Re: CST branch -- April 13, 2010 - 20:14

This is perfect!  Note that 'None' should not be a sting in the lists
but the special None object.  You will also have to append an empty
list between the two loops, and inside the second loop have a new data
container initialised and appended to the list at the current spin
position.  This should be safe to implement.

Cheers,

Edward


On 13 April 2010 19:48, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx> wrote:
> Hi,
> My idea is feeding Mf class with a list of spin-data in form of lists of
> parameters for each interaction. Considering following example of data for
> one particular spin:
>
> interactions      internuclei_distance  gratio_ext     csa      unit_vector
> 'dipole-dipole'               1.02e-10           2.67522e8   'None'
> [0.707,0.707,0.000]
> 'dipole-dipole'               1.50e-10           6.7283e7     'None'
> [0,866,0.000,0.500]
> 'csa1'                           'None'              'None'
> 120e-6    [0.000,0.000,1.000]
> 'csa2'                           'None'              'None'
> 50e-6      [1.000,0.000,0.000]
>
> each column represents a list containing internuclei_distances, gratio_exts,
> csas, unit_vectors ...
>
> So Mf class would get the lists of "interactions", "internuclei_distance",
> "gratio_ext"  ... for each spin and in the __init__() the loop will go first
> over the number of spins and then over the number of interactions i.e.:
>
> for i in xrange( self.num_spin )
>    for j in xrange( self.num_interactions[i] ):
>       self.data[i].interactions[j]=interactions[i][j]
>       self.data[i].internuclei_distance[j]=internuclei_distance[i][j]
>       self.data[i].gratio_ext[j] = gratio_ext[i][j]
>        .
>        .
>        .
>
> Best regards,
> Pavel
>
>
> On 12 April 2010 09:00, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > On 8 April 2010 17:23, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx> wrote:
> > > Hi,
> > > I would do it as you suggested by "list of list" architecture, the outer
> > > loop would correspond to the loop over spins and the inner loop over the
> > > interactions.
> > > to sum up, here are the suggested changes in the __init__() method
> > > (class
> > > Mf, file mf.py)
> > > currently it is necessary to load for all spins
> > > one unit vector for xh
> > > one bond length for xh
> > > one gyromagnetic ratio of attached nucleus (proton)
> > > one csa
> >
> > Hi,
> >
> > This is correct.
> >
> >
> > > this needs to be changed to:
> > > list of units vectors over all dipole-dipole interactions and two unit
> > > vectors for CST (this correspond to two axially symmetric chemical
> > > shielding
> > > tensors to which the asymmetric chemical shielding tensor can be
> > > decomposed)
> >
> > This is good.  What do you think of having special arguments for
> > these?  For example in the future someone may come up with a better
> > way to handle rhombic and non-collinear CSA (i.e. the spectral
> > densities are different in different directions).  So we could have a
> > system whereby the interactions are classified.  The first dimension
> > of the unit vector list of lists would be the interaction, the second
> > the spin pair, and the third are the 3D coordinates.  A second
> > argument such as 'interactions' could be added to identify each one.
> > I.e. it could be something like:
> >
> > ..., interactions=['dipole-dipole', 'dipole-dipole', 'csa_split1',
> > 'csa_split2'], ...
> >
> >
> > > list of bond lengths
> >
> > This first dimension can match the above 'interactions' arg.
> >
> >
> > > list of gyromagnetic constants of attached nuclei
> >
> > This can also match the interactions arg.  The 'gx' arg could be
> > renamed to gratio_spin and be a single value - the spin being looked
> > at doesn't change, just the interactions.  The 'gh' arg could be
> > changed to something like 'gratio_ext' and turned into a list matching
> > 'interactions'  It would then have a value if the interaction is
> > dipole-dipole, and be set to None for the CSA interactions.  We don't
> > need to specify that the interacting remote spin is covalently
> > attached though.
> >
> >
> > > two "csa" corresponding to mentioned CST tensors mentioned above
> >
> > This could also be a list corresponding to 'interactions'.  Set the
> > values when needed, otherwise use None for dipole-dipole, etc.  The
> > point of having these all lists of the same length is just so that you
> > don't have to deconvolute the incoming data to work out what belongs
> > to what.  You loop over 'interactions' in __init__() and pack the data
> > container using the appropriate data.  It will make the code much
> > cleaner.  What do you think?
> >
> > Regards,
> >
> > Edward