LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Initialization
units           metal
boundary        p p p
atom_style      full
processors      * * 1     # domain decomposition over x and y
read_data       ./gra_water.data
Reading data file ...
  orthogonal box = (0 0 0) to (46.92336 44.331078 200)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  936 atoms
  reading velocities ...
  936 velocities
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  96 bonds
  reading angles ...
  48 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.014 seconds
mass            1 12.0107   # carbon   	mass (g/mole)
mass            2 15.9994   # oxygen    mass (g/mole)
mass            3 1.008     # hydrogen 	mass (g/mole)
# Separate atom groups
group 		gr    molecule 1
792 atoms in group gr
group 		water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style  hybrid/overlay  aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff  1 1   none
pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
pair_coeff  * *   aip/water/2dm/opt        COH.aip.water.2dm C Ow Hw  # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style  	  harmonic
bond_coeff  	  1 	0.0  0.9572
angle_style 	  harmonic
angle_coeff 	  1 	0.0  104.52
# define kspace calculation
kspace_style      pppm/tip4p 1E-5
# Neighbor update settings
neighbor        2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute   	1 all pair lj/cut/tip4p/long
compute   	2 all pair aip/water/2dm/opt
compute		wt water temp
variable  	TIP4P  equal  c_1
variable  	EILP   equal  c_2     # total interlayer energy
variable	temp_wt equal c_wt
############# Output ##############
thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
thermo          100
thermo_modify   lost error

fix		subf gr setforce 0.0 0.0 0.0
fix 		1    water shake 0.0001 20 100 b 1 a 1
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
      48 = # of frozen angles
  find clusters CPU = 0.000 seconds

timestep	1e-3
velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
fix		2 water nve
run		1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
 author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
 title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
 journal = {Nano Letters},
 volume =  18,
 pages =   6009,
 year =    2018,
}

- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
@Article{Ouyang2021
  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
  title = {Anisotropic Interlayer Force Field for Transition
    Metal Dichalcogenides: The Case of Molybdenum Disulfide},
  journal = {J.~Chem.\ Theory Comput.},
 volume   = 17,
 pages    = {7237--7245}
 year     = 2021,
}

- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
 author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
 title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
 journal = {J. Phys. Chem. C},
 volume =  127,
 pages =   {8704-8713}
 year =    2023,
}

- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
@inproceedings{gao2021lmff
 author = {Gao, Ping and Duan, Xiaohui and Others},
 title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
 year = {2021},
 isbn = {9781450384421},
 publisher = {Association for Computing Machinery},
 address = {New York, NY, USA},
 url = {https://doi.org/10.1145/3458817.3476137},
 doi = {10.1145/3458817.3476137},
 booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
 articleno = {42},
 numpages = {14},
 location = {St. Louis, Missouri},
 series = {SC'21},
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  extracting TIP4P info from pair style
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.28684806
  grid = 25 24 80
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0001640931
  estimated relative force accuracy = 1.1395635e-05
  using single precision MKL FFT
  3d grid and FFT values/proc = 30685 12480
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 100000, page size: 1000000
  master list distance cutoff = 18
  ghost atom cutoff = 18
  binsize = 9, bins = 6 5 23
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair aip/water/2dm/opt, perpetual
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair lj/cut/tip4p/long, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual, half/full from (1)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
SHAKE stats (type/ave/delta/count) on step 0
Bond:   1   0.957201  2.19705e-06       96
Angle:  1   104.52    0.000203056       48
Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 Mbytes
   Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
         0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
SHAKE stats (type/ave/delta/count) on step 100
Bond:   1   0.9572    9.54949e-07       96
Angle:  1   104.52    6.01522e-05       48
       100  -17.494869     -20.796995      3.3021253      188.4955      -1.8981262      268.90898    
SHAKE stats (type/ave/delta/count) on step 200
Bond:   1   0.9572    9.63922e-07       96
Angle:  1   104.52    7.7021e-05        48
       200  -17.48627      -21.194892      3.7086213      188.14561     -1.9871708      302.01203    
SHAKE stats (type/ave/delta/count) on step 300
Bond:   1   0.9572    1.4264e-06        96
Angle:  1   104.52    6.48393e-05       48
       300  -17.502843     -20.993703      3.4908599      188.23268     -1.8457229      284.27861    
SHAKE stats (type/ave/delta/count) on step 400
Bond:   1   0.9572    1.33728e-06       96
Angle:  1   104.52    7.6239e-05        48
       400  -17.495285     -20.82835       3.333065       188.48003     -1.8429074      271.42856    
SHAKE stats (type/ave/delta/count) on step 500
Bond:   1   0.9572    1.14685e-06       96
Angle:  1   104.52    8.58621e-05       48
       500  -17.491436     -20.443043      2.9516075      188.7589      -1.8566335      240.36452    
SHAKE stats (type/ave/delta/count) on step 600
Bond:   1   0.9572    9.17601e-07       96
Angle:  1   104.52    8.24517e-05       48
       600  -17.505682     -20.608456      3.1027734      188.72078     -1.9560795      252.67474    
SHAKE stats (type/ave/delta/count) on step 700
Bond:   1   0.9572    9.50425e-07       96
Angle:  1   104.52    5.62423e-05       48
       700  -17.496706     -21.072664      3.575958       188.2777      -1.9833951      291.20858    
SHAKE stats (type/ave/delta/count) on step 800
Bond:   1   0.9572    1.15256e-06       96
Angle:  1   104.52    7.02177e-05       48
       800  -17.478628     -20.819507      3.340879       188.37868     -1.9113009      272.0649     
SHAKE stats (type/ave/delta/count) on step 900
Bond:   1   0.9572    9.14163e-07       96
Angle:  1   104.52    6.98849e-05       48
       900  -17.480868     -20.728506      3.2476383      188.5902      -1.8922108      264.47182    
SHAKE stats (type/ave/delta/count) on step 1000
Bond:   1   0.9572    1.00568e-06       96
Angle:  1   104.52    0.000111707       48
      1000  -17.498472     -20.331605      2.8331335      188.87466     -1.8121689      230.71657    
Loop time of 4.24862 on 4 procs for 1000 steps with 936 atoms

Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.25749    | 1.1806     | 2.6872     |  89.0 | 27.79
Bond    | 0.00018656 | 0.00020786 | 0.00025377 |   0.0 |  0.00
Kspace  | 1.4259     | 2.9204     | 3.8414     |  56.3 | 68.74
Neigh   | 0.057504   | 0.057852   | 0.05818    |   0.1 |  1.36
Comm    | 0.041952   | 0.053593   | 0.05876    |   3.0 |  1.26
Output  | 0.0004296  | 0.00046809 | 0.00055317 |   0.0 |  0.01
Modify  | 0.026204   | 0.027251   | 0.028382   |   0.6 |  0.64
Other   |            | 0.008209   |            |       |  0.19

Nlocal:            234 ave         302 max         198 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost:         2876.5 ave        3122 max        2632 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:              0 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:       107846 ave      150684 max       82181 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:04
