| name | arguments | returns |
|---|
| save_rxn_data | rxn_index :int, system_time, time_step,
increment_vector_single_rxn: Union[np.array, None],
aborted=False,
rate=None,
caption="" | None |
Save up diagnostic data for 1 reaction, for a simulation step
(by convention, regardless of whether the step is completed or aborted)
:param rxn_index: The integer index (0-based) to identify the reaction of interest
:param system_time: The START time of the reaction step
:param time_step: The duration of the current simulation step
:param increment_vector_single_rxn: A Numpy array of size equal to the total number of chemical species,
containing the "delta concentrations" caused by this reaction
for ALL the chemicals (whether involved in the reaction or not);
it may be None if the current reaction step was aborted
Note: diagnostic data is saved only for the chemicals involved in this reaction
:param aborted: True is the current reaction step was aborted (i.e. will get repeated);
False (default) for normal situations
:param rate: [OPTIONAL] The value of the reaction rate (aka reaction velocity) at this step
:param caption: [OPTIONAL] string to describe the snapshot
:return: None
|
| name | arguments | returns |
|---|
| save_diagnostic_aborted_rxns | system_time, time_step,
caption="" | None |
Save up diagnostic data, for ALL reactions, in case of aborted simulation step
:param system_time: The START time of the reaction step
:param time_step: The duration of the current simulation step
:param caption: [OPTIONAL] string to describe the snapshot
:return: None
|
| name | arguments | returns |
|---|
| annotate_abort_rxn_data | msg: str | None |
Store the given value in the caption field of the last record
for EACH of the reaction-specific dataframes.
Also, set the "aborted" fields to "True"
:param msg: Value to set the comment field to
:return: None
|
| name | arguments | returns |
|---|
| get_rxn_rates | rxn_index :int | Union[pd.DataFrame, None] |
Return a Pandas dataframe with 2 columns: "START_TIME" and "rate",
with the rates of the specified reaction at those times.
Note that the dataframe will have 1 LESS ROW than a corresponding dataframe of concentration history,
because the rate at the final time won't be known (since that time would be the start of a simulation step
that has not been done)
Also, aborted time steps are eliminated (only the rate of the final "re-do" is included)
:param rxn_index: The integer index (0-based) to identify the reaction of interest
:return: A Pandas dataframe with times and their corresponding reaction rates
|
| name | arguments | returns |
|---|
| get_rxn_data | rxn_index :int, head=None, tail=None,
t=None, print_reaction=True | Union[pd.DataFrame, None] |
Return a Pandas dataframe with the diagnostic run data of the requested SINGLE reaction,
from the time that the diagnostics were enabled by instantiating this class.
In particular, the dataframe contains the reaction rate at the start time,
and the "Delta" values for each of the chemicals
involved in the reaction - i.e. the change in their concentrations
over the time interval that *STARTS* at the value in the "START_TIME" column.
(So, there'll be no row with the final current System Time)
Note: entries are always added, even if an interval run is aborted and automatically re-done;
therefore, some entries will be duplicates in the "START_TIME" column.
Those entries with have a value of True in the "aborted" column.
Optionally, print out a brief description of the reaction.
Optionally, limit the dataframe to a specified numbers of rows at the end,
or just return one entry corresponding to a specific time
(the row with the CLOSEST time to the requested one, which will appear in an extra column
called "search_value")
:param rxn_index: The integer index (0-based) to identify the reaction of interest
:param head: (OPTIONAL) Number of records to return,
from the start of the diagnostic dataframe.
:param tail: (OPTIONAL) Number of records to return,
from the end of the diagnostic dataframe.
If either the "head" arguments is passed, this argument will get ignored
:param t: (OPTIONAL) Individual time to pluck out from the dataframe;
the row with closest time will be returned.
If this parameter is specified, an extra column - called "search_value" -
is inserted at the beginning of the dataframe
If either the "head" or the "tail" arguments are passed, this argument will get ignored
:param print_reaction: (OPTIONAL) If True (default), concisely print out the requested reaction
:return: If present, return a Pandas data frame with (all or some of)
the diagnostic data of the specified reaction.
