE:BiogemTutorial moved to GENIE BiogemTutorial: make public

Genie-user: /* Exercise 3a. Transient run from spin-up [optional] */

2007-07-25T14:17:35Z

Exercise 3a. Transient run from spin-up [optional]

Genie-user: /* Instructions */

2007-07-25T14:04:25Z

Instructions

Genie-user at 10:33, 25 July 2007

2007-07-25T10:33:24Z

Genie-user: /* Instructions */

2007-07-25T10:22:09Z

Instructions

Genie-user: /* Instructions */

2007-07-25T09:44:28Z

Instructions

Genie-user: /* Instructions */

2007-07-25T09:39:53Z

Instructions

Genie-user: /* Instructions */

2007-07-25T08:49:04Z

Instructions

Genie-user: /* Instructions */

2007-07-25T08:18:15Z

Instructions

Genie-user: /* Instructions */

2007-07-25T08:05:58Z

Instructions

@@ Line 142: / Line 142: @@
 #	Try repeating Exercise #3, but using the re-start of the run generated in Exercise #2a, in which a large-scale pattern of circulation was already starting to be well established. You can use a re-start by adding an extra parameter to the list passed to the run script, e.g.:
-## $ ./rungenie genie_eb_go_gs_ac_bg_itfclsd_08l n 1931 70 biogem_exp_2 biogem_exp_3
+## $ ./rungenie genie_eb_go_gs_ac_bg_itfclsd_08l n 1931 70 biogem_exp_3 biogem_exp_2
 #	Re-analyze the year 1994 CFC distributions in the ocean.

@@ Line 123: / Line 123: @@
 ### biogem_force_*_sig.dat
 ## and contains two columns of information - the first is a time marker (year) and is paired with a corresponding magnitude modifier value in the second column.
-## The values assigned to the time markers in the signal file define the time-varying information. For a model year falling outside of the maximum or minimum time markers specified in the signal file, no forcing will be applied (this in effect allows a restoring forcing to be turned 'on' and then 'off' again later). For model years inbetween specified time points, the bounding modifier values are linearly interpolation. It should be noted that biogem_force_*_sig.dat file must contain at least one (row) entry.
+## The values assigned to the time markers in the signal file define the time-varying information. For a model year falling outside of the maximum or minimum time markers specified in the signal file, no forcing will be applied (this in effect allows a restoring forcing to be turned 'on' and then 'off' again later). For model years inbetween specified time points, the bounding modifier values are linearly interpolated. It should be noted that biogem_force_*_sig.dat file must contain at least one (row) entry.
 ## The way in which these three files are employed to define a spatially-explicit time-varying input field is as follows. The first field file (*_I.dat) defines the baseline distribution and the second (*_II.dat) an alternative distribution. The difference between the two fields defines the spatial component of a time-varying forcing. The 2nd value of each data pair in the signal file is used to modify the difference between the two spatial fields.
 ## Puting it another way - the magnitude of the forcing that is applied at any point in time is equal to the baseline field, defined in:

@@ Line 26: / Line 26: @@
 #### WARNING -> Originating location in code [module,subroutine]: biogem_data,sub_init_data_save -> ERROR MESSAGE: No time-slice dates listed in file biogem_save_timeslice.dat fall within the model start and end years -> ERROR ACTION:  CONTINUING
 ### No data categories for time-slice saving have been selected in biogem_config.par.
-#	Re-run the model, but with a time-slice mid-point of 0.5 years set in biogem_save_timeslice.dat (any earlier or later that this will not work because the integration interval is set as 1.0 years by default in biogem_config.par (near the bottom of the I/O - TIME-SERIES section) and the run is only 1 year long …), and select (as t) ocean 'physical' properties as a time-slice data save in biogem_config.par. Explore the contents of fields_biogem_3d.nc. Note that much of the physical grid information is as dull as ditchwater (and also note that ocn_sal and ocn_temp fields are erroneously created, but with no data saved to them – a bug to be fixed :o) ). Also note that nothing is being saved yet in the 2-D netCDF file: fields_biogem_2d.nc.
+#	Re-run the model, but with a time-slice mid-point of 0.5 years set in biogem_save_timeslice.dat (any earlier or later that this will not work because the integration interval is set as 1.0 years by default in biogem_config.par (near the bottom of the I/O - TIME-SERIES section) and the run is only 1 year long …), and select (as t) the following parameters in biogem_config.par:
 #	The important ‘physics’ is saved by selecting miscellaneous properties as a time-slice data save. Select miscellaneous properties in 'time slice' section of biogem_config.par and re-run.
 #	A second type of data that can be saved is ‘time-series’ data: i.e., time series of global of surface averaged properties. The time-series configuration file: biogem_save_sig.dat is already populated for you. This file contains the mid-point years at which a time-series data point are to be saved. Again the data is time-integrated, with the integration interval specified in biogem_config.par (near the bottom of the I/O - TIME-SERIES section). Try selecting miscellaneous properties in 'time-series' section and re-run the model. The results directory now contains time-series files in ASCII (plain text) format. There is a header describing the information and units of each column.

