Anode Materials Design Lab

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Introduction

  • Example : Lobby of Anode Materials Design Lab
  • Example : Working Studio of Anode Materials Design Lab

Anode Materials Design Lab is for in-silico experiments of lithiation or delithiation of the anode materials that you design.

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

  • In the lobby, you can review the anode structures you worked with and all of your previous and on-going jobs. You can also filter the jobs by the anode material, volume expansion, lithiated Li concentration and resulting voltage. If you go to working studio after selecting an anode structure or job, you can continue to work with that anode or review the details of the job, respectively.
  • In the working studio, you can design your anode and perform in-silico experiment of lithiation or delithiation. After the in-silico experiment, various properties of the anode can be characterized. If you selected the anode in the lobby, you can work with the anode you made previously. You can also load the previous jobs to review the condition and results of the job.

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

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 three sections:

  • Visualization Window to show the atomic structure of anode or the final configuration of the job.
  • Anode Table to list the anode you have worked in the present project.
  • Job Table to list the jobs you have executed in the present project.

Visualization window

  • Example : Visualization window showing a Si nanotube

On the left of the lobby is the visualization window that shows the atomic structure or final configuration of the job. Anode structure (final configuration of the job) is displayed depending on your selection in the Anode table (Job 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 left button to change the viewing angle
  • Drag with 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 bond


Control Buttons in the Window

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

  • Display of the sample information

  • Filtering atoms by x-position and Si

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.


Anode Table

  • Example : Anode Table

All anodes you and your colleagues have worked with are listed in sample table. Data of the sample table is generated in the Working Studio when you save the designed anode.

  • Name : Anode name (as you input in Working Studio) with the generation date and time.
  • Owner : User name (not user ID)
  • Materials : Starting materials of the designed anode
  • Description : Brief description of the anode. When you generated the anode, no information appears. You can add description in this table by clicking the empty table. You can edit the description whenever you want.
  • Del.JPG : This button is to delete the anode. PI of the project has the right to delete any anode, but participant can delete only the anode that he/she created.

Once you delete, you won't be able to recover the anode. Please be cautious when you delete an anode.


Job Table

  • Example : Anode Job Table

All jobs you and your colleagues have done are listed in this job table. Data in the job table is generated in the Working Studio when the user execute the lithiation or delithiation experiment.

  • Name : Name of jobs (as you input in the Working Studio) with the job execution date and time.
  • Owner : Name of the user (not user ID).
  • Anode : Name of anode used in the job.
  • Temperature : Temperature (in Kelvin) for the virtual experiment of lithiation or delithiation.
  • Time : Time (in picosecond) for the virtual experiment of lithiation or delithiation.
  • [math]V_{final}/V_{initial}[/math] : Ratio of the anode volume after the experiment to the initial volume.
  • [math]x_{Li}[/math] : Concentration of Li in anode materials
  • Voltage : Anode potential
  • Status [F|R] : status of the job. F means finish and R running.
  • Del.JPG : This button is to delete the job. PI of the project has the right to delete any job, but participant can delete only the job that he/she performed.

Once you delete, you won't be able to recover the job. Please be cautious when you delete a job.

The job 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. See the example below.

  • Filtered by the volume



User Manual : Working Studio

  • Example : Working Studio of Anode Materials Design Lab

Working studio can be devided in 4 sections.

On the left of the window, menu column provides the input area of all parameters or options for anode design, lithiation or delithiation simulation and analysis of the sample.

Visualization window provide the atomic structure viewer. Color of atom is based on the CPK coloring convention, with slight modification for better distinction. See color of atom page for the color list.

On the right side of the viewer, three graphs shows the temperature, potential energy and total energy of the sample.

Top of the viewer, we provide mainpulation toolkit for anode materials design and simulation box set-up.


How to Make Anode Sample

Select Materials

In Anode section of Menu Column, you can choose the materials for anode from pull-down menu. As of July 1st, 2015, Si (100), Si (111) and graphite of both AB stacking and AA stacking are provided as the anode materials. Other materials of interest will be added as the virtual fab is developed.

When you load the materials by clicking Load button, basic unit cell of the materials appears on the visualization window. You can then start to design your anode sample.

  • Load materials from anode section : the case of Si (001)


Manipulate Materials to Design Your Anode

On the top of the visualization window, several tools for anode maniputation can be found. The manipulation functions can be groupd in three groups.

  1. Cell-base manipulation
  2. Atom-base manipulation
  3. Pretreatments


Cell-base manipulations
  • Anode-strain-button.JPG Strain : to apply strain on the sample in [math]x[/math], [math]y[/math] and [math]z[/math] direction of the simulation box, respectively. Unit is in percent of the present dimension of the box. When you click Anode-strain-button.JPG, 3 input windows appear in the lower area of the Manipulation toolkit section. If you want to cancel the operation, you have to load materials again.
  • Strain input window


  • Anode-clone-button.JPG Clone : to clone the simulation box in [math]x[/math], [math]y[/math] and [math]z[/math] direction respectively. This tool is useful for making larger anode sample from the unit cell. Example below shows the example to make Si anode made from Si(001) materials by clonning 5 in [math]x[/math] direction, 5 in [math]y[/math] direction and 2 in [math]z[/math] direction.
  • Example of making Si 5X5X2 anode made from Si(001) unit cell


