Errors encountered in the pyrolysis of organic polymers under ReaxFF force field

LAMMPS LAMMPS Beginners
1

Dear community,

I’m sorry to bother you. But after many times of debugging, I still can not solve the problem of error. So I had to ask for your help again. (Again, sorry for wasting everyone’s time.)

What I’ve done is pyrolytic PI films to simulate laser production of graphene, and the force field is ReaxFF Force field, using a version of LAMMPS 64-bit 2Aug2023-MSMPI for windows. However, an error was reported at runtime.

LAMMPS (2 Aug 2023 - Update 3)

job aborted:

[ranks] message

[0] application aborted

aborting MPI_COMM_WORLD (comm=0x44000000), error 1, comm rank 0

[1-3] terminated

---- error analysis -----

[0] on LAPTOP-K8KKF285

lmp aborted the job. abort code 1

---- error analysis -----

After checking the in file for several times, I made different concatenation between the wrong file and the file that could run successfully before, so as to find out the cause of the error.

Since most of the programs in the initialization phase were copied directly from files that worked successfully, the reason was to focus on modeling and force field Settings. The following are the details of the data file and the Force field file.

My modeling was done using Material studios software, converted into data files using msi2lmp program under pcff force field. The vmd software is then used to change the atomic type into charge. Here is the data file and its corresponding OVITO image.

PI_OVITO
PI_OVITO692×544 160 KB

PI.data (98.0 KB)

For the force field file, my force field file is downloaded from Included force fields — ReaxFF 2023.1 documentation (scm.com), from the literature:

L.Z. Zhang, S.V. Zybin, A.C.T. van Duin, S. Dasgupta, W.A. Goddard, and E.M. Kober Carbon Cluster Formation during Thermal Decomposition of Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine and 1,3,5-Triamino-2,4,6-trinitrobenzene High Explosives from ReaxFF Reactive Molecular Dynamics Simulations Journal of Physical Chemistry A (2009) 113, 10619-10640 http://dx.doi.org/10.1021/jp901353a

I converted it from a PDF file to a txt file and then manually reformatted the force field. Finally, the format was adjusted using the fromdos applet in the Ubuntu subsystem. I attached the force field file I used below.

reaxff.chon.txt (17.4 KB)

To avoid making the stupid mistake of typing the wrong file name again, I typed the dir command on the command line and compared it with the run command to rule out the cause of the error.

avoid_name_error

This is the second molecular dynamics model I’ve done. My study is inseparable from the support and advice of the community. Thank you very much for your advice. Any advice will benefit me a lot, and every reply will become my motivation to move forward. Sorry again for my ignorance.

Best regards，

Ripples

2

You cannot get comments on how to correct your input file if you don’t provide it.
I only see the data file and the ReaxFF force field file.

3

Dear Alex,

Thank you for your response, which has guided me in improving my writing standards. I sincerely apologize for any shortcomings. Here are my revisions.

My input file is divided into several sections: initialization, data reading, force field setting, relaxation, heating, equilibration, cooling, and each section is separated by a row of # symbols.

I apologize for the poor organization of this file. Regarding temperature control, I have used the fix temp/berendsen command. In the paper I am trying to replicate, the timestep for relaxation and heating is 0.01 fs, but due to my limited technical knowledge, I have not been able to find an example of changing the timestep midway, so I have standardized all timesteps to 0.1 fs.

I would greatly appreciate any suggestions you may have.

Best regards,

Ripples916

(Below is my input file and specific code)
in.pi2.lmp (1.2 KB)

#Preparation of graphene by pyrolysis of PI

#initialize

units real

dimension 3

boundary p p p

atom_style charge

neighbor 2.0 bin

neigh_modify every 1 delay 0 check no

read_data PI.data

#Force field:ReaxFF

pair_style reaxff NULL

pair_coeff * * reaxff.chon.txt C H N O

#####################

timestep 0.1

velocity all create 1000.0 4928459 rot yes dist gaussian

thermo 100

thermo_style custom step temp pe ke

thermo_modify flush yes

dump 1 all custom 200000 dump-eq.dsw id type q x y z

dump_modify 1 sort id

dump 2 all xyz 200000 dump-eq.xyz

dump_modify 2 sort id

fix 1 all nve

fix 2 all temp/berendsen 300.0 300.0 10

fix 3 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff

fix 4 all reaxff/species 1 1 200000 species-eq.txt element C H N O

fix 5 all reaxff/bonds 200000 bonds.reaxff

run 4000000

unfix 2

##############################

#500ps 300k-2800k 0.01fs

reset_timestep 0

fix 2 all temp/berendsen 300.0 2800.0 10

run 5000000

unfix 2

##############################

#700ps 2800k 0.1fs

fix 2 all temp/berendsen 2800.0 2800.0 10

run 7000000

unfix 2

##############################

#600ps 2800k-300k 0.1fs

fix 2 all temp/berendsen 2800.0 300.0 10

run 6000000

PS：During the process of troubleshooting, I combined different parts of this file with a previously successful run file (pyrolysis of glucose). I found a combination that works, which is the first three parts of the glucose pyrolysis (initialization, data reading, and force field setting) combined with the second half of the current file. The specific file is as follows:
in.pi4.lmp (1.5 KB)
PTT500reaxff.data (594.8 KB)
ffield.reax.cho (8.1 KB)

4

You need to find somebody local(!) that can sit down with you and help you at all levels. If something as simple as this is a major stumbling block, then you need more help than an online forum and scavenging for examples can ever lead you. You have to make choices for the right reasons and not because it is convenient or you don’t know how to implement the alternative.

One major thing is still missing: there is no mention of the error that you are encountering and that you cannot resolve except by “randomizing” input files from different setups.