Tutorials¶
Tutorial 1. Using GEMS from command line¶
Note
Updated for GEMS 0.4
If you are familiar with Linux, you must be familiar with the use of a terminal prompt.
Command line options¶
From the prompt you can type $ ./gems.py -h will print all available options.
usage: gems.py [-h] [-s MOLECULE] [-f FILE] [-p] [-o ORDER] [-w FILE]
GEMS: The GEneral Microspeciation Solver v0.5
optional arguments:
-h, --help show this help message and exit
-s MOLECULE, --symmetry MOLECULE
display information on the molecule
-f FILE, --fit FILE load data in file and start computation
-p, --plot display window with plots
-o ORDER, --order ORDER
order of interactions to fit
-w FILE, --write FILE
write results in numpy array for later use
The most important option is -f FILE which loads an input file FILE, starts the calculation and output the result.
Tutorial 2: Obtaining information based on molecule symmetry¶
GEMS when used with the option -s
displays information about the microstates
and microsteps based on the symmetry provided. The symmetry of the molecule is described
by using characters to tag each one of the protonation centres and a number indicating
the multiplicity of said centres. For example, A2B
indicates a molecule with three
protonation centres where two of them are chemically equivalent. Any letter can be used
to indicate a protonation centre. A2B
, X2P
, BA2
and AAB
are equivalent and should yield the same result except with different labels and in
different order.
molecule symmetry: A2B
n = 0, 1 microstate(s): Ø
Ø + A -> A
Ø + B -> B
2 microstep(s)
n = 1, 2 microstate(s): B, A
B + A -> AB
A + A -> A2
A + B -> AB
3 microstep(s)
n = 2, 2 microstate(s): AB, A2
AB + A -> A2B
A2 + B -> A2B
2 microstep(s)
n = 3, 1 microstate(s): A2B
total microstates = 6
total microsteps = 7
Fitting information
first order parameters: 2
second order parameters: 2
third order parameters: 1
- - - - - - - - - - - - - -
total parameters: 5
The output is a list of each one of the macrostates, from n =0 to n =3. Inside each one of the macrostates there is a list of the possible microstates and microsteps.
You can try with any symmetry.
$./rungems.py -s A4B2
$./rungems.py -s A6B2C