WARNING: H matrix size has been exceeded

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1

Dear LAMMPS-users,

I am trying to simulate the kerogen molecule with REAX/C package. But I got the following warning:

WARNING: H matrix size has been exceeded: m_fill=6424 H.m=6237
(…/fix_qeq_reax.cpp:623)

I build a low density file and try to compress the system with NPT ensemble (400 K, 30 MPa). The input file is as follows:

ReaxFF potential for kerogen system

units real
atom_style full
dimension 3
boundary p p p

read_data data.kerogen_II_D_configuration_1

ReaxFF

pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N S

minimize 1.0e-4 1.0e-6 100 10000

compute reax all pair reax/c

variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]

velocity all create 400.0 4928459 rot yes dist gaussian
neighbor 2.5 bin
neigh_modify every 10 delay 20 check yes

thermo_style custom step temp epair etotal vol press &
v_eb v_ea v_elp v_emol v_epen v_ecoa v_ehb &
v_et v_eco v_ew v_ep v_efi v_eqeq
thermo 10000

timestep 0.1

fix 1 all npt temp 400.0 400.0 10.0 iso 300.0 300.0 100.0
fix 2 all qeq/reax 10 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 400000 bonds_400_p_30.reaxc

dump 1 all xyz 2000 kerogen_reax_npt_400_p_30.xyz
dump 2 all image 200000 kerogen_reax_npt_400_p_30.*.png type type size 1280 720
dump 3 all custom 200000 kerogen_reax_npt_400_p_30.txt id type mass x y z q

info all out simulation_log.txt
run 4000000 # 400 ps
write_restart kerogen_reax_npt_p_30_t_400.restart
write_data kerogen_reax_npt_p_30_t_400.data

reset_timestep 0
unfix 1
fix 5 all nve
run 4000000 # 400 ps

Please find the data file in the attached. Any help would be appreciated. Thanks in advance.

Bests,
Shuai

data.kerogen_II_D_configuration_1 (77.3 KB)

2

It is not recommended to use a nevery that is not 1 for fix qeq/reax. Have you tried using 1 instead of 10? Can you try incrasing safezone and mincap keywords? This usually occurs when an atom has too many neighbors within the non-bonded cutoff.

Ray

3

Hi Ray,

Thanks for the apply. I changed safezone to 1.6 and mincap to 100. No warning has been reported right now and simulation is running. Does this occurs because I have a bad initial data structure? OR should I change my non-bonded cutoff (current is 4.5) ? Will the change of safezone and mincap affect the simulation result?

Bests,
Shuai

4

No, it is not because of bad structure or bad setup (e.g. cutoff) but simply due to the numbers of atoms’ neighbors changing significantly during a simulation. This can be the case when you have a very reactive system or when box dimensions change significantly. This is a flaw in reax/c’s dynamic memory allocation, and we get pass by it by allocating a larger buffer in advance. Your setup is fine. Please note that non-bonded cutoff is usually around 10-11, while the 4.5 is a short range cutoff.

Ray

5

Hi Ray,

Sorry, I think I misunderstand the meaning of non-bond cutoff with nbrhood_cutoff in control file. I set the nbrhood_cutoff as 4.5 and I didn’t find the place to change this nonbond_cutoff. Is there any option I can set to change the nonbond-cutoff?