Anode SEI Simulation Lab

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Introduction

Solid electrolyte interface (SEI) on anode surface is especially important to understand the reliability and charge-discharge behavior of anode materials. SEI simulation lab is for simulating the chemical interaction between electrolyte and anode materials. This understanding will be used to optimize the electrolyte design for a given anode materials or vice versa. iBat provides all required tools from design of electrolyte, building the interface between the electrolyte and anode, reaction simulation at SEI and characterization tools for investigating the reaction in molecular scale.

  • Example : Lobby of Anode SEI Simulation Lab
  • Example : Working Studio of Anode SEI Simulation Lab

As in other laboratories, this lab is composed of "Lobby" (left figure) and "Working Studio" (right figure).

  • In the lobby, you can review all your previous works. It includes the SEI structures, electrolytes you built and your previous and on-going simulations. You can also filter the simulation jobs by SEI structure, simulation temperature and simulation time. If you go to working studio after selecting one of them, you can continue to work with that SEI structure or review/resume the simulation job.
  • In the working studio, you can build electrolte and SEI interface, preform in-silico experiment of SEI interaction. After the in-silico experiment, SEI product can be analyzed.

Status bar

  • Status-bar.JPG

Both lobby and working-studio pages in the lab have common status bar on the top. It contains the buttons for lobby Lobby-button.JPG and working studio Working-studio-button.JPG. It also shows the present user ID (e-mail address) and the present project name in bold with login time (In this example, krlee@kist.re.kr in project "3rd year demo" (20-15-09-15 10:59:01)). On the right corner of the status bar are the help button Help.JPG to see this document and the job status button Job-status-button.JPG that shows the present status of on-going jobs in this lab.

User Manual : Lobby

  • Example : Lobby of Anode SEI Simulation Lab.

When you first come to the anode materials design lab, you are in lobby. This is the default setting of the lab.
You can go to working studio anytime by clicking the working studio button Working-studio-button.JPG in the status bar.
You can come to lobby anytime by clicking the lobby button Lobby-button.JPG in the status bar.

Lobby has four sections:

  • Visualization Window to show the atomic structure of anode SEI or the final configuration of the simulations.
  • SEI Structure Table to list the anode you have worked in the present project.
  • Electrolyte Table to list the electrolytes you prepared in the present project.
  • Simulations Table to list the simulations performed or being performed in the present project.

Visualization window

  • Example : Visualization window showing a SEi structure built in anode SEI simulation lab.

On the left of the lobby is the visualization window that shows the atomic structure or final configuration of the simulation job. Anode SEI structure (final configuration of the job) is displayed depending on your selection in the SEI Structure table (Simulations table). Color of atom in this visualization is based on the CPK coloring convention. However, slight modification is applied for better distinction. See color of atom page for the color list.

Number of mouse actions can be used to change the visualization.

  • Scrolling the center wheel to zoom in & zoom out
  • Drag with pressing left button to change the viewing angle
  • Drag with pressing right button to move the image


Short Keys

  • Visualization with larger balls
  • Visualization with smaller balls
  • Visualzation with smaller balls without bonds

Some short-keys are defined as followings.

  • < : reduce the ball size for atoms
  • > : increase the ball size for atoms
  • b : toggle to show the atomic bonds (default is on)
  • p : simple and fast drawing of atoms (useful for fast loading of data)
  • s : rendered sphere drawing of atoms (default)


Control Buttons in the Visulation Window

  • Visualization of Si nanotube from +z direction
  • Visualization of Si nanowire from +y direction
  • Display of the axis by pressing x key

  • Display of the sample information

Three bottons on the left lower corner, Xyz-button.JPG will align the image from +x, +y and +z directions, respectively.

[math] x, y, z [/math] axis appear by pressing x key in keyboard. The axis disappears by pressing x key again.

Button F.jpg is for a filtering. You can filter atoms by x,y,z position, element, and the number of bonds.

Info.JPG is a toggle switch for displaying the sample information: Box dimension, Box volume and Atoms in the box.


