> Please always reply to the mailing list and not only to individual
people.
> Thanks, Axel.
>
>
>> good day sir,
>> i have a script for deposition but i'm having problem with the
>> potential for the Nickel and Copper atoms. I'm planning to use EAM
>> potentials for both element, but i don't know how to incorporate the
>> potential into the script.
good day everyone,
i’m currently depositing Ni atoms in a copper substrate surface, i fixed some of the bottom layer, then the top layer are simulated in NVE ensemble and finally, i need to anneal the whole system (from 300.0 K to 1000.0 K). I used the pair_style eam/alloy for calling the potential CuNi.eam.alloy for the EAM forcefield and set the Cu as the substrate and Ni as the incident atom. but i’m having a major problem since during the simulation, the copper substrate rises up as the simulation goes on, resulting to loss of atoms. the two atoms won’t stick together. here is my script:
units lj
atom_style atomic
boundary p p f
lattice fcc 1.0
region box block 0 7.5 0 7.5 0 15
create_box 2 box
region substrate block INF INF INF INF INF 3.6
create_atoms 1 region substrate
pair_style eam
pair_coeff 1 1 Cu_u3.eam
pair_coeff 2 2 Ni_u3.eam
pair_style eam/alloy
pair_coeff * * CuNi.eam.alloy Cu Ni
neigh_modify delay 0
group deposition type 2
region mobile block 0 7.5 0 7.5 2 3.6
group mobile region mobile
region anneal block 0 7.5 0 7.5 2 INF
group anneal region anneal
compute add deposition temp
compute_modify add dynamic yes extra 0
fix 1 deposition nve
fix 2 mobile nve
fix 3 anneal nvt temp 300.0 1000.0 100.0
region film block 0 7.5 0 7.5 10 12
fix 4 deposition deposit 1000 2 100 12345 region film near 1.0 &
vz -1.0 -1.0
fix 5 deposition wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add
what is wrong with my script? and what is there a problem with the fix that i’ve been using?
hoping for a positive response
Ed Michael Joil D. Fajardo
Physics Department
Mindanao State University
good day everyone,
i'm currently depositing Ni atoms in a copper substrate surface, i fixed
some of the bottom layer, then the top layer are simulated in NVE ensemble
and finally, i need to anneal the whole system (from 300.0 K to 1000.0 K).
I used the pair_style eam/alloy for calling the potential CuNi.eam.alloy
for the EAM forcefield and set the Cu as the substrate and Ni as the
incident atom. but i'm having a major problem since during the simulation,
the copper substrate rises up as the simulation goes on, resulting to loss
of atoms. the two atoms won't stick together. here is my script:units lj
units lj ???
atom_style atomic
boundary p p flattice fcc 1.0
region box block 0 7.5 0 7.5 0 15
create_box 2 boxregion substrate block INF INF INF INF INF 3.6
create_atoms 1 region substratepair_style eam
pair_coeff 1 1 Cu_u3.eam
pair_coeff 2 2 Ni_u3.eampair_style eam/alloy
pair_coeff * * CuNi.eam.alloy Cu Ni
this overrides and eliminates the previous pair_style and pair_coeff
commands.
neigh_modify delay 0
group deposition type 2
region mobile block 0 7.5 0 7.5 2 3.6
group mobile region mobileregion anneal block 0 7.5 0 7.5 2 INF
group anneal region annealcompute add deposition temp
compute_modify add dynamic yes extra 0fix 1 deposition nve
fix 2 mobile nve
fix 3 anneal nvt temp 300.0 1000.0 100.0region film block 0 7.5 0 7.5 10 12
fix 4 deposition deposit 1000 2 100 12345 region film near 1.0 &
vz -1.0 -1.0
fix 5 deposition wall/reflect zhi EDGEthermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp addwhat is wrong with my script? and what is there a problem with the fix
that i've been using?
what problem with what fix where?
the core problems is *much* more fundamental. see above.
axel.
should i use real for units sir?
whenever i use real as the units, this error comes out “Neigbor list overflow”
and sometimes it also results to loss of atoms.
and i’ll just remove the pair_style eam for the Cu-Cu and Ni-Ni atoms.
and lastly, what do you mean by “much more fundamental” sir?
should i use real for units sir?
please read the documentation carefully for all commands and styles that
you are using. the answer will reveal itself to you.
whenever i use real as the units, this error comes out "Neigbor list
overflow"
and sometimes it also results to loss of atoms.and i'll just remove the pair_style eam for the Cu-Cu and Ni-Ni atoms.
and lastly, what do you mean by "*much* more fundamental" sir?
something like using the wrong units. e.g. in reduced units you don't have
300K or 1000K.
also the lattice constant has a different meaning in reduced units (see in
the documentation)
that said, i am just seeing, that you are using a lattice constant for 1.0.
that don't make much sense either.
no wonder, this input will fly right in your face.
axel.
i’m actually using the real units sir, with lattice constant of 3.615 for the copper atoms. it just that sometimes, the simulation won’t work because of the loss of atoms. i used the thermo_modify lost ignore for the simulation to continue.
for the pair_style eam/alloy, is it automatic that the copper atom becomes the substrate and nickel as the incident atom for the pair_coeff * * CuNi.eam.alloy that i got from the potential files?
and my major problem really is that when i annealed the whole system (excluding the bottom fixed layer), the substrate tends to rise up. but when i only use fix nve for the substrate and anneal only the incident atoms, the simulation goes well, but still, the incident atom won’t stick to the surface of the copper substrate. any suggestion for the fix that i need to use in order for the deposited atom to stick to the surface of the substrate atom?
sorry, please don’t take what is said below the wrong way. i am not trying to dress you down, but give you the kind of jolt to get you off the track of disaster that you are currently on.
at this point i am a bit overwhelmed by your lack of studying the LAMMPS documentation and ignorance toward very serious problems with the physics of your model and results of your simulations. you do need some serious help with your simulations and MD in general, much more than can be provided through e-mail.
before you should even attempt to start as complex a simulation as the kind of deposition you want to do, you need to learn how to run simpler simulations correctly and reproduce some published data. if you had done that, you would have never made most of the mistakes that you have in your input.
e,g. you can try running a bulk copper system, or a bulk nickel system at fixed temperature. then experiment with temperature ramps. then with slab configurations. then with regions and groups …and given how much you seem to be struggling with understanding, you must find yourself a tutor with knowledge in MD simulations that can properly advise you what to do and how to check that your simulations are correct, and with whom you can discuss the results of your practice simulations.
also, when starting to work on your actual project, i strongly advise to assemble your input in small steps and at each step you need to experiment with each command and make absolutely certain you understand properly what each command is doing before your proceed to the next.
…and always be certain to thoroughly study the documentation. e.g. the question of the proper choice of units is explained very prominently in the documentation for the eam/alloy pair style. the fact, that you haven’t noticed it should worry you a lot. there are likely other issues that you have overlooked, especially because some problems with getting simulations to provide physically meaningful answers are not quite so obvious.
axel.