Dear Lammps Users,
I was trying to minimize my initial system and while doing so, I stumbled upon this warning " System is not charge neutral, net charge = 100 " I checked the total charge using variable equal command it is indeed coming out to be neutral. What I don’t understand is how it has picked up net charge = 100?
One more thing, I’m not able to make sense of “estimated absolute RMS force accuracy” & “estimated relative force accuracy” they seem to be too low. Is the geometry of my initial system too bad? What could be the reason?
LAMMPS (23 Jun 2022 - Update 1)
Reading data file ...
orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
2 by 1 by 4 MPI processor grid
reading atoms ...
1008 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
3 = max angles/atom
reading bonds ...
1467 bonds
reading angles ...
2846 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
3 = max # of 1-2 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:140)
Deleted 4 atoms, new total = 1004
Deleted 9 bonds, new total = 1458
Deleted 24 angles, new total = 2822
Created 100 atoms
using lattice units in orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
create_atoms CPU = 0.000 seconds
Created 100 atoms
using lattice units in orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
create_atoms CPU = 0.000 seconds
Created 100 atoms
using lattice units in orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
create_atoms CPU = 0.000 seconds
Created 100 atoms
using lattice units in orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
create_atoms CPU = 0.000 seconds
Created 100 atoms
using lattice units in orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
create_atoms CPU = 0.000 seconds
Setting atom values ...
200 settings made for charge
Setting atom values ...
200 settings made for charge
Setting atom values ...
100 settings made for charge
Resetting atom IDs ...
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 100 (../kspace.cpp:327)
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.53224709
grid = 60 60 150
stencil order = 5
estimated absolute RMS force accuracy = 0.00012031676
estimated relative force accuracy = 0.00012031676
using double precision KISS FFT
3d grid and FFT values/proc = 97825 68400
Generated 0 of 10 mixed pair_coeff terms from geometric 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 = 4.9
ghost atom cutoff = 4.9
binsize = 2.45, bins = 25 25 82
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
3 = max # of 1-2 neighbors
3 = max # of special neighbors
special bonds CPU = 0.001 seconds
Reading data file ...
orthogonal box = (-6.04 -4.86 -100) to (53.94 54.44 100)
2 by 1 by 4 MPI processor grid
reading atoms ...
100 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
99 bonds
reading angles ...
98 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
3 = max # of 1-2 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
1004 atoms in group carbon
200 atoms in group cl
200 atoms in group k
100 atoms in group counter
100 atoms in group polymer
1004 atoms in group gcar
200 atoms in group gnegative
200 atoms in group gpositive
100 atoms in group gcounter
100 atoms in group gpoly
24 atoms in group gright
24 atoms in group gleft
917 atoms in group gmid
21 atoms in group gtop
21 atoms in group gbot
97 atoms in group gmovep
3 atoms in group gstill
400 atoms in group gions
500 atoms in group gcions
600 atoms in group gcp
595 atoms in group gcp2
1516 atoms in group g1
1512 atoms in group g2
1016 atoms in group g3
Changing box ...
orthogonal box = (-2.228024 -4.86 -100) to (50.12096 54.44 100)
Changing box ...
orthogonal box = (-2.228024 -1 -100) to (50.12096 50.630001 100)
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.55114466
grid = 60 60 160
stencil order = 5
estimated absolute RMS force accuracy = 0.00010245694
estimated relative force accuracy = 0.00010245694
using double precision KISS FFT
3d grid and FFT values/proc = 102375 72000
Generated 0 of 10 mixed pair_coeff terms from arithmetic mixing rule
Setting up cg style minimization ...
Unit style : lj
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 19.11 | 19.21 | 19.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.2334685 13546.881 8.4807628 13555.712 160.82539
1000 0.2334685 -0.05865352 0.14719725 0.43852814 0.00055982023
Loop time of 119.848 on 8 procs for 1000 steps with 1604 atoms
98.7% CPU use with 8 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
13555.3617637139 0.0885840599875491 0.0885437295034541
Force two-norm initial, final = 6.6860196e+08 9.1834272
Force max component initial, final = 4.2201969e+08 1.9281637
Final line search alpha, max atom move = 0.012476214 0.024056184
Iterations, force evaluations = 1000 1981
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026485 | 0.21159 | 0.43755 | 31.7 | 0.18
Bond | 0.0070498 | 0.065725 | 0.13038 | 20.4 | 0.05
Kspace | 118.97 | 119.27 | 119.52 | 1.9 | 99.52
Neigh | 0.066244 | 0.071282 | 0.077214 | 1.5 | 0.06
Comm | 0.079118 | 0.10795 | 0.14064 | 7.1 | 0.09
Output | 4.0129e-05 | 4.2255e-05 | 5.5743e-05 | 0.0 | 0.00
Modify | 0.018069 | 0.021414 | 0.027532 | 2.3 | 0.02
Other | | 0.0963 | | | 0.08
Nlocal: 200.5 ave 355 max 53 min
Histogram: 2 1 1 0 0 0 0 1 2 1
Nghost: 337.5 ave 677 max 49 min
Histogram: 3 1 0 0 0 0 0 1 1 2
Neighs: 1991.25 ave 4543 max 27 min
Histogram: 3 1 0 0 0 0 0 2 1 1
Total # of neighbors = 15930
Ave neighs/atom = 9.9314214
Ave special neighs/atom = 1.9413965
Neighbor list builds = 287
Dangerous builds = 0
Total wall time: 0:01:59