Snapshots

  • Example : Snapshots of the lithiated Si nanotube taken by the camera

You can take the snapshot of the image of the visualization window by using the camera button on the right upper corner, Camera.JPG. As you click the camera button, new window with the sanpshot opens. Every snapshot appears in separate windows so that the user can compare the images. The snapshot image can be stored as a file that can be used later for the user's purpose. In order to save the image, place the cursor on the snapshot image then right click to invoke the menu of Chrome browser.

SEI Structure Table

  • Example : SEI Structure Table

All anode SEI structures you and your colleagues have built and worked with are listed in this table. Data in this table can be filtered by Anode name or/and Electrolyte name using the radio buttons and pull-down menu to select filtered condition.

  • Name : SEI structure name (as you input in Working Studio) with the generation date and time when you saved the designed SEI structure.
  • Owner : the user name. (not user ID)
  • Anode : The anode used for this SEI structure. This name is the same as the anode name in the Anode Table of Anode Materials Design Lab.
  • Electrolyte  : The electrolyte used in this SEI structure design. Details of the electrolyte can be found in the Electrolyte Table. Before building SEI structure, an electrolyte is to be modeled with electrolyte molecules, salt and additives in the working studio and saved in the Electrolyte Table.
  • Del.JPG : This button is to delete the SEI structure. PI of the project has the right to delete any SEI structure, but participant can delete only the structure that he/she created. (Once you delete, you won't be able to recover the SEI structure. Please be cautious when you delete structure. )

The SEI Structure data can be filtered by many factors. To filter the data, click the title of the list that you want to filter with. Then the filtering box will be shown. choose the condition and type the value. Click the Apply to apply. Multiple filters can be applied in once.

Electrolyte Table

  • Example : Electrolyte Table

All Electrolytes models designed in this project are listed in this table.

  • Name : Electrolyte name (as you input in Working Studio) with the date and time when you saved the designed electrolyte.
  • Owner : the user name. (not user ID)
  • SEI Comp. (ratio) : Molecules and their ratio in this electrolyte model.
  • Density : Equilibrium density of the electrolyte. The equilibrium density is calculated when user design new electrolyte.
  • Del.JPG : This button is to delete the SEI structure. PI of the project has the right to delete any SEI structure, but participant can delete only the strudture that he/she created. (Once you delete, you won't be able to recover the SEI structure. Please be cautious when you delete structure. )

Simulations Table

  • Example : Simulations Table

All simulation jobs you and your colleagues have done are listed in Simulations table. Data in this table show only the SEI structure, temeprature and time for the simulation. All the details of the simulation can be reviewed in the Working Studio after reloading the data. Please refer to the Working Studio section.

  • Name : Name of simulation job (as you input in the Working Studio) with the simulation execution date and time.
  • Owner : The user name. (not user ID)
  • SEI Name : SEI structure name as appears in SEI Structure Table.
  • Status : Status of the simulation work. F means finish and R running.
  • Del.JPG : This button is to delete the SEI structure. PI of the project has the right to delete any SEI structure, but participant can delete only the strudture that he/she created. (Once you delete, you won't be able to recover the SEI structure. Please be cautious when you delete structure. )

The simulation data can be filtered with same way as mentioned on SEI Structure Table.

User Manual : Working Studio

Introduction

In the SEI simulation working studio, users can build interface between anode (usually lithiated) and electrolyte to investigate the reactions at the interface. Details of gas evolution and molecular interactions within the electrolyte or at the interface can be easily analyzed.

Working flow for simulate the SEI inteface is usually

  1. Build SEI structure
  2. Set temperature and time for simulating interactions
  3. Analyze the product of the reaction as a function of time and position from anode surface

Windows in Working Studio

  • SEI working studio

Working studio is composed of 4 windows. On the left side are three windows for controlling the work: SEI builder, Simulations and Analysis, following the general working flow of SEI interface study. On the right side is the visualization window with manipulation tools on top. Please refer to Manipulate Materials to Design Your Anode of Anode Materials Design Lab for the details of the tools. The manipulation tools would be used to modify further the SEI structure and simulation box after building the interface. On the far right of the manipulate tools bar, user will find a molecule filter icon, Mol-filter.JPG. This icon will turn on the Molecule Filter window where users can select the molecules displayed in the visualization window.

How to build SEI

In order to design SEI interface, users will take three steps.