  • Anode-vacuum-button.JPG Vacuum : to make a vacuum space in simulation box in [math]\pm x, \pm y, \pm z[/math] directions respectively. Unit is in Angstrom. Whenever you click the Apply button, the space of selected dimension is added. This tool is typically used to supply Li for the lithiation simulation. Example below shows the case to make 20 Angstrom in [math] +z[/math] direction.
  • Example of making 20 Angstrom vacuum space on Si 5X5X2 anode


Atom-base Manipulators
  • Anode-select-button.JPG Select Atom : to provide various atom selection options. Click Anode-select-button.JPG will display the options in the lower area of the manipulation toolkit.
  • Various options for atom selection appears by click Select Atom tool.
  • Option Description How to release
    Anode-select-single.JPG Single atom selection toggle
    Anode-select-element.JPG Select by element Click other options
    Anode-select-square-in.JPG Select all atoms projected in the square Click other options
    Anode-select-square-out.JPG Slect all atoms projected outside of the square Click other options
    Anode-select-circle-in.JPG Select all atoms projected in the circle Click other options
    Anode-select-circle-out.JPG Select all atoms projected outside of the circle Click other options
    Anode-select-sphere-in.JPG Select all atoms in the sphere Click other options
    Anode-select-sphere-out.JPG Select all atoms outside of the sphere Click other options
    Anode-select-bond.JPG Select all atoms bonded to the selected atom Click other options
    Anode-select-unbond.JPG Select all atoms that are not bonded to the selected atom Click other options
  • Selected atoms are blue colored. Number of selected atom appears in the lower right corner of the visualization window. All selection functions are applied to the atoms defined by the pull-down selection menu next to "Select atom" in the manipulation menu bar. If the All is chosen, you can select any atoms in the sample. If you specify the atom by selecting element in the pull-down menu, your selection is applied only to the element. See below for example.
  • Selected atoms without element filtering :
    Select option = all

  • Selected atoms with element filtering :
    Select option = Si
  • Selected atoms with element filtering :
    Select option = Li
  • Once you select atoms, you can manipuate the selected atoms. Delete the atoms by using Delete keyboard on your system. In addition, you can Add atom, Move, Rotate, Strain, Substitute and Copy & Paste. These functions can be used by the buttons right to Anode-select-button.JPG button.


  • Anode-add-atom-button.JPG Add Atom : This is to add atom(s) near the selected atom(s). Once you click, options appear in the lower area of the toolkit.
  • Option menus when selecting Anode-add-atom-button.JPG button
  • Here, H, C, N, O, Si atom can be added at the relative position from the selected atom(s). Added atom is to be selected in the pull-down element menu. Two adding options are possible. Add One is to add one atom selected in the pull-down menu at the relative position defined by the [math]x, y, z[/math] position input from the center of the selected atom(s). Add Atoms is to add atom(s) of the same number of selected atom(s) at the relative position defined by the [math]x, y, z[/math] position input from the center of each atom.
  • The first example is to add hydrogen atom at 1 Angstrom higher at the center of the selected atoms.
  • Central 9 Si surface atoms are selected



  • By clicking Add One with hydrogen select and set 0, 0, 1 for [math] x, y, z[/math] values respectively, one hydrogen atom is added at 1 Angstrom above from the center of the 9 selected Si surface atoms.
  • Please note that after addition, added hydrogen atom is selected with the selected Si atoms are released. This function enables one to add more atoms at this hydrogen atom.
  • With the previously added hydrogen selected, carbon atom is added to make CH surface functionalization. After addition, carbon atom is now selected while hydrogen is released.
  • In order to release the atom selection, please click ESC key in PC keyboard.

  • The second example is to add hydrogen atoms at 1 Angstrom higher at each selected atom.
  • Central 9 Si surface atoms are selected


  • By clicking Add Atoms with hydrogen select and set 0, 0, 1 for [math] x, y, z[/math] values respectively, 9 hydrogen atoms are added at 1 Angstrom above from the center of 9 Si surface atoms.
  • Tip with Add atom
  • You can add atoms to empty box. If you don't have anything in the visualization window (This is the starting status when you come to working studio.), you will add an atom by clicking Add One. The selected atom is added at the [math]x, y, z[/math] position from the origin. You can then consecutively add more atoms by defining the element to be added and the relative position from this atom. Using this function, you can add an arbitrary molecule in the simulation box.


  • Anode-move-atom-button.JPG Move Atom : This is to move the selected atom(s). The selected atom(s) is(are) moved by the amount of the move option value in [math]\pm x, \pm y [/math] and [math]\pm z[/math] directions by pressing the corresponding button.
  • Option menus when selecting Anode-move-atom-button.JPG button


  • Anode-rotate-atom-button.JPG Rotate Atom : This is to rotate the selected atom(s) in either clockwise(cw) or counter clockwise (ccw). The selected atom(s) is(are) rotated by the amount of the rotation step size option whenever cw or ccw button is clicked. Radio button is provided to define the rotation axis.
  • Option menus when selecting Anode-rotate-atom-button.JPG button


  • Anode-strain-atom-button.JPG Apply Strain to the Group of Atoms : This is to apply strain to the selected atom(s). In the menu, minimum dimension of the cube that can contain the selected atoms are presented. User may set the [math] x, y, z[/math] values for new dimension after applying strain to the selected atom(s). Pressing Apply will change the dimension to the new values.
  • Option menus when selecting Anode-strain-atom-button.JPG button
  • Following is the example of applying strain in the center of the Si slab anode. Dimension in [math]z[/math] direction is sqeezed from 6.6749 to 4 Angstrom.
  • Select the center atoms for applying strain
  • The atoms are squeezed in [math]z[/math] direction.


