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+ + + + + + + + + + + + + + + + + + +To adjust the system to a different set of temperature and/or pressure conditions, use adjust
:
co2s_adj = co2s.adjust(
+ temperature=25,
+ pressure=1000,
+ store_steps=1,
+ method_fCO2=1,
+ opt_which_fCO2_insitu=1,
+ bh_upsilon=None,
+)
+
The result co2s_adj
is a new CO2System
with all values at the new conditions (above, temperature of 25 °C and hydrostatic pressure of 1000 dbar).
For more on the store_steps
kwarg, see Advanced results access.
The adjust
method can be used if any two carbonate system parameters are known, but also if only one of pCO2, fCO2, [CO2(aq)] or xCO2 is known. In this case, adjust
can take additional kwargs:
method_fCO2
: how to do the temperature conversion.
1
: using the parameterised υh equation of H24 (default). 2
: using the constant υh fitted to the TOG93 dataset by H24.3
: using the constant theoretical υx of H24.4
: following the H24 approach but using a user-provided b_h value (given with the additional kwarg bh_upsilon
).5
: using the linear fit of TOG93.6
: using the quadratic fit of TOG93 (default before v1.8.3).opt_which_fCO2_insitu
: whether the input (1
, default) or output (2
) condition pCO2, fCO2, [CO2(aq)] and/or xCO2 values are at in situ conditions, for determining b_h with the parameterisation of H24. Only applies when method_fCO2
is 1
.
bh_upsilon
: If this is a single-parameter system and method_fCO2
is 4
, then the value of b_h in J/mol must be specified here.
Marine carbonate system calculations in Python.
+ + + + + + + + +CO2System
+
+
+¶
+ Bases: UserDict
PyCO2SYS/engine.py
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|
adjust(temperature=None, pressure=None, store_steps=1, method_fCO2=1, opt_which_fCO2_insitu=1, bh_upsilon=None)
+
+¶Adjust the system to a different temperature and/or pressure.
+ + +Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ temperature
+ |
+
+ float
+ |
+
+
+
+ Temperature in °C to adjust to. If |
+
+ None
+ |
+
+ pressure
+ |
+
+ float
+ |
+
+
+
+ Hydrostatic pressure in dbar to adjust to. If |
+
+ None
+ |
+
+ store_steps
+ |
+
+ int
+ |
+
+
+
+ Whether/which non-requested parameters calculated during intermediate +calculation steps should be stored. The options are: +
|
+
+ 1
+ |
+
+ method_fCO2
+ |
+
+ int
+ |
+
+
+
+ If this is a single-parameter system, which method to use for the +adjustment. The options are: +
|
+
+ 1
+ |
+
+ opt_which_fCO2_insitu
+ |
+
+ int
+ |
+
+
+
+ If this is a single-parameter system and |
+
+ 1
+ |
+
+ bh_upsilon
+ |
+
+ float
+ |
+
+
+
+ If this is a single-parameter system and |
+
+ None
+ |
+
Returns:
+Type | +Description | +
---|---|
+ CO2System
+ |
+
+
+
+ A new |
+
PyCO2SYS/engine.py
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|
get_grad(var_of, var_wrt)
+
+¶Compute the derivative of var_of
with respect to var_wrt
and store it in
+sys.grads[var_of][var_wrt]
. If there is already a value there, then that
+value is returned instead of recalculating.
Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ var_of
+ |
+
+ str
+ |
+
+
+
+ The name of the variable to get the derivative of. + |
+ + required + | +
+ var_wrt
+ |
+
+ str
+ |
+
+
+
+ The name of the variable to get the derivative with respect to. This must
+be one of the fixed values provided when creating the |
+ + required + | +
PyCO2SYS/engine.py
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|
get_grads(vars_of, vars_wrt)
+
+¶Compute the derivatives of vars_of
with respect to vars_wrt
and store
+them in sys.grads[var_of][var_wrt]
. If there are already values there, then
+those values are returned instead of recalculating.
Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ vars_of
+ |
+
+ list
+ |
+
+
+
+ The names of the variables to get the derivatives of. + |
+ + required + | +
+ vars_wrt
+ |
+
+ list
+ |
+
+
+
+ The names of the variables to get the derivatives with respect to. These
+must all be one of the fixed values provided when creating the |
+ + required + | +
PyCO2SYS/engine.py
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|
plot_graph(ax=None, exclude_nodes=None, prog_graphviz='neato', show_tsp=True, show_unknown=True, show_isolated=True, skip_nodes=None)
+
+¶Draw a graph showing the relationships between the different parameters.
