Commonly used parameters

This is a detailed explanation of a few input parameters that are most commonly used by MDANSE. A full list can be found in section Input Parameter Types.

Frames

Parameter	Format	Default Value	Description
First frame	int	0	The frame from which the analysis will begin, the first frame taken into account.
Last frame	int	Last frame	The frame until which the analysis proceeds. The last frame taken into account.
Frame step	int	1	Determines the periodicity of which steps are used and which are skipped. 1 means that all frames are read, 2 means every other is read, etc.

Correlation Frames

Parameter	Format	Default Value	Description
First frame	int	0	The frame from which the analysis will begin, the first frame taken into account.
Last frame	int	Last frame	The frame until which the analysis proceeds. The last frame taken into account.
Frame step	int	1	Determines the periodicity of which steps are used and which are skipped. 1 means that all frames are read, 2 means every other is read, etc.
Correlation frames	int	Last frame / 2	Determines the size of the correlation window (in frames). This determines the time range of the output of the analysis. See also Time Series.

Q shells

Input	Format	Default	Description
from	float	0	The lowest value of \(q\) to be used in \(\mathbf{q}\)-vector generation.
to	float	10	The highest value of \(q\) to be used in \(\mathbf{q}\)-vector generation.
by step of	float	1	The step by which \(q\) is incremented when changing from one \(\mathbf{q}\)-shell to the next one. Please adjust the width input parameter accordingly when changing the step.

The unit of the \(\mathbf{q}\)-vector length in MDANSE is \(\text{nm}^{-1}\).

Output trajectory

This is used in every converter, and a few analysis jobs that also output a trajectory (CenterOfMassesTrajectory, TrajectoryEditor).

Input	Format	Default	Description
filename	str		The full path to the new file that will be created by this run.
precision	int	64	Number of bits used for writing out floating point numbers. 64, 32 and 16 are possible
chunk size	int	128	Number of atoms to be included in a single chunk of the HDF5 datasets in the output trajectory. An entire chunk must be loaded to access any number in that chunk. Smaller number means faster analysis, but also larger files. There rarely any advantage to chunks smaller than 128.
compression	str	gzip	Can be ‘none’, ‘gzip’ or ‘lzf’. ‘none’ means no compression. For most trajectories, compressing the atom coordinate arrays visibly reduces the file size at an expense of only a minor slowing down.
log level	str	no logs	Can be “no logs”, “DEBUG”, “INFO”, “WARN”, “ERROR” or “CRITICAL”. Not relevant to the output trajectory itself, but will change the amount of output in the log file of the converter run.

Output files

Most analysis types define their output file using this.

Input	Format	Default	Description
filename	str		The full path to the new file that will be created by this run. Since multiple formats can be selected, it can be used as the base name to which different exten- sions will be appended for different output formats.
format	list[str]	MDAFormat	Can be [“MDAFormat”], [“TextFormat”] or both can be used with [“MDAFormat”, “TextFormat”]. MDA format is the only format used by the MDANSE_GUI.
log level	str	no logs	Can be “no logs”, “DEBUG”, “INFO”, “WARN”, “ERROR” or “CRITICAL”. Not relevant to the output trajectory itself, but will change the amount of output in the log file of the converter run.

Atom Selection

Atom Selection allows you to select any set of atoms and/or other particles. These selected particles are then the ones that are made the target of the analysis. There is no limit to which particles can be included in a selection, or to how many selections can be used simultaneously. Atom Selection is entirely optional; if it is omitted, all the particles in the simulation are used.

More information about atom selection can be found here: Atom Selection.

Atom Transmutation

Atom transmutation uses the same interface as atom selection. Once you have selected the atoms you wanted to transmute, you can choose what chemical elements to replace them with, and add this change to the total transmutation mapping.