  • Anode-substitute-atom-button.JPG Substitute Atom : This function is to substitute selected atom(s) by the chosen element. As of Sep. 27, 2015, H, C, N, O, Si can be used for the substitute atom(s).
  • Substitute atom selection option appears when selecting Anode-substitute-atom-button.JPG button


  • Anode-copy-atom-button.JPG Copy Atom : This function is coupled with paste atom(s) function. This is to store atomic configuration of the selected atom(s) in buffer. The atomic configuration stored in the buffer can be pasted using Anode-paste-atom-button.JPG function.
  • Anode-paste-atom-button.JPG Paste Atom : This function is coupled with copy atom(s) function. The atomic configuration stored in the buffer by Anode-copy-atom-button.JPG function is pasted at the position defined by selecting reference atom and relative distance from it. Before starting paste, reference atom should be selected by Anode-select-button.JPG.
  • Paste atom options appear when selecting Anode-paste-atom-button.JPG button


  • Anode anchor button.jpg Anchor Atom : This function is to make atoms anchored, so that they don't disappear from the boundary. The atoms,which are anchored, turn into the black, so the user can see which atoms are anchored.
  • Anchored atoms turn into the black


Pretreatments

We provide two virtual reactors for pretreatment of your anode: Annealing Furnace and Surface Modification Equipment.

Caution : Pretreatments is done by molecular dynamics simulation. However, the pretreatment simulation job is not to be recorded in the database. This means that your work should be finished during present live session. Even when you close the pretreatment window, your job is alive in the computation server. However, there is no way to check the status of the job at present. This will be improved in the later version.


  • Anode-pretreat-anneal-button.JPG Annealing Furnace : The furnace can be used for annealing of your sample. One of the typical example would be to relax the artificially built anode sample. The artificially built structure can be so unstable that lithiation simulation may disintegrate your anode. This furnace is to anneal the anode sample by molecular dynamics simulation. Technical details of the simulation is provided in the Molecular Dynamics Simulation section of the Technical Information of this page.
  • NOTE : When you save the anode sample, your sample will be always annealed at 300K for 1.5 ps to guarantee the stability. However, the low temperature annealing would not affect the annealed structure by using this annealing furnace.
  • When you click the Annealing Furface button, you will get the input window for the annealing temperature in K and annealing time in ps. Process button is for starting the pretreatment process. Following is the example of the annealing of Si NW.
  • Example of annealing of Si-NW at 1000K for 3 ps
  • When starting the annealing, variation of system temperature, potential energy and total energy are monitored on the right side of the visualization window.


  • Anode-pretreat-modification-button.JPG Surface Modification Equipment : Surface modification is widely used for enhancing the performance of anode. In this function, the platform provides amorphous carbon deposition, C60 deposition, oxidation and hydrization of the surface. Modification icon will open pop-up window in the center of the anode working studio. You can select the modification method from the pull-down menu as shown in the following examples.


  • C Deposition
  • For the carbon deposition on the surface of the anode, you need to provide deposition temperature, time interval between atoms supplied for the deposition, total number of atoms to be deposited and the kinetic energy of the deposited carbon atoms. C deposition on the anode surface is simulated by the molecular dynamics simulation. Please refer to section Technical Information of this page for the details of the simulation method. C atoms are supplied randomly near the anode surface and always directed to the center of the anode sample.
  • Example : 50 carbon atoms of 5 eV will be deposited at 1000K at the interval between C atom depositions of 2 ps, i.e. for 100 ps.


  • C60 Deposition
  • Same as the carbon deposition, except the deposited precursor is C60. This is to reproduce the simulation work published in Carbon in 2014.
  • Example : 20 C60 molecules of 180 eV will be deposited at 1000K at the interval between C60 molecule depositions of 5 ps, i.e. for 100 ps.


  • Gas Treatment (N2, O2, H2)
  • These treatments are for nitridation, oxidation and hydrogenation of the anode surface, respectively. This treatment process is composed of two step; Fill and Process. Fill button will fill the selected gas in the simulation box as much as possible: the gas molecules are randomly supplied as far as the distance to the neighbor molecule is larger than 0.3 nm. This value was determined by experience for the stable simulation.
  • Example : Nitrogen gas treatment at 1000K for 100 ps.

Caution : Pretreatments is done by molecular dynamics simulation. However, the pretreatment simulation job is not to be recorded in the database. This means that your work should be finished during present live session. Even when you close the pretreatment window, your job is alive in the computation server. However, there is no way to check the status of the job at present. This will be improved in the later version.


Save Your Anode

After making your anode, it must be saved in the anode database with assigned name. Pressing Save button will save the anode AFTER additional annealing at 300K for 1.5 ps by MD simulation. This additional annealing is for relaxing the structure after design the anode using Manipulation and Pretreatment functions. During the relaxation, progress of the relaxation can be seen in the [relax.%] next to the anode name in Simulations section. See below.

  • Before save the anode, the structure is relaxed automatically at 300K for 1.5 ps. Progress of the relaxation is presented in the [relax. %] next to the anode name in Simulations section

After finishing the relaxation, your can load the relaxed anode by using anode Load button in the Simulations section.

How to perform simulation

Simulations section in the Menu Column has 5 areas. In Anode area, you can choose the anode for this simulation. Fill Lithium area is to fill lithium in appropriate region of the simulation box. Mode can choose the lithiation or delithiation simulation. Default is lithiation where no electric field is applied. Temp.(K), Time(ps) is for setting simulation temperature in K and time in ps. Finally, Job name area is for job name input and start simulation by pressing <simulate> button.