Columns of the dataframes:
'START_TIME','time_step','aborted','Delta A','Delta B'...,'rate','caption'
If not present, return None
|
| name | arguments | returns |
|---|
| save_diagnostic_conc_data | system_data, system_time, caption="" | None |
Save the diagnostic concentration data during the run, indexed by the current System Time.
Note: if an interval run is aborted, by convention NO entry is created here
:return: None
|
| name | arguments | returns |
|---|
| get_diagnostic_conc_data | self | pd.DataFrame |
Return the diagnostic concentration data saved during the run.
This will be a complete set of simulation steps,
even if the user elected to only save part of the history during the run.
Note: if the run of an interval step is aborted,
by convention NO entry is created here
:return: A Pandas dataframe, with the columns:
'TIME' 'A' 'B' ... 'caption'
where 'A', 'B', ... are the labels of all the chemicals
|
| name | arguments | returns |
|---|
| save_diagnostic_decisions_data | system_time, data :dict,
delta_conc_arr :Union[np.ndarray, None], caption="" | None |
Used to save the diagnostic concentration data during the run, indexed by the given System Time.
Note: if an interval run is aborted, by convention an entry is STILL created here
:param system_time:
:param data:
:param delta_conc_arr: A Numpy array of "delta concentrations". EXAMPLE: array[1.23, 52.2]
:param caption: [OPTIONAL] String with a caption for this record
:return: None
|
| name | arguments | returns |
|---|
| get_decisions_data | self | pd.DataFrame |
Determine and return the diagnostic data about concentration changes at every step - by convention,
EVEN aborted ones
:return: A Pandas dataframe with a "TIME" column, and columns for all the "Delta concentration" values
|
| name | arguments | returns |
|---|
| explain_reactions | self | bool |
Provide a detailed explanation of all the steps of the reactions,
from the saved diagnostic data
WARNING: Currently designed only for exactly 2 reactions!
:return: True if the diagnostic data is consistent for all the steps of all the reactions,
or False otherwise
|
| name | arguments | returns |
|---|
| explain_time_advance | return_times=False, silent=False, sys_history=None | Union[None, tuple] |
Use the saved-up diagnostic data, to print out details of the timescales of the reaction run
If diagnostics weren't enabled ahead of calling this function, an Exception is raised
EXAMPLE of output:
From time 0 to 0.0304, in 17 FULL steps of 0.0008
(for a grand total of 38 FULL steps)
:param return_times: If True, all the critical times (times where the interval steps change)
are saved and returned as a list
:param silent: If True, nothing gets printed out
:param sys_history: [OPTIONAL] The system history.
If passed, use it in lieu of the diagnostic data;
a consideration is the fact that the user might only have asked
for PART of the history to be saved
:return: Depending on the argument "return_times", it returns either None, or a pair with 2 lists:
1 - list of time values
2 - list of step sizes (will have one less element than the first list)
|
| name | arguments | returns |
|---|
| stoichiometry_checker | rxn_index :int, conc_arr_before: np.array, conc_arr_after: np.array | bool |
For the indicated reaction, investigate the change in the concentration of the involved chemicals,
to ascertain whether the change is consistent with the reaction's stoichiometry.
See https://life123.science/reactions
IMPORTANT: this function is currently meant for simulations involving only 1 reaction
NOTE: the concentration changes in chemicals not involved in the specified reaction are ignored
:param rxn_index: The integer index (0-based) to identify the reaction of interest
:param conc_arr_before: Numpy array with the concentrations of ALL the chemicals (whether involved
in the reaction or not), in their index order, BEFORE the reaction step
:param conc_arr_after: Same as above, but after the reaction
:return: True if the change in reactant/product concentrations is consistent with the
reaction's stoichiometry, or False otherwise
|
| name | arguments | returns |
|---|
| stoichiometry_checker_entire_run | self | bool |
Verify that the stoichiometry is satisfied in all the reaction steps,
using the diagnostic data from an earlier run
IMPORTANT: this function is currently meant for simulations involving only 1 reaction
:return: True if everything checks out, or False otherwise
|