1. Phonopy-Spectroscopy : It is a project to add the capability to simulate vibrational spectra to the Phonopy code. Features: Calculate infrared (IR) intensities from Phonopy or VASP calculations; Calculate Raman-activity tensors and scalar-averaged intensities within the far-from-resonance approximation; Prepare peak tables including assigning modes to irreducible representations (Phonopy interface); Output customisable simulated spectra with support for multiple unit systems and simulated instrumental broadening; Include first-principles mode linewidths from Phono3py calculations (Phonopy interface). https://github.com/JMSkelton/Phonopy-Spectroscopy When using this code, please cite the following article: Phy. Chem. Chem. Phy. 19, 12452 (2017). 2. IR : Python Package to Calculate IR Intensities from the Dipole Approximation with Phonopy and VASP. This python package can calculate infrared intensities based on the dipole approximation. To do so, you need VASP and Phonopy . https://github.com/JaGeo/IR When using this code, please cite the following article: J. Chem. Phys. , 1994 , 100 , 8537; J. Phys.:Condens. Matter. , 2010 , 22 , 265006. 3. INTENS : The BASH script for evaluation of IR intensities within DFPT by VASP. As of VASP 5.* version, the DFPT linear response calculations are available. Among others, the user can obtain the matrix of Born effective charges ( BEC ), which refers to change of atoms'polarizabilities at an external electric field. The BEC tensor is a key to calculate the vibrational intensities using the most modern method available , using the formula by Gianozzi Baroni. http://homepage.univie.ac.at/david.karhanek/downloads.html 4. raman-sc : Python program to evaluate off-resonance Raman activity using VASP code as the backend. In order to calculate off-resonance Raman activity of a mode, one needs to compute the derivative of the polarizability (or macroscopic dielectric tensor) with respect to that normal mode coordinate: dP/dQ (or de/dQ). Thus, two ingredients are required: Phonons at Γ-point; Macroscopic dielectric tensor. https://github.com/raman-sc/VASP 5. VASP2NMR : Convert VASP files to NMR spectra. https://github.com/smeerten/VASP2NMR 6. opticsVASP : Program to plot optical properties from VASP results Program to plotoptical properties from VASP results. compile the program with :$g++ -oopticsVASP opticsVASP.2.0.c. run the executable file on the folder where theVASP output files are located. https://github.com/gmsn-ita/opticsVASP
from http://www.st-andrews.ac.uk/seeinglife/science/research/Raman/Raman.html Raman spectroscopy Raman spectroscopy relies on the scattering of light. In the same way that particles can be scattered through collisions with other particles, light can also be deflected when it interacts with matter. Upon interaction with matter, there can be four different types of energy exchange . Why is the sky blue? The sky looks blue because the tiny particles of dust and water in the air scatter the light from the sun. Blue light has a shorter wavelength and is scattered more than red light so the sky appears blue. As the light from the sun travels through more atmosphere more of the colours of light are scattered and the sun appears red. Raman Scattering Only 1 in every 30 million photons are inelastically, scattered and the photon transfers some of its energy to the molecule Rayleigh (ordinary) scattering is when the photon is absorbed to a higher virtual level and is instantly scattered (emitted) elastically back to the initial level. The photons emitted by Stokes-Raman scattering usually have a lower energy and frequency than that of the photons absorbed and these photons are inelastically scattered, transferring some of their energy to the molecule. The reverse is also possible; the photons emitted have a higher energy and frequency than the photons absorbed. This is called Anti-Stokes-Raman, but it is not likely at room temperature as electrons prefer to be in the ground state. Raman Spectroscopy Raman Spectroscopy is a vibrational spectroscopy technique used to collect a unique chemical fingerprint of molecules. Each molecule has a different set of vibrational energy levels, and the photons emitted have unique wavelength shifts. Vibrational spectroscopy involves collecting and examining these wavelength shifts and using them to identify what is in a sample. Different peaks in the spectrum correspond to different Raman excitations. Uses Raman Spectroscopy produces information about a cell. It tells you about the state of the cell, and possibly whether or not it is virally infected and whether or not it is cancerous, precancerous, or not cancerous. It can be used to study HIV and malaria. A laser is shone at the cell and the information needed is extracted from the spectra obtained. Enhancements Unfortunately Raman scattering is a rare event, roughly 1 in every 30 million photons is Raman scattered. This means that it takes a long time to get a signal, which can also be highly masked by fluorescence or other interference. An improved signal to noise ratio is required to reduce acquisition time. A laser is normally used as a light source to increase the photon density. The photons from the laser, with frequency in the visible range, provide monochromatic excitation. Another way to enhance Raman spectroscopy is to make the virtual level in the Jablonski diagram above a real level. Normally no energy level actually exists at this energy value. This process is called resonance Raman scattering . It chooses an incident wavelength at which the molecular unit absorbs and selectively excites the vibrations of this unit. Surface enhanced Raman spectroscopy (SERS), is another technique used to improve Raman based on metallic surfaces that has proved to be very successful, and by combining Raman spectroscopy with optical trapping we get the Raman tweezers that can be used to study the behaviour of entire cells simultaneously. Advantages Although another vibrational spectroscopy technique, infrared spectroscopy (IR), is more sensitive than Raman, it does not work well for aqueous solutions since it suffers from large water absorption effects. Raman does not suffer from these absorption effects and needs little or no sample preparation. It also has the added advantage that the spectra are generally unaffected by temperature changes, and that the concentration of the particular species is directly proportional to the intensity of spectral features shown. Raman gives an objective and accurate result reducing the time delay for receiving diagnosis and does not require chemicals to be added to samples. This was a contribution from Kirsty Scott, one of our undergraduate project students.
标签: Spectroscopy
