Dear contributors of LAMMPS-Interface.
I have been using this code for around a year already and I am very pleased with the results. Thank you all for this excellent work.
I always have to modify the topology though, in order to describe properly the crystal structure of the Metal-Phosphonate MOFs that I synthesize in the lab.
I usually have to do one of these two things.
1)Either I define, new atom types, bonds, angles, etc and manually change the topology of the unit-cell until I am done, and then I replicate the cell with other external codes like OVITO and export the new lmp.data file of the supercell.
or
2) I modify the CIF file of my structures and replace some atoms that need higher verbosity with dummy atoms so lammps-interface attach to them different FF parameters, that I later modify manually (again after that I replicate with same methodology as in case 1)
I should also add that I start with the UFF force field in order to get parameters for all types of atoms, and later I modify a lot of stuff. I add DFT calculated bond and angle terms. I add the partial charges calculated via plane wave DFT. I replace the UFF Lennard-Jones parameters with the OPLS parameters except for metal ions that I keep them UFF. This way I get the minima and overall structure closer to the original crystal structure of my materials.
My experience as a simple user of this code leads me naturally to the idea that it would be very beneficial to add the following features:
1)Add 2-3 levels of verbosity for FF parameterization minimum (as it is), Medium, High
2)It would also help if there was the choice to export the lmp.data file with empty tables for the FF parameters but the topology printed as described above in order for the user to add their own parameters
Either way, great work guys.
I hope that with the years lammps-interface will evolve along with us :)
Dear contributors of LAMMPS-Interface. I have been using this code for around a year already and I am very pleased with the results. Thank you all for this excellent work. I always have to modify the topology though, in order to describe properly the crystal structure of the Metal-Phosphonate MOFs that I synthesize in the lab.
I usually have to do one of these two things.
1)Either I define, new atom types, bonds, angles, etc and manually change the topology of the unit-cell until I am done, and then I replicate the cell with other external codes like OVITO and export the new lmp.data file of the supercell.
or
2) I modify the CIF file of my structures and replace some atoms that need higher verbosity with dummy atoms so lammps-interface attach to them different FF parameters, that I later modify manually (again after that I replicate with same methodology as in case 1)
I should also add that I start with the UFF force field in order to get parameters for all types of atoms, and later I modify a lot of stuff. I add DFT calculated bond and angle terms. I add the partial charges calculated via plane wave DFT. I replace the UFF Lennard-Jones parameters with the OPLS parameters except for metal ions that I keep them UFF. This way I get the minima and overall structure closer to the original crystal structure of my materials.
My experience as a simple user of this code leads me naturally to the idea that it would be very beneficial to add the following features:
1)Add 2-3 levels of verbosity for FF parameterization minimum (as it is), Medium, High 2)It would also help if there was the choice to export the lmp.data file with empty tables for the FF parameters but the topology printed as described above in order for the user to add their own parameters
Either way, great work guys. I hope that with the years lammps-interface will evolve along with us :)