Displaying trajectory and chart data

Depending on the type of calculation performed, a CASTEP run may produce a trajectory document and one or more chart documents. These documents have a special association with each other because each of the points on the graphs correspond to a frame in the trajectory.

CASTEP produces a trajectory (.xtd) file whenever you run a geometry optimization, molecular dynamics or elastic constants calculation, or a transition state search. In all cases, a history of the optimization is returned in a file called <name> Trajectory.xtd, where <name> is the name used for the job description on the Job Control tab of the CASTEP Calculation dialog.

When you run a geometry optimization, two chart documents are generated:

<name> Energies.xcd: Contains a plot of total energy vs. frame for all steps of the calculation
<name> Convergence.xcd: Contains three (possibly four) plots that describe the degree of convergence of the optimization as a function of frame:
- Change in energy vs. frame
- Maximum Cartesian force vs. frame
- Maximum Cartesian step size vs. frame
- Maximum stress tensor component vs. frame (for cell optimization runs)

Because these values span several orders of magnitude, the data are plotted on a log₁₀ scale.

Similar charts are produced for each structure in an elastic constants calculation.

When you run a transition state search, a single chart containing a graph of energy vs. reaction coordinate for each step of the calculation, <name> TSSearch.xcd, is generated. This includes an individual graph for each LST or QST 'uphill' cycle as well as a graph for each conjugate gradient minimization. The CASTEP Transition State Search task topic contains more details.

When you run a molecular dynamics simulation, either two or three chart documents are generated:

<name> Constant.xcd: Contains a plot of the constant of motion vs. simulation time
<name> Temperature.xcd: Contains a plot of temperature vs. simulation time
<name> Pressure.xcd: Contains a plot of pressure vs. simulation time (only produced by the NPH or NPT ensemble)

Trajectory files can be animated using the controls on the Animation toolbar.

If you have access to the Forcite module, you may find some of its dynamics, statistical, and structural analysis features useful for analyzing trajectories. Refer to the Using Forcite Analysis topic for details.

Creating a trajectory and chart

When you run CASTEP using the Materials Studio interface, the creation and display of these trajectories and charts is automatic. If you selected Automatically view output on the CASTEP Job Control Options dialog, the graphs will be displayed automatically on completion of the run. If you selected Update graphs on the CASTEP Job Control Options dialog, these graphs will be displayed and updated with intermediate results throughout the course of the calculation.

To create charts from output files generated by a standalone calculation

Download the files from the compute server to your PC using the procedure described in Running CASTEP in standalone mode. Be sure to retrieve the .check, .castep, and .geom, .md, or .ts files.
Select Modules | CASTEP | Analysis from the menu bar.
Select Energy evolution from the list on the CASTEP Analysis dialog.
Make sure that the .castep file is the currently active document.
Click the View button.

If you used the Materials Studio interface to set up and launch your job, you can regenerate the chart documents by following a similar procedure.

To regenerate charts

Open either the .xsd or .castep file and make it the currently active document.
Select Modules | CASTEP | Analysis from the menu bar.
Select Energy evolution from the list on the CASTEP Analysis dialog.
Click the View button.

Animating the trajectory

You can use the controls on the Animation toolbar to animate the trajectory, stepping through each of the frames of the document. If the chart is open during the animation, the point corresponding to the active frame will be highlighted.

Chart Viewer point selection

Alternatively, you can use Chart Viewer point selection to display the trajectory frames of the points you select from the chart document.

To display a trajectory frame for a point on a chart document

Choose the Selection tool on the Chart Viewer toolbar to enter selection mode.
Making sure you have the corresponding trajectory document open, select a data point on the chart document.
The corresponding trajectory frame is displayed.
Drag the mouse over other data points on the chart document to display their corresponding trajectory frames.
If CASTEP generated multiple chart documents, the related data points will be highlighted on all of them.

To make it easier to see the chart and trajectory documents, close all the other documents and then maximize the sizes of these two documents by selecting Window | Tile Vertically from the menu bar.

Displaying trajectory and chart data

Creating a trajectory and chart

Animating the trajectory

Chart Viewer point selection

See Also: