Hi
I am running some MD cases, where I need to tag some atoms based on their kinetic energies. I want to run the case for 200 ps then tag the atoms, then run it for longer time to visualize their trajectory.
Is it possible to change the type of atoms after 200 ps and set up the script considering the proper pair style and coeff. and let it to run for longer time so that I can recognize them in VMD for visualization?
I am using TIP4P-Ew water model. I run the case for 200 ps using 1 and 2 as the atom type for water. then based on their velocities I changed the type of some of them from 1,2 to 4,5. But I could not let it run again. The error message I am getting is:
ERROR: Pair coeff for hybrid has invalid style (pair_hybrid.cpp:348)
I really appreciate if someone help or suggest me. Thank you.
The input script I am trying to do is attached here.
dimension 3
units metal
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
pair_style hybrid eam lj/cut/tip4p/long 1 2 1 1 0.125 9.0 lj/cut/tip4p/long 4 5 1 1 0.125 9.0 lj/cut/tip4p/long 1 5 1 1 0.125 9.0 lj/cut/tip4p/long 4 2 1 1 0.125 9.0 lj/cut 9.0
read_data testing_in_note.data
pair_coeff 1 1 lj/cut/tip4p/long 0.0070575098 3.16435
pair_coeff 2 2 lj/cut/tip4p/long 0.0 0.0
pair_coeff 1 2 lj/cut/tip4p/long 0.0 0.0
pair_coeff 3 3 eam Au_u3.eam
pair_coeff 1 3 lj/cut 0.08602 2.95 9.0
pair_coeff 2 3 lj/cut 0 0
pair_coeff 1 4 lj/cut/tip4p/long 0.0070575098 3.16435
pair_coeff 2 4 j/cut/tip4p/long 0.0 0.0
pair_coeff 1 5 lj/cut/tip4p/long 0.0 0.0
pair_coeff 2 5 lj/cut/tip4p/long 0.0 0.0
pair_coeff 4 4 lj/cut/tip4p/long 0.0070575098 3.16435
pair_coeff 5 5 lj/cut/tip4p/long 0.0 0.0
pair_coeff 4 5 lj/cut/tip4p/long 0.0 0.0
pair_coeff 4 3 lj/cut 0.08602 2.95 9.0
pair_coeff 5 3 lj/cut 0 0
kspace_style pppm/tip4p 10e-6
…
Thanks
Hi
I am running some MD cases, where I need to tag some atoms based on their
kinetic energies. I want to run the case for 200 ps then tag the atoms, then
run it for longer time to visualize their trajectory.
Is it possible to change the type of atoms after 200 ps and set up the
script considering the proper pair style and coeff. and let it to run for
longer time so that I can recognize them in VMD for visualization?
that is far to complex and complicated. you can simply output to the
kinetic energy for each atom via "compute kepa all ke/atom" and then
as additional field in a dump custom trajectory file.
before loading the traejctory into VMD, you can set the environment
variable LAMMPSREMAPFIELDS to vx=c_kepa and when loading the
trajectory, the value of ke/atom will be loaded into the "vx" field
for each atom at each time step. you can then refer to the vx field,
e.g. in atom selections or use it for color mapping.
in fact, even simpler would be to simply output velocities (vx, vy,
vz) in the custom dump and VMD will read those automatically, then you
can compute the particle's kinetic energy directly from the velocities
via 1/2 k_b mv**2, you just need to figure out the right way for the
conversion factor, so your get the kinetic energy in the desired units
(VMD will always assume "real" units).
I am using TIP4P-Ew water model. I run the case for 200 ps using 1 and 2 as
the atom type for water. then based on their velocities I changed the type
of some of them from 1,2 to 4,5. But I could not let it run again. The error
message I am getting is:
ERROR: Pair coeff for hybrid has invalid style (pair_hybrid.cpp:348)
your input is incorrect. when you specify the same pair style multiple
times in a hybrid pair style, you need to label the individual
pair_coeff statements with a number, to indicate *which* of those pair
sub-styles you are referring to. for details, please see the pair
style hybrid documentation.
You can also use dump_modify thresh to only
output atoms which meet a criteria, e.g. high kinetic
energy.
Steve