AIMD / Trajectory Analysis
This tutorial explains how to analyze VASP AIMD trajectories with VQkit.
VQkit provides nine AIMD / trajectory-analysis workflows under:
Main menu
[2] Post-processing
[6] AIMD / trajectory analysis
The same menu can also be opened directly by typing:
aimd
at any VQkit Enter your choice prompt.
Required files
Most AIMD analyses use the VASP XDATCAR trajectory file.
Depending on the selected analysis, VQkit can also use:
INCAR— preferred source for the MD time stepPOTIM.OUTCAR— fallback source forPOTIMand energy data.OSZICAR— preferred source for MD temperature and energy records.
The basic calculation directory therefore commonly contains:
INCAR
OUTCAR
OSZICAR
XDATCAR
VQkit performs the analysis directly in the active working directory.
Time convention
VQkit uses the XDATCAR configuration number multiplied by the VASP MD time
step POTIM:
where POTIM is in femtoseconds.
VQkit attempts to detect POTIM automatically:
INCARis checked first.OUTCARis used as a fallback.If the time step cannot be detected, VQkit asks you to enter it manually.
When VQkit detects the time step, a prompt similar to the following appears:
MD time step POTIM in fs [1, detected from INCAR]:
Press Enter to accept the detected value, or type a different value to override it.
Variable-cell trajectories
For workflows that read XDATCAR, VQkit asks:
Variable-cell / NPT XDATCAR? [y/N]:
For a normal fixed-cell NVT trajectory, press:
Enter
For a variable-cell or NPT trajectory, enter:
y
VQkit then uses the lattice associated with each trajectory frame.
1. Trajectory summary
Purpose
Trajectory summary provides a quick overview of the AIMD trajectory before performing more detailed analysis.
Select:
[1] Trajectory summary
VQkit asks for the XDATCAR filename:
XDATCAR file in current directory [XDATCAR]:
Press Enter if the file is named XDATCAR.
Then choose whether the trajectory is variable-cell and confirm the MD time step.
Output
VQkit creates:
VQkit_AIMD_summary/
Inside the directory, the summary file is:
VQkit_AIMD_trajectory_summary.txt
The summary reports:
XDATCAR path
number of trajectory frames
number of atoms
atomic species
detected or user-specified time step
first and last configuration numbers
last-frame simulation time
variable-cell status
minimum, maximum, and mean cell volume
Example use
Use the trajectory summary first to confirm that:
the correct trajectory is being read;
the atom count is correct;
POTIMis correct;the number of frames is reasonable.
2. Atomic positions versus time
Purpose
This workflow follows the position of one or more selected atoms throughout the AIMD trajectory.
Select:
[2] Atomic position coordinates vs time (XDATCAR)
VQkit asks for the XDATCAR file and whether the trajectory is variable-cell.
It then reports the detected atoms and species and asks:
Atom index/indices (1-based; e.g. 1 or 1,5,10-12):
Examples
One atom:
5
Several atoms:
1,5,10
Atom range:
10-15
Mixed selection:
1,5,10-12
After confirming POTIM, VQkit asks:
Output directory [VQkit_AIMD_positions]:
Press Enter to use the default.
Output
VQkit creates:
VQkit_AIMD_positions/
Important output files include:
VQkit_XDATCAR_position_vs_time.csv
VQkit_XDATCAR_position_vs_time.dat
VQkit_XDATCAR_position_vs_time_summary.txt
For every selected atom, VQkit also creates PNG and PDF plots.
The exported coordinates include:
fractional coordinates
wrapped Cartesian coordinates
PBC-unwrapped Cartesian coordinates
The unwrapped Cartesian coordinates are particularly useful when following long-range atomic motion through periodic boundaries.
3. Energy versus time
Purpose
This workflow extracts AIMD energy information and plots it against simulation time.
Select:
[3] Energy vs time
VQkit determines the time step and then searches for energy records.
Energy source priority
VQkit first checks:
OSZICAR
If suitable MD records are not found, it falls back to:
OUTCAR
When OSZICAR is available, VQkit can export:
temperature
EFE0EK
when those quantities are present.
