HOW TO CREATE ATOMS AT A TIMESTEP INTERVAL AND HOW TO PASSIVATE ATOMS IN LAMMPS

Dear all,

I am a newbie to lammps and i have two major challenges.

1. I need to know how to create atoms at a given timestep (say 0.5 ps). Actually my work involves creating about 100 atoms but not at once. it should be one by one at a regular time interval.

2.In another case, I am interested in passivating half of the atoms i have created with hydrogen but cannot simply figure out how to do it.

please your advice and help will be much appreciated.

Thanks.

Ogunbunmi Michael
Msc Theoretical Physics
AUST Abuja
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Comments below.

Steve

Dear all,

I am a newbie to lammps and i have two major challenges.

1. I need to know how to create atoms at a given timestep (say 0.5 ps). Actually my work involves creating about 100 atoms but not at once. it should be one by one at a regular time interval
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  • |

The question is where you want to add them, particularly so
they don’t overlap other atoms.

You can look at the fix deposit command which adds atoms in
a specific way. You can also do a loop and use a create_atoms single
command, to add atoms periodically.

2.In another case, I am interested in passivating half of the atoms i have created with hydrogen but cannot simply figure out how to do it |

  • |

If by passivated, you mean add bonds between atoms, then
you need to create a data file that lists the bond topology.
Several of the example scripts use data files with bonds.

There is no automagic way to create bond topologies in LAMMPS,
that’s a pre-processing step.

Dear all,

I am a newbie to lammps and i have two major challenges.

1. I need to know how to create atoms at a given timestep (say 0.5 ps).
Actually my work involves creating about 100 atoms but not at once. it
should be one by one at a regular time interval.

2.In another case, I am interested in passivating half of the atoms i
have created with hydrogen but cannot simply figure out how to do it.

passivate what from what? and for what model?

axel.