  1. Select an anode material from the results of the simulation work in Anode Materials Design Lab
  2. Build an electrolyte model by using the electrolyte molecules data of the Electrolyte Molecule Table of Electrolyte Design Lab. If you already have the electrolyte models, you can select the model for the SEI simulation.
  3. Build SEI interface using the anode and the electrolyte selected.

Select Anode

First of all, users have to choose anode materials for the SEI interface. This platform enables one to choose the anode from the simulation results performed in the Anode Materials Design Lab.

SEI builder window where user can select anode materials

If users click Search button in the builder window, new window entitled Search Result listing the simulation jobs of the Anode Materials Design Lab will appear.

Anode Table Window where users can select anode materials for SEI simulation

Users can filter the data by the materials, anode models or calculated results such as the volume expansion ratio or the open circuit voltage. By selecting the data, you can observe the final configuration of the simulation performed in the Anode Materials Design Lab in the visualization window. OK is used for selecting the anode of the selected simulation data. (Close can be used to close the window without choosing anode.)

The selected anode then appears in the visualization window of the working studio as shown below.

Selected anode appears in the working studio.

If users want to change the dimension of the simulation box or manipulate further the anode structure, manipulation tools on the top of the visualization window can be used. See more details in Manipulate Materials to Design Your Anode of Anode Materials Design Lab.

Select Electrolyte

For the electrolyte, users can build new electrolyte or load the previously built electrolyte.

Build New Electrolyte
  • Build new electrolyte
  • New Electrolyte button in SEI builder window is used to open the window for electrolyte design as below.

  • Electrolyte Builder
  • Left side of the Electrolyte Builder has the electrolyte Molecule Selector, Molecule Mixer of the electrolyte molecules and salt and Find Density button. On the right side, a data window is prepared to show the process to find the equilibrium density of the prepared electrolyte mixture. Equilibrium density is found by simulating the variation of potential energy vs. density of the electrolyte mixture using the molecular mechanics calculation with reactive force field of C-H-O-Li-P-F system. Algorithm for building the electrolyte and details of the calculation condition including the interatomic potential will be found in the technical information of this document.


  • Molecule Selector Window to be used in electrolyte
  • Molecule Mixer Window for building electrolyte
  • Molecule Selector window is to choose the molecule used for the electrolyte. Search button will list the molecules that meet the condition of the input box from the electrolyte table of the Electrolyte Design Lab. You can input partial formula of the molecule as the search condition: C3, C5 or C5H9 for searching the molecules containing 3 carbons, 5 carbons or 5 carbons and 9 hydrogens, respectively. Search results include the formula, the name assigned in the Electrolyte Design Lab and the molecule structure. Selected molecule by clicking the data row will appear in the list of Molecule Mixer window.
  • Molecule Mixer window provides the way to control the composition of the electrolyte including salt. In the present platform, only two salts LiPF6 and LIBF4 that are most common in industry can be added. First two rows of the table are the salt. Following data result from selecting the molecules in the Molecule Selector window. Gravimetric fraction can be changed for building electrolyte mixture.
  • When you put the electrolyte name and click Find Density, the platform automatically generate the electrolyte mixture with the density of 0.7 g/cm^3, start to find the equilibrium density, and save the data.


  • Finding Equilibrium Density of Electrolyte
  • The Electrolyte data is saved automatically after Finding Equilibrium Density
  • The platform start to find the equilibrium density of the electrolyte by molecular mechanics calculation using reactive force field. Data window shows the variation of potential energy vs density of the electrolyte. In order to find the equilibrium density, the platform performs a sequence of potential energy calculation for various values of density. Box volume of electrolyte is changed to manipulate the density. While calculating, Running.. message appears in the Electrolyte Name window.
  • Below the window, the status bar shows the progress of the calculation to find the equilibrium density. Current Density and Current Energy shows the current values during finding the equilibrium density.
  • Note: Finding equilibrium density needs a lot of calculations and patience. Better algorithm will be studied and implemented in the future.

    Caution: As of Jan. 13, 2016, available reactive force fields are of C-H-O-Li-P-F system. Please note that if you select the molecules containing the element beyond C-H-O-Li-P-F, procedure for finding equilibrium density wouldn't work properly.

