Dear lammps-users,
I now know how to model a diamond lattice using the lammps lattice command, but I have to model water molecules and combined them together. I have the water data file from moltemplate, and I am wondering that is there any method to make lammps not only read my data file with water but also the commands that I create for diamond lattice? Or is there anyone can tell me how to make a diamond lattice in moltemplate? I am a beginner in this area, and also will like to know any recommendation for learning conducting models.
Thank you!
Miao-Chun Wang
Dear lammps-users,
I now know how to model a diamond lattice using the lammps lattice command,
but I have to model water molecules and combined them together. I have the
water data file from moltemplate, and I am wondering that is there any
method to make lammps not only read my data file with water but also the
commands that I create for diamond lattice? Or is there anyone can tell me
how to make a diamond lattice in moltemplate? I am a beginner in this area,
and also will like to know any recommendation for learning conducting
models.
you can create atoms based on a lattice *after* you have read a data
file. take your data file with the water, load it into a text editor
and change the number of atom types to make room for one more atom
type and write it out again. remember that number and create atoms
for that atom type to build your diamond structure via lattice and create_atoms.
if you want to create a periodic diamond structure, then you have to
make certain that the box dimensions for your water system are
suitably commensurate with the grid defined by the lattice command for
your diamond structure.
then you should look for overlapping atoms and delete all the water
molecules where at least one atom overlaps with a carbon atom.
axel.
Thanks for Axel answering my question.
I try to make lattice after let lammps read the water data file but I reach to an error.
My script shows as below:
units real
dimension 3
atom_style full
boundary p p p
neighbor 3.0 bin
neigh_modify delay 0 every 1 check yes
pair_style hybrid lj/cut/coul/long 9.0
bond_style hybrid harmonic
angle_style hybrid harmonic
kspace_style pppm 0.0001
read_data system.data
lattice diamond 5.431
region box block -5 22 -5 22 -8 -2
create_atoms 1 box
mass 3 28.0855
and in log file, I see the error stop at mass, and it said "ERROR: Numeric index is out of bounds (../force.cpp:753)"
I search for this error meaning but still do not know why.
I have enlarge the boundary in the water data file but it still remain error.
Can anyone tell me what has happened?
Thank you!
Miao-Chun Wang
you just posted the exact same reply only 10 minutes ago and i already
gave you an answer reminding you to pay more close attention to the
advice been given, as the error you get is a direct consequence of
skipping over some of the details.
axel.