Simple energy model
The energy input is a simple mapping of coordination number to energy in eV. The input can be a direct mapping of every coordination number to a distinct energy. Alternatively, a linear energy increase with coordination number can be used, which speeds up the simulation.
High performance
By using a simple energy model, the simulation can perform up to 10^11 iterations in one day. With a linear coordination number to energy mapping it can reach up to 10^12 iterations in one day. This allows for the simulation of larger nanoparticles.
Multithreaded
The code allows for as many parallel simulations as cores available on the computing node. This enables the user to obtain a statistically relevant ensemble of low-energy structures. Adding parallel simulations has negligible increase in required RAM.
Track the Simulation using the .xyz-format
Throughout the simulation it is possible to track the energy and save snapshots of the particle. Furthermore the particle with the lowest energy will be saved as an .xyz-file.
Support
The simulation can simulate the effect a support can have on the particle.
A monometallic support can be created by giving a vector that is orthogonal to the support pane.
Usage
Requirements
Rust
Python used version 3.11.10
ASE used version: ase-3.22.1
Install from git
git clone git@github.com:T-136/MC-Cluster.git
Build the binary
Build the program with:
cargo build -r
After the build step is complete the compiled program can be found in your project folder under "./target/release/mc".
Run the simulation
./target/release/MC-Cluster -a Pt,1000 --support Al,1,1,1 -t 1000 -i 1e7 -r 0-1 --e-cn ./example_data/cn_input_example.json -o 9/10 -g ./example_data/303030-grid --support-e 0 --xyz-trajectory
Use "-h" or "--help" to see the available flags and how to use them.
-s, --start-cluster <START_CLUSTER>
-a, --atoms
Atom name and number of that atom seperated by a comma. "Pt,4000"
-s, --support
When creating a new particle using the atoms flag, write the Atom name and a vector orthogonal to the support surface Al,1,1,1. When starting from a xyz file only the support atom is required
-f, --folder
Output folder [default: ./sim/]
-i, --iterations
Determines the length of the simulation
-b, --begin-temperature <BEGIN_TEMPERATURE>
Temperature where the annealing process starts [default: 5000]
-t, --temperature
Temperature at which the annealing process stops [default: 300]
-o, --optimization-cut-off-fraction <OPTIMIZATION_CUT_OFF_FRACTION>
Fraction of the simulation after which the annealing process is completed. After that, the temperature remains constant [default: 1 2]
--support-e <SUPPORT_E>
Support energy
--e-l-cn <E_L_CN>
File path or string containing a JSON-formatted list of energies
--e-cn <E_CN>
File path or string containing JSON-formatted energies
-r, --repetition
How many times the same simulation is run. Multiple runs allow for convergence tests. The number will be part of the simulation folder name. After running -r 0-1, you can run -r 1-2 and the previous simulation will not be overwritten [default: 0 1]
-g, --grid-folder <GRID_FOLDER>
Folder containing the setup files like neighbor sites. It can be created using the Python script create_sites.py [default: ../303030-pair]
-x, --xyz-trajectory
Track the simulation by taking snapshots of the cluster throughout the simulation
--heat-map
Generate a heat map
-h, --help
Print help
-V, --version
Print version