[lammps-users] A molecule isn't inserted in a system

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1

I’m trying to simulate deposition of silicon on Silicon Nitride using BDIPAS as a precursor.

To insert BDIPAS, I used “molecule + group + fix deposit mol” commands.

This is my input file.

# LAMMPS input - silicon nitride with reaxff

boundary p p f

units real

atom_style charge

read_data practice.data

molecule BDIPAS BDIPAS.data

group ADD type 1

timestep 0.1

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.SiN C H N Si

region bulk prism 0 30.3364067078 0 26.2720988685 2.0 INF -15.1682033539 0 0

group bulk region bulk

neigh_modify delay 0

region slab prism 0 30.3364067078 0 26.2720988685 8 10 -15.1682033539 0 0

group slab region slab

fix mynve all nve

fix Temp bulk temp/berendsen 500.0 500.0 100.0

fix qeq all qeq/reax 1 0.0 10.0 1e-6 param.qeq

fix please ADD deposit 96 0 100 12345 region slab global 2.0 3.0 &

mol BDIPAS vz -1.0 -1.0

dump dp1 all atom 50 bfadd.lammpstrj

minimize 1.0e-4 1.0e-6 500 1000

thermo 100

run 1000

It is running well, but I can’t find BDIPAS in trj file

I’ll put data file and molecule file.

# LAMMPS data file written by OVITO Basic 3.4.2

832 atoms

4 atom types

0.0 30.3364067078 xlo xhi

0.0 26.2720988685 ylo yhi

0.0 50.1672267914 zlo zhi

-15.1682033539 0.0 0.0 xy xz yz

Masses

1 12.0107 # C

2 1.00784 # H

3 14.0067 # N

4 28.0855 # Si

Atoms # charge

1 2 0.0 4.5262087782 0.3085315949 0.4312125653

2 2 0.0 -3.0578932931 13.4445817123 0.4312125653

3 2 0.0 19.694411677 0.3085315949 0.4312125653

4 2 0.0 12.1103096057 13.4445817123 0.4312125653

… (There is no atom#1 in data file)

The molecule file

# LAMMPS data file written by OVITO Basic 3.4.2

48 atoms

Coords

1 11.59037847 12.77372215 20.5230708

2 10.36811233 14.83822682 20.59840347

3 5.939217115 9.439932308 20.21971871

4 9.056769688 15.53765678 20.21511855

…

Types

1 1

2 1

3 1

4 1

5 1

6 1

7 1

8 1

9 1

10 1

11 1

12 1

13 2

14 2

15 2

16 2

17 2

18 2

19 2

20 2

21 2

22 2

23 2

24 2

25 2

26 2

27 2

28 2

29 2

30 2

31 2

32 2

33 2

34 2

35 2

36 2

37 2

38 2

39 2

40 2

41 2

42 2

43 2

44 2

45 3

46 3

47 4

48 4

2

It is rarely useful to provide incomplete files or excerpts. It is rarely possible to tell what is causing a problem reliably since there are usually other causes that are not shown.
It also makes it impossible to reproduce your observations. The best approach is to construct a minimal test case with as few atoms as possible that can reliably showcase the issue with a short simulation run. since there are size limitations for mailing list emails, it is best to combine those into a .zip or .tar.gz archive and attach it to the email.

You didn’t say by which method you determined that there were no deposits.

Please provide the log file or screen output so we can see if there were any relevant warnings from LAMMPS.

Axel.

3

Thanks Axel for reply

tar.gz file I sent includes the log, input, molecule, trajectory file.

These are slightly different to files in the previous email, but the result is same.

Hankyu

2021년 3월 5일 (금) 오전 1:17, Axel Kohlmeyer <akohlme[email protected]>님이 작성:

log.tar.gz (141 KB)

4

Thanks Axel for reply

tar.gz file I sent includes the log, input, molecule, trajectory file.

These are slightly different to files in the previous email, but the result is same.

Input and log files don’t match and the package is incomplete. It is not possible to re-run your calculation.
If this is representative of the level of care that you apply to your research, then you should be very happy to not have me for an adviser.

At least the log file seems to be consistent with your previous reports and it was possible to reconstruct a demonstration input.
The issue is that you define a fix (deposit) that is dependent on “normal” timestep progression, but then first run a minimization, which disrupts this. It will advance the timestep number without calling fix deposit, since the fix is not called during minimization. that in turn prevents the fix from being executed during the following run statement, since the fix is expecting to be run first on step 0 and thus waits for that step, but that step has already been executed during the minimization when the fix is inactive and thus fix deposit will never run. move the minimize command ahead of the definition of fix deposit and it should work as expected.

axel