Output
VQkit creates:
VQkit_AIMD_energy/
with files such as:
VQkit_AIMD_energy_vs_time.csv
VQkit_AIMD_energy_vs_time.dat
VQkit_AIMD_energy_vs_time_summary.txt
VQkit_AIMD_energy_vs_time.png
VQkit_AIMD_energy_vs_time.pdf
Use this plot to inspect energy equilibration, drift, and fluctuations during the AIMD simulation.
4. Volume and lattice parameters versus time
Purpose
This workflow tracks simulation-cell geometry during the trajectory.
Select:
[4] Volume / lattice parameters vs time
VQkit reads XDATCAR and calculates for each frame:
abcalphabetagammacell volume
This is especially useful for variable-cell or NPT simulations.
Output
VQkit creates:
VQkit_AIMD_cell/
with numerical data and PNG/PDF plots of the lattice lengths and cell volume.
For fixed-cell AIMD, these quantities should remain constant unless the trajectory file itself contains changing lattice information.
5. Bond distance versus time
Purpose
This workflow follows the distance between two selected atoms throughout the trajectory.
Select:
[5] Bond distance vs time
VQkit asks for the XDATCAR file and then requests two atom indices:
First atom index (1-N):
and:
Second atom index (1-N):
where N is the total number of atoms.
Example
To monitor the distance between atoms 5 and 18:
First atom index: 5
Second atom index: 18
VQkit uses the periodic minimum-image convention when calculating the pair distance.
Output
The default output directory is:
VQkit_AIMD_bond/
VQkit generates numerical data together with PNG and PDF plots of bond distance versus time.
This analysis is useful for monitoring:
bond formation;
bond breaking;
structural fluctuations;
coordination changes.
6. Mean-squared displacement
Purpose
The mean-squared displacement (MSD) measures the average displacement of a selected group of atoms from the first XDATCAR configuration.
Select:
[6] Mean-square displacement (MSD)
VQkit accepts several selection styles.
All atoms:
all
One element:
Li
Several atom indices:
1,5,10-12
VQkit unwraps trajectories across periodic boundaries before calculating the MSD.
Output
The default output directory is:
VQkit_AIMD_MSD/
Files include:
VQkit_AIMD_MSD.csv
VQkit_AIMD_MSD.dat
VQkit_AIMD_MSD_summary.txt
VQkit_AIMD_MSD.png
VQkit_AIMD_MSD.pdf
The MSD has units of:
Angstrom^2
Scientific note
For variable-cell trajectories, Cartesian MSD contains contributions from cell deformation. Interpret NPT or strongly deforming trajectories carefully.
7. Diffusion coefficient
Purpose
VQkit estimates a diffusion coefficient from the MSD using the Einstein relation.
Select:
[7] Diffusion coefficient
Select the diffusing atoms using:
allan element symbol such as
Liexplicit atom indices
Example:
Diffusing atoms [all]: Li
VQkit then asks:
Diffusion dimensionality [3]:
Use:
1for one-dimensional diffusion;2for two-dimensional diffusion;3for three-dimensional diffusion.
For normal bulk diffusion, press Enter to use 3.
Fit region
VQkit asks:
Fraction of trajectory to discard before linear fit [0.5]:
The default 0.5 means that the first 50% of the trajectory is excluded
from the linear MSD fit.
The diffusion coefficient is calculated from:
where d is the selected dimensionality.
Output
The default output directory is:
VQkit_AIMD_diffusion/
Files include:
VQkit_AIMD_diffusion_fit.csv
VQkit_AIMD_diffusion_fit.dat
VQkit_AIMD_diffusion_summary.txt
VQkit_AIMD_diffusion_fit.png
VQkit_AIMD_diffusion_fit.pdf
VQkit reports:
MSD slope in
Angstrom^2/fsdiffusion coefficient in
Angstrom^2/fsdiffusion coefficient in
cm^2/slinear-fit
R^2
Important
VQkit does not automatically identify the physically valid diffusive regime.
You must choose a fit-start fraction corresponding to a region where MSD is approximately linear with time.
Always inspect the MSD and diffusion-fit plot before reporting the diffusion coefficient.
8. Radial distribution function
Purpose
The radial distribution function describes the probability of finding one
group of atoms at distance r from another group.
Select:
[8] Radial distribution function (RDF)
Group selection
The group-selection prompt accepts:
allelement symbols
atom indices
Example for Li-O RDF:
Group A [all]: Li
Group B [all]: O
VQkit then asks:
Maximum r in Angstrom [automatic]:
Press Enter to use the automatically determined value.
