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Warning, /doc/phys_pkgs/gchem.rst is written in an unsupported language. File is not indexed.
view on githubraw file Latest commit bf89a37a on 2019-03-17 03:29:27 UTCbf89a37abc Phob*0001 .. _sub_phys_pkg_gchem: 0002 9ce7d74115 Jeff*0003 GCHEM Package 0004 ------------- 0005 0006 Introduction 0007 ~~~~~~~~~~~~ 0008 0009 This package has been developed as interface to the PTRACERS package. 0010 The purpose is to provide a structure where various (any) tracer 0011 experiments can be added to the code. For instance there are 0012 placeholders for routines to read in parameters needed for any tracer 0013 experiments, a routine to read in extra fields required for the tracer 0014 code, routines for either external forcing or internal interactions 0015 between tracers and routines for additional diagnostics relating to the 0016 tracers. Note that the gchem package itself is only a means to call the 0017 subroutines used by specific biogeochemical experiments, and does not** Warning **
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0018 “do” anything on its own. 0019 0020 There are two examples: **cfc** which looks at 2 tracers with a simple 0021 external forcing and **dic** with 4,5 or 6 tracers whose tendency terms 0022 are related to one another. We will discuss these here only as how they 0023 provide examples to use this package. 0024 0025 Key subroutines and parameters 0026 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0027 0028 | **FRAMEWORK** 0029 | The different biogeochemistry frameworks (e.g. cfc of dic) are 0030 specified in the packages\_conf file. *GCHEM\_OPTIONS.h* includes the 0031 compiler options to be used in any experiment. An important compiler 0032 option is #define GCHEM\_SEPARATE\_FORCING which determined how and 0033 when the tracer forcing is applied (see discussion on Forcing below). 0034 See section on dic for some additional flags that can be set for that 0035 experiment. 0036 | There are further runtime parameters set in *data.gchem* and kept in 0037 common block *GCHEM.h*. These runtime options include: 0038 | :math:`\bullet` Parameters to set the timing for periodic forcing 0039 files to be loaded are: *gchem\_ForcingPeriod*, *gchem\_ForcingCycle*. 0040 The former is how often to load, the latter is how often to cycle 0041 through those fields (eg. period couple be monthly and cycle one 0042 year). This is used in *dic* and *cfc*, with gchem\_ForcingPeriod=0 0043 meaning no periodic forcing. 0044 | :math:`\bullet` **nsubtime** is the integer number of extra timesteps 0045 required by the tracer experiment. This will give a timestep of 0046 **deltaTtracer**\ :math:`/`\ **nsubtime** for the dependencies between 0047 tracers. The default is one. 0048 | :math:`\bullet` File names - these are several filenames than can be 0049 read in for external fields needed in the tracer forcing - for 0050 instance wind speed is needed in both DIC and CFC packages to 0051 calculate the air-sea exchange of gases. Not all file names will be 0052 used for every tracer experiment. 0053 | :math:`\bullet` **gchem\_int\_** are variable names for run-time set 0054 integer numbers. (Currently 1 through 5). 0055 | :math:`\bullet` **gchem\_rl\_** are variable names for run-time set 0056 real numbers. (Currently 1 through 5). 0057 | :math:`\bullet` Note that the old **tIter0** has been replaced by 0058 **PTRACERS\_Iter0** which is set in data.ptracers instead. 0059 | 0060 | **INITIALIZATION** 0061 | The values set at runtime in data.gchem are read in using 0062 *gchem\_readparms.F* which is called from packages\_readparms.F. This 0063 will include any external forcing files that will be needed by the 0064 tracer experiment. 0065 | There are two routine used to initialize parameters and fields needed by 0066 the experiment packages. These are *gchem\_init\_fixed.F* which is 0067 called from *packages\_init\_fixed.F*, and *gchem\_init\_vari.F* called 0068 from packages\_init\_variable.F. The first should be used to call a 0069 subroutine specific to the tracer experiment which sets fixed 0070 parameters, the second should call a subroutine specific to the tracer 0071 experiment which sets (or initializes) time fields that will vary with 0072 time. 0073 | 0074 | **LOADING FIELDS** 0075 | External forcing fields used by the tracer experiment are read in by a 0076 subroutine (specific to the tracer experiment) called from 0077 *gchem\_fields\_load.F*. This latter is called from *forward\_step.F*. 0078 | 0079 | **FORCING** 0080 | Tracer fields are advected-and-diffused by the ptracer package. 0081 Additional changes (e.g. surface forcing or interactions between 0082 tracers) to these fields are taken care of by the gchem interface. For** Warning **