General procedure for the lithiation simulation is

  1. Load anode
  2. Fill lithium
  3. Set temperature in K and lithiation time in ps
  4. Assign job name and start simulation

Load anode

There are three ways to load anode for the lithiation simulation.

  1. If you design and save your anode in the current session, that anode appears as default in the Anode window.
  2. You can also use anodes you made previously. In the pull-down menu of the Anode window, you will be able to find the list of the anodes.
  3. You can also select the anode in the lobby. If you caome to the working studio after selecting the anode in the lobby, the anode you selected will appear in the Anode window.

Once the anode you want appears in the Anode window, you can load the anode by using Load button next to the window.

Fill Lithium

This function is to supply Li to react with the anode materials. If you click Fill button, vaccum space in the box will by filled by Li atoms. Li atoms are randomly filled that the final density of Li is 0.53g/cc, which is the density of bcc Li. If you need more space for the simulation, you can use Vaccum function in manipulation toolkit.

In some anode geometry, such as tube or shell, inner space of anode should not be filled by Li. For this purpose, the masking function of both square and circile shape is provided. You can also use the Select Atom> in the manipulation toolkit for selecting and removing unwanted Li atoms from the simulation box.

  • Example 1 : Unmaksed Fill can be done by simply pressing Fillbutton
  • Simple unmasked fill of Li
  • Example 2 : Masked Fill for Si Nanotube is to keep inner space of tube empty. After aligning the tube in z direction, press square or circle mask. Blue square or circle appears in the visualization window. You can move or resize the mask by left click on the mask line. Changing the size is possible in vertical and hotizontal directions. Your cursor changes to two-direction-arrow when the size of the mask is adjustable. Once you set up the mask, pressing Fill button will fill Li atoms in the vacuum except the masked space. (NOTE : the projected space of the 2-D mask shape is not filled by Li.)
  • Masked fill of Li to keep the inner space of Si nanotube empty.


Set Mode of Simulation

Radio button to select the simulation mode is provided. Choose appropriate simulation mode.

Set Temperature and Time

Input temperature in K and time for simulation in ps.

Start Simulation

Input job name and press Simulate button to start the simulation. Lithiation or delithiation simulation occurs depending on the mode of simulation. Technical details of the simulation is provided in the technical information section in this document.

As the simulation proceeds, temperature, potential energy and total energy of the system are displayed in real time on the right graph window. Progress of the simulation is displayed by the horizontal bar below the visualization window.

The simulation job status can be seen in the account page or status button Status-button.JPG on the right corner of the status bar in this Anode Disign Lab.

  • Lithiation Simulation : Lithiation reaction is spontaneous when Li and anode materials contact with each other. Lithiation reaction thus occurs once you fill Li atoms near the anode.
  • Example 1 : Lithiation of Si nanotube at 600K for 5 ps.
  • Lithiation of Si Nanotube
  • After the Lithiation of Si Nanotube


  • Delitiation Simulation : For delithiation, external electric field is applied to the anode. The platform finds the geometry of the anode and automatically set a uniform electric field (1 V/&Aring) from the center of the anode.
  • Example 2 : Delithation of the Lithiated Si Nanotube (Example 1) at 600K for 3 ps. For delithiation simulation, lithiated sample should be saved as anode and concentric electric field is applied.
  • Before Delithiation of Lithiated Si Nanowire
  • Delithiation of Lithiated Si Nanowire


How to characterize the (de)lithiated anode

When you just finish the simulation, the job name of the simulation appears in the Job window of the Analysis section. Load button will load the result and the final atomc configuration appears in the visualization window. When loading the result, you can choose the option "clean" that removes the unlithiated free Li from the system. Please refer to Clean section in Technical Information for algorithm to select free Li. You can also select the previous jobs by using pull-down menu of the Job window in Analysis section or by selecting the job from the Job Table in the Lobby.

Once you load the job, all the information in the Menu Column are set to those associated with the job. Right side of the visualization window shows the recorded variation of the temperature, potential energy and the total energy of the simulation job.

All the analysis tools will be applied to the atomic configuration appeared in the visualization window.

Please note that the Fill button disappears to prevent possible confusion.

Review of Simulation

Your simulation can be reviewed once loaded.

Below the visualization window is the movie control panel. Play button (Anode-play.jpg) is to replay the simulation movie with the moving arrow in the temperature and energy graphs on the right side. The simulation movie includes all atoms regardless of the "clean" option when loading the job.

Pause button (Anode-pause.jpg) will pause the movie. You can also visualize the snapshot at any simulation time by selecting the simulation time on the horizontal time scale bar in the movie control panel. Using this function, you can apply all anaysis tools in the middle of the simulation.

  • Example of simulation replay. Captured at 47% of the Lithiation Simulation of Si Nanotube at 600K for 5 ps


Log files of the simulations can be downloaded by using Download Log button below the graphs. You will get a file named vfab_anode.zip. In this zip file exist initial (Initial.dat) and final atomic configuration (Final.dat) and LAMMPS log file (log.dat) of the simulation job. If you are familiar with the LAMMPS code and molecular dynamics simulation, you would be able to use the data for further analysis.

Charge

Charge button will represent the Li atoms based on their charge. Color-scale on the top-right side of the screen shows the range of the charge. Here, the darker color indicates the larger atomic charge of Li. With this function, user can compare the atomic charges of Li near the anode surface with those in the bulk.