Atom Charges

The partial charge setting uses the same interface as the atom selection. You will most likely need to create several selections one after another. Every time you have selected atoms which should have the same charge assigned, set their charge and reset the selection. Once all the charges have been set, confirm the changes by clicking “Use setting”.

q-vectors

\(\mathbf{q}\)-vectors can be created using several generators. The generators use different input parameters. The details are given here.

For vector generators requiring “shells” and “width” input, the “shell” input defines a range of bin centres, and “width” gives the bin width used for assigning vectors to shells. For example, shells = (4.0, 8.0, 2.0) will generate 3 bins, centred on 4.0, 6.0 and 8.0 \(\text{nm}^{-1}\). The bins will contain vectors with \(q\) in the ranges of 3.5-4.5, 5.5-6.5 and 7.5-8.5, respectively. That is, for each bin the range of accepted \(q\) is \((\text{centre}-0.5*\text{width},\, \text{centre}+0.5*\text{width})\).

Vector generators with “Lattice” in their name generate vectors commensurate with the reciprocal lattice of the simulation box. This is important for analysis types which calculate correlations of pairs of atoms (Current Correlation Function and Dynamic Coherent Structure Factor).

While Dynamic Incoherent Structure Factor does not require a Lattice vector generator, it is still necessary to use one if you intend to combine the coherent and incoherent parts into the total signal using Neutron Dynamic Total Structure Factor.

Spherical Lattice Vectors

Parameter	Format	Default	Description
seed	int	0	RNG seed used to generate the vectors. Setting the same seed ensures reproducibility of random numbers.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors (Number of hkl vectors)	int	50	Number of hkl vectors in each shell. Higher values result in higher accuracy but longer computation time.
width	float	1.0	Accepted tolerance of each shell. Often identical to the “by step of” parameter.

The most commonly used vector generator, appropriate for isotropic systems. Generates vectors in all directions, and groups them into spherical shells of finite thickness. The results for each shell are averaged over all the component vectors, resulting in an approximation of random orientation. Only vectors commensurate with the reciprocal lattice of the simulation box are generated.

Circular Lattice Vectors

Parameter	Format	Default	Description
seed	int	0	The RNG seed used to generate the vectors. Setting the same seed ensures reproducibility of random numbers.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors	int	50	Number of hkl vectors in each shell. Higher values result in higher accuracy but at the cost of longer computational time.
width	float	1.0	Accepted tolerance of each shell. Often identical to the “by step of” parameter.
axis_1	3*[float]	[1,0,0]	\([h,k,l]\)
axis_2	3*[float]	[0,1,0]	\([h,k,l]\)

The reciprocal space vectors “axis_1” and “axis_2” define a plane in which the vectors are generated. Only vectors commensurate with the reciprocal lattive defined by the simulation box will be generated.

Linear Lattice Vectors

Parameter	Format	Default	Description
seed	int	0	The RNG seed used to generate the vectors. Setting the same seed ensures reproducibility of random numbers.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors	int	50	Number of hkl vectors in each shell. Higher values result in higher accuracy but at the cost of longer computational time.
width	float	1.0	Accepted tolerance of each shell. Often identical to the “by step of” parameter.
axis	3*[float]	[1,0,0]	\([h,k,l]\)

The Q vectors will be generated along the reciprocal space direction “axis”. Only vectors commensurate with the reciprocal lattive defined by the simulation box will be generated.

Miller Indices Lattice Vectors

Parameter	Format	Default	Description
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
width	float	1.0	Accepted tolerance of each shell. Often identical to the “by step of” parameter.
h	3*[int]	[0,8,1]	Integer values of [first, last, step]
k	3*[int]	[0,8,1]	Integer values of [first, last, step]
l	3*[int]	[0,8,1]	Integer values of [first, last, step]

Only reciprocal space vectors with integer values of \(h\), \(k\), \(l\) will be generated. Once generated, they will still be grouped into shells based on their \(q\).