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0083 tracers that are essentially passive (e.g. CFC’s) but may have some 0084 surface boundary conditions this can easily be done within the regular 0085 tracer timestep. In this case *gchem\_calc\_tendency.F* is called from 0086 *forward\_step.F*, where the reactive (as opposed to the advective 0087 diffusive) tendencies are computed. These tendencies, stored on the 3D 0088 field **gchemTendency**, are added to the passive tracer tendencies 0089 **gPtr** in *gchem\_add\_tendency.F*, which is called from 0090 *ptracers\_forcing.F*. For tracers with more complicated dependencies 0091 on each other, and especially tracers which require a smaller timestep 0092 than deltaTtracer, it will be easier to use *gchem\_forcing\_sep.F* 0093 which is called from forward\_step.F. There is a compiler option set 0094 in *GCHEM\_OPTIONS.h* that determines which method is used: #define 0095 GCHEM\_SEPARATE\_FORCING does the latter where tracers are forced 0096 separately from the advection-diffusion code, and #undef 0097 GCHEM\_SEPARATE\_FORCING includes the forcing in the regular 0098 timestepping. 0099 | 0100 | **DIAGNOSTICS** 0101 | This package also also used the passive tracer routine 0102 *ptracers\_monitor.F* which prints out tracer statistics as often as 0103 the model dynamic statistic diagnostics (dynsys) are written (or as 0104 prescribed by the runtime flag **PTRACERS\_monitorFreq**, set in 0105 *data.ptracers*). There is also a placeholder for any tracer 0106 experiment specific diagnostics to be calculated and printed to files. 0107 This is done in *gchem\_diags.F*. For instance the time average CO2 0108 air-sea fluxes, and sea surface pH (among others) are written out by 0109 *dic\_biotic\_diags.F* which is called from *gchem\_diags.F*. 0110 | 0111 0112 .. _gchem_diagnostics: 0113 0114 GCHEM Diagnostics 0115 ~~~~~~~~~~~~~~~~~ 0116 0117 These diagnostics are particularly for the **dic** package. 0118 0119 :: 0120 0121 0122 ------------------------------------------------------------------------ 0123 <-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) 0124 ------------------------------------------------------------------------ 0125 DICBIOA | 15 |SM P MR |mol/m3/sec |Biological Productivity (mol/m3/s) 0126 DICCARB | 15 |SM P MR |mol eq/m3/sec |Carbonate chg-biol prod and remin (mol eq/m3/s) 0127 DICTFLX | 1 |SM P L1 |mol/m3/sec |Tendency of DIC due to air-sea exch (mol/m3/s) 0128 DICOFLX | 1 |SM P L1 |mol/m3/sec |Tendency of O2 due to air-sea exch (mol/m3/s) 0129 DICCFLX | 1 |SM P L1 |mol/m2/sec |Flux of CO2 - air-sea exch (mol/m2/s) 0130 DICPCO2 | 1 |SM P M1 |atm |Partial Pressure of CO2 (atm) 0131 DICPHAV | 1 |SM P M1 |dimensionless |pH (dimensionless) 0132** Warning **
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0133 Do’s and Don’ts 0134 ~~~~~~~~~~~~~~~ 0135 0136 The pkg ptracer is required with use with this pkg. Also, as usual, the 0137 runtime flag **useGCHEM** must be set to **.TRUE.** in **data.pkg**. By 0138 itself, gchem pkg will read in **data.gchem** and will write out gchem 0139 diagnostics. It requires tracer experiment specific calls to do anything 0140 else (for instance the calls to dic and cfc pkgs). 0141 0142 Reference Material 0143 ~~~~~~~~~~~~~~~~~~ 0144 0145 Experiments and tutorials that use gchem 0146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0147 0148 - Global Ocean biogeochemical tutorial, in 0149 tutorial\_global\_oce\_biogeo verification directory, described in 0150 section [sec:eg-biogeochem\_tutorial] uses gchem and dic 0151 0152 - Global Ocean cfc tutorial, in tutorial\_cfc\_offline verification 0153 directory, uses gchem and cfc (and offline) described in 0154 [sec:eg-offline-cfc] 0155 0156 - Global Ocean online cfc example in cfc\_example verification 0157 directory, uses gchem and cfc
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