  • Presented by Atom Color Code of Li
  • Presented by Charge Color Code of Li


RDF

Pressing RDF opens a new window for radial distribution function graph. RDF spectrum can be used to understand the atomic structure of the sample. All the possible atomic pairs are listed on the left upper corner of the window with colors of the data. You can select atomic pair for the partial RDF spectra.

  • Example of RDF Graph

You can capture the RDF data screen by using Camera.JPG button. RDF data can be downloaded by Download botton below the graph. Pressing Close will close the window.

Line Profile

Pressing Line Profile button opens a new window for line profile analysis. On the top left, there are buttons to select the atom to be displayed and to choose the cross section plane. Below the selection area, projected image of the selected atom on the selected cross section plane is displayed as a contour map. Numbers are dimension of the map in Angstrom.

On the contour map, a horizontal or vertical red line moved at the mouse position on the map. Switching between vertical and horizontal line occurs by clicking the right button of the mouse. When you click the left button of the mouse, line profile of the selected atom will be displayed on the graph of right side. If you move the mouse further, new red line appears and moves with the mouse position, while the red line displaying the line profile data changes to white and fixed in the selected position.

  • Example of Line Profile. White line in the contour map corresponds to the present line profile data in graph, while the red line shows the present mouse position.

You can capture the line profile data screen by using Camera.JPG button. Line profile data can be downloaded by Download botton below the graph. Pressing Close will close the window.

Volume

Pressing Volume will open the new window to show the volume change during the simulation job.

  • Example of Volume Change

You can capture the volume change data screen by using Camera.JPG button. Volume change data can be downloaded by Download botton below the graph. Pressing Close will close the window.

Voltage

Pressing Voltage button will open the new window to show the voltage change during the simulation job.

A problem has occurred while calculating the accurate voltage. So the graph below doesn't show the correct voltage. This will be improved in the later version.

  • Example of Anode Voltage

You can capture the voltage chage graph screen by using Camera.JPG button. Voltage change data can be downloaded by Download botton below the graph. Pressing Close will close the window.

Diffusion

Pressing Diffusion button will open the new window to show the mean square displacement vs. time graph to characterize the diffusivity. You can select the range of time by scrolling the mouse while pressing left button. It will draw red line on the graphe showing linear regression of the data. Inset is the log-log plot of the selected range of the data to check the linearity that is important to judge the validity of the analysis. Calculated diffusivity and a coefficient of determination, [math]R^2[/math] appear below the log-log plot.

  • Example of Diffusivity Characterzation

You can capture the MSD vs time graph screen by using Camera.JPG button. Pressing Close will close the window.

Clean

Clean button will be used when you need to clean the free Li atoms in more elaborate manner. After the cleaning, you can also use the lithiated sample for additional lithiation simulation.

As in the Fill Lithium section, you can use masks of square or circular shape to prevent cleaning free Li atoms in some specific space, such as inner space of tube or hollow ball. Examples below shows the difference between the masked and unmasked cleaning of the lithiated Si nanotube. Loaded data with clean option is also included for more comparison. Unmasked cleaning is almost the same as the loading data with cleaning option. In the case of masked cleaning, all Li atoms inside of the nanotube were kept after the cleaning.

  • Cleaning with masking whole inner volume of the Si nanotube
  • Cleaning without mask

  • Loaded sample with cleaning option


Manipulation of the mask is the same as the mask in Fill Lithium. (NOTE : Project 3 dimensional space is masked by the 2 dimensional mask. 3 dimensional mask will be provided in the future.) After putting mask on the sample, pressing Select button in Criterion section will change the color of Li atoms to be removed into blue. Then the Select button changes to Unselect to cancel the selection. (see below)

  • Example of Masked Selecton to clean free Li atoms that are not involved in lithiation reaction

Pressing Clean button will remove the blue colored Li atoms. Following is the resulting sample.

  • Result of the Masked Cleaning

Another important function of Clean is to prepare the anode sample for repeating lithiation. After cleaning free Li, you can save the lithiated anode as the new anode materials for consecutive lithiation. New anode name section provides the option.

Technical Information

Molecular Dynamics Simulation

Molecular dynamics (MD) simulation is employed for annealing, modification for anode design and lithiation/delithiation simulation. For the MD simulation, the platform is using the LAMMPS software with reactive force field (ReaxFF). (Click this link for details of MD scripts) Please refer to the Interatomic Potential section for more details of the force field.

Annealing

A user will make his/her anode structure based on a unit cell of crystalline Si or C, which might be unstable. Therefore, a user needs to ‘anneal’ the structure in order to obtain an optimized structure at a given temperature by MD simulations. For the annealing process, the iBat performs ReaxFF-MD simulations under a canonical NVT ensemble condition at a temperature that a user assigns. Also, a user can assign his/her MD time; however, he/she must make sure whether total energies of a system converge with MD time. Usually, the longer MD time would provide the more reliable structure.

Modification

For improved design of an anode material, a user would probably consider a composite structure such as carbon-coated Si or SiOx. The iBat currently supports four processes to make a composite: C-deposition, C60-depostion, O2-treatment, and H2-treatment. The deposition simulations are performed by shooting carbon or C60 molecules with a specific kinetic energy that a user assigns on an anode structure one by one every a specific time that a user also assigns [14]. Here, several layers far from surfaces of the anode structure (e.g. the core regions for a nanowire structure and the bottom layers for a slab structure) are fixed to maintain the bulk structure, while several surface layers remain free without constraints to avoid interrupting C or C60-surface interactions during deposition. And the in-between layers are heat reservoirs to prevent temperature increases upon deposition. A thermostat is not applied to the free layers. The O2- or H2-treatment simulations are performed by filling with O2 or H2 molecules in the vacuum region of a MD simulation box. Here, the O2 or H2 molecules are randomly filled until the van der Waals radius of O2 or H2 is no longer overlapped. And the MD simulation is performed under a NVT ensemble at a specific temperature that a user assigns [15].

