Class PdfFitSandbox

Get resulting list of Fitting and Calculations
        

Create sandbox dictionary suitable for script evaluation

returns sandbox dictionary

Execute scriptfile in this sandbox.  Before it is executed, change
to script directory and shadow pdffit and pdffit2 modules

scriptfile  --  path to the script to be loaded

Read structure from file into memory.

filename  -- name of file from which to read structure

Raises:
    pdffit2.calculationError when a lattice cannot be created from the
    given structure
    pdffit2.structureError when a structure file is malformed
    IOError when the file cannot be read from the disk

Read structure from a string into memory.

s    -- string containing the contents of the structure file
name -- tag with which to label structure

Raises:
    pdffit2.calculationError when a lattice cannot be created from the
    given structure
    pdffit2.structureError when a structure file is malformed

Read pdf data from file into memory.

filename -- name of file from which to read data
stype    -- 'X' (xray) or 'N' (neutron)
qmax     -- maximum q value
qdamp    -- instrumental q-resolution factor

Raises:
    IOError when the file cannot be read from disk

Read pdf data from a string into memory.

s       -- string containing the contents of the data file
stype   -- 'X' (xray) or 'N' (neutron)
qmax    -- maximum q value
qdamp   -- instrumental q-resolution factor
name    -- tag with which to label data

Read pdf data into memory from lists.

All lists must be of the same length.
stype       -- 'X' (xray) or 'N' (neutron)
qmax        -- maximum q value
qdamp       -- instrumental q-resolution factor
r_data      -- list of r-values
Gr_data     -- list of G(r) values
dGr_data    -- list of G(r) uncertainty values
name        -- tag with which to label data

Raises:
    NotImplementedError

Set the range of the fit in specified dataset.

iset    -- data set to consider, indexed from 1 or 'ALL'
rmin    -- minimum r-value of fit
rmax    -- maximum r-value of fit

Allocate space for a PDF calculation.

The structure from which to calculate the PDF must first be imported with
the read_struct() or read_struct_string() method.
stype   -- 'X' (xray) or 'N' (neutron)
qmax    -- maximum q value
qdamp   -- instrumental q-resolution factor
rmin    -- minimum r-value of calculation
rmax    -- maximum r-value of calculation
rlen    -- number of data points in calculation

Calculate the PDF of the imported structure.

Space for the calculation must first be allocated with the alloc()
method.

Raises:
    ControlRuntimeError when space for calculation has not been
    allocated

Fit the theory to the imported data.

toler   --  tolerance of the fit, ignored for now

Run a single step of the fit.

toler   --  tolerance of the fit

Raises:
    NotImplementedError - I am not importing such beast

Save calculated or fitted PDF to file.  Ignored.
        

Save calculated or fitted PDF to string.

iset    -- data set to save, indexed from 1

Raises:
    NotImplementedError - we cannot return anything without engine.

Save data and fitted PDF difference to file.  Ignored.

iset    -- data set to save
fname   -- file to write to

Save data and fitted PDF difference to string.

iset    -- data set to save

Raises:
    NotImplementedError - we cannot return anything without engine.

Save fit-specific data to file.  Ignored.
        

save_res_string() --> Save fit-specific data to a string.

Raises:
    NotImplementedError - we cannot return anything without engine.

Save structure resulting from fit to file.  Ignored.

ip    -- phase to save

Save structure resulting from fit to string.

ip    -- phase to save

Raises:
    NotImplementedError - we cannot return anything without engine.

Print structure resulting from fit.  Ignored.

ip    -- phase to display

Constrain a variable to a parameter.

A variable can be constrained to a number or equation string.
var     -- variable to constrain, such as x(1)
par     -- parameter which to constrain the variable. This can be
           an integer or an equation string containing a reference
           to another parameter. Equation strings use standard c++
           syntax. The value of a constrained parameter is accessed
           as @p in an equation string, where p is the parameter.
           e.g.
           >>>  constrain(x(1), 1)
           >>>  constrain(x(2), "0.5+@1")
fcon    -- 'IDENT', 'FCOMP', or 'FSQR', old-style constraint formulas:
               'IDENT'  @par
               'FCOMP'  1.0-@par
               'FSQR'   @par*@par

Set value of constrained parameter.

idx     --  parameter index
val     --  Either a numerical value or a reference to variable

Raises:
    KeyError when parameter is yet to be constrained

Get value of parameter.

idx     --  parameter index

Raises:
    KeyError if parameter does not exists

Fix a parameter.

idx     --  parameter index

Fixed parameters are not fitted in a refinement. Passed parameter can be
'ALL', in which case all parameters are fixed.

Raises:
    ControlKeyError if parameter does not exists

Free a parameter.

idx     --  parameter index

Freed parameters are fitted in a refinement. Passed parameter can be
ALL, in which case all parameters are freed.

Raises:
    ControlKeyError if parameter does not exists

Set the value of a variable.

Raises:
    ControlKeyError if variable does not yet exist

Get stored value of a variable.

Raises:
    ControlKeyError if variable index does not exist

returns value of variable var.

Get goodness of fit value, rw.
Raises:
    NotImplementedError - we cannot return anything without engine.

Get r-points used in the fit.

This function should only be called after data has been loaded or
calculated. Before a refinement, the list of r-points will reflect the
data. Afterwords, they will reflect the fit range.

Raises:
    NotImplementedError - we cannot return anything without engine.

Get fitted PDF.

This function should only be called after a refinement or refinement
step has been done.

