About FIX file


How to import configuration files for FIX

During analysis, it is sometimes necessary to reload the results of a previous analysis. Currently, when the program FIX is restarted, the context of FIX when it was last terminated is reloaded.

For example, in the situation

  • First run: Searched bifurcation of equilibrium point A.
  • Second run: Searched bifurcation of limit cycle.
  • Third run: Searched bifurcation of equilibrium point B.
  • Fourth run: Searched bifurcation of equilibrium point A again.

At the fourth start of FIX, the information on equilibrium point B calculated at the third run of FIX is reloaded. To resume bifurcation point search of equilibrium point A conducted in the first run, PP must be restarted to obtain the information on equilibrium point A and pass the information to FIX.

To reduce such inconvenience, when the program FIX is terminated, it is possible to save the current status, including information of the configuration for FIX, into a file.*1

The current status of FIX are saved as an XML formatted file. The following is an example of a configuration file for an equilibrium point observed in the Hodgkin-Huxley equation.

index.php?plugin=attach&refer=aboutFIX_file&openfile=dataFIX.png

The following steps are used to import the configuration files saved for each condition.

  1. Start up FIX ( Select PP: Program-> FIX.)

    index.php?plugin=attach&refer=aboutFIX_file&openfile=startFIX.png

  2. The following shows the state when FIX starts up at first time.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=startFIX2.png

  3. Select File -> Import -> FIX save file.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX.png

  4. Start up FIX save file selection window.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX2.png

  5. Select the FIX save file.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX3.png

  6. When the file have imported, the saved data are reflected to each field.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX4.png



How to save the configured state of FIX

During analysis, it is sometimes necessary to reload the results of a previous analysis. Currently, when the program FIX is restarted, the context of FIX when it was last terminated is reloaded.

For example, in the situation

  • First run: Searched bifurcation of equilibrium point A.
  • Second run: Searched bifurcation of equilibrium point B.
  • Third run: Searched bifurcation of limit cycle.
  • Fourth run: Searched bifurcation of equilibrium point B again.

At the fourth start of FIX, the information on the bifurcation search of the limit cycle calculated at the third run of FIX is reloaded. If the information regarding the search of the bifurcation point of equilibrium point B was saved, it can be reused for analysis at another time.

Therefore, it is possible to save the current status, including the configuration information. To save the configurations into a file, follow the steps shown below.

  1. Select File -> Export -> FIX save file.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX.png

  2. Write the save file name. The default extension is .fixd. It's also able to change the extension.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX2.png

  3. The produced file is an XML formatted file as follows:

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX3.png



How to import an initial value file edited as a text file

0 is the input for all Initial state fields and 1 is the input for all Parameters fields (figure below) when starting for the first time. Correct information on the attractor to be analyzed must be given in the Initial state and Parameters fields when searching for bifurcation points. This indicates that information such as the values of the state variables, the parameters, the period of a periodic solution, and the return time of a limit cycle, and the configuration of Poincare section are necessary. Although such information can be manually entered from a GUI panel, the contents of a file can be reflected in the respective fields by making a text file following the rules below and importing the file, at least for values of state variable and parameters.

index.php?plugin=attach&refer=aboutFIX_file&openfile=startFIX2.png

  1. Prepare a text file describing parameters and state variables in this order.*2.Check the order of the parameters using a web browser.*3 State variables are placed from above in the order x[1], x[2], ・・・, x[n].
    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX5.png

  2. Select File -> Import -> Text data.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX6.png

  3. Select the text file from the file selection window, and import the file.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX7.png

  4. The state after the import are reflected to the field of the state variables and parameters.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=importFIX8.png

Actually, knowledge of only state variable and parameter variables does not mean FIX will operate normally. Additional information is necessary, such as the period of a periodic solution or the return time of a limit cycle. Usage of this mode is meaningful only if such necessary additional information is known. If not, this mode should not be used.



How to produce a text file composed of initial values and parameters

This is how to produce a text file composed of a list of state variables and parameters.

  1. Assume that the values in the fields of Initial states and Parameter in the Main panel were the values in the following figure.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX4.png

  2. Select File -> Export -> Text Data.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX5.png

  3. Write the save file name. The default extension is .iv. It's also able to change the extension.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX6.png

  4. After Export, the following text file is produced.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=exportFIX7.png



How to import initial conditions to run FIX

The following figure shows a situation when FIX is started right after a Project is generated. Arbitrary values are input in the fields of Initial states and Parameters. FIX cannot run from this state, and apropriate initial conditions must be given. Thus, PP is used to find attractors. The following steps are used to import the values of state variables and parameters of an attractor fonoud using PP, into FIX.

  1. Find some attractor with a simulation using PP, and export the conditions from PP. For the steps, see How to pass the attractor information to FIX tool (part 1) or How to pass the attractor information to FIX tool (Part 2).
  1. Start up FIX as PPProgram -> FIX.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=startFIX.png

  2. The following shows the state when FIX starts up at first time.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=startFIX2.png

  3. Select Tools -> Import initial point.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=PPtoFIX.png

  4. The attractor information is imported to each fields.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=PPtoFIX2.png

Aside from the values of the state variables and parameters, the following necessary information can also be transferred from PP to FIX:

  1. Is the attractor an equilibrium point or a limit cycle ?
  2. In case of a limit cycle, where is the Poincare section configured ?
  3. What is the period of a limit cycle ?
  4. How long is the period of a periodic point ?
  5. What type of ODE Solver was used ?



How to save various information as data when the bifurcation of an equilibrium point are searched by changing system parameters

When bifurcations of an equilibrium point are searched by changing system parameters, it may need to know the change of statuses such as coordinates of the equilibrium point or the values of the eigenvalues later. Here, if various information during the search of a bifurcation point can be saved as data, it is easier to reproduce the change in status. The following steps show how to save various information as data when users investigate bifurcations of the equilibrium point.