@@ Line 27: / Line 27: @@
 ### No data categories for time-slice saving have been selected in biogem_config.par.
 #	Re-run the model, but with a time-slice mid-point of 0.5 years set in biogem_save_timeslice.dat (any earlier or later that this will not work because the integration interval is set as 1.0 years by default in biogem_config.par (near the bottom of the I/O - TIME-SERIES section) and the run is only 1 year long …), and select (as t) ocean 'physical' properties as a time-slice data save in biogem_config.par. Explore the contents of fields_biogem_3d.nc. Note that much of the physical grid information is as dull as ditchwater (and also note that ocn_sal and ocn_temp fields are erroneously created, but with no data saved to them – a bug to be fixed :o) ). Also note that nothing is being saved yet in the 2-D netCDF file: fields_biogem_2d.nc.
-#	The important ‘physics’ is saved by selecting miscellaneous properties as a time-slice data save. De-select ocean 'physical' properties and select miscellaneous properties instead and re-run.
+#	The important ‘physics’ is saved by selecting miscellaneous properties as a time-slice data save. Select miscellaneous properties in 'time slice' section of biogem_config.par and re-run.
-#	A second type of data that can be saved is ‘time-series’ data: i.e., time series of global of surface averaged properties. The time-series configuration file: biogem_save_sig.dat is already populated for you. This file contains the mid-point years at which a time-series data point are to be saved. Again the data is time-integrated, with the integration interval specified in biogem_config.par (near the bottom of the I/O - TIME-SERIES section). Try selecting miscellaneous properties time-series data saving and re-run the model. The results directory now contains time-series files in ASCII (plain text) format. There is a header describing the information and units of each column.
+#	A second type of data that can be saved is ‘time-series’ data: i.e., time series of global of surface averaged properties. The time-series configuration file: biogem_save_sig.dat is already populated for you. This file contains the mid-point years at which a time-series data point are to be saved. Again the data is time-integrated, with the integration interval specified in biogem_config.par (near the bottom of the I/O - TIME-SERIES section). Try selecting miscellaneous properties in 'time-series' section and re-run the model. The results directory now contains time-series files in ASCII (plain text) format. There is a header describing the information and units of each column.
 #	Do any other playing with the options you like.

@@ Line 16: / Line 16: @@
 ## Note that the only tracers selected are temperature and salinity (humidity in the case of the atmospheric tracers).
 ## Also note that in biogem_config.par, no biological option is selected (or rather, the ‘null’ option NONE is selected, with the corresponding biological configuration file biogem_bio_NONE_config.par containing no parameter information.
-# Get the necessary genie config file [http://source.ggy.bris.ac.uk/subversion/genie/trunk/genie-main/configs/genie_eb_go_gs_ac_bg_itfclsd_08l.config http://source.ggy.bris.ac.uk/subversion/genie/trunk/genie-main/configs/genie_eb_go_gs_ac_bg_itfclsd_08l.config] and put it in genie-main/configs/
+# Get the necessary genie config file [http://researchpages.net/media/resources/2007/07/25/genie_eb_go_gs_ac_bg_itfclsd_08l.config genie_eb_go_gs_ac_bg_itfclsd_08l.config ] and put it in genie-main/configs/
 #       Get the [http://researchpages.net/media/resources/2007/07/25/rungenie   rungenie script]. (Just in case that one doesn't work, here's a backup:[http://researchpages.net/media/resources/2007/07/24/rungenie  rungenie]). Put it at the same level as your genie and genie_input directories (i.e. probably in your home directory). Make it executable:
 ## chmod u+x rungenie

← Older revision	Revision as of 08:49, 6 March 2008
(No difference)

@@ Line 16: / Line 16: @@
 ## Note that the only tracers selected are temperature and salinity (humidity in the case of the atmospheric tracers).
 ## Also note that in biogem_config.par, no biological option is selected (or rather, the ‘null’ option NONE is selected, with the corresponding biological configuration file biogem_bio_NONE_config.par containing no parameter information.
-#       Get the [http://researchpages.net/media/resources/2007/07/24/rungenie   rungenie script]. (Just in case that one doesn't work, here's a backup:[http://researchpages.net/media/resources/2007/07/24/rungenie  rungenie]). Put it at the same level as your genie and genie_input directories (i.e. probably in your home directory).
+#       Get the [http://researchpages.net/media/resources/2007/07/24/rungenie   rungenie script]. (Just in case that one doesn't work, here's a backup:[http://researchpages.net/media/resources/2007/07/24/rungenie  rungenie]). Put it at the same level as your genie and genie_input directories (i.e. probably in your home directory). Make it executable:
 #	Run the model for 1 year (refer to the [[http://researchpages.net/media/resources/2007/07/25/RELEASENOTES.readme.txt rungenie.README]] file for the description of the options passed to the rungenie configuration script), i.e.:
 ## $ ./rungenie genie_eb_go_gs_ac_bg_itfclsd_08l n 0 1 biogem_exp_1

@@ Line 87: / Line 87: @@
 === Instructions ===
-#	Download and unpack configuration set biogem_exp_3.tar.gz.
+#	Download and unpack configuration set [[http://www.seao2.org/genie_workshop/biogem_exp_3.tar.gz http://www.seao2.org/genie_workshop/biogem_exp_3.tar.gz]].
 #	Select the following atmospheric (gaseous) tracers: CFC-11, CFC-12, together with the equivalent dissolved tracers in the ocean.
 #	Select some data to save and then run the model for 10 years. It should run … but there is nothing (interesting) going on – the ocean and atmosphere have been initialized with a zero concentration of CFCs, and irrespective of the establishment of large scale ocean circulation and adjustment of climate, zero is where their concentrations are going to remain everywhere (hopefully!).