    Load Previously Built Electrolyte
    • Select electrolyte from pull-down menu
    • Users can load the previously built electrolyte by selecting the electrolyte from the pull-down menu of the Load option. Details of the electrolyte, such as density and composition appears below the pull-down menu as the user selects an electrolyte. Details of the electrolyte can be also found in the electrolyte table in the Lobby.


    Build Interface

    • Build SEI button will build the interface.
    • Build SEI is to make interface between the anode and the electrolyte that are selected, previously. Empty space of the simulation box is filled by the electrolyte selected.
    • SEI is modelled by filling the emptry space with the electrolyte
    • SEI model made by filling the electrolyte in the empty space of simulation box
    • After the SEI model is built, the Build SEI in the SEI builder window changed to Save.

      How to Simulate

      Once users save the SEI structure using the SEI builder window, the saved SEI structure appears in the SEI window of the Simulations window. Then the reaction simulation is ready to go.

      Previously built SEI structure can be also loaded by using the pull down menu of SEI window and Load button.

      • Saved SEI structure is loaded for reaction simulation

      All to do for starting simulation are to input temperature, simulation time and job name and press Simulate button.

      • Simulation of the SEI reaction

      As the simulation starts, Molecule Filter window appears and shows the list of all molecules involved in this simulation. The list in the Molecuel Filter is continuously updated during simulation.

      Analysis of the Simulation

      iBat provides many useful analysis tools for the SEI reaction study. Before analysis, simulation results should be loaded in SEI working studio.

      The input window, which is on the left side of the Load button, is for typing the number of data. If user put 10 and the total simulation time is 2ps, for example, 10 data will be given every 0.2ps of the simulation.

      Users can load not only the present simulation job but any previous jobs using the pull down menu of Analysis window.

      When loaded, the visualization window shows the initial structure of SEI with the list of the molecules involved in the simulation job in Molecules Filter window.

      Please also note that all data in the Simulations window are those for the simulation jobs.

      • Reload the simulation job for analysis

      Review of Simulation

      Users can review the simulation by clicking any time in the progress bar below the visualization window, or review step by step using [,] button on a keyboard. 1 step is 0.005ps.

      • Review simulation at any time by the click in the progress bar

      It is also possible to see the simulation results at a given interval. Input window, which is next to the progress bar, is the time interval in ps of the snapshots consecutively displayed when pressing Anode-play.jpg button. Example below shows the snapshots obtained with 1 ps interval using this function.

      • At O ps
      • At 1 ps
      • At 2 ps
      • At 3 ps

      Analysis is always based on the present snapshot displayed in the visualization window. Hence, users can analyze the result at any time of the simulation.


      Molecules Filter

      Molecules filter can be used to control the display of the simulation result.

      Molecules Filter window will be open as a default when users load the simulation job. Users can also open the filter by using Filter-icon.JPG icon.

      Molecules Filter window lists anode and all molecules appeared in the present simulation result. Selected molecules will be displayed in the visualization window. Examples below show the flexibility of the Molecules Filter.

      • Display of all molecules including anode
      • Display of nothing by deselecting all
      • Display of electrolyte molecules
      • Display of CO2 gas molecule

      Two buttons All Inverse and Electrolyte Inverse are provided to inverse the selection. All Inverse button is to inverse any selection for all molecules, while Electrolyte Inverse button is applied only for electrolyte molecules.

      SEI Product

      This function is to display the product of reaction as a function of simulation time or position.

      SEI-Product-icon.JPG icon will open new window as following.

      • SEI Product Window

      Data in the graph show the variation of the number of molecules. Displayed molecule is filtered by the Molecules Filter on the left side of the SEI Product window. All and Electrolyte are the selection inverse function for all molecules and only electrolyte, respectively.

      The x-axis can be selected either simulation time or distance in z direction from the origin of the simulation box. X-axis control can be found on the bottom of the graph.

      • When selecting Time for x-axis, the data are for all molecules in the simulation box.
      • When selecting z for x-axis, users are asked to input dz and time values. The displayed data are for the molecules in the volume from z to z+dz. Users can observe the time variation of the molecules in the system. Time can be changed by the input of the time input window or up and down arrow of keyboard to observe the consecutive change. The time step is determined to the value of total simulation time divided by 200.
      • Selected display of product molecules with simulation time
      • Selected dispaly of product in z direction at 1 ps

      Reaction Table

      Reaction table is to provide detail information of the reaction by identifying the source molecule for a specific product or vice versa.

