# 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