Rearrangement of crystal structure during equilibrium

Hello

I simulated uniaxial compression model on Nickel oxide (NiO) and Cobalt oxide (CoO) separately by meam potential. Given the visualization part (OVITO), I faced rearrangement of crystal structure during equilibrium (NPT). How can I address the issue? I used the unit cell from Materials Project, and then extended it to 8000 atoms through Atomsk. I would be thankful if you could advise me.

Best,
Niki

Atoms go where the forces tell them to go. Thus when your atoms change to a different structure, then this is either what should happen, or your choice of potential(s) is not properly representing your system.

Thanks for your response.

Hi Axel

Given our previous discussion, I might need to use Hybrid command for meam and coul/streitz potentials through adding qeq parameters from relevant studies. However, I unfortunately faced this error: ERROR: Unrecognized fix style ‘qeq/slater’ is part of the QEQ package which is not enabled in this LAMMPS binary.

On the other hand, I also received this error for the current example of LAMMPS (streitz) for Al2O3, so I did not manage to run the simulation! I would appreciate if you could give me your advice.

I am using LAMMPS package through Compute Canada servers. The version and modules are:
module load StdEnv/2020 intel/2020.1.217 openmpi/4.0.3 lammps-omp/20210929

Best,
Niki

The error message is self-explanatory and something you need to discuss with the people that provide the binaries or you need to compile your own.

Thanks for your quick reply.
How should I address the issue for the available example in LAMMPS directory? I mean AlO, which is a sample for streitz force field

Same problem, same solution. You need a LAMMPS executable that includes the QEQ package. The one you are using obviously does not.

Thank you very much for your explanation.

Hi Axel

Given our previous conversation, I want to modify the lammps with the relevant QEQ package, and compile it in the separate environment. According to the advice of the potential parameter files’ producer, I followed below instruction:

  • Modified_source_code : LAMMPS codes that should be modified before compiling. ( to calculate 2NNMEAM+Qeq )
  • Use “lammps-14 May 2016” version
  • Recompile LAMMPS after modifying the initial source code (copy 1.Modified source code/ files into both src/ , src/QEQ/ folder and then compile)

Moreover, I removed GPU and USER-INTEL packages which are not compatible with QEQ. I also added KSPACE package. However, once I added MEAM package too, I cannot install lammps in mpi or serial! How should I solve this problem?

Make mpi error:

make[1]: Entering directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_mpi’
Makefile.package.settings:4: …/…/lib/meam/Makefile.lammps: No such file or directory
make[1]: *** No rule to make target ‘…/…/lib/meam/Makefile.lammps’. Stop.
make[1]: Leaving directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_mpi’
make[1]: Entering directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_mpi’
Makefile.package.settings:4: …/…/lib/meam/Makefile.lammps: No such file or directory
make[1]: *** No rule to make target ‘…/…/lib/meam/Makefile.lammps’. Stop.
make[1]: Leaving directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_mpi’
make: *** [Makefile:142: mpi] Error 2

Make serial error:

make[1]: Entering directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_serial’
Makefile.package.settings:4: …/…/lib/meam/Makefile.lammps: No such file or directory
make[1]: *** No rule to make target ‘…/…/lib/meam/Makefile.lammps’. Stop.
make[1]: Leaving directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_serial’
make[1]: Entering directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_serial’
Makefile.package.settings:4: …/…/lib/meam/Makefile.lammps: No such file or directory
make[1]: *** No rule to make target ‘…/…/lib/meam/Makefile.lammps’. Stop.
make[1]: Leaving directory ‘/project/6003103/niki88/NiOCoO_env/just_lammps/lammps-14May16/src/Obj_serial’
make: *** [Makefile:142: serial] Error 2

This is a new topic and should thus not be appended to an existing conversion.

That means the new topic should be posted into the “LAMMPS Development” subcategory.

Sorry, but this is a deal breaker. I have no time and interest to dig out how to make an over seven year old version of LAMMPS work. Such older versions have many known bugs that we have systematically eliminated in the last few years through more careful auditing of changes, writing loads of tests, and using a variety of static code analysis tools.

For starters, the current MEAM package is different from what MEAM was at that time. The current version is implemented in C++, the older one was written as a lightweight wrapper around a Fortran library. For a while both existed concurrently with the C++ version listed as USER-MEAMC.