Dear LAMMPS users,
I need to build a system with dual resolution (CG-ELBA + all-atom). The combination of the atomic styles that gave me the necessary attributes was,
atom_style hybrid molecule dipole sphere
(atom-ID atom-type x y z molecule-ID q mux muy muz diameter density) ----> CG sites
(atom-ID atom-type x y z molecule-ID q ) ----> AA sites
In an attempt to define the explicit atom (point particle), the magnitude of the electric dipole moment and diameter is set to 0.0,
...
6151 1 20.4554 -16.4525 23.5537 129 0.00 0.44575 0.29934 -0.06879 3.0 2.7 ----> CG site
6152 1 19.8678 -13.5254 -29.7945 129 0.00 0.53449 0.02447 0.08219 3.0 2.7 ----> CG site
6153 7 -1.718 7.358 41.954 130 0.1 0.00000 0.00000 0.00000 0.0 0.0 ----> AA atom
6154 7 -2.148 5.987 41.967 130 -0.15 0.00000 0.00000 0.00000 0.0 0.0 ----> AA atom
...
lammps return 'ERROR: Invalid density in Atoms section of data file'
*Questions*
1)How to define a density for a point particle ? (Would be physically reasonable set the density equal to the atomic mass of the point particle, when diameter is set to 0?)
2)If not, how to define both atomic types (point particles + finite-size particles), in data file?
Thanks,
Siani
Dear LAMMPS users,
I need to build a system with dual resolution (CG-ELBA + all-atom). The
combination of the atomic styles that gave me the necessary attributes was,
atom_style hybrid molecule dipole sphere
(atom-ID atom-type x y z molecule-ID q mux muy muz diameter density)
----> CG sites
(atom-ID atom-type x y z molecule-ID q ) ----> AA sites
In an attempt to define the explicit atom (point particle), the
magnitude of the electric dipole moment and diameter is set to 0.0,
...
6151 1 20.4554 -16.4525 23.5537 129 0.00 0.44575 0.29934 -0.06879
3.0 2.7 ----> CG site
6152 1 19.8678 -13.5254 -29.7945 129 0.00 0.53449 0.02447 0.08219 3.0
2.7 ----> CG site
6153 7 -1.718 7.358 41.954 130 0.1 0.00000 0.00000 0.00000 0.0
0.0 ----> AA atom
6154 7 -2.148 5.987 41.967 130 -0.15 0.00000 0.00000 0.00000 0.0
0.0 ----> AA atom
...
lammps return 'ERROR: Invalid density in Atoms section of data file'
*Questions*
1)How to define a density for a point particle ? (Would be physically
reasonable set the density equal to the atomic mass of the point
particle, when diameter is set to 0?)
for point particle interactions, only the total mass of each particle matters.
LAMMPS uses density and radius to determine the per atom mass via
4/3*pi*r^3*density. however for radius set to 0.0, then the convention
is to use the density value directly as per atom mass. please see the
read_data documentation for confirmation.
2)If not, how to define both atomic types (point particles + finite-size
particles), in data file?
for hybrid styles, all atoms have to have valid parameters for all
properties, even if not used, unless particular conventions exist (see
above). that is independent from whether those properties are used in
the pair calculations or not.
axel.