      SEI-Reaction-icon.JPG icon will open Reaction Table window.

      • SEI Reaction Table Window

      Reaction table consists of 3 columns. It shows which atom is moved from source molecule to product molecule. If the user wants to see how the certain product molecule is made, the user may use filter. See the example below.

      • SEI Reaction Table Filtered by product molecule

      As you see on the example, the user can easily know that Li is from anode and other atoms are from C3H2O3.

      Technical Information

      To simulate SEI components that are evolved from chemical reactions between electrolyte and anode, the iBat employed molecular dynamics (MD) simulations with the reactive force field (ReaxFF). (Click this link for details of MD scripts) The current SEI module in the iBat (as of Jan. 2, 2017) includes the ReaxFF for Si-Li-C-O-H-P-F systems, and the anode module is also operated with the same ReaxFF parameters. This implies that with the ReaxFF one can simulate interfaces between anodes including carbon/silicon and liquid electrolytes including LiPF6 salts. The detail information on development of ReaxFF for Si-Li-C-O-H systems is explained in technical information of the anode module. Here, only the ReaxFF development for new systems (F-F, C-F, H-F, Li-F, O-F, Si-F, P-P, P-F, Li-P, C-P, O-P, and relevant angle and torsion terms) generated by adding P and F into the Si-Li-C-O-H system is explained below. We will also publish the more details and open them on this site sooner or later. Moreover, we are currently developing ReaxFF parameters for other Li salts such as LiBF4 and LiClO4. The results will also open on this site after their publication.

      • Fig.1 Comparison of DFT and ReaxFF through bond dissociation curves of a F-F bond
      • Fig.2 Comparison of DFT and ReaxFF through bond dissociation curves of a C-F bond
      • Fig.3 Comparison of DFT and ReaxFF through angle bending curves of a C-F-C angle(left) and F-C-F angle(right)
      • Fig.4 Comparison of DFT and ReaxFF through bond dissociation curves of a Li-F bond(left) and H-F bond(right)
      • Fig.5 Comparison of DFT and ReaxFF through bond dissociation curves of a P-F bond in LiPF6(left) and PF5(right)
      • Fig.6 Comparison of DFT and ReaxFF through bond dissociation curves of a Li-P bond in Li3P
      • Fig.7 Comparison of DFT and ReaxFF through bond dissociation curves of a C-P bond in P(CH3)4
      • Fig.8 Comparison of DFT and ReaxFF through bond dissociation curves of a O-P bond in H3PO(left) and H3PO4(right)
      • Fig.9 Comparison of DFT and ReaxFF through bond dissociation curves of a O-F bond in OF2(left) and O2F2(right)
      • Fig.10 Comparison of DFT and ReaxFF through bond dissociation curves of a O-F bond in OF radical
      • Fig.11 Comparison of DFT and ReaxFF through angle bending curves of a F-O-F angle bending in OF2(left) and O-O-F andgle bending in O2F2(right)
      • Fig.12 Comparison of DFT and ReaxFF through bond dissociation curves of a Si-F bond in SiF4(left) and SiF2(right)
      • Fig.13 Comparison of DFT and ReaxFF through angle bending curves of a F-Si-F angle bending in SiF4(left) and SiF2(right)
      • Fig.14 Comparison of DFT and ReaxFF through bond dissociation curves of a PF5-LiF in LiPF6


      With the developed ReaxFF for Si-Li-C-O-H-P-F systems, we can perform MD simulation on the iBat to investigate SEI components at the atomic level, using the LAMMPS [6] software with a Verlet [7] integration time step of 1 fs (femtosecond). The simulations were run in a canonical NVT ensemble at a given temperature, in which the temperature was maintained by a Nosé-Hoover thermostat [8] with a damping parameter of 0.01 fs-1.

      How to determine densities of liquid electrolytes?

