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[lammps-users] Problem with PPPM
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[lammps-users] Problem with PPPM


From: <jony.castagna@...3299...>
Date: Wed, 21 Jun 2017 12:42:12 +0000

Hi there,

  I tried to run the attached input file with1-32 cores, but I get the following error (see also the putput.txt file attached):

“ERROR on proc 1: Out of range atoms - cannot compute PPPMDisp (../pppm_disp.cpp:4300)”

 

Any idea?

 

Best Regards,

Jony

 

Dr Jony Castagna

Sci-Tech Daresbury

Keckwick Lane

Daresbury

Warrington

WA4 4AD

Tel.: +44 (0)1925 603682

 

Attachment: in.lj
Description: in.lj

Attachment: log.lammps
Description: log.lammps

LAMMPS (17 Nov 2016)
  using 1 OpenMP thread(s) per MPI task
Reading data file ...
  orthogonal box = (-0.000163 -0.005763 0.003035) to (31.5409 31.5353 31.5441)
  1 by 1 by 2 MPI processor grid
  reading atoms ...
  23328 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
0 atoms in group insert
Neighbor list info ...
  1 neighbor list requests
  update every 20 steps, delay 0 steps, check yes
  max neighbors/atom: 12000, page size: 200000
  master list distance cutoff = 5.5
  ghost atom cutoff = 5.5
  binsize = 2.75, bins = 12 12 12
Setting up Verlet run ...
  Unit style    : lj
  Current step  : 0
  Time step     : 0.005
Memory usage per processor = 17.5593 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0            0   -4.4471047            0   -4.4471047    2.3401163    31378.257 
     100   0.72229476    -5.471664            0   -4.3882683  -0.64450061    30542.978 
     200   0.83204726    -5.537041            0   -4.2890236   0.16982224    29620.442 
     300   0.92776925   -5.5421008            0   -4.1505066   0.99252832    28819.881 
     400    1.0573422   -5.5682478            0   -3.9823025     1.778802    28146.669 
     500    1.1503269   -5.5201563            0   -3.7947399       2.9113     27608.96 
     600    1.2509424   -5.4802039            0   -3.6038707    3.7236997    27229.089 
     700    1.3312462   -5.4267533            0   -3.4299697    4.3605857    27034.089 
     800    1.3887174   -5.3769988            0   -3.2940121    4.6116589    27061.383 
     900    1.4197145   -5.3277699            0   -3.1982895    4.4865901    27297.297 
    1000    1.4415026   -5.2713111            0   -3.1091498    4.3450061    27574.195 
Loop time of 102.259 on 2 procs for 1000 steps with 23328 atoms

Performance: 4224.550 tau/day, 9.779 timesteps/s
59.5% CPU use with 2 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 89.574     | 89.683     | 89.792     |   1.2 | 87.70
Bond    | 0.00074649 | 0.00077128 | 0.00079608 |   0.1 |  0.00
Neigh   | 5.4726     | 5.5306     | 5.5887     |   2.5 |  5.41
Comm    | 5.0794     | 5.1765     | 5.2735     |   4.3 |  5.06
Output  | 0.00051713 | 0.0018551  | 0.0031931  |   3.1 |  0.00
Modify  | 1.6972     | 1.7463     | 1.7953     |   3.7 |  1.71
Other   |            | 0.1205     |            |       |  0.12

