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Merge remote-tracking branch 'upstream/master'

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This commit is contained in:
Gareth Tribello
2018-10-26 22:01:05 +01:00
parent 2e79d9f340 2428c1c1f3
commit ff9f836be4
1856 changed files with 103330 additions and 24994 deletions
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7
examples/USER/diffraction/BulkNi.in
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@ -17,10 +17,11 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed

35
examples/USER/diffraction/Output/BulkNi.in
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@ -1,35 +0,0 @@
variable A string bulkNi
log $A.log
boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
dump 1 all custom 1 $A.dump id x y z
run 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED

2467
examples/USER/misc/mop/data.mop Normal file
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File diff suppressed because it is too large Load Diff

40
examples/USER/misc/mop/in.compute_stress_mop Normal file
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@ -0,0 +1,40 @@
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 1000
thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0

111
examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 Normal file
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@ -0,0 +1,111 @@
LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 1 by 1 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms
167.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 1224 ave 1224 max 1224 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2975 ave 2975 max 2975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40241 ave 40241 max 40241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

111
examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 Normal file
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@ -0,0 +1,111 @@
LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 2 by 2 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms
65.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.065e-05 | | |100.00
Nlocal: 306 ave 320 max 295 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1450.25 ave 1485 max 1422 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 10060.2 ave 10866 max 9507 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