      For many cases, a user might consider an electrolyte in a liquid-mixture phase composing of more than two molecular compounds. Thus, prior to prediction of chemical reactions between the electrolyte and anode, a density of the liquid electrolyte should be determined. To determine a liquid density of electrolytes, the SEI module proceeds with the following procedures:

      1. Randomly fill electrolyte molecules in the vacuum volume that a user selects, where the electrolyte are occupied as much as possible by calculating overlaps between molecules based on their van der Waals radii.
      2. The electrolyte system obtained from the 1. process would be very unstable. To relieve the high energy of the system, insert an additional vacuum volume by increasing 20 % of z-axis length of the system.
      3. Perform molecular mechanics to relax the simulation cell obtained from the 2. process without a cell optimization
      4. Squeeze the simulation cell obtained from the 3. process by 5% of z-axis length of the cell.
      5. Perform molecular mechanics to relax the simulation cell obtained from the 4. process without a cell optimization and then compare a potential energy of the system with the previous one (3. process). If the current potential energy is more stable (more negative) than the previous one, repeat the step 4. and 5. Otherwise, save the system density as an optimal liquid density as well as a potential energy, and then go to step 6.
      6. Additionally, the iBat double-checks the optimal liquid density obtained from the 5. process. Squeeze the cell and calculate the potential energy as steps 4. and 5. Repeat this process 4 times to confirm that the current energy is higher than the potential energy at the minimum density point from the 5. process. If a new point with a lower potential energy (more stable point) during this process appears, save the system density as an optimal liquid density as well as a potential energy, and then do this process (step 6) again.

      The below graph shows a potential energy versus system density curve obtained in finding an optimal liquid density on the iBat.


      • Example plot of the determination about density of liquid electrolytes by a potential energy versus system density curve. Remark the red square as optimal density that we can obtain in the system


      • Description of the process to search optimal density of liquid electrolytes. Remark the red square as optimal density that we can obtain in the system

      How to analyze chemical products from ReaxFF-MD simulations?

      The main purpose of the iBat SEI module is to predict chemical products in the SEI created by chemical reactions between anode and electrolyte. The iBat analyzes the chemical products from outputs (e.g. bond order) of ReaxFF-MD simulations. The chemical molecule information computed by the ReaxFF potential can be written by using “pair_style reax/c” command in LAMMPS. The bond order value is used to determine chemical bonds, in which the bond order depends on bond distance. In ReaxFF, the bond order (BOij) is defined as followings:


      • Description(Left) and Equation(Right) of Bond Order Definition for bonding distance

        For identifying chemical bonds between pairs of atoms, “cutoff” distance should be assigned. The default cutoff of 0.3 usually gives good results, and, in practice, LAMMPS set the default cutoff as well. Normally, LAMMPS should match the chemical identity of each atom type, as specified using the reax/c pair_coeff command and the ReaxFF force field file. The LAMMPS writes the output containing the following information: molecule ID, number of atoms in this molecule, chemical formula, total charge, and center-of-mass xyz positions of this molecule. Finally, the SEI module of the iBat version utilizes the molecule information in LAMMS to show bonding and decomposition mechanism at each time step in the simulation.

        References

        [1] Jung, H.; Lee, M.; Yeo, B.; Lee, K.-R.; Han, S. S. J. Phys. Chem. C 2015, 119, 3447.

        [2] van Duin, A. C. T.; Strachan, A.; Stewman, S.; Zhang, Q.; Xu, X.; Goddard, W. A. III. J. Phys. Chem. A 2003, 107, 3803.

        [3] Han, S. S.; van Duin, A. C. T.; Goddard, W. A. III.; Lee, H. M. J. Phys. Chem. A 2005, 109, 4575.

        [4] Newsome, D. A.; Sengupata, D.; Foroutan, H.; Russo, M. F.; van Duin, A. C. T. J. Phys. Chem. C 2012, 116, 16111.

        [5] Bedrov, D.; Smith, G. D.; van Duin, A. C. T. J. Phys. Chem. A 2012, 116, 2978.

        [6] Plimpton, S. J. Comput. Phys. 1995, 117, 1.

        [7] Verlet, L. Phys. Rev. 1967, 159, 98.

        [8] Hoover, W. G. Phys. Rev. A 1985, 31, 1695.

        Contact

        Dr. Sanng Soo Han, Korea Institute of Science and Technology (Tel: +82-2-958-5441)

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