Nlocal:    11664 ave 11691 max 11637 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost:    25887.5 ave 25931 max 25844 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs:    3.4382e+06 ave 3.44834e+06 max 3.42806e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 6876402
Ave neighs/atom = 294.77
Ave special neighs/atom = 0
Neighbor list builds = 23
Dangerous builds = 0
PPPMDisp initialization ...
WARNING: Charges are set, but coulombic solver is not used (../pppm_disp.cpp:328)
  Dispersion G vector (1/distance)= 0.8
  Dispersion grid = 45 45 45
  Dispersion stencil order = 5
  Dispersion estimated absolute RMS force accuracy = 0.00103578
  Dispersion estimated absolute real space RMS force accuracy = 5.17315e-05
  Dispersion estimated absolute kspace RMS force accuracy = 0.00103449
  Dispersion estimated relative force accuracy = 0.00103578
  using double precision FFTs
  3d grid and FFT values/proc dispersion = 81120 46575
Neighbor list info ...
  1 neighbor list requests
  update every 20 steps, delay 0 steps, check yes
  max neighbors/atom: 12000, page size: 200000
  master list distance cutoff = 5.5
  ghost atom cutoff = 5.5
  binsize = 2.75, bins = 11 11 11
Setting up Verlet run ...
  Unit style    : lj
  Current step  : 1000
  Time step     : 0.005
Memory usage per processor = 25.2109 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
    1000    1.4415026   -5.3819963            0    -3.219835    4.1579182    27574.195 
    1100    1.4647046   -5.3132922            0   -3.1163295    4.1946301    27775.915 
    1200    1.5090683   -5.2718097            0   -3.0083044    4.1964049    27945.513 
    1300    1.5439451   -5.2197114            0    -2.903893    4.2089386    28123.759 
    1400    1.5834414   -5.1777395            0   -2.8026792    4.1877084    28307.233 
    1500     1.613491   -5.1245331            0   -2.7044004     4.185539    28493.986 
    1600    1.6382537   -5.0659211            0   -2.6086459    4.2210686     28679.58 
    1700    1.6755585   -5.0298455            0   -2.5166155    4.1826769    28868.055 
    1800    1.7054114   -4.9859205            0    -2.427913    4.1877353    29055.969 
    1900     1.733693   -4.9418891            0    -2.341461    4.1663636    29237.412 
    2000    1.7588021   -4.8961481            0    -2.258058    4.1550032     29413.12 
Loop time of 209.987 on 2 procs for 1000 steps with 23328 atoms

Performance: 2057.272 tau/day, 4.762 timesteps/s
60.0% CPU use with 2 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 105.91     | 107.46     | 109        |  14.9 | 51.17
Bond    | 0.00075889 | 0.00079596 | 0.00083303 |   0.1 |  0.00
Kspace  | 23.603     | 25.128     | 26.653     |  30.4 | 11.97
Neigh   | 5.6799     | 5.7033     | 5.7267     |   1.0 |  2.72
Comm    | 5.2342     | 6.4853     | 7.7365     |  49.1 |  3.09
Output  | 0.00052881 | 0.0012099  | 0.0018909  |   2.0 |  0.00
Modify  | 63.563     | 64.817     | 66.071     |  15.6 | 30.87
Other   |            | 0.3936     |            |       |  0.19

Nlocal:    11664 ave 11675 max 11653 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost:    25071 ave 25118 max 25024 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs:    3.21839e+06 ave 3.25785e+06 max 3.17892e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 6436771
Ave neighs/atom = 275.925
Ave special neighs/atom = 0
Neighbor list builds = 25
Dangerous builds = 0
PPPMDisp initialization ...
WARNING: Charges are set, but coulombic solver is not used (../pppm_disp.cpp:328)
  Dispersion G vector (1/distance)= 0.8
  Dispersion grid = 54 54 54
  Dispersion stencil order = 5
  Dispersion estimated absolute RMS force accuracy = 0.000324219
  Dispersion estimated absolute real space RMS force accuracy = 5.00883e-05
  Dispersion estimated absolute kspace RMS force accuracy = 0.000320327
  Dispersion estimated relative force accuracy = 0.000324219
  using double precision FFTs
  3d grid and FFT values/proc dispersion = 126514 78732
Setting up Verlet run ...
  Unit style    : lj
  Current step  : 2000
  Time step     : 0.005
Memory usage per processor = 29.2665 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
    2000    1.7588021   -4.8961456            0   -2.2580555    4.1550036     29413.12 
    2100    1.7883762   -4.8609455            0   -2.1784962    4.1283671    29583.864 
    2200    1.8124506   -4.8210581            0   -2.1024987    4.1413281    29749.269 
    2300    1.8317922   -4.7794555            0    -2.031885    4.1397474    29916.602 
    2400    1.8601677   -4.7554229            0    -1.965291    4.0786182    30078.412 
    2500    1.8794173   -4.7213551            0     -1.90235    4.0752349    30227.037 
    2600    1.8917404   -4.6808812            0   -1.8433922    4.1285486    30355.446 
    2700    1.9163752   -4.6636493            0   -1.7892097    4.0722449      30481.3 
    2800    1.9422027   -4.6543351            0    -1.741156    4.0039759    30598.429 
ERROR on proc 1: Out of range atoms - cannot compute PPPMDisp (../pppm_disp.cpp:4300)