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 (58.46592 29.23296 43.42768)
1 by 1 by 1 MPI processor grid
reading atoms ...
4128 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 = 0.023 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
4128 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]
log 2.2_NVT.out
#-------------------------------------------------------------------------------
# Stage 2.2: NVT integration for 100 ps with a timestep of 1 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 1000 drag 0.0
fix 2 movable ave/time 1 10000 10000 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 10 1 10 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 100000 2.2.restart
dump trj all custom 10000 2.2.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 10000 1 10000 v_etotal v_pe v_ke file 2.2.energies.txt
dump sci all custom 10000 2.2.xyz id mol type q xs ys zs
timestep 1
run 100000
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 = 5 3 4
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 : 1
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) = 94.31 | 94.31 | 94.31 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 -5372.4239 74223.633 1.0950134 0 0 0 0 0 -382310.95 -66556.846 0 0 -448867.79 0