+ + +Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ ax
+ |
+
+ matplotlib axes
+ |
+
+
+
+ The axes on which to plot. If |
+
+ None
+ |
+
+ exclude_nodes
+ |
+
+ list of str
+ |
+
+
+
+ List of nodes to exclude from the plot, by default |
+
+ None
+ |
+
+ prog_graphviz
+ |
+
+ str
+ |
+
+
+
+ Name of Graphviz layout program, by default "neato". + |
+
+ 'neato'
+ |
+
+ show_tsp
+ |
+
+ bool
+ |
+
+
+
+ Whether to show temperature, salinity and pressure nodes, by default
+ |
+
+ True
+ |
+
+ show_unknown
+ |
+
+ bool
+ |
+
+
+
+ Whether to show nodes for parameters that have not (yet) been calculated,
+by default |
+
+ True
+ |
+
+ show_isolated
+ |
+
+ bool
+ |
+
+
+
+ Whether to show nodes for parameters that are not connected to the graph,
+by default |
+
+ True
+ |
+
+ skip_nodes
+ |
+
+ bool
+ |
+
+
+
+ List of nodes to skip from the plot, by default |
+
+ None
+ |
+
Returns:
+Type | +Description | +
---|---|
+ matplotlib axes
+ |
+
+
+
+ The axes on which the graph is plotted. + |
+
PyCO2SYS/engine.py
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|
propagate(uncertainty_in, uncertainty_from)
+
+¶Propagate independent uncertainties through the calculations. Covariances +are not accounted for.
+New entries are added in the uncertainty
attribute, for example:
co2s = CO2System(dic=2100, alkalinity=2300)
+co2s.propagate("pH", {"dic": 2, "alkalinity": 2})
+co2s.uncertainty["pH"]["total"] # total uncertainty in pH
+co2s.uncertainty["pH"]["dic"] # component of ^ due to DIC uncertainty
+
Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ uncertainty_in
+ |
+
+ list
+ |
+
+
+
+ The parameters to calculate the uncertainty in. + |
+ + required + | +
+ uncertainty_from
+ |
+
+ dict
+ |
+
+
+
+ The parameters to propagate the uncertainty from (keys) and their +uncertainties (values). + |
+ + required + | +
PyCO2SYS/engine.py
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solve(parameters=None, store_steps=1)
+
+¶Calculate parameter(s) and store them internally.
+ + +Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ parameters
+ |
+
+ str or list of str
+ |
+
+
+
+ Which parameter(s) to calculate and store, by default None, in which case +all possible parameters are calculated and stored internally. + |
+
+ None
+ |
+
+ store_steps
+ |
+
+ int
+ |
+
+
+
+ Whether/which non-requested parameters calculated during intermediate +calculation steps should be stored, by default 1. The options are + 0 - store only the specifically requested parameters, + 1 - store the most used set of intermediate parameters, or + 2 - store the complete set of parameters. + |
+
+ 1
+ |
+
PyCO2SYS/engine.py
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|
to_pandas(parameters=None, store_steps=1)
+
+¶Return parameters as a pandas Series
or DataFrame
. All parameters should
+be scalar or one-dimensional vectors of the same size.
Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ parameters
+ |
+
+ str or list of str
+ |
+
+
+
+ The parameter(s) to return. These are solved for if not already available.
+If |
+
+ None
+ |
+
+ store_steps
+ |
+
+ int
+ |
+
+
+
+ See |
+
+ 1
+ |
+
Returns:
+Type | +Description | +
---|---|
+ Series or DataFrame
+ |
+
+
+
+ The parameter(s) as a |
+
PyCO2SYS/engine.py
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|
to_xarray(parameters=None, store_steps=1)
+
+¶Return parameters as an xarray DataArray
or Dataset
.
Parameters:
+Name | +Type | +Description | +Default | +
---|---|---|---|
+ parameters
+ |
+
+ str or list of str
+ |
+
+
+
+ The parameter(s) to return. These are solved for if not already available.
+If |
+
+ None
+ |
+
+ store_steps
+ |
+
+ int
+ |
+
+
+
+ See |
+
+ 1
+ |
+
Returns:
+Type | +Description | +
---|---|
+ DataArray or Dataset
+ |
+
+
+
+ The parameter(s) as a |
+
PyCO2SYS/engine.py
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