LAMMPS (2 Jun 2022)
KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:105)
will use up to 1 GPU(s) per node
using 1 OpenMP thread(s) per MPI task
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
atom_modify map array
box tilt large
read_data structure.dat
Reading data file ...
orthogonal box = (0 0 0) to (248.585 100 20.7669)
1 by 1 by 1 MPI processor grid
reading atoms ...
7366 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.013 seconds
pair_style reax/c NULL checkqeq no safezone 10.0 mincap 1000
pair_coeff * * parameters.dat H O Si
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+23
variable sysdensity equal v_sysmass/v_sysvol/1.0e-24
variable coulomb equal ecoul+elong
variable etotal equal etotal
variable pe equal pe
variable ke equal ke
variable evdwl equal evdwl
variable epair equal epair
variable ebond equal ebond
variable eangle equal eangle
variable edihed equal edihed
variable eimp equal eimp
variable lx equal lx
variable ly equal ly
variable lz equal lz
variable Nthermo equal 0
variable cella equal lx
variable cellb equal sqrt(ly*ly+xy*xy)
variable cellc equal sqrt(lz*lz+xz*xz+yz*yz)
variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc))
variable cellbeta equal acos(xz/v_cellc)
variable cellgamma equal acos(xy/v_cellb)
variable p equal press
variable pxx equal pxx
variable pyy equal pyy
variable pzz equal pzz
variable pyz equal pyz
variable pxz equal pxz
variable pxy equal pxy
variable sxx equal -pxx
variable syy equal -pyy
variable szz equal -pzz
variable syz equal -pyz
variable sxz equal -pxz
variable sxy equal -pxy
variable fmax equal fmax
variable fnorm equal fnorm
variable time equal step*dt+0.000001
variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz)
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo_modify flush yes
#
# Set up the fixed and movable groups
#
group movable union all
7366 atoms in group movable
group fixed subtract all movable
0 atoms in group fixed
compute sum_f1 movable reduce sum fx fy fz
variable sum_fx equal c_sum_f1[1]
variable sum_fy equal c_sum_f1[2]
variable sum_fz equal c_sum_f1[3]
#
# Subsets
#
group subset_Surface_O id 80 92 104 188 200 212 296 308 320 404
10 atoms in group subset_Surface_O
group subset_Surface_O id 416 428 512 524 536 620 632 644 728 740
20 atoms in group subset_Surface_O
group subset_Surface_O id 752 836 848 860 944 956 968 1052 1064 1076
30 atoms in group subset_Surface_O
group subset_Surface_O id 1160 1172 1184 1268 1280 1292 1376 1388 1400 1484
40 atoms in group subset_Surface_O
group subset_Surface_O id 1496 1508 1592 1604 1616 1700 1712 1724 1808 1820
50 atoms in group subset_Surface_O
group subset_Surface_O id 1832 1916 1928 1940 2024 2036 2048 2132 2144 2156
60 atoms in group subset_Surface_O
group subset_Surface_O id 2240 2252 2264 2348 2360 2372 2456 2468 2480 2564
70 atoms in group subset_Surface_O
group subset_Surface_O id 2576 2588 2672 2684 2696 2780 2792 2804 2888 2900
80 atoms in group subset_Surface_O
group subset_Surface_O id 2912 2996 3008 3020 3104 3116 3128 3212 3224 3236
90 atoms in group subset_Surface_O
group subset_Surface_O id 3320 3332 3344 3428 3440 3452 3536 3548 3560 3644
100 atoms in group subset_Surface_O
group subset_Surface_O id 3656 3668 3752 3764 3776 3860 3872 3884 3968 3980
110 atoms in group subset_Surface_O
group subset_Surface_O id 3992 4076 4088 4100 4184 4196 4208 4292 4304 4316
120 atoms in group subset_Surface_O
group subset_Surface_O id 4400 4412 4424 4508 4520 4532 4616 4628 4640 4724
130 atoms in group subset_Surface_O
group subset_Surface_O id 4736 4748 4832 4844 4856 4940 4952 4964 5048 5060
140 atoms in group subset_Surface_O
group subset_Surface_O id 5072 5156 5168 5180 5264 5276 5288 5372 5384 5396
150 atoms in group subset_Surface_O
log 2.2_NVT.out
#-------------------------------------------------------------------------------
# Stage 2.2: NVT integration for 1000 ps with a timestep of 0.2 fs
# Temperature 300 K
#-------------------------------------------------------------------------------
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nvt temp 300 300 100 drag 0.0
fix 2 movable ave/time 1 500000 500000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.2_averages.txt off 1
fix 3 movable ave/time 500 1 500 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.2_instantaneous.txt
fix 4 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
restart 5000000 2.2.restart
dump trj all custom 50000 2.2.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.2.energies.txt
dump sci all custom 500000 2.2.xyz id mol type q xs ys zs
timestep 0.2
run 5000000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
- fix qeq/reaxff command:
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 12, bins = 21 9 2
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c/kk, perpetual
attributes: half, newton off, ghost, kokkos_device
pair build: half/bin/ghost/kk/device
stencil: full/ghost/bin/3d
bin: kk/device
(2) fix qeq/reax/kk, perpetual
attributes: full, newton off, kokkos_device
pair build: full/bin/kk/device
stencil: full/bin/3d
bin: kk/device
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.2
WARNING: Fixes cannot yet send exchange data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:581)
Per MPI rank memory allocation (min/avg/max) = 119.6 | 119.6 | 119.6 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 -25895.949 516233.98 0.41097661 0 0 0 0 0 -830235.34 -134185.12 0 0 -964420.45 0