185
examples/USER/misc/mop/moppz.time.reference Normal file
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@ -0,0 +1,185 @@
# Time-averaged data for fix moppzt
# TimeStep Number-of-rows
# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
0 181
1 -2 0 0 0 0 0 0
2 -1.9 0 0 0 0 0 0
3 -1.8 0 0 0 0 0 0
4 -1.7 0 0 0 0 0 0
5 -1.6 0 0 0 0 0 0
6 -1.5 0 0 0 -9.81273e-05 0.000228605 -0.00421138
7 -1.4 0 0 0 -9.81273e-05 0.000228605 -0.00421138
8 -1.3 0 0 0 -9.81273e-05 0.000228605 -0.00421138
9 -1.2 0 0 0 -9.81273e-05 0.000228605 -0.00421138
10 -1.1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
11 -1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
12 -0.9 0 0 0 -9.81273e-05 0.000228605 -0.00421138
13 -0.8 0 0 0 -9.81273e-05 0.000228605 -0.00421138
14 -0.7 0 0 0 -0.000370675 -0.00240125 -0.26848
15 -0.6 0 0 0 -0.000370675 -0.00240125 -0.26848
16 -0.5 0 0 0 -0.000370675 -0.00240125 -0.26848
17 -0.4 0 0 0 -0.000370675 -0.00240125 -0.26848
18 -0.3 0 0 0 -0.000370675 -0.00240125 -0.26848
19 -0.2 0 0 0 -0.000370675 -0.00240125 -0.26848
20 -0.1 0 0 0 -0.000370675 -0.00240125 -0.26848
21 0 0 0 0 -0.000370675 -0.00240125 -0.26848
22 0.1 0 0 0 0.190761 -0.491728 0.287704
23 0.2 0 0 0 0.190761 -0.491728 0.287704
24 0.3 0 0 0 0.190761 -0.491728 0.287704
25 0.4 0 0 0 0.190761 -0.491728 0.287704
26 0.5 0 0 0 0.190761 -0.491728 0.287704
27 0.6 0 0 0 0.190761 -0.491728 0.287704
28 0.7 0 0 0 0.190761 -0.491728 0.287704
29 0.8 0 0 0 -0.181602 -0.198457 -0.0964774
30 0.9 0 0 0 -0.15138 0.183353 0.206848
31 1 0 0 0 0.174362 1.27701 0.600545
32 1.1 0 0 0 0.160987 0.563442 0.494994
33 1.2 0 0 0 0.218876 0.59796 0.398527
34 1.3 0 0 0 0.187614 0.558909 0.372353
35 1.4 0 0 0 0.118586 0.410013 0.331945
36 1.5 0 0 0 -0.0514208 0.40381 0.128097
37 1.6 3.08628 0.241189 5.90817 -0.198262 0.324128 -0.0449302
38 1.7 0 0 0 -0.104542 0.256677 -0.332854
39 1.8 0.222123 2.43524 1.10089 -0.324638 -0.168682 -1.06238
40 1.9 0 0 0 -0.175732 -0.186846 -0.163062
41 2 0 0 0 -0.137995 0.0920401 -0.260106
42 2.1 -0.179621 -2.59775 1.80077 -0.480624 -0.0439511 -0.0824913
43 2.2 0 0 0 -0.499868 -0.0106185 -0.108924
44 2.3 0 0 0 -0.703301 0.124555 -0.0880158
45 2.4 0 0 0 -0.581211 -0.244281 -0.250071
46 2.5 1.05274 -2.86043 3.36339 -0.575104 -0.148715 -0.249092
47 2.6 0 0 0 0.66061 -0.157649 -0.357141
48 2.7 0 0 0 0.299971 -0.302298 -0.572714
49 2.8 0 0 0 0.33107 -0.201699 -0.470466
50 2.9 0 0 0 0.822686 1.08427 -0.390511
51 3 0 0 0 0.716428 0.750998 -0.698174
52 3.1 0.805189 0.571878 4.31938 0.121891 0.922727 -0.932582
53 3.2 0 0 0 0.0442642 1.02537 -1.03066
54 3.3 2.54289 -1.93701 4.88355 0.0731321 1.09091 -0.83075
55 3.4 0 0 0 0.426589 0.821174 -0.765855
56 3.5 0 0 0 0.445135 0.299996 -1.48972
57 3.6 0 0 0 0.362916 -1.28673 -0.853897
58 3.7 0.952867 -1.07044 1.04141 0.12517 -1.00353 -0.785272
59 3.8 0.617661 0.991499 1.80973 -0.182369 -1.04057 -1.00435
60 3.9 0.60295 -2.41888 3.98011 0.0347345 -1.01302 -0.88314
61 4 -2.97421 -2.01531 2.98586 0.43463 -0.465643 -0.801128
62 4.1 -3.23318 -3.31281 0.956525 0.732752 0.140718 -1.10583
63 4.2 0 0 0 0.969872 0.298566 -0.823464
64 4.3 0 0 0 0.7707 0.557002 -0.836549
65 4.4 0 0 0 0.395828 0.66755 -1.53454
66 4.5 0 0 0 0.104451 0.46777 -1.32358
67 4.6 0 0 0 0.402084 0.464983 -1.22051
68 4.7 0 0 0 0.352808 0.0794986 -1.31292
69 4.8 0 0 0 0.0215512 0.284343 -0.975326
70 4.9 0 0 0 -0.133637 0.250925 -1.33918
71 5 0 0 0 -0.066208 0.104514 -1.27412
72 5.1 0 0 0 -0.184391 0.479805 -1.15139
73 5.2 0 0 0 -0.200251 0.527142 -1.34307
74 5.3 0 0 0 0.043532 -0.0788824 -0.998406
75 5.4 0 0 0 -0.531846 0.126289 -1.05818
