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forcite dynamics tutorial

The document outlines a step-by-step procedure for conducting molecular dynamics calculations using Forcite software, starting from building a crystal structure to analyzing oxygen ion self-diffusion. It includes instructions for geometry optimization, dynamics calculations, and data analysis to obtain mean square displacement values. The final analysis allows for the calculation of oxygen diffusion coefficients using the Einstein equation.

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أحمد النهدي
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87 views12 pages

forcite dynamics tutorial

The document outlines a step-by-step procedure for conducting molecular dynamics calculations using Forcite software, starting from building a crystal structure to analyzing oxygen ion self-diffusion. It includes instructions for geometry optimization, dynamics calculations, and data analysis to obtain mean square displacement values. The final analysis allows for the calculation of oxygen diffusion coefficients using the Einstein equation.

Uploaded by

أحمد النهدي
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Forcite Dynamics Calculations

Step 1: Build crystal to run molecular dynamics calculations


Build crystal structure in 3D atomistic file

Select build_crystals_Build Crystal

Enter required space group and lattice parameters value of the crystal in terms of (a, b, c (Å); α, β, γ)
Forcite Dynamics Calculations

Add Individual atoms

Build_Add Atoms
Forcite Dynamics Calculations
Choose every atom from inbuilt period table and add

Similarly, add the fractional co-ordinate values in terms of a, b, c which are originally provided in
terms of x, y, z in the literature.

Apply “make P1” symmetry to the structure


Forcite Dynamics Calculations
Make super cell of 4 x 4 x 2 in order to get the symmetric structure in all the direction.

Build_Symmetry_Super cell

Delete bonds

Assign charge on each atom

Example: select all “O” atom _ click charge (on left properties) _assign -2 for oxygen atom

Similarly, assign charge on all other atoms (Gd=3, Ba=2, Co=3, O=-2)
Forcite Dynamics Calculations
Create alternative vacancies in Gd-O plane (z-y plane in material studio.xsd file) by removing oxygen
atom manually to fix the stoichiometry to δ= 0.5

All the Dynamic calculation will be run on GdBaCo2O5.5 (GBCO5.5)


Arrow indicating Gd layer

Step 2: Geometry optimization


Select all the oxygen atom except Ba plane to make edit set

Click edit_ edit set _ new_ name it (O)

Check cell Empirical formula to be GBCO5.5


Forcite Dynamics Calculations

Click module_ choose forcite_calculation

Setup _click task choose Geometry optimization _ quality fine


Forcite Dynamics Calculations
Energy _ Forcefield _ browse created Buckingham potential force field file

Keep other parameters by default like,

Electrostatic = Ewald summation

Van der Waals = atom based

run

Step 3 = Dynamics Calculation


Choose generated .xsd geometric optimized file

Choose module_ forcite_calcultion_task_ dynamics_click more

Change ensemble: example for GBCO5.5

Ensemble NPT_Temperature = 773K_ pressure = 0.0 _ Time step = 1fs_ Total simulation time = 10 ps

Other parameters are set by defaults in calculation like:

Thermostat = Nose, Q ratio = 0.01

Barostat = Berendsen

Run
Forcite Dynamics Calculations

Select .xtd file from the forcite dynamics folder which created after first NPT run
Forcite Dynamics Calculations

Module_ Forcite_ Calculation_ Task (dynamics)_ click on more_ ensemble (NVT) _ total simulation
time_10ps

Keeping other parameters constant as used before for NPT run.

Setup_ Restart_ click on append to current trajectory_ run


Forcite Dynamics Calculations

Final run

Choose generated .xtd file in “forcite Restart folder”

Module_ forcite _ calculation_ setup_ Task (Dynamics), More_ ensemble = NVT_ Change Total
simulation Time = 100ps

Setup_Restart_Append_ Run

Step 4: Analysis to calculate oxygen ion self-diffusion


Choose the structure .xtd final Forcite Restart file generated after100ps run and analyse the results
Forcite Dynamics Calculations
Modules_ forcite_ Analysis

Choose mean square displacement: dynamics_ Set choose edit set name O_

Length from 1.0 to 25 frames

Time = 5 ps to 25 ps

Click analyse
Forcite Dynamics Calculations

Two files generated after analysis run

Forcite MSD. xcd and Forcite MSD. std

Choose forcite MSD. std file and select the time versus MSD values given in the right column

MSD versus t plot will be a straight and slope will give oxygen diffusion using

Einstein equation of MSD

MSD = 6Dt + B

D (cm2 .s-1) = (slope/6)* 10-4

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