Lithiation or delithiation simulation

For a modeled or selected anode structure, a user can predict lithiation or delithiation behavior of the anode material by molecular dynamics (MD) simulation with a reactive force field (ReaxFF). The details on ReaxFF will be discussed below. The ReaxFF-MD simulations on the iBat platform are performed by using the LAMMPS software [1] with a Verlet [2] integration time step of 0.5 fs (femtosecond). The simulations are run in a canonical NVT ensemble at a constant temperature that a user selects. The MD simulation temperature is maintained by a Nosé-Hoover thermostat [3] with a damping parameter of 0.01 fs-1. For a lithiation simulation, an anode material need to be immersed in Li sources. For doing this, a user must first make a MD simulation box where a vacuum region includes along with the anode structure. And then, click button ‘Fill Lithium’. The iBat randomly fills Li atoms in the vacuum region by considering van der Waals (vdW) radius (3 Å) of Li. In other words, Li atoms are filled until the vdW radius of an added Li atom is no longer overlapped with the previous ones. The delithiation simulation is performed by applying a two-dimensional or three-dimensional electric field to the simulation box. In the iBat, the electric field of 1 V/Å is used as the default value. We (the developer) confirmed that the default value would provide reasonable results.

Interatomic Potential

Importing ReaxFF Potential

A current anode module of the iBat version (as of Jan. 3, 2016) includes the ReaxFF for Si-Li-C-O-H systems. Developments order is as follows. First, we developed the ReaxFF for Si-Li systems such as Si-Si, Li-Li, and Si-Li bond terms by ourselves.[6] In developing the ReaxFF parameters for the Si-Li systems, we initially used Li-Li parameters fitted by Han et al. [8] respectively, which were further trained to model several Li-Si systems. Validation results of the Si-Li ReaxFF are shown in Figures 1-4. To consider SiOx anode systems, we extended the ReaxFF to the Si-Li-O ternary system,[20] where the ReaxFF was developed based on the our Si-Li parameters reported in Ref. 8. In particular, we newly developed the Si-O and Li-O parameters. In developing the parameters, we used a reported parameter for O atom and O-O bond parameters.[7] Validation results regarding the ReaxFF development are shown in Figures 5-8. And then, we additionally extended the ReaxFF to the Si-Li-O-C-H systems to consider carbon anodes as well as carbon-coated Si-based anodes. We developed the ReaxFF parameters for Si-C, Li-C, O-C, and Li-H bonds. Here, the parameters for atoms, bonds, angle and torsion regarding C and H were from Ref. 4 and the O-H parameters were from Ref. 5. Validation results regarding the ReaxFF development are shown in Figures 9-11. The more details will be published soon.


  • Interatomic Types Developing Group Year Reference
    C-C, C-H, H-H Other Group 2012 [4]
    O-H Other Group 2012 [5]
    Li-Li KIST 2005 [8]
    Si-Si, Li-Li KIST 2015 [6]
    Si-O, Li-O KIST 2016 [20]
    Si-C, Li-C, O-C, and Li-H KIST 2017 to be published

Validation of ReaxFF <Si-Li>

An accuracy of the MD simulations relies on an accuracy of the ReaxFF used in this work. Basic concepts and formulas of ReaxFF can be found in [10] and [11]. The ReaxFF for a Si-Li system implemented on the iBat was developed by Jung et al. [6], where the ReaxFF parameters of the Li-Si system were optimized against a training set obtained from density functional theory (DFT) calculations using a Li4Si molecule in figure 1 and several LixSi crystals (Li21Si5, Li15Si4, Li13Si4, Li7Si3, Li12Si7, and LiSi) in figure 2 that are thermodynamically stable. And, Jung et al. [6] successfully showed an anisotropic volume expansion behavior of Si nanowires during lithiation by MD simulations with the developed ReaxFF. Figure 1 shows a comparison of the DFT and developed ReaxFF for calculating Li-Si bond dissociation energy in a Li4Si molecule with C2v symmetry because our DFT calculation revealed that the C2v structure is the most stable among C2v, C3v, C4v, and Td structures, which is consistent with a previous ab initio calculation. Additionally, when calculating the bond dissociation energy using DFT calculations, two spin states (singlet and triplet) were considered. The ReaxFF well reproduces the bond dissociation energy for the Li-Si bond obtained from the DFT calculation (DFT: 48.5 kcal/mol versus ReaxFF: 50.9 kcal/mol), although the energies calculated using ReaxFF are higher than those of DFT over the bond distance range of 2.5 ~ 4.5 Å.

  • Figure 1. Comparison of DFT and ReaxFF through bond dissociation curves of a Li-Si bond in the Li4Si molecule.
  • Figure 2. Comparison of DFT (left) and ReaxFF (right) for the EOSs of several LixSi crystals.

Figure 2 shows the equation of states (EOSs) for several LixSi crystals obtained from DFT and ReaxFF, in which the formation energies for each LixSi crystal relative to pure Si (diamond structure) and Li (bcc structure) crystals are included. Overall, the ReaxFF reproduces the EOSs obtained from the DFT calculations, although for the Li21Si5 crystal, the EOS calculated using ReaxFF is broader than that calculated using DFT. Additionally, the formation energies for the LixSi crystals calculated using ReaxFF are similar to the DFT values, which indicates that the developed ReaxFF can provide reasonable results regarding the thermodynamic behaviors for the Li-Si system.

