search

peteboyd / lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs
MIT License
125 stars 63 forks source link

Cannot find coordination type for Zr8f4 when convert CIF of UiO type MOF #7

Closed zmzeng closed 6 years ago

zmzeng commented 6 years ago

cif and log.zip Thanks for your attention. There is a structure of an UiO type MOF, consist of Zr cluster and BTB linker. Now I want to use lammps_interface to convert the CIF generated by Material Studio 2017 to the lammps data file with UFF4MOF, but I got an error when I tried to. No error with UFF, but UFF4MOF seems better for my structure.

[zeng@localhost lammps_interface]$ python lammps_interface.py -ff UFF4MOF ZrBTB-MOL-NiOPT-supercell.cif 
Molecules found in the framework, separating.
ERROR: Cannot find coordination type for Zr8f4
[zeng@localhost lammps_interface]$ python lammps_interface.py ZrBTB-MOL-NiOPT-supercell.cif 
Molecules found in the framework, separating.
WARNING: Atom 1 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 21 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 41 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 71 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 81 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 111 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 121 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 141 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 161 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 165 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 169 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 173 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 197 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 217 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 237 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 267 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 277 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 307 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 317 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 337 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 357 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 361 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 365 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Atom 369 element Zr has 8 neighbors, but was assigned Zr3+4 as a force field type!
WARNING: Molecule 1 with atoms (Ni, O, H, H, O, H, H) will be using the UFF force field as no  value was set for molecules. To prevent this warning set --molecule-ff=[some force field] on the command line.
WARNING: Atom 393 element Ni has 2 neighbors, but was assigned Ni4+2 as a force field type!
Files created! -> /home/zeng/lammps_interface