CHANGES

From KaSim 3 to KaSim 4
=======================

- Options '-t' '-e' and '-p' are removed!

You should specify the limit of simulation by '-l' and the plot period
(how often you want a data line) by the "new" '-p'. These options are
by default in "simulated time unit" but you can switch to event using
'-u event'.

The motivation is interactivity. If you don't specify any limit, the
simulation will run forever.  (Use Ctrl-c to stop).

- Data files are printed using the comma separated value format
  (instead of space separated value) by default.

The default name of the output file is therefore 'data.csv'.

KaSim can also generate (based on the extension of the output file)
tsv or svg files.

The motivation is to deal with weird values (e.g. infinity, not a number) in a
way understood by (at least) Gnuplot, Python, Matlab, ...

- There is no special case for "observables"

Number of occurrences of the pattern pat is now written |pat| and it can
be placed in any algebraic expression.

To be concrete, you need to write
%var: 'o' |A(x!1),B(x!1)|
instead of
%var: 'o' A(x!1),B(x!1)
But you can write directly
%var: 'o' 1 + |A(x!1),B(x!1)| / 2
instead of
%var: 'tmp_o' A(x!1),B(x!1)
%var: 'o' 1 + 'tmp_o' / 2

As a (more or less direct) consequence, you can write
%init: "any algebraic expression" "mixture"
and
$TRACK "pattern" [true]

- Modification $STOP without argument does not dump a snapshot

Use $STOP "something" to get one

- Ctrl-c does not stop the simulation

It pauses and launches a toplevel in which you can do modification
(as in perturbations) and then (optionally) continue the simulation.

You can use '-mode batch' to get a Ctrl-c that does kill the simulation
(and more generally to get a KaSim that never asks questions) or '-mode
interactive' to pause the simulation just after the initialization
phase.

Concretely the old behavior of Ctrl-c and then y(es I want a snapshot)
is recovered by Ctrl-c and the modification $STOP "dump.ka"

- Rates for unary instances of rule involving ambiguous molecularity
  are in {} instead of ()