  • Figure 3. Potential energy profiles of DFT and ReaxFF for the insertion of Li into the surface and sub-surface sites of Si(100) (left) and Si(111) (right).

Jung et al. [6] also compared the thermodynamic behaviors for the insertion of Li into the surface and sub-surface sites of Si(100) and Si(111) between DFT and ReaxFF, as shown in Figure 3. Here, the DFT values were obtained from Ref. [9]. The ReaxFF shows a similar Li insertion behavior to the DFT. Both the ReaxFF and DFT indicate that a Li atom on the surface is more stable than one inside the Si bulk. Note that this comparison was performed for the insertion of one Li atom. If more Li atoms are considered, the Li insertion behavior would change; in other words, a Li atom inside the Si bulk is more stable than one on the Si surface.

  • Figure 4. (left) Mean-square displacements of Li atoms in a Si crystal from ReaxFF-MD simulations at several temperatures (300 – 1000 K), and (right) calculation of the energy barrier for the diffusion of Li in a Si crystal using the Arrhenius equation.

Using the developed ReaxFF, we performed MD simulations to investigate the diffusion properties of Li atoms in a Si crystal in figure 4. From the mean-square displacements of Li atoms in the Si crystal, we calculated the diffusion coefficients of Li atoms at a given temperature (300 ~ 1,000 K). Furthermore, using the calculated diffusion coefficient and the Arrhenius equation, D=D0exp⁡(-Ea/kRT) , we calculated the energy barrier for the diffusion of Li in a Si crystal and found that the value is 0.5 eV, which is close to the reported DFT (0.6 eV) and experimental values (0.57 – 0.79 eV) [12].


  • Figure 5. Comparison of DFT and ReaxFF through bond dissociation curves of Li-O bond in Li2O (left) and Li2O2 (right) molecules.

The reactive force field (ReaxFF) parameters of the Li-Si-O system were developed based on the Li-Si parameters that we have previously developed [6]. For the ternary Li-Si-O system, additional ReaxFF parameters with regard to Li-O bonds are required. Here, the parameters concerning the Li-O bond were obtained from figure 5-7 and figure 12.

  • Figure 6. Comparison of DFT and ReaxFF through a dissociation curve of the Li-O bond in Li4SiO4.
  • Figure 7. Comparison of DFT and ReaxFF through an equation of state of the Li2O crystal.

In addition, using the developed ReaxFF, we calculated bulk moduli for c-Si and a-SiO2, which is shown in Figure 8. The ReaxFF predicts the bulk modulus of 70.3 GPa for c-Si, which is comparable to experimental (97.6 GPa) [16] and DFT (88.7 GPa) [17] values. And, the ReaxFF predicts 47.9 GPa for a-SiO2, which is also in the reasonable range between the previous experimental (36.7 GPa) [18] and theoretical (51.5 GPa) [19] values.

  • Figure 8. Bulk moduli of c-Si (left) and a-SiO2 (right) calculated by the developed ReaxFF.
  • Figure 9. Comparison of DFT and ReaxFF through an equation of state of the 4H, 6H, 8H and beta Si-C crystal.

In addition, the ReaxFF parameters for Si-C, C-Li, and O-Li were developed by our KIST team. Some validation results of the developed ReaxFF are shown in Figure 8-11. The details on development of the ReaxFF parameters for Si-C and C-Li will be published soon.

  • Figure 10. Comparison of DFT and ReaxFF through bond dissociation curves of a Si(Yellow)-C(Gray) bond in the CH3SiH3 (Left) and CH2SiH2(Right).
    • Figure 11. Comparison of DFT and ReaxFF through bond dissociation curves of a C(Gray)-Li(Violet) bond in the CH3Li (Left) and NEB(Right).

    Analysis

    Charge

    The atomic charge is calculated by the QEq [13] scheme. It also clarifies the difference of atomic charges by color-gradation along with a charge spectrum on the top-right side of the screen. Here, the darker color indicates the positively higher atomic charge of Li. For example, with this function, a user can compare atomic charges of Li near the anode surface with in the bulk.

    Clean

    A user would sometimes want to remove free Li atoms which are not lithiated in an anode material. With the Clean function, a user can find only Li atoms interacted with the anode material. Here, the free Li atoms are selected by the following conditions: bond order Li = 0 or potential energy Li > -55 kcal/mol. The potential energy criterion is based on our (the developer) experience.

    RDF

    The RDF indicates how density varies as a function of distance from a reference particle. Let [math]n(r)[/math] be the average number of particles found at distances between [math]r[/math] and [math]r+\Delta r[/math] from a reference particle. The RDF, [math]g(r)[/math], is then defined as follows;

    [math]g(r)= \frac{1}{\rho} (4\pi{r}^2 \Delta r) [/math]

    where [math]\rho = \frac{N}{V}[/math] is the density of the material and [math]4\pi r^2 \Delta r[/math] is the volume between two spheres of radii [math]r[/math] and [math]r+\Delta r[/math], centered at the reference particle. This function measures the average correlation among the particles. It is the density of particles at a distance [math]r[/math] from a reference particle, normalized by the average density of the material.