Raises:
    NotImplementedError - we cannot return anything without engine.

Get observed PDF.

This function should only be called after data has been loaded or
calculated. Before a refinement, the list of r-points will reflect the
data. Afterwords, they will reflect the fit range.

Raises:
    NotImplementedError - we cannot return anything without engine.

Get atoms in the structure.

This function should only be called after a structure has been loaded.

Raises:
    NotImplementedError - we cannot return anything without engine.

Switch to phase ip.

ip  --  phase index starting from 1

All parameters assigned after this method is called refer only to the
current phase.

Raises:
    IndexError if phase ip does not exist

Set specified dataset in focus.

iset  --  dataset index starting from 1

Raises:
    IndexError if dataset iset does not exist

Associate the current data set with phase ip.

ip -- phase index starting from 1

Raises:
    NotImplementedError

Unassociate the current data set with phase ip.

ip -- phase index starting from 1

Raises:
    NotImplementedError

Select atoms for calculating partial PDF

ip  --  phase index starting from 1, if set to 'ALL' isel applies
        to all phases
i  --   atom index starting from 1, if set to 'ALL', select all atoms

Raises: 
    NotImplementedError

Deselect atoms for calculating partial PDF

ip  --  phase index starting from 1, if set to 'ALL' isel applies
        to all phases
i  --   atom index starting from 1, if set to 'ALL', select all atoms

Raises: 
    NotImplementedError

Select atoms for calculating partial PDF

ip  --  phase index starting from 1, if set to 'ALL' jsel applies
        to all phases
i  --   atom index starting from 1, if set to 'ALL', select all atoms

Raises: 
    NotImplementedError

Deselect atoms for calculating partial PDF

ip  --  phase index starting from 1, if set to 'ALL' jsel applies
        to all phases
i  --   atom index starting from 1, if set to 'ALL', select all atoms

Raises: 
    NotImplementedError

bang(ia, ja, ka) --> Get the bond angle defined by atoms ia, ja, ka.

Raises:
    NotImplementedError

blen(ia, ja) --> Get bond between atoms ia and ja.  Ignored.

blen(a1, a2, lb, ub) --> Print length of all a1-a2 bonds in range
[lb,ub], where a1 and a2 are integers representing atom types. 1
represent the first type of atom in the phase, 2 represents the second
type of atom in the structure, an so on. Either a1 or a2 can be the
keyword ALL, in which all atom types are used for that end of the
calculated bonds.

Print scattering length for all atoms.  Ignored.

stype -- 'X' (xray) or 'N' (neutron).

Get string with scattering length for all atoms.

stype -- 'X' (xray) or 'N' (neutron).

Raises:
    NotImplementedError

Return scattering factor of given element.
Not supported.

Raises: 
    NotImplementedError

set_scat() --> Change neutron or x-ray scattering factor for given
element.  Not supported.

Raises: 
    NotImplementedError

reset_scat() --> reset scattering factor.  Not supported.

Raises: 
    NotImplementedError

Get number of atoms in current phase.

Raises:
    ControlKeyError if phase does not exists

lat(n) --> Get reference to lattice variable n.

n can be an integer or a string representing the lattice variable.
1 <==> 'a'
2 <==> 'b'
3 <==> 'c'
4 <==> 'alpha'
5 <==> 'beta'
6 <==> 'gamma'

u11(i) --> Get reference to U(1,1) for atom i.

U is the anisotropic thermal factor tensor.

u22(i) --> Get reference to U(2,2) for atom i.

U is the anisotropic thermal factor tensor.

u33(i) --> Get reference to U(3,3) for atom i.

U is the anisotropic thermal factor tensor.

u12(i) --> Get reference to U(1,2) for atom i.

U is the anisotropic thermal factor tensor.

u13(i) --> Get reference to U(1,3) for atom i.

U is the anisotropic thermal factor tensor.

u23(i) --> Get reference to U(2,3) for atom i.

U is the anisotropic thermal factor tensor.

pscale() --> Get reference to pscale.

pscale is the fraction of the total structure that the current phase
represents.

pfrac() --> Deprecated reference to pscale.

pscale is the fraction of the total structure that the current phase
represents.

spdiameter() --> Get reference to spdiameter.

Diameter value for the spherical particle PDF correction. 
Spherical envelope is not applied when spdiameter equals 0.

stepcut() --> Get reference to stepcut.

stepcut is cutoff radius for empirical step-function PDF envelope.
Step cutoff is not applied when stepcut equals 0.
Non-refineable variable.  

sratio() --> Get reference to sigma ratio.

The sigma ratio determines the reduction in the Debye-Waller factor for
distances below rcut.

srat() --> Deprecated reference to sigma ratio.

The sigma ratio determines the reduction in the Debye-Waller factor for
distances below rcut.

delta2() --> Get reference to delta2

The phenomenological correlation constant in the Debye-Waller factor.
The (1/R^2) peak sharpening factor.

dscale() --> Get reference to dscale.

The data scale factor.

qsig() --> Deprecated reference to qdamp.

instrument q-resolution factor.

qdamp() --> Get reference to qdamp.

instrument q-resolution factor.

qalp() --> Deprecated reference to qbroad.

Quadratic peak sharpening factor.

qbroad() --> Get reference to qbroad.

Quadratic peak sharpening factor.

rcut() --> Get reference to rcut.

rcut is the value of r below which peak sharpening, defined by the sigma
ratio (sratio), applies.