LAMMPS (7 Jan 2022)
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
pair_style lj/class2/coul/long 12
pair_modify mix sixthpower
pair_modify tail yes
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0
box tilt large
read_data structure.dat
Reading data file ...
orthogonal box = (0 0 0) to (38.8222 38.2464 46.9556)
4 by 2 by 4 MPI processor grid
reading atoms ...
3120 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
1824 bonds
reading angles ...
1680 angles
reading impropers ...
768 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
4 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.022 seconds
include parameters.dat
bond_coeff 1 1.5325 277.56 -433.25 2922.8 # o1S- s4o-
bond_coeff 2 0.97 563.28 -1428.2 1902.1 # h* o*
angle_coeff 1 109.47 87.637 -98.528 174.89 # o1S- s4o- o1S-
angle_coeff 2 103.7 49.84 -11.6 -8 # h* o* h*
dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx
improper_coeff 1 0 0 # * s_ * *
angle_coeff 1 bb 130.45 1.5325 1.5325 # o1S- s4o- o1S-
angle_coeff 2 bb -9.5 0.97 0.97 # h* o* h*
angle_coeff 1 ba 0.0 0.0 1.5325 1.5325 # o1S- s4o- o1S-
angle_coeff 2 ba 22.35 22.35 0.97 0.97 # h* o* h*
dihedral_coeff 1 mbt 0.0000 0.0000 0.0000 0.0 # xxx xxx xxx xxx
dihedral_coeff 1 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx
dihedral_coeff 1 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx
dihedral_coeff 1 aat 0.0000 0.0 0.0 # xxx xxx xxx xxx
dihedral_coeff 1 bb13 0.0 0.0 0.0 # xxx xxx xxx xxx
improper_coeff 1 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * s_ * *
pair_coeff 1 1 0.05899 5.1728 # Cl -
pair_coeff 2 2 0 1.098 # hw -
pair_coeff 3 3 0.4691 3.292 # K+ -
pair_coeff 4 4 0.2951 2.3959 # mg+ -
pair_coeff 5 5 0.148 3.7824 # o* -
pair_coeff 6 6 0.1436 3.6173 # o1S- -
pair_coeff 7 7 0.24 4.08 # s4o- -
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
kspace_style pppm 0.00001
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
3120 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 fast
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
minimize 0.0 1.0 1000 10000
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 0.0192 (../kspace.cpp:325)
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.25812978
grid = 30 30 36
stencil order = 5
estimated absolute RMS force accuracy = 0.003608555
estimated relative force accuracy = 1.0867056e-05
using double precision KISS FFT
3d grid and FFT values/proc = 4928 1800
generated 0 of 21 mixed pair_coeff terms from sixthpower mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : real
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 11.22 | 12.26 | 12.94 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 1139.3168 3178.5228 -608.65763 69720.116 1.1179105 4166.203 -3443.317 1103.0869 -606.44425 419.69789 836.36035 -177414.03 38.8222 38.2464 46.9556 1.5707963 1.5707963 1.5707963 9.876544e-13 1.1368684e-12 -1.3287149e-12
1 9015.2122 25464.474 -1556.0383 69720.116 1.1179105 6652.2 -3387.9141 1403.8291 -543.46367 1230.1249 954.42467 -179454.37 38.8222 38.2464 46.9556 1.5707963 1.5707963 1.5707963 1.3454127e-11 -2.6361135e-12 -1.2398971e-12
Loop time of 0.161826 on 32 procs for 1 steps with 3120 atoms
98.3% CPU use with 32 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-177414.032213651 -177414.032213651 -179454.365147643
Force two-norm initial, final = 3178.5228 25464.474
Force max component initial, final = 1139.3168 9015.2122
Final line search alpha, max atom move = 4.8234773e-05 0.43484672
Iterations, force evaluations = 1 50
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0424e-05 | 0.055424 | 0.10442 | 19.2 | 34.25
Bond | 2.9022e-05 | 0.00040518 | 0.00074598 | 0.0 | 0.25
Kspace | 0.044949 | 0.094287 | 0.1502 | 14.8 | 58.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0057861 | 0.0082012 | 0.0095739 | 1.4 | 5.07
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003509 | | | 2.17
Nlocal: 97.5 ave 189 max 0 min
Histogram: 8 0 0 8 0 0 0 8 0 8
Nghost: 3048 ave 3562 max 2602 min
Histogram: 16 0 0 0 0 0 0 8 0 8
Neighs: 36914.1 ave 69175 max 0 min
Histogram: 8 8 0 0 0 0 0 0 0 16
Total # of neighbors = 1181250
Ave neighs/atom = 378.60577
Ave special neighs/atom = 2.2461538
Neighbor list builds = 0
Dangerous builds = 0
undump sci
log 2.3_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.3: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity all create 298.2 72489 dist gaussian mom yes rot no
log 2.4_NPT.out
#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 3 ns with a timestep of 1 fs
# Temperature 298.2 K
# Pressure 1 atm
#-------------------------------------------------------------------------------
# Fix shake is needed for water in pcff+
fix shaken all shake .0001 20 50000 a 2 b 2
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
528 = # of frozen angles
find clusters CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (38.8222 38.2464 46.9556) with tilt (0 0 0)
kspace_style pppm 0.00001
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
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (38.8222 38.2464 46.9556) with tilt (0 0 0)
fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000
fix 2 movable ave/time 1 299999 300000 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 300 1 300 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
restart 3000000 2.4.restart
dump sci all custom 300000 2.4.xyz id mol type q xs ys zs
timestep 1
run 3000000
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 0.0192 (../kspace.cpp:325)
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.26069637
grid = 32 32 36
stencil order = 5
estimated absolute RMS force accuracy = 0.002976358
estimated relative force accuracy = 8.9632137e-06
using double precision KISS FFT
3d grid and FFT values/proc = 5520 2048
generated 0 of 21 mixed pair_coeff terms from sixthpower mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
SHAKE stats (type/ave/delta/count) on step 0
2 1.01212 0.677128 1584
2 96.2954 10.096 528
Per MPI rank memory allocation (min/avg/max) = 11.04 | 12.01 | 12.48 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 -10815.5 69720.116 1.1179105 358.96789 143.89384 565.43667 0 0 16018.647 -57997.644 -98.483661 -140321.85 -181591.51 2772.4091