    Line Profile

    A ‘Line Profile’ indicates how many atoms are distributed along the line of a MD simulation system. In the current platform, the line implies a thin rectangular shape with a width of 0.5 Å, where it counts atoms within the rectangular body. With this ‘Line Profile’, a user can observe evolution of an interface (e.g. LixSi/Si) in an anode material during lithiation. For example, a user can analyze position, thickness, and mobility of an interface by the function. Please refer Ref. 1 where a user can find several study cases of the Line Profile.

    Volume

    In designing anode materials, a volume expansion of the material during lithiation is a very important indicator. Our iBat platform provides a change of the volume expansion with a MD simulation time. The volume is calculated by using van der Waals (vdW) radii of elements in the anode material. For example, for a pristine Si nanowire as an anode material, the vdW radius of only Si is considered. In lithiated phases of Si (LixSi), Si-Si bonds are broken, and then low-coordinated components of Si such as atoms or dumbbells are created, leading to significant volume expansion. For measuring more accurately, it is necessary to consider a larger radius than the vdW radius reported in literatures. The iBat uses a vdW radius of 6 Å for Si.

    Voltage

    An open-circuit voltage (V) is also a very important indicator to be considered in designing a anode material. The voltage is calculated for a given Li concentration as follows;

    [math]V=-\frac{E_{final}-E_{init}-\mu_{Li} N_{Li}}{N_{Li}}[/math] ,

    where [math]E_{init}[/math] and [math]E_{final}[/math] and are a system energy for initial state and final state, [math]\mu_{Li}[/math] is a chemical potential for Li atom, and [math]N_{Li}[/math] is a Li concentration.

    Diffusion

    For investigating battery performances, it is also necessary to investigate how fast Li atoms can diffuse in an anode material. In studying kinetic properties of atoms, a mean squared displacement (MSD) is the most common measure. And, a diffusion coefficient ([math]D[/math]) can be calculated by the following Einstein equation;

    [math] MSD = (\mathbf{X}(t)-\mathbf{X}_0)^2=6Dt[/math],

    where [math]\mathbf{X}(t) [/math] and [math]\mathbf{X}_0 [/math] are the position of the particle, and [math]t[/math] is the time.

    Then, [math]D[/math] can be calculated from the slope of [math]MSD[/math] versus [math]t[/math]. The iBat performs a least square fitting procedure to obtain the [math]D[/math] value. However, the Einstein equation is applicable when [math]t[/math] → ∞, and the [math]D[/math] is an independent value on the time ([math]t[/math]). Accordingly, a user would usually need a long MD simulation to obtain a reliable [math]D[/math]. To make sure an accuracy of the calculated diffusion coefficient, a user also needs to consider a curve for [math]\log MSD[/math] vs [math]\log t[/math]. Here, please find the following equation derived from the ‘[math]MSD = 6Dt[/math]’ equation along with the fact that [math]D[/math] is an independent value on [math]t[/math]:

    [math]\log MSD = \log t + \log 6D [/math]

    From the above equation, it can be found that a reliable [math]D[/math] can be obtained when a slope of [math]MSD[/math] vs [math]t[/math] is 1. In other words, a user needs to perform his/her MD simulation until the slope approaches to 1. To show how accurate the calculated [math]D[/math] is, the iBat also provides a [math]R^2[/math] value for a line of [math]\log MSD[/math] vs [math]\log t[/math]. In other words, the [math]R^2[/math] value indicates how far the slope of [math]\log MSD[/math] vs [math]\log t[/math] does deviate from 1. As the [math]R^2[/math] value is close to 1, the calculated [math]D[/math] value is more reliable.

    References

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

    [2] “Verlet, L. Phys. Rev. 1967, 159, 98.”

    [3] “Hoover, W. G. Phys. Rev. A 1985, 31, 1695.”

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

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

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

    [9] “Jung, S. C.; Han, Y.-K. Phys. Chem. Chem. Phys. 2011, 13, 21282.”

    [10] “van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. III. J. Phys. Chem. A 2001, 105, 9396.”

    [11] “van Duin, A.C.T.; Strachan, A.; Stewman, S.; Zhang, Q.; Xu, X.; Goddard, W. A. J. Phys. Chem. A 2003, 17, 3803.”

    [12] “Kim, H.; Kweon, K. E.; Chou, C.-Y.; Ekerdt, J. G.; Hwang, G. S. J. Phys. Chem. C 2010, 114, 17942.”

    [13] “Rappé, A. K.; Goddard, W. A. III. J. Phys. Chem. 1991, 95, 3358.”

    [14] “Joe, M.; Han, Y. K.; Lee, K. R.; Mizuseki, H.; Kim, S.; Carbon 2014, 77, 1140-1147.”

    [15] “Kim, B. H.; Pamungkas, M. A.; Park, M.; Kim. G.; Lee, K. R.; Chung, Y. C.; App. Phys. L. 2011, 99, 143115.”

    [16] “M. A. Hopcroft, W. D. Nix, T. W. J. Kenny, J. Microelectromech. Syst. 2010, 19, 229.”

    [17] “E. Ziambaras, E. Schröder, Phys. Rev. B 2003, 68, 064112.”

    [18] “W. H. Wang, Prog. Mater. Sci. 2012, 57, 487–656.”

    [19] “L. Si, D. Guo, G. Xie, J. Luo, ACS Appl. Mater. Interfaces 2014, 6, 13850.”

    [20] “Jung, H.; Yeo, B.; Lee, K.-R.; Han, S. S. Phys. Chem. Chem. Phys., 2016,18, 32078-32086.”

    Contact

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

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