Glossary of Parameters
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. |
Q shells
Input |
Format |
Default |
Description |
|---|---|---|---|
from |
float |
0 |
The lowest value of \(|Q|\) to be used in Q-vector generation. |
to |
float |
10 |
The highest value of \(|Q|\) to be used in Q-vector generation. |
by step of |
float |
1 |
The step by which \(|Q|\) is incremented when changing from one Q-shell to the next one. Please adjust the width input parameter accordingly when changing the step. |
The unit of the Q-vector length in MDANSE is \(\text{nm}^{-1}\).
Output files
This is one of the two parameters that are present in each analysis, the other being param-frames. It usually appears at the bottom of an analysis window (Analysis), right above the buttons.
output files
Output Files |
|
|---|---|
Format: |
str |
Default: |
trajectory_directory_path<trajectory_filename>_ <analysis_acronym> |
Browse: |
The Browse button opens a system file browser window, allowing the navigation of the filesystem. |
Description: Specifies the location where analysis results will be stored. It’s typically composed of a directory path, the name of the HDF file being analyzed, and a shortened analysis acronym (e.g., “disf” for dynamic incoherent structure factor). If a file with the same name already exists, a unique number (n) is appended to avoid overwriting.
output formats
Output Formats |
|
Format Default |
Drop-down HDF5 (for analysis), HDF (for trajectory conversion) |
Description: specifies the Supported File Formats in which the analysis results are saved. HDF5 File Format and GUI Integration, DAT File Format, or cominbations of those can be selected. The name of these files is given in the ‘Basename’ string.
Creating selections
There are the following Selections in MDANSE, each of which provides a variety of ways to alter the analysis:
param-atom-selection
Q Vectors (explored separately in the next section)
The ones relevant to the analysis are present in its window, but some can also be performed from Molecular Viewer. By default, there are no Selections saved in MDANSE; they all have to be created manually. Each selection is unique to a trajectory HDF file, but all selections are stored in the same folder, $APPDATA/mdanse. Therefore, if a selection is to be reuse, it is important to give selections unique names even when creating the same selection for multiple trajectories. To help with that, all existing saved selection can be viewed in the User Definition Viewer which can be accessed from the toolbar. To save a selection, type a name in the field next to the Save button, and then click on the button. This will save the selection without closing the window.
Axis Selection/Reference Basis
Inside an analysis window, Axis Selection looks like this:
The drop-down menu is used to choose one of the existing definitions. Only the definitions with the format matching the analysis, i.e. those with the same number of selected atoms as the analysis expects, will appear. New ones can be created by clicking on the New definition button, which will open the window below. The details of the currently selected definition can be viewed in the User Definition Viewer by clicking on the View selected definition.
When this window is opened from an analysis window, the ‘Number of atoms’ field at the top will be set to the number of atoms that must be selected for the selection to work in the analysis from whose window it was opened. The field will also not be editable. Thus, when the New definition button is clicked in Angular Correlation analysis, the field will be set to 2, because that is how many it requires.
The number of atoms indicates how many atoms from one molecule must be selected. To select an atom, click on the + button in the ‘Molecules’ list to show which atoms that molecule contains, and then double-click the atom. That will cause the chosen atom to appear in the ‘Selected atoms’ list, and its details in the box below. An atom can be removed from selection by clicking on it in the ‘Selected atoms’ list and hitting the Delete key on the keyboard.
Axis selection is available for Angular Correlation and analysis-op analyses, which both require 2 atoms to be selected, and the Spatial Density analysis, which requires 3 atoms.
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. There can even be none; Atom Selection is entirely optional.
Inside an analysis window, Atom Selection appears thusly:
The green button adds a line for another selection, allowing you to choose one more selection to apply to that analysis:
The line can be removed by clicking on the red button. The drop-down menu and the View selected definition button work the way they do in Axis Selection <link>. The Set new selection button opens the following window:
The Filter by field contains different ways to access the various particles in the loaded trajectory. Clicking on a filter will make all the relevant particles appear in the top right box:
Clicking on the particles/groups in that window will highlight them and make them appear in the Selection box. Together with the buttons for logical operations, it is possible to make complex selections, like so:
The large box below the Selection box should show information about your selection, but it is broken for complex selections. The box at the very bottom, next to the Save button, is used for naming the selection. Each selection must be named with a unique name. The Save button saves the selection for the loaded trajectory, but it will not close the Atom Selection window. Once selection has been saved, it should appear in the drop-down menu in the analysis window.
