Ionic Conductivity Panel

Calculate the ionic conductivity, and optionally diffusion coefficient, for either a type of atom or a type of molecule from an MD trajectory. The trajectory can be generated for the calculation, or an existing trajectory can be used.

To display this panel: click the Tasks button and browse to Materials → Classical Mechanics → Ionic Conductivity → Ionic Conductivity Calculations

The following licenses are required to use this panel: MS Maestro, OPLS (optional), MS Force Field Applications (optional), MS Transport, Desmond

  • Using
  • Features
  • Additional Resources

Using the Ionic Conductivity Panel

In this panel, you can set up and run MD simulations which are analyzed to obtain the ionic conductivity, ambipolar diffusivity, and the cation transference of an ionic system. Optionally the isotropic and anisotropic diffusion coefficients for a particular type of atom or molecule can be calculated. You can use the results of an existing calculation, if you have the output of an MD simulation with a trajectory. Otherwise, for Desmond model systems (.cms), you can run the simulation as part of the job.

The input structure must be an all-atom Desmond model system (.cms) prepared with OPLS2005, OPLS4, OPLS5, or MLFF with or without a trajectory. The output from a Quantum ESPRESSO MD simulation (.maegz) with a trajectory can also be used. If you are running the MD simulation as part of the job, you should make sure that the Desmond system is already fully relaxed, as the simulation does not include relaxation stages.

Ionic conductivity can be determined for a system consisting of a solvent and an ionic solute via the calculation of Onsager coefficients based on Maxwell-Stefan diffusion.

The diffusion coefficient can optionally be calculated for individual atoms or individual molecules. The atoms or the molecules must all be of the same type: same element for atoms, same molecular structure for molecules. This is necessary because the results are averaged over all selected molecules or atoms. When selecting the atoms or molecules for the diffusion calculations, therefore, you must ensure that you choose only atoms or molecules of the same type. The easiest way to do this is probably to enter an ASL expression in the text box in the Atoms for diffusion parameters picking tools section. For an atom, you can enter the expression a.e element-symbol to specify the element whose symbol is element-symbol. For a molecule you can use SMARTS, with the expression smarts. smarts-pattern to specify the molecules that match smarts-pattern. (Make sure that the SMARTS pattern doesn't match anything else.)

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see diffusion_coefficient_msd_driver.py Command Help.

To visualize the results, you can use the Ionic Conductivity Viewer Panel (Clickclick the Tasks button and browse to Materials → Classical Mechanics → Ionic Conductivity → Ionic Conductivity Results). To open this panel from the entry group for the results of a job, and load the results, use the Workflow Action Menu .

Ionic Conductivity Panel Features

Use structures from option menu

Choose the structure source for calculation.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Method tab
Trajectory options

Select an option for the source of the trajectory.

  • Generate from MD simulation—select this option if the structure does not have an associated trajectory (there is no T button in the Entry List for the structure). With this option, a simulation is run to generate the trajectory. This option is not available for Quantum ESPRESSO MD simulations.
  • Use existing—select this option if the structure has a trajectory that you want to use (there is a T button in the Entry List for the structure). The simulation is skipped, and the trajectory is analyzed to obtain the ionic conductivity and diffusion coefficients.
Start with trajectory frame box

Start the calculations of the MSD against time difference (tau) from the specified trajectory frame. Earlier frames in the trajectory are discarded.

Ionic Conductivity Calculation section

Specify parameters for the ionic conductivity calculation which computes Stefan-Maxwell diffusivities.

Method options

Choose the method for calculating the ionic conductivity, from MS1 (90), MS2 (91), and MS3 (92). All three methods are based on Maxwell-Stefan diffusion but differ in how they calculate the Onsager coefficients, leading to differing ionic conductivity values.

Parameters for averaging relative displacements section
Window size text box

Specify the window size, in ns, to perform block averaging.

Interval text box

Specify the window interval, in ns, to perform block averaging.

Diffusion Coefficient Calculation (via MSD) option and section

Choose to run a diffusion coefficient calculation and specify the parameters for it. The mean squared displacement method is used.

