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[lammps-users] Lammps run.


From: "swarnimaa B." <swarnimaa39@...16...>
Date: Thu, 16 Nov 2017 10:29:30 +0000 (UTC)

Dear Steve Sir,

I am runing my lammps simulation. But it is not progressing further. From last 2-3 days it is with held. I am unable to find reason for this.
Please help me out of this. I would always be thankful to you.

My lammps input-script:
units        real
dimension    3
boundary     p p p
atom_style     full
#atom_modify    map array
neigh_modify    delay 0 every 1 check yes
processors     * * *

variable timecoef equal 1.00
variable T equal 300
variable thermo_itv equal 50
variable seed equal 2012

# atom definition:
read_data     graphene.data

###############################################
# group definition:
group           oxygen type 1
group           hydrogens type 2
group           fluidmols type 1 2
group           potassium type 3
group           chloride type 4
group           ions type 3 4
group           graphene type 5
group           solutions type 1 2 3 4 5
#################################################
# force fields
variable        rcF equal 12.0
pair_style      lj/cut/coul/long  ${rcF} ${rcF}
                      #epsi     #sig
pair_coeff      1 1  0.15539   3.1656       # O
pair_coeff      2 2  0.0       0.0          # H
pair_coeff      3 3  0.43      2.84         # K
pair_coeff      4 4  0.0128    4.83         # Cl
#----------Graphene-Water interaction------------------
pair_coeff      5 5   0.06844   3.407        # C
pair_coeff      1 5   0.1039    3.372        # C-O
pair_coeff      2 5   0.0256    2.640        # C-H
pair_modify    mix arithmetic
############################################
kspace_style    pppm 1e-05
dielectric      1.0
bond_style      harmonic
bond_coeff      1 450.0 1.0
angle_style     harmonic
angle_coeff     1 100.0 109.47
print "Angle"

# minimization
min_style       sd
minimize        1.0e-4 1.0e-5 1000 10000
print "Min"
###############################################3
reset_timestep 0
timestep       ${timecoef}
compute        fluidtemp solutions temp
velocity       solutions create ${T} ${seed} dist gaussian temp fluidtemp mom yes rot yes units box
######################################################################################
fix   1 fluidmols shake 0.0001 20 0 b 1 a 1
fix   GD ions flow/gauss 0 0 1 energy yes
dump  2 ions dcd 1000 ions.dcd
dump  3 all custom 5000 system.lammpstrj id type x y z
dump  4 ions custom 1000 ions.lammpstrj id type x y z
fix   fxnpt solutions npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0
run   1000
################################################
fix   fxnvt solutions nvt temp 300 300 100.0
run   1000
#####################################################
fix   ef all efield 0.0 0.0 0.0167    #L=60A 1lammps=V/A*60A=1V
dump  5 ions dcd 1000 ions2.dcd
dump  6 ions custom 1000 ions2.lammpstrj id type x y z
################################################################################################=
reset_timestep 0
thermo ${thermo_itv}
thermo_style    multi
restart         1000 extend_01.restart1 extend_01.restart2
run 1500

-------------- log.lammps file: ---------------------

LAMMPS (11 Aug 2017)
units           real
dimension    3
boundary     p p p
atom_style     full
#atom_modify    map array
neigh_modify    delay 0 every 1 check yes
processors     * * *

variable timecoef equal 1.00
variable T equal 300
variable thermo_itv equal 50
variable seed equal 2012

# atom definition:
read_data     graphene.data
  orthogonal box = (0 0 0) to (40 40 60)
  2 by 4 by 4 MPI processor grid
  reading atoms ...
  9442 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  5780 bonds
  reading angles ...
  2890 angles
  2 = max # of 1-2 neighbors
  1 = max # of 1-3 neighbors
  1 = max # of 1-4 neighbors
  2 = max # of special neighbors

###############################################
# group definition:
group           oxygen type 1
2890 atoms in group oxygen
group           hydrogens type 2
5780 atoms in group hydrogens
group           fluidmols type 1 2
8670 atoms in group fluidmols
group           potassium type 3
58 atoms in group potassium
group           chloride type 4
58 atoms in group chloride
group           ions type 3 4
116 atoms in group ions
group           graphene type 5
656 atoms in group graphene
group           solutions type 1 2 3 4 5
9442 atoms in group solutions
#################################################
# force fields
variable        rcF equal 12.0
pair_style      lj/cut/coul/long  ${rcF} ${rcF}
pair_style      lj/cut/coul/long  12 ${rcF}
pair_style      lj/cut/coul/long  12 12
                      #epsi     #sig
pair_coeff      1 1  0.15539   3.1656       # O
pair_coeff      2 2  0.0       0.0          # H
pair_coeff      3 3  0.43      2.84         # K
pair_coeff      4 4  0.0128    4.83         # Cl
#----------Graphene-Water interaction------------------
pair_coeff      5 5   0.06844   3.407        # C
pair_coeff      1 5   0.1039    3.372        # C-O
pair_coeff      2 5   0.0256    2.640        # C-H
pair_modify    mix arithmetic
############################################
kspace_style    pppm 1e-05
dielectric      1.0
bond_style      harmonic
bond_coeff      1 450.0 1.0
angle_style     harmonic
angle_coeff     1 100.0 109.47
print "Angle"
Angle

# minimization
min_style       sd
minimize        1.0e-4 1.0e-5 1000 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.253785
  grid = 30 30 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.00272313
  estimated relative force accuracy = 8.20064e-06
  using double precision FFTs
  3d grid and FFT values/proc = 5236 1800
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 9
  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/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.95 | 9.188 | 9.793 Mbytes
Step Temp E_pair E_mol TotEng Press
       0            0 1.6872437e+16    8614.2937 1.6872437e+16 4.8204844e+16
      99            0 -1.7287911e+16    54505.399 -1.7287911e+16 -4.5570136e+15
Loop time of 9.58775 on 32 procs for 99 steps with 9442 atoms

99.8% CPU use with 32 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final =
     1.68724368706e+16 -1.72879105926e+16 -1.72879105926e+16
  Force two-norm initial, final = 2.92716e+18 3.00343e+30
  Force max component initial, final = 1.87617e+18 1.85376e+30
  Final line search alpha, max atom move = 1.53319e-45 2.84217e-15
  Iterations, force evaluations = 99 600

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.5797     | 5.0425     | 7.8305     |  66.4 | 52.59
Bond    | 0.01009    | 0.013746   | 0.016436   |   1.5 |  0.14
Kspace  | 1.3422     | 4.1382     | 6.6094     |  73.6 | 43.16
Neigh   | 0.037211   | 0.037409   | 0.037693   |   0.1 |  0.39
Comm    | 0.21014    | 0.24252    | 0.2688     |   3.8 |  2.53
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.1134     |            |       |  1.18

Nlocal:    295.062 ave 331 max 243 min
Histogram: 2 1 4 3 5 1 0 4 6 6
Nghost:    7378.94 ave 7800 max 6982 min
Histogram: 11 5 0 0 0 0 0 0 9 7
Neighs:    168631 ave 225962 max 116482 min
Histogram: 1 6 6 2 3 4 2 0 2 6

Total # of neighbors = 5396191
Ave neighs/atom = 571.509
Ave special neighs/atom = 1.83648
Neighbor list builds = 3
Dangerous builds = 0


Thanks,
Swarnimaa