Atom selection is available for all the analyses for which Atom Transmutation is available, as well as all analysis-trajectory analyses, analysis-gacf, Molecular Trace, Root Mean Square Fluctuation, Radius of Gyration, Solvent Accessible Surface, and Spatial Density.
Atom Transmutation
To use Atom Transmutation, simply select an Atom Selection in the grey drop-down menu on the left, and then choose the element into which the atoms in that Atom Selection will be transmuted from the white drop-down menu next to the red button. For example, the below Atom Transmutation will transmute all sodium ions into potassium ions:
This parameter is available for the following analyses: Coordination Number, Current Correlation Function, Density Of States, Density Profile, Dynamic Coherent Structure Factor, Dynamic Incoherent Structure Factor, Eccentricity, Elastic Incoherent Structure Factor, Gaussian Dynamic Incoherent Structure Factor, General Auto Correlation Function, Mean Square Displacement, Neutron Dynamic Total Structure Factor, Order Parameter, Pair Distribution Function, Position Auto Correlation Function, Root Mean Square Deviation, Static Structure Factor, Velocity Auto Correlation Function, X-Ray Static Structure Factor.
Atom Charges
This selection works inside an analysis window exactly the same as Axis Selection/Reference Basis. The only difference is the window that opens when Set new selection button is clicked. The Partial Charges window appears as below, and allows you to edit the charges at each atom inside the system. To do that, simply click on a field in the charge column and type in a number. The change will be confirmed once you hit enter or click outside the field. Once all changes have been made, name the selection using the box at the bottom, then click the Save button, and finally close the window.
This parameter is only available for the analysis-dacf analysis.
Q vectors
Similar to the selections above but specific to Scattering Plugins, Q vectors give the opportunity to change how the analysis is performed. Each window has a part like this:
This section must be filled for analysis to be able to run. Like for other selections, there are no definitions by default. Therefore, one has to be created by clicking on the New definition button. This will open a window like in one of the following subsections, which show how Q Vectors are defined for each type of Q Vector. There are many types, and it is up to you to choose which is the best for a given experiment.
Once a definition of choice exists, it can be selected from the drop-down menu. The View selected definition opens the User Definition viewer <link> at the currently selected definition.
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. |
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. |
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width). Must be clicked before saving. |
||
Name |
str |
None |
Allows you to name the generated vectors. Name must be set before saving the vectors. |
Save button |
Saves the generated vectors. It doesn’t close the Q Vectors window. Saved vectors may be in a specific format. |
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. |
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. |
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width). Must be clicked before saving. |
||
Name |
str |
None |
Allows you to name the generated vectors. Name must be set before saving the vectors. |
Save button |
Saves the generated vectors. It doesn’t close the Q Vectors window. Saved vectors may be in a specific format. |
axis 1
Component
Format
Default
Description
x-component
int
1
X-component for plane
y-component
int
0
Y-component for plane
z-component
int
0
Z-component for plane
axis 2
Component
Format
Default
Description
x-component
int
0
X-component for plane
y-component
int
1
Y-component for plane
z-component
int
0
Z-component for plane
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. |
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 |
|||
x-component | int | 1 | The x-components of the specified axis. |
|||
y-component | int | 0 | The y-components of the specified axis. |
|||
z-component | int | 0 | The z-components of the specified axis. |
|||
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors. This must be set before saving the vectors. |
Save button |
Saves the generated vectors. It doesn’t close the Q Vectors window. Saved vectors may be in a specific format. |
||
Miller Indices 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. |
width |
float |
1.0 |
Accepted tolerance of each shell. Often identical to the “by step of” parameter. |
h (and the same goes for k and l fields)
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. |
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. |
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors before saving. |
Save button |
Saves the generated vectors. It doesn’t close the Q Vectors window. |
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. |
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 |
|
||
axis 2 |
|
||
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width, axis components). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors before saving. Must be set before saving. |
