diffpy.pdffit2.pdffit2

Module pdffit2

pdffit2 - interface to the core calculation routines in C++

Functions

[hide private]

alloc(...)
Allocate space for pdf data

bond_angle(...)
Return bond angle between three atoms.

bond_length_atoms(...)
Return a tuple of (dij, ddij) for distance between two atoms and its standard deviation.

bond_length_types(...)
Return bond lengths between two elements within given bounds

calc(...)
calculate pdf from data

constrain_int(...)
Constrain refined variable to integer.

constrain_str(...)
Constrain refined variable to string.

create(...)

delta1(...)
Pointer to variable delta1.

delta2(...)
Pointer to variable delta2.

dscale(...)
Pointer to variable dscale.

fixpar(...)
Fix value of parameter.

freepar(...)
Free parameter.

getR(...)
Get list of r-values for plotting.

get_atom_types(...)
Get ordered unique symbols of atoms in the phase.

get_atoms(...)
Get element symbols of atoms in the phase.

get_scat(...)
Return scattering factor for given element.

get_scat_string(...)
Return string with scatter details.

getcrw(...)
Get cumulative Rw for the current dataset.

getpar(...)
Get value of parameter

getpdf_diff(...)
Get list of differences between observed and fitted PDF points.

getpdf_fit(...)
Get list of calculated pdf points.

getpdf_obs(...)
Get list of observed (theory) pdf points.

getrw(...)
Get rw of fit.

getvar(...)
Get variable value.

is_element(...)
Check if element or isotope is defined in the built-in periodic table.

lat(...)
Pointer to refinable variable lat.

num_atoms(...)
Get the number of atoms in the current phase.

num_datasets(...)
Get the number of loaded datasets.

num_phases(...)
Get the number of loaded phases.

occ(...)
Pointer to refinable variable occ.

pdesel(...)
Deselect phase in focus.

pdfrange(...)
Set r-range of pdf.

phase_fractions(...)
Return relative phase fractions for current dataset scattering type

pscale(...)
Pointer to variable pscale.

psel(...)
Select phase in focus.

qbroad(...)
Pointer to variable qbroad.

qdamp(...)
Pointer to variable qdamp.

rcut(...)
Pointer to nonvariable rcut.

read_data(...)
Read data file into memory.

read_data_arrays(...)
Read data from arrays into memory.

read_data_string(...)
Read data from string into memory.

read_struct(...)
Read structure file into memory.

read_struct_string(...)
Read structure file into memory from a c-string.

redirect_stdout(...)
Redirect engine output to a file-like object.

refine(...)
refine model to pdf data

refine_step(...)
Make one step in the refinement process.

reset(...)
reset pdf data

reset_scat(...)
Reset scattering factor for given element.

save_dif(...)
Save pdf difference to file

save_pdf(...)
Save calculated pdf to file

save_res(...)
Save residual to file

save_struct(...)
Save refined structure to file

selectAll(...)
Include all atoms in 'i' or 'j' pair of PDF calculation.

selectAtomIndex(...)
Include atom of given index in 'i' or 'j' pair of PDF calculation.

selectAtomType(...)
Include element in 'i' or 'j' pair of PDF calculation.

selectNone(...)
Include all atoms in 'i' or 'j' pair of PDF calculation.

set_scat(...)
Set custom scattering factor for given element.

setdata(...)
Set data in focus.

setpar_RV(...)
Set parameter value via refined variable.

setpar_dbl(...)
Set parameter value.

setphase(...)
Set phase in focus.

setvar(...)
Set variable to value.

show_struct(...)
Show structure.

spdiameter(...)
Pointer to variable spdiameter.

sratio(...)
Pointer to variable sratio.

stepcut(...)
Pointer to nonvariable stepcut.

u11(...)
Pointer to refinable variable u11.

u12(...)
Pointer to refinable variable u12.

u13(...)
Pointer to refinable variable u13.

u22(...)
Pointer to refinable variable u22.

u23(...)
Pointer to refinable variable u23.

u33(...)
Pointer to refinable variable u33.

x(...)
Pointer to refinable variable x.

y(...)
Pointer to refinable variable y.

z(...)
Pointer to refinable variable z.

Variables

[hide private]

__package__ = None

Function Details

[hide private]

bond_length_types(...)

Return bond lengths between two elements within given bounds

a1    -- symbol of the first element in pair or 'ALL'
a2    -- symbol of the second element in pair or 'ALL'
lb    -- lower bound for bond lengths
ub    -- upper bound for bond lengths

Return a dictionary of distance data containing:

dij  : list of bond lenghts within given bounds
ddij : list of bond legnth standard deviations
ij0  : list of tupled pairs of indices starting at 0
ij1  : list of tupled pairs of indices starting at 1

phase_fractions(...)

Return relative phase fractions for current dataset scattering type

Return a dictionary of relative phase fractions:

atom    -- list of fractions normalized to atom count
stdatom -- errors of atom count fractions
cell    -- list of fractions normalized to unit cell count
stdcell -- errors of unit cell count fractions
mass    -- list of relative weight fractions
stdmass -- errors of relative weight fractions