Structure modules#

Saxs#

Description#

Compute SAXS scattering intensities.

The q vectors are binned by their length using a binwidth given by -dq. Using the -nobin option the raw intensity for each q_{i,j,k} vector is saved using. Note that this only works reliable using constant box vectors! The possible scattering vectors q can be restricted by a miminal and maximal angle with the z-axis. For 0 and 180 all possible vectors are taken into account. For the scattering factor the structure fator is multiplied by a atom type specific form factor based on Cromer-Mann parameters. By using the -sel option atoms can be selected for which the profile is calculated. The selection uses the MDAnalysis selection commands.

Parameters#

atomgroupAtomGroup

Atomgroup on which the analysis is executed

noboindatabool

Do not bin the data. Only works reliable for NVT!

startqfloat

Starting q (1/nm)

endqfloat

Ending q (1/nm)

dqfloat

binwidth (1/nm)

mintheta float

Minimal angle (°) between the q vectors and the z-axis.

maxthetafloat

Maximal angle (°) between the q vectors and the z-axis.

outputstr

Output filename

concfreqint

Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.

verbosebool

Turn on more logging and debugging

Attributes#

results.qnp.ndarray

length of binned q-vectors

results.q_indicesnp.ndarray

Miller indices of q-vector (only if noboindata==True)

results.scat_factornp.ndarray

Scattering intensities

Diporder#

Description#

Calculate dipolar order parameters.

Calculations include the projected dipole density P_0⋅ρ(z)⋅cos(θ[z]), the dipole orientation cos(θ[z]), the squared dipole orientation cos²(Θ[z]) and the number density ρ(z).

Parameters#

atomgroupAtomGroup

Atomgroup on which the analysis is executed

dimint

Dimension for binning (x=0, y=1, z=2)

binwidthfloat

binwidth (nanometer)

comgroupAtomGroup

Perform the binning relative to the center of mass of the selected group.

centerbool

Perform the binning relative to the center of the (changing) box.

symbool

symmetrize the profiles

binmethodstr

binning method: center of mass (COM) or center of charge (COC)

make_wholebool

Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup

outputstr

Output filename

concfreqint

Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.

verbosebool

Turn on more logging and debugging

Attributes#

results.zlist

bins

results.P0np.ndarray

P_0⋅ρ(z)⋅cos(θ[z]) [e/nm²]

results.cos_thetanp.ndarray

cos(θ[z])

results.cos_2_thetanp.ndarray

cos²(Θ[z])

results.rhonp.ndarray

ρ(z) [1/nm³]

Debyer#

Description#

Calculate scattering intensities using the debye equation.

Parameters#

atomgroupAtomGroup

Atomgroup on which the analysis is executed

outfreq float :

Number of frames after which the output is updated.

outputstr

Output filename

startqfloat

Starting q (1/nm)

endqfloat

Ending q (1/nm)

dqfloat

binwidth (1/nm)

sincbool

Apply sinc damping

debyerstr

Path to the debyer executable

verbosebool

Turn on more logging and debugging

Attributes#

results.qnp.ndarray

length of binned q-vectors

results.scat_factornp.ndarray

Scattering intensities