Then:
Bin width in Angstrom [0.05]:
Press Enter to use 0.05 Angstrom.
Output
The default output directory is:
VQkit_AIMD_RDF/
Files include:
VQkit_AIMD_RDF.csv
VQkit_AIMD_RDF.dat
VQkit_AIMD_RDF_summary.txt
VQkit_AIMD_RDF.png
VQkit_AIMD_RDF.pdf
VQkit uses periodic minimum-image distances and per-frame cell-volume normalization.
Important
For unambiguous normalization, the two RDF groups must be either:
identical; or
disjoint.
Partially overlapping but non-identical groups are not accepted.
9. Coordination number versus time
Purpose
This workflow follows the coordination environment of selected atoms over the AIMD trajectory.
Select:
[9] Coordination number vs time
VQkit asks for:
Center atoms [all]:
Neighbor atoms [all]:
Selections can be:
allelement symbols
atom indices
Example for Li coordinated by O:
Center atoms [all]: Li
Neighbor atoms [all]: O
Then choose the distance cutoff:
Coordination cutoff in Angstrom [3.0]:
Example:
2.8
Output
The default output directory is:
VQkit_AIMD_coordination/
Files include:
VQkit_AIMD_coordination_vs_time.csv
VQkit_AIMD_coordination_vs_time.dat
VQkit_AIMD_coordination_summary.txt
VQkit_AIMD_coordination_vs_time.png
VQkit_AIMD_coordination_vs_time.pdf
For every trajectory frame, VQkit reports:
mean coordination number;
minimum coordination number;
maximum coordination number.
Self-pairs are excluded and periodic minimum-image distances are used.
Example: Li-ion AIMD analysis
Assume your AIMD calculation directory contains:
INCAR
OUTCAR
OSZICAR
XDATCAR
and you want to analyze Li-ion mobility.
Step 1 — Open the calculation directory
Start VQkit and set the AIMD calculation directory as the working directory.
Step 2 — Open AIMD analysis
At any VQkit menu prompt type:
aimd
Step 3 — Check the trajectory
Choose:
1
Confirm the number of frames, atoms, species, and MD time step.
Step 4 — Check temperature and energy behavior
Choose:
3
Inspect the resulting energy plot and temperature data exported from
OSZICAR when available.
Step 5 — Calculate Li MSD
Choose:
6
For the atom selection enter:
Li
Inspect:
VQkit_AIMD_MSD/VQkit_AIMD_MSD.png
Step 6 — Estimate Li diffusion coefficient
Choose:
7
Enter:
Diffusing atoms [all]: Li
Diffusion dimensionality [3]: 3
Fraction of trajectory to discard before linear fit [0.5]: 0.5
Inspect the diffusion-fit plot and R^2 before using the reported
diffusion coefficient.
Step 7 — Calculate Li-O RDF
Choose:
8
Enter:
Group A [all]: Li
Group B [all]: O
Maximum r in Angstrom [automatic]:
Bin width in Angstrom [0.05]:
Inspect the first-shell peak in the resulting RDF plot.
Step 8 — Follow Li-O coordination
Choose:
9
For example:
Center atoms [all]: Li
Neighbor atoms [all]: O
Coordination cutoff in Angstrom [3.0]: 2.8
The resulting plot shows how the Li coordination environment changes through the trajectory.
Recommended AIMD workflow
For a typical trajectory, the following order is recommended:
Trajectory summary.
Energy and temperature inspection.
Cell / volume inspection when relevant.
Selected atomic-position or bond-distance analysis.
MSD.
Diffusion coefficient.
RDF.
Coordination number.
Scientific cautions
Diffusion fitting
A diffusion coefficient is meaningful only when the fitted MSD interval is in a physically linear diffusive regime.
Do not report the automatically calculated value without inspecting the MSD and fit.
Variable-cell MSD
For variable-cell or NPT simulations, Cartesian MSD can include contributions from cell deformation.
RDF normalization
For RDF analysis, the selected groups must be identical or disjoint.
Trajectory quality
AIMD analysis cannot compensate for insufficient simulation time, poor equilibration, unsuitable thermostat settings, inadequate sampling, or incorrect DFT parameters.
The physical reliability of the analysis depends on the quality of the underlying AIMD simulation.