Save button |
Saves the generated vectors. It does not close the Q Vectors window. The saved vectors may be in a specific format, such as a table format. |
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. |
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 |
|
||
Generate button |
Generates hkl vectors based on the specified parameters (seed, n vectors, width, axis components). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors before saving. Must be set before saving. |
Save button |
Saves the generated vectors. It does not close the Q Vectors window. |
Grid 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. |
hrange (krange , lrange fields) |
|
||
qstep |
float |
0.01 |
Determines how the hkl vectors are grouped. |
Generate button |
Generates hkl vectors based on the specified parameters (seed, hrange, krange, lrange, qstep). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors before saving. Must be set before saving. |
Save button |
Saves the generated vectors. It does not close the Q Vectors window. Saved vectors may be in a specific format. |
Approximated Dispersion Vectors
Parameter |
Format |
Default |
Description |
|---|---|---|---|
generator |
drop-down |
circular_lattice |
The selection of which type of Q Vectors is being defined. |
Q start (nm^-1) |
|
||
Q step (nm^-1) |
float |
0.1 |
The increment by which Q is increased when tracing the line between the two points. |
Generate button |
Generates hkl vectors based on the specified parameters (generator, Q start, Q step). Must be clicked before saving. |
||
Name |
str |
None |
This is the empty box at the bottom of the window. It allows you to name the generated vectors before saving. Must be set before saving. |
Save button |
Saves the generated vectors. It does not close the Q Vectors window. Saved vectors may be in a specific format. |
Group coordinates
This parameter is available in the following analyses: trajectory-comt, Density Of States, analysis-disf, analysis-eisf, analysis-gdisf, analysis-gacf, Mean Square Displacement, analysis-op, Rigid Body Trajectory, Root Mean Square Deviation, Root Mean Square Fluctuation, Velocity Auto Correlation Function.
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', {})
This parameter is available for the following analyses: Current Correlation Function, Density of States, Dynamic Coherent Structure Factor, Dynamic Incoherent Structure Factor, Gaussian Dynamic Incoherent Structure Factor, Neutron Dynamic Total Structure Factor, Structure Factor From Scattering Function.
Interpolation order
Analyses that require atomic velocity data have an option to interpolate this data from atomic positions. By default, no interpolation is performed and instead MDANSE attempts to use the velocities stored int the HDF trajectory. Of course, depending on the way your simulation was set up, it is possible that the atoms velocities were not even stored in the output. It is still possible to derive the velocities of atoms from their positions at known time intervals, which is the subject of this section.
Interpolation order is available for the following analyses: Current Correlation Function, Density of States, Temperature, Velocity Auto Correlation Function. However, please note that due to the nature of the Current Correlation Function analysis, the interpolation there is more complicated, the details of which can be found in its section.
Normalize
Normalisation is available for the following analyses: Current Correlation Function, General Auto Correlation Function, Position Auto Correlation Function, Velocity Auto Correlation Function.
Project coordinates
This parameter is available for the following analyses: Density of States, Dynamic Incoherent Structure Factor, Elastic Incoherent Structure Factor, Gaussian Dynamic Incoherent Structure Factor, Mean Square Displacement, Position Auto Correlation Function, Velocity Auto Correlation Function.
Weights
This parameter is available in the following analyses: Current Correlation Function, Density of States, Density Profile, Dynamic Coherent Structure Factor, Dynamic Incoherent Structure Factor, Eccentricity, Elastic Incoherent Structure Factor, Gaussian Dynamic Incoherent Structure Factor, General Auto Correlation Function, Mean Square Displacement, Pair Distribution Function, Radius of Gyration, Rigid Body Trajectory, Root Mean Square Deviation, Static Structure Factor, Velocity Auto Correlation Function.
Running mode
Running mode is available for most analyses: all Dynamics analyses, all Trajectory analyses, all Thermodynamics analyses, Area Per Molecule, Coordination Number, Current Correlation Function, Density Profile, Dipole Auto Correlation Function, Dynamic Coherent Structure Factor, Dynamic Incoherent Structure Factor, Eccentricity, Elastic Incoherent Structure Factor, Gaussian Dynamic Incoherent Structure Factor, McStas Virtual Instrument, Molecular Trace, Neutron Dynamic Total Structure Factor, Order Parameter, Pair Distribution Function, Radius of Gyration, Rigid Body Trajectory, Root Mean Square Deviation, Root Mean Square Fluctuation, Spatial Density, Static Structure Factor, Voronoi, X-Ray Static Structure Factor.