LAMMPS (7 Jan 2022)
KOKKOS mode is enabled (../kokkos.cpp:105)
will use up to 0 GPU(s) per node
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
box tilt large
read_data structure.dat
Reading data file ...
orthogonal box = (0 0 0) to (12.5214 12.5214 10.6652)
2 by 4 by 2 MPI processor grid
reading atoms ...
216 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 = 0.002 seconds
pair_style reax/c NULL checkqeq no safezone 10.0 mincap 1000
pair_coeff * * parameters.dat C N O Si
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+023
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
216 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_Minimization.out
#-------------------------------------------------------------------------------
# Stage 2.2: Minimization
#-------------------------------------------------------------------------------
min_style cg
min_modify dmax 0.05 line quadratic
reset_timestep 0
thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888)
dump sci all custom 1000 2.2.xyz id mol type q xs ys zs
thermo 100
fix 2_2_qeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
minimize 0.0 1.0 1000 10000
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
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 3 3 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, copy from (1)
attributes: half, newton off, ghost, kokkos_device
pair build: copy/kk/device
stencil: none
bin: none
Setting up cg/kk style minimization ...
Unit style : real
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 26.45 | 26.58 | 26.74 Mbytes
Step Fmax Fnorm Press Volume v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy PotEng v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz
0 8489.2432 17945.011 4257565.3 1672.1483 4.1674486 -3661617.3 -3909405.9 -5201672.9 -164771.75 -183759.27 10264.193 -9030.2725 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 3.1832315e-12 2.8421709e-12 0
100 1935.6774 2783.8347 2505218.9 1672.1483 4.1674486 -2350294 -2339882.7 -2825480 -20967.76 6214.4454 -16551.109 -17607.149 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 1.8189894e-12 -2.8421709e-14 -8.9528385e-13
200 2833.1934 5969.1529 2539676.1 1672.1483 4.1674486 -2524742.6 -2543799.1 -2550486.7 43659.649 35718.033 -53353.141 -17842.211 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 1.0231815e-12 9.094947e-13 3.1832315e-12
300 1153.2751 2003.34 2567536.1 1672.1483 4.1674486 -2450836.7 -2500870.5 -2750901.3 33785.405 -24344.131 -56813.758 -18063.368 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 -1.3784529e-12 -1.3073986e-12 2.0321522e-12
400 354.46868 863.44821 2526940.9 1672.1483 4.1674486 -2363278.1 -2416112.4 -2801432 -4430.408 -24056.646 -27023.428 -18202.657 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 7.6738615e-13 -1.4779289e-12 -2.2737368e-13
500 154.92111 647.90402 2564871.3 1672.1483 4.1674486 -2419235.5 -2449425.8 -2825952.6 309.35492 -20778.358 -45469.033 -18548.378 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 -9.3791641e-13 2.8421709e-12 -9.9475983e-13
600 2447.2082 4834.071 2485763.7 1672.1483 4.1674486 -2180831.6 -2170843 -3105616.5 -48926.414 -110542.21 -35387.496 -18678.871 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 -2.543743e-12 -3.2400749e-12 -1.3642421e-12
700 487.88628 1133.9384 2576433.8 1672.1483 4.1674486 -2435958.1 -2484478.4 -2808865.1 23766.309 -12855.669 -29256.899 -18828.789 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 1.1368684e-13 -4.5474735e-13 -9.9475983e-13
800 479.65689 1271.4578 2545770.9 1672.1483 4.1674486 -2386095.4 -2434461.7 -2816755.5 -1066.3457 -14860.217 -28682.859 -18867.01 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 -1.9468871e-12 2.1032065e-12 7.0201622e-12
900 590.01789 1352.796 2576099.1 1672.1483 4.1674486 -2414164.4 -2424344.1 -2889788.7 -18436.301 2207.1881 -60435.703 -18970.011 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 3.399947e-12 -3.9790393e-13 -7.2475359e-13
1000 587.97816 1358.6475 2513646.8 1672.1483 4.1674486 -2307592.3 -2351002.4 -2882345.7 -13224.327 -17060.841 -26762.085 -19015.645 12.5214 12.5214 10.6652 1.5707963 1.5707963 1.5707963 6.6791017e-13 5.9117156e-12 1.2221335e-12
Loop time of 955.45 on 16 procs for 1000 steps with 216 atoms
99.9% CPU use with 16 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-9030.27246733301 -19015.6327742922 -19015.6450632365
Force two-norm initial, final = 17945.011 1358.6475
Force max component initial, final = 8489.2432 587.97816
Final line search alpha, max atom move = 3.4244012e-07 0.00020134731
Iterations, force evaluations = 1000 9605
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 879.31 | 893.77 | 912.21 | 25.0 | 93.54
Bond | 0.0028657 | 0.0044308 | 0.011561 | 3.4 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.2706 | 19.708 | 34.173 | 168.0 | 2.06
Output | 0.0018321 | 0.0018568 | 0.0020434 | 0.1 | 0.00
Modify | 41.533 | 41.548 | 41.557 | 0.1 | 4.35
Other | | 0.4166 | | | 0.04
Nlocal: 13.5 ave 16 max 11 min
Histogram: 1 0 4 0 1 0 8 0 0 2
Nghost: 3107.56 ave 3127 max 3084 min
Histogram: 1 1 2 3 0 2 1 2 2 2
Neighs: 12423.2 ave 14713 max 10129 min
Histogram: 1 0 4 0 1 6 2 0 0 2
Total # of neighbors = 198771
Ave neighs/atom = 920.23611
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 2_2_qeq
log 2.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.3: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity all create 300 72489 dist gaussian mom yes rot no
log 2.4_NPT.out
#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 100 ps with a timestep of 1 fs
# Temperature 300 K
# Pressure 0 atm
#-------------------------------------------------------------------------------
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
thermo 0
fix 1 movable npt temp 300 300 100 iso 0 0 100 drag 0 mtk yes nreset 2000
fix 2 movable ave/time 1 9999 10000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt
fix 4 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
restart 100000 2.4.restart
dump sci all custom 10000 2.4.xyz id mol type q xs ys zs
timestep 1
run 100000
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 = 6, bins = 3 3 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, copy from (1)
attributes: half, newton off, ghost, kokkos_device
pair build: copy/kk/device
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 26.25 | 26.41 | 26.53 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 2518902.2 1672.1483 4.1674486 300 0 0 0 0 -16307.386 -2708.2588 0 0 -19015.645 192.26225