The LoDiS package is a 0D classical molecular dynamics Fortran 90 - Python hybrid software designed to simulate processes for finite-size systems between 10-10000 atoms. Incorporated tools allow for investigations into growth, coalescence, quenching, phase transition, canonical esemble (NVT), microcanonical esemble (NVE) and metadynamics with the choice of either a gas phase or ligand environment, and the addition of a MgO substrate.
Supported nanosystems include:
- Mono- and bi-metallic clusters (metal-metal interactions are modelled by the Rosato-Guillope-Legrand potential) [1]
- Noble gases (Lennard-Jones potential) [2]
- Carbon-based systems (Pacheco-Girifalco potential) [3]
For more general information and publications visit Baletto group website
Copyright 2020 KCL-LoDiS-Baletto
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Clone the repository into a local directory:
git clone https://github.com/kcl-tscm/LoDiS.git
Modify the Makefile in the LoDiS_GIT/base directory to run your local Fortran compiler and its libraries (openmp required).
Compile all the .f90 files by running the Makefile:
cd LoDiS/LODIS_GIT
make -f Makefile
Before configuring the simulation, several files must be prepared beforehand:
- .xyz file with the initial nanocluster atom positions
- .pot file with the potential parameters
- .pot file with the MgO substrate parameters (only when MgO substrate is present)
- .xyz file with second cluster atom positions (only during coalescence)
LoDiS comes equipped with two input schemes: an interactive interface and an input.in file. The former is a more user friendly method for those unfamiliar with the program, providing visual aids and error checks before simulation. In addition, post-simulation analysis unique to the scheme can be automatically run. To run the interface and by extension LoDiS, use the following command on terminal:
python /PATH/LoDiS_GIT/py_interface/lodis_gui.py
/PATH is either the relative from the input.in file directory (i.e the current directory) to the LoDiS_GIT directory, or the absolute path. After allocaring values to all the necessary parameters and confirming, an input.in file will be created and LoDiS will begin the simulation.
The second method involves copying the complete input.in file from the /LoDiS_GIT/base directory into the output directory and modifying the parameter values within it. The .yxz and .pot files paths are included in the input.in and should be given as the relative path for the best result. After altering the input.in file, begin the simulation by running the executable generated by compiling the Makefile, which should be called LODIS_all:
/PATH/LoDiS_GIT/base/LODIS_all <input.in> output.out
Background information regarding each procedure as well tutorials on inputs and outputs are presented in the manual. Supporting descriptions about the input parameters can be found in the LoDiS Documentation.
Running a simulation regardless of the procedure will output the following six files:
- energy.out - the caloric data over the course of the simulation
- movie.xyz - the trajectory data.
- error.out - a file listing any errors that may have occurred over the course of the run period or may have halted the process altogether
- definition.out - a binary file
- pr.out - the final positions of the components
- output.out - a file containing a runthorugh of the process, inluding parameters and errors.
Depending on the procedure, additional files may be generated such as meta.out for Metadynamics and coalescing.out for Coalescence.
A rapid 100K/ns melting simulation of an Ag 147 atom icosahedron is readily available with the use of the provided files in the example_input_files directory.
Edit the paths to the for Ag147.xyz and Ag_Ag.pot files before running the simulation:
filepos = '~/Documents/LoDiS/input_example_files/Ag147.xyz', ! Initial atom positions file, ONLY .xyz format
filepot = '~/Documents/LoDiS/input_example_files/Ag_Ag.pot', ! Potential parameters file, ONLY .pot format
NOTE: neither Ag_309.xyz nor Ag_Ag.MgO.pot are used in this particular run.
- Francesca Baletto (francesca.baletto@kcl.ac.uk)
- Luca Pavan (luca.pavan@kcl.ac.uk)
- Kevin Rossi (k1992@hotmail.it)
- Raphael Pinto-Miles (raphpmx@gmail.com)
- Laia Delgado-Callico (laia.delgado@kcl.ac.uk)
- Matteo Tiberi (matteo.tiberi@kcl.ac.uk)
- Robert Jones (robert.m.jones@kcl.ac.uk)
- Alejandro Santana-Bonilla (alejandro.santana_bonilla@kcl.ac.uk)
- Riccardo Ferrando (ferrando@fisicaunige.it)
- Christine Mottet (mottet@cinam.univ-mrs.fr)
[1] V. Rosato, M. Guillope and B. Legrand, Philosophical Magazine A 59, 321 (1989)
[2] J. E. Jones, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 106, 463 (1924)
[3] L. A. Girifalco, The Journal of Physical Chemistry 95, 5370 (1991)
[4] K. Rossi, Journal of Physics: Condensed Matter 29, 145402 (2017)
[5] K. Rossi and F. Baletto, Physical Chemistry Chemical Physics 19, 11057 (2017)