Home
The documentation has been moved to a HackMD page !
COSMOSS is a Matlab based spectral simulation package. The simulation focuses on vibrational excitations, where each of the locally excited modes is treated as a harmonic oscillator (ωi) that coupled (βij) to each other. To simulate 2D spectrum, we add the anharmonic shift (Δ) in the Hamiltonian (H).
The easiest way to install COSMOSS is to download from the Matlab File Exchange:
https://www.mathworks.com/matlabcentral/fileexchange/64433-cosmoss
The package integrates with the Matlab App Installation process. Once installed, you can directly access COSMOSS from your App banner of Matlab.
The package currently wraps up v1.7.3 so it may be outdated. If you want to use the newest version, please clone or download it from GitHub and place the whole folder in your Matlab path. Executing the "COSMOSS.m" file will bring up the main GUI. You might also need to download the GUI Layout Toolbox (See note below) for proper GUI display.
Note: The GUI is built upon the "GUI Layout Toolbox", written by David Sampson. Further information about GUI Layout Toolbox can be found in here
There are three major GUIs of COSMOSS:
- Main GUI: Spectrum simulation (COSMOSS.m)
- Model_GUI: Molecule construction (Model_XXX.m)
- Modes_GUI: Mode Visualization (Plot_Mode.m)
- Run COSMOSS.m
- Construct a model structure
- Adjusting simulation parameters
- Do simulation
A typical working flow starts from initiating COSMOSS.m, which brings up the Main GUI. On the top-left of the Main GUI, one can select a molecule construction model, which will bring up a Model_GUI associated with the selected model. In the Model_GUI one can construct a molecule with some optional parameters. One can also visualize the molecule to confirm the structure. At this point, one can start to simulate spectrum by clicking on the button on the corresponding Model_GUI. If necessary, to visualize the vibrational modes the Modes_GUI can be brought up by clicking the "Plot Modes" button on Model GUI.