  1. Check the checkbox File name in Output field in the FIX main panel. By default, the checkbox is not checked the first time.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC.png

  2. Input a File name. In default settings, the data file is saved as fix.out. The file name can be changed into something easier to identify.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC2.png

    (a) Default settings

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveEq.png

    (b) Example where the file name was changed to Eq.out because it is the bifurcation search data of an equilibrium point.

  3. Start the bifurcation point search. Click the Start Button. Various information will be shown in the list box during the search.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveEq2.png

  4. The data is saved in the FIX_data directory in the Project directory.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC5.png

  5. The data is a text formatted file as shown below.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveEq3.png

The data is described in the following order:

  • Iterations to convergence in the Newton method, para(X), para(Y), x[1], x[2],・・・,x[n], first eigenvalue (real part) , first eigenvalue (imaginary part), first eigenvalue (absolute value), ・・・, ・・・, n-th eigenvalue (real part), n-th eigenvalue (imaginary part), n-th eigenvalue (absolute value), Jacobian, period.

However, since there is no period for the equilibrium point, zero is always displayed.



How to save various information as data when bifurcations of a limit cycle are searched by changing system parameters

When bifurcations of a limit cycle are searched by changing system parameters, it may need to know the change of statuses such as the period of the limit cycle, the local coordinates on the Poincare section or the values of the eigenvalues later. Here, if various information during the search of a bifurcation point can be saved as data, it is easier to reproduce the change in status. The following steps show how to save various information as data when users investigate bifurcations of limit cycles.

  1. Check the checkbox File name in Output field in the FIX main panel. By default, the checkbox is not checked the first time.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC.png

  2. Input a File name. In default settings, the data file is saved as fix.out. The file name can be changed into something easier to identify.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC2.png

    (a) Default settings

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC3.png

    (b) Example where the file name was changed to LC.out because it is the bifurcation search data of a limit cycle.

  3. Start the bifurcation point search. Click the Start Button. Various information will be shown in the list box during the search.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC4.png

  4. The data is saved in the FIX_data directory in the Project directory.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC5.png

  5. The data is a text formatted file as shown below.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC6.png

The data is described in the following order:

  • Iterations to convergence in the Newton method, para(X), para(Y), x[1], x[2],・・・,x[n], first eigenvalue (real part) , first eigenvalue (imaginary part), first eigenvalue (absolute value), ・・・, ・・・, n-th eigenvalue (real part), n-th eigenvalue (imaginary part), n-th eigenvalue (absolute value), Jacobian, period.

Here, notice that each value of the state variables represents ''local coordinates on the Poincare section. Thus, the coordinates of the periodic point of the Poincare map are saved. Also, note that the period is the return time of the limit cycle.



How to save various information as data when bifurcations of a periodic solution or periodic point (fixed point) are searched by changing system parameters

When bifurcations of a periodic solution or a periodic point are searched by changing system parameters, it may need to know the change of statuses such as the period of the periodic solution or the values of the eigenvalues later. Here, if various information during the search of a bifurcation point can be saved as data, it is easier to reproduce the change in status. The following steps show how to save various information as data when users investigate bifurcations of periodic solutions or periodic points.

  1. Check the checkbox File name in Output field in the FIX main panel. By default, the checkbox is not checked the first time.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC.png

  2. Input a File name. In default settings, the data file is saved as fix.out. The file name can be changed into something easier to identify.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=saveLC2.png

    (a) Default settings

    index.php?plugin=attach&refer=aboutFIX_file&openfile=savePD.png

    (b) Example where the file name was changed to 5PD.out because it is the bifurcation search data of a 5-periodic point.

  3. Start the bifurcation point search. Click the Start Button. Various information will be shown in the list box during the search.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=savePD2.png

  4. The data is saved in the FIX_data directory in the Project directory.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=savePD3.png

  5. The data is a text formatted file as shown below.

    index.php?plugin=attach&refer=aboutFIX_file&openfile=savePD4.png

The data is described in the following order:

  • non-autonomous system
    • Iterations to convergence in the Newton method, para(X), para(Y), x[1], x[2],・・・,x[n], first eigenvalue (real part) , first eigenvalue (imaginary part), first eigenvalue (absolute value), ・・・, ・・・, n-th eigenvalue (real part), n-th eigenvalue (imaginary part), n-th eigenvalue (absolute value), Jacobian, period,
  • discrete system
    • Iterations to convergence in the Newton method, para(X), para(Y), x[1], x[2],・・・,x[n], first eigenvalue (real part) , first eigenvalue (imaginary part), first eigenvalue (absolute value), ・・・, ・・・, n-th eigenvalue (real part), n-th eigenvalue (imaginary part), n-th eigenvalue (absolute value), Jacobian, period,

Here, notice that each value of the state variables represents ''local coordinates on the Poincare section. Thus, the coordinates of the periodic point of the Poincare map are saved. Also, note that the period is the return time of the periodic solution in the non-autonomous system.




*1 see How to save the configured state of FIX
*2 This file is also text files produced by using non-BunKi program (However, to run FIX, it is not enough to prepare the set of the values of parametes and state variables. The additonal information such as the configuration of the Poincare section, the period of a limit cycle, a periodic solution or a periodic point must be set.). The text file can be also produced from PP using a method How to produce a text file composed of initial values and parameters.
*3 See also How to check the generated system.

Front page   Edit Freeze Diff Backup Upload Copy Rename Reload   New List of pages Search Recent changes   Help   RSS of recent changes
Last-modified: 2009-07-23 (Thu) 20:13:30 (3592d)