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PBS script for Gaussian Calculations on HPC Systems

  Creating a PBS script A PBS script is a text file that contains the information that PBS needs to set up the job, followed by the commands to be executed.  In the PBS script, the lines beginning with “#PBS” are PBS directives that specify the resource requirements and various other attributes of the job. Note that the directives must come first in the script as any directives after the first executable statement are ignored. Since the R program we will be running doesn't require any interaction, we want to submit the job to the batch queue. In this example, the job we will be running has the following requirements: ·         the job will need 1 node, 10 processors and 64 GB of RAM ·         the job will not require more than 48 hours to complete ·         the name of the job will be 'myscript', with the output written to myscript.out and errors written to myscript.err ·         we want email notifications to be sent to your_email@abc.edu when the job starts and stops
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All about DFT Calculations of Molecules

  Density Functional Theory (DFT) is a computational quantum mechanical modeling method used in chemistry, physics, and materials science to investigate the electronic structure (the distribution of electrons) of molecules and solids. Here's a basic overview of how DFT calculations of molecules work:   1. **Formulation of the Problem**: In DFT, the problem is formulated as finding the electronic density that minimizes the total energy of the system. The electronic density is a function of position and represents the probability of finding an electron at a particular location.   2. **Approximations**: DFT involves several approximations, the most notable being the exchange-correlation functional. This functional captures the effects of electron-electron interactions, including exchange (the antisymmetry of the wave function) and correlation (the classical electrostatic repulsion between electrons).   3. **Choice of Basis Set**: In practical calculations, the electronic wavefunctions

Geometry Optimization Using DFT method in Gaussian Software

  Geometry optimization using Density Functional Theory (DFT) in Gaussian involves finding the minimum energy configuration of a molecule or molecular system by adjusting the nuclear coordinates iteratively until reaching convergence. Here's how you can perform geometry optimization using the DFT method in Gaussian:   1. **Input Preparation**:    Begin by preparing the input file for Gaussian. This file includes specifications for the molecule's geometry, the DFT method to be used, and any additional settings required for the calculation.   2. **Specify the DFT Method**:    Choose a DFT functional and basis set suitable for your system and the level of accuracy you require. Common DFT functionals include B3LYP, PBE, TPSS, etc. You'll also need to specify a basis set for describing the electronic structure, such as 6-31G(d), 6-311G(d,p), etc.   3. **Specify Optimization Keyword**:    Include the keyword "Opt" to indicate that a geometry optimization should be perfo

HOMO-LUMO Calculation and Analysis Using DFT method in Gaussian Software

  HOMO and LUMO are terms used in chemistry to refer to the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), respectively. These orbitals are important in understanding the electronic structure and reactivity of molecules, especially in the context of organic and inorganic chemistry and chemical reactions.   HOMO (Highest Occupied Molecular Orbital):   The HOMO represents the highest energy level of molecular orbitals that contain electrons. It is typically involved in chemical bonding and determines the electron-donating properties of a molecule. In terms of significance: It dictates the reactivity of a molecule in nucleophilic reactions. Molecules with higher energy HOMOs are more prone to donate electrons and act as nucleophiles. It plays a crucial role in determining the absorption spectrum of molecules. Absorption of light often involves promotion of electrons from the HOMO to the LUMO or higher energy orbitals, depending on the energy

IRC Calculation in Gaussian

  IRC (Intrinsic Reaction Coordinate) calculations in Gaussian are used to explore the reaction pathways of chemical reactions. They allow you to follow the path of the reaction from reactants to products, revealing important intermediates and transition states along the reaction coordinate. Here's how you can perform IRC calculations in Gaussian: Performing the Reaction Coordinate Scan : Before running the IRC calculation, you typically perform a single-point energy calculation or a geometry optimization at each point along the reaction coordinate. This involves scanning the reaction coordinate by varying the geometry of the system along the desired direction. Specify the IRC Keyword : To request an IRC calculation in Gaussian, you need to include the "IRC" keyword in your input file. This tells Gaussian to perform the IRC calculation starting from a specified transition state or reaction intermediate. Transition

Phonon Calculations Using CASTEP tool in Materials Studio

Phonon dispersion calculations are a crucial aspect of computational materials science and condensed matter physics. They play a significant role in understanding the vibrational properties of crystalline materials, which are essential for predicting various physical properties and phenomena. Here's an introduction to the significance of phonon dispersion calculations:   Understanding Lattice Dynamics: Phonon dispersion calculations provide insights into the lattice dynamics of crystalline materials. Phonons are quantized lattice vibrations, and their dispersion relation (relationship between phonon frequency and wave vector) characterizes the vibrational behavior of the crystal lattice.   Thermal Properties: Phonon dispersion calculations are fundamental for understanding thermal properties such as heat capacity, thermal conductivity, and lattice thermal expansion. These properties are crucial for engineering materials for specific applications, such as thermoelectric materials or