I am trying to parametrize a UiO-66 mof using lammps-interface. This UiO-66 structure was obtained from CSD and has the deposition number 733458. I added H bonds on the linkers using the MOFUN software (attached here is the CIF file). 733458-H.cif.txt
When performing lammps-interface 733458-H.cif, the program does not find any neighbors with Zr atoms. Thus counting the cif file as having "2 molecules"
From the images, we see Zr is considered "Molecule 1" and all other atoms as "Molecule 2". Because of this, no bonding terms are made with Zr.
When visualizing the structure using VESTA, the Zr-O bond distance is 2.3358 A, which is normal.
I tried lammps-interface 733458-H.cif --neighbor-sze 8, but this didn't change the results.
May I kindly ask if there are any additional command-line options I should do for Zr to bond with the other atoms? (specifically O atoms)
Hello dear community,
I am trying to parametrize a UiO-66 mof using lammps-interface. This UiO-66 structure was obtained from CSD and has the deposition number 733458. I added H bonds on the linkers using the MOFUN software (attached here is the CIF file). 733458-H.cif.txt
When performing
lammps-interface 733458-H.cif, the program does not find any neighbors with Zr atoms. Thus counting the cif file as having "2 molecules"From the images, we see Zr is considered "Molecule 1" and all other atoms as "Molecule 2". Because of this, no bonding terms are made with Zr.
When visualizing the structure using VESTA, the Zr-O bond distance is 2.3358 A, which is normal.
I tried
lammps-interface 733458-H.cif --neighbor-sze 8, but this didn't change the results.May I kindly ask if there are any additional command-line options I should do for Zr to bond with the other atoms? (specifically O atoms)