Fitting range for diffusion parameters section
Include Tau values from t1 ns to t2 ns for linear fit boxes

Perform the linear fit of the MSD for the diffusion coefficient between the specified time difference (tau) values. These text boxes allow you to discard small and large tau values where the relationship might not be linear. You can adjust the fit after the calculation is run, in the Diffusion Coefficient Viewer Panel.

Simulation protocols tab

Specify parameters for the simulation from which the ionic conductivity and diffusion coefficients are calculated.

Ensemble class option menu

Choose the ensemble class for the simulation, from NVT, NPT, or NVE. The default is NVE.

Temperature text box

Set the temperature in kelvin for the simulation and thus for the diffusion coefficients. If the ensemble is NVE, this text box supplies the initial temperature for the simulation, and is labeled Initial temperature.

Pressure text box

Set the pressure in bar for the simulation and thus for the diffusion coefficients. Only available when the Ensemble class is NPT.

Simulation time text box

Specify the desired simulation time in ns.

Time step text box

Specify the time step for the simulation in fs.

Trajectory recording interval text box

Set the recording interval for saving points on the trajectory, in ps. This is the amount of time between frames in the trajectory. The entered value is rounded to an integer multiple of the far time step size. The resultant number of records to be written is reported to the right.

Set random number seed option and text box

Select this option to specify a random seed to be used in the simulations. Specifying the seed allows you to reproduce the results, unless other factors affect them. If this option is not selected, a seed is chosen at random.

Save trajectory option

Save the trajectory when the simulation is done. If this option is not selected, the trajectory is used to evaluate the ionic conductivity and diffusion coefficients, then it is discarded.

Diffusion parameters tab

Make settings for the calculation of the diffusion coefficient. If you have coarse-grained systems, you will not be able to use SMARTS patterns for selection.

Center of mass for diffusion parameters section
Use center of mass of each object option menu

Choose the substructure for which the MSD (mean square displacement) of the center of mass is calculated. The center of mass is calculated for the atoms or particles in each of these substructures represented in the atom selection. The default is to do the MSD calculation for each molecule. If you choose SMARTS, the SMARTS tools are activated.

SMARTS text box and Use Workspace Selection button

Enter the SMARTS pattern for the center of mass atoms in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Use Workspace Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace.

Atoms for diffusion parameters picking tools

Select atoms for the calculation of diffusion parameters, using these standard picking tools. The mean square displacement (MSD) is averaged over all instances in the selection of the substructure chosen from the Use center of mass of each object option menu, i.e. for all molecules, all monomers, all atoms or particles, or all SMARTS-defined functional groups in the selection.

You can make a selection by picking in the Workspace, using the other tools, or entering an ASL expression in the text box (see Atom Specification Language). Useful ASL expressions are all, water, or a SMARTS pattern with the syntax smarts. smarts-pattern. The default setting of the Pick option menu is coordinated with the choice from the Use center of mass of each object option menu: Molecules for Molecule, Residues for Monomer, Atoms for Atom and SMARTS. (Monomers in a polymer are the same as residues in this context, and coarse-grained particles are the same as atoms.) For coarse-grained systems, it may be helpful to use the Atom Selection Dialog Box (click the + button then click Select), as the coarse-grained particles and molecules and their properties are listed in the various tabs.

Note: Make sure you have the right structure in the Workspace! If your source of structures is the selected entries rather than the Workspace, picking atoms in the Workspace might not give a meaningful atom set for the selected entries.

Anisotropic diffusion coefficient section

Select options for calculating anisotropic diffusion coefficients in addition to the isotropic diffusion coefficient.

Along the x, y, and z axes, respectively option

Select this option to calculate the diffusion coefficient parallel to the x, y, and z axes, respectively.

In the plane perpendicular to vector option and Modify button

Select this option to calculate the diffusion coefficient in a plane perpendicular to a vector. The currently selected vector is printed next to this option. Click Modify to define the plane, for which the diffusion coefficient is computed. Opens the Define Interface Dialog Box

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Diffusion Coefficient - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

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