File doc/controls.txt; TRANSIENT V3.11; 18 Feb. 2006
(C) 2001-06 Miroslav Kolar

Control parameters, their default values and their purpose:
-------------------

monitor = 1
   Controls the level of diagnostic output (on screen) for transient calculations:
  -1 - Only t printed at "pr_Other" output times.
   0 - Only values of t and cDiffM printed at "pr_Other" output times.
   1 - Values of t, cDiffM (max c change), # of attempts, and total # of
	 runband Newton-Raphson (NR) iterations in all attempts are printed
	 after EACH time step.
   2 - During EACH time step a line with iter #, (fresidT), fresidM, node and equ #
	 where fresidM occurs, (cresidT), cresidM, and the corresponding node and
	 and equ #, are printed after each iteration; then a line which starts
	 with t, cDiffM, tStep, Scale = next_tStep/tStep ratio.
	 Also some details about repeated attempts are given, and output
	 to the two output files is flagged as outOTH and out.
   3 - In addition to 2, one more line is inserted indicating where
	 the maximum of cDiff occurs.
   In the last 4 cases the last line ends with the cumulative #s of time
   steps, attempts (calls to runband), and NR iterations (incl. those in
   unsuccessful attempts).

CmntC = #
   Character to mark the beginning of comment
   (i.e., not to be plotted) lines in the output files.
   May start a valid input line in input files.

steady = 0
   0 - The main purpose of this program: transient solution of
	 coupled reaction-diffusion equations in one spatial
	 variable; all control parameters listed below are used.
   1 - Only the steady state is calculated using the same evalf()
	 function as for transient solution, provided that it consistently
	 uses the global variable 'tStepInv' to calculate the contribution
	 of discretized time derivatives of concentrations to B[k][k]
	 (tStepInv = 1/tStep); only monitor (1=2) and CmntC are used.
   2 - Calculate steady state and then use it as the initial state for
	 the transient calculation (e.g., to check its stability).

Tau = 0.1
   "Implicitness" of the differencing scheme (in time; 0 <= Tau <= 1):
		 0	fully implicit
		 0.5	Crank-Nicholson
		 1	explicit
   Preferably use Tau = 0.5; if there are problems, try Tau < 0.5;
   in some cases, Tau = 0 may be the best.

NIG = 0.5
   New Initial Guess extrapolation factor (0<=NIG<=1) for the next time step:
   c_New_Initial_Guess = c + NIG * scale * (c - c_previous); where
   scale = (t_new - t) / (t - t_previous); t & c: current time and concentration

nIter = 10
   Desired number of NR iterations in runband() in each attempt

Prec = 0
   0 = default precision; reasonable values between -3 and 10;
   as Prec increases, the precision of the results increases but execution slows down

tStart = 0 sec
   Initial time (start of integration)

tEnd = 1.600000000000e+16 sec
   Final time (end of integration)

tStepInit = 0.01 sec
   Magnitude of the initial time step tStep

tStepMin = -1e-05 sec
   If > 0: the smallest allowed magnitude of the time step tStep;
   If < 0: |tStep| >= -tStepMin*tt, where tt is the (always positive) time
                elapsed from the beginning of a run

tStepMax = -0.1 sec
   If > 0: the largest allowed magnitude of the time step tStep;
   If = 0: |tStep| <= 0.1*|tEnd-tStart|;
   If < 0: |tStep| <= tStepInit-tStepMax*tt, where tt is the (always positive)
                time elapsed from the beginning of a run

tOutInit = 2.629800000000e+06 sec
   Initial time (tOut) for c profiles output

tOutMulF = 1.4
   Rate of increase of the time interval between subsequent c profiles outputs:
   Next_tOut = tOut + (tOut - previous_tOut) * tOutMulF

nOutOTH = -20
   pr_Other() is called at |nOutOTH|-1 regularly spaced time instants
   between 2 consecutive tOut (can be used for additional output).
   If nOutOTH<0, pr_Other calls need not be exactly equidistant in time.

sepProf = 1
   0 - Concentration profiles for all output times will be placed
	 into a single output file.
   1 - Profiles for each time will be placed into a separate file.
  -1 - No profiles file created. In addition, no diag file created.

strict = -1
   strict < 0: cDifMxf(t) is not used at all to calculate next tStep
	 which is determined only by nIter.
   strict = 0: cDiffM does usually not exceed cDifMxf(t) too much.
   strict = 1: cDiffM <= cDifMxf(t) is strictly enforced.
	 Here cDiffM is the maximum magnitude of the change in all c[][k]
	 over the whole tStep (while cresidM is over a single NR iteration only).
	 cDifMxf(t) is determined by input parameters cDifMxMode, cDifMxInit and
	 cDifMxEnd. Often strict<0 is good enough, and fast.

cDifMxMode = 2
   Mode of interpolating between cDifMxInit and cDifMxEnd in cDifMxf(t):
   0 - Max allowed change in c is constant and equal to cDifMxInit
   1 - Linear interpolation
   2 - Log-log linear: ln(cDifMxf) = linear function of ln(|t|)

cDifMxInit = 0.1
   Value of cDifMxf at t = tStart+sign(tEnd-tStart)*tStepInit

cDifMxEnd = 1e-09
   Value of cDifMxf at t = tEnd (needed only for cDifMxMode>0)

init_from_file = 
   Name of file containing the initial profiles; if nonnull, the
   user supplied function read_profiles() will be invoked just after
   Initialize(), and initial profiles set in Initialize() will be
   overwritten by those read in in read_profiles(). Can be used to
   continue an interrupted calculation (possibly after changing some
   parameters).