Spherical Vectors

Parameter	Format	Default	Description
seed	int	0	The RNG seed used to generate the vectors. Setting the same seed ensures reproducibility of random numbers.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors	int	50	The number of \(hkl\) vectors in each shell. Higher values result in higher accuracy but longer computational time.
width	float	1.0	The accepted tolerance of each shell. Often identical to the “by step of” parameter.

Circular Vectors

Parameter	Format	Default	Description
seed	int	0	The RNG seed used to generate the vectors. Setting the same seed ensures that the same random numbers are generated, making the calculation reproducible.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors	int	50	The number of hkl vectors in each shell. Increasing this value improves accuracy but also increases computational time.
width	float	1.0	The accepted tolerance of each shell. It often matches the “by step of” parameter.
axis_1	3*[float]	[1,0,0]	\([h,k,l]\) vector 1
axis_2	3*[float]	[0,1,0]	\([h,k,l]\) vector 2

The reciprocal space vectors “axis_1” and “axis_2” define a plane in which the vectors are generated.

Linear Vectors

Parameter	Format	Default	Description
seed	int	0	The RNG seed used to generate the vectors. Setting the same seed ensures that the same random numbers are generated, making the calculation more reproducible.
shells	3*[float]	[0, 5.0, 0.5]	A [first, last, step] definition of a range of \(q\) values used as centres of vector shells.
n_vectors	int	50	The number of hkl vectors in each shell. Higher values result in higher accuracy but longer computational time.
width	float	1.0	The accepted tolerance of each shell. It is often identical to the “by step of” parameter.
axis	3*[float]	[1,0,0]	\([h,k,l]\)

Grid Vectors

Parameter	Format	Default	Description
hrange	3*[int]	[0,8,1]	Integer values of [first, last, step]
krange	3*[int]	[0,8,1]	Integer values of [first, last, step]
lrange	3*[int]	[0,8,1]	Integer values of [first, last, step]
qstep	float	0.01	Size of the \(q\) bin for grouping vectors in shells.

Approximated Dispersion Vectors

Parameter	Format	Default	Description
q_start	3*[float]	[0,0,0]	\(\mathbf{q}_0 = [q_x, q_y, q_z] (\text{nm}^{-1})\)
q_end	3*[float]	[1,0,0]	\(\mathbf{q}_1 = [q_x, q_y, q_z] (\text{nm}^{-1})\)
q_step	float	0.1	The increment (in \(\text{nm}^{-1}\)) by which \(q\) is increased when tracing the line between the two points.

Generates a line between any two arbitrary points in reciprocal space. The input values are in inverse nanometers, and NOT in reciprocal lattice units.

Dispersion Lattice Vectors

Parameter	Format	Default	Description
start	3*[int]	[0,0,0]	\([h,k,l]\)
direction	3*[int]	[1,0,0]	\([h,k,l]\)
n steps	int	10	The increment (in \(\text{nm}^{-1}\)) by which \(q\) is increased when tracing the line between the two points.

Generates reciprocal lattice vectors (integer indices only) from the starting point in the selected direction.

Instrument resolution

This option is available in all the analyses performing a time Fourier Transform, e.g. for the calculation of the density of states or the dynamic structure factor. The following resolution shapes are supported in MDANSE at the moment:

• Gaussian

  ('gaussian', {'mu': 0.0, 'sigma': 1.0})

• Lorentzian

  ('lorentzian', {'mu': 0.0, 'sigma': 1.0})

• Pseudo-Voigt

  The corresponding MDANSE input is:

  ('pseudo-voigt', {'eta': 0.5, 'mu_lorentzian': 0.0, 'sigma_lorentzian': 1.0, 'mu_gaussian': 0.0, 'sigma_gaussian': 1.0})

• square

  The corresponding MDANSE input is:

  ('square', {'mu': 0.0, 'sigma': 1.0})

• triangular

  The corresponding MDANSE input is:

  ('triangular', {'mu': 0.0, 'sigma': 1.0})

• ideal The corresponding MDANSE input is:

  ('ideal', {})