76 5.5 0 0 0 -0.259593 0.0818463 -1.58939
77 5.6 0 0 0 -0.373828 -0.343977 -1.50908
78 5.7 -0.294161 -1.07567 3.46536 -0.0644873 -0.424333 -1.28548
79 5.8 0 0 0 -0.293233 -0.201133 -1.19085
80 5.9 0.961568 -1.44949 2.42101 -0.632816 -0.0669315 -0.85119
81 6 0 0 0 -0.0559892 -0.0194478 -1.04541
82 6.1 0 0 0 -0.339753 0.286693 -1.24366
83 6.2 0 0 0 -0.376208 0.444053 -1.7662
84 6.3 0 0 0 -0.718923 0.555398 -1.93862
85 6.4 0 0 0 -1.10631 0.263525 -1.79723
86 6.5 0 0 0 -0.217948 -0.0489491 -2.07833
87 6.6 0 0 0 -0.376248 -0.0588682 -2.45322
88 6.7 -2.12742 4.22609 2.36568 -0.236703 -0.279582 -1.56434
89 6.8 0.869072 -0.141389 3.92123 0.0540986 -0.00271606 -0.930143
90 6.9 0 0 0 1.08829 -1.11737 -0.808187
91 7 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
92 7.1 0 0 0 1.03324 -0.470631 -0.486767
93 7.2 0 0 0 0.950164 -0.112451 -0.479409
94 7.3 -2.66121 -0.326607 7.83093 0.359 -0.482493 0.154384
95 7.4 0 0 0 0.359089 -1.12337 0.409711
96 7.5 -1.88971 1.34806 3.56893 0.394677 -1.0109 0.548348
97 7.6 -1.34494 -0.896214 2.06959 0.231398 -0.728529 0.313513
98 7.7 0 0 0 0.415681 -0.45268 0.507181
99 7.8 0 0 0 0.259423 -0.11638 0.464208
100 7.9 -1.97572 -1.20836 3.95731 0.252257 -0.0845701 -0.249345
101 8 0 0 0 0.0688154 0.290386 -0.462467
102 8.1 0.25925 -0.458269 3.33086 0.360399 -0.0409494 -0.656911
103 8.2 0 0 0 -0.0587033 0.347698 -0.340604
104 8.3 0 0 0 -0.377192 0.153096 -0.914654
105 8.4 0 0 0 -0.431553 0.274996 -0.946252
106 8.5 0 0 0 -0.898366 0.146653 -1.36383
107 8.6 0 0 0 -0.889593 0.385951 0.125116
108 8.7 0 0 0 -0.0139171 -0.162302 -0.0287854
109 8.8 0 0 0 -0.266284 -0.148945 0.393533
110 8.9 0 0 0 -0.00920376 -0.0770818 0.334642
111 9 0 0 0 -0.0949156 0.0113352 -0.0761263
112 9.1 0 0 0 0.0688045 0.104558 -0.101891
113 9.2 3.79773 0.0255401 3.75032 0.419832 0.295402 0.652533
114 9.3 0 0 0 0.594267 0.70396 0.836434
115 9.4 0 0 0 0.174722 1.00483 1.42787
116 9.5 0 0 0 0.0626835 0.518952 0.269158
117 9.6 0 0 0 -0.302859 -0.265212 -0.0145578
118 9.7 0 0 0 -0.114026 -0.201336 -0.539522
119 9.8 0 0 0 0.104008 -0.30236 -0.0789062
120 9.9 0 0 0 -0.0482778 -0.553118 0.45214
121 10 0 0 0 -0.0554938 -0.402692 0.141112
122 10.1 0 0 0 0.174338 0.556958 -0.0922154
123 10.2 0 0 0 -1.06045 0.541565 -0.0409312
124 10.3 0 0 0 -1.20782 0.464574 -0.413871
125 10.4 0 0 0 -0.891701 0.327653 -0.286438
126 10.5 0 0 0 0.231227 -0.064277 -0.89684
127 10.6 -1.27989 -4.87365 9.40433 0.211278 0.230826 -1.23536
128 10.7 -2.1001 -0.417817 1.17745 0.425856 0.078728 -1.44229
129 10.8 0 0 0 0.30965 0.450884 -1.74985
130 10.9 0 0 0 0.36735 0.990032 -1.19971
131 11 0.253834 -1.84303 3.91828 1.01826 0.0660896 -0.481086
132 11.1 0 0 0 0.744006 0.0906555 -0.897417
133 11.2 0 0 0 0.339073 0.361038 -0.545084
134 11.3 -1.9974 -0.431998 3.46296 0.611295 0.17282 0.0341483
135 11.4 0 0 0 -0.491432 -0.958871 1.28001
136 11.5 0 0 0 0.0431048 -1.50924 1.24037
137 11.6 0 0 0 -0.684419 -0.0163951 1.06179
138 11.7 0 0 0 -0.425278 -0.127741 0.757298
139 11.8 -2.09164 0.00894897 2.22812 -0.0955178 -0.310572 0.661289
140 11.9 0 0 0 0.156959 -0.233409 0.802568
141 12 0 0 0 -0.05541 -0.346448 0.541571
142 12.1 0 0 0 0.706767 0.182767 0.25767
143 12.2 0 0 0 0.4791 0.464612 -0.212887
144 12.3 0 0 0 0.81454 0.440323 -0.461359
145 12.4 0 0 0 -0.110025 0.200698 -0.996706
146 12.5 0 0 0 -0.149791 0.165599 -1.02233
147 12.6 0 0 0 -0.170933 0.0644682 -0.866174
148 12.7 0 0 0 -0.122869 -0.0196287 -0.801348
149 12.8 0 0 0 -0.0693832 -0.0673091 -0.382802
150 12.9 0 0 0 -0.0693832 -0.0673091 -0.382802
151 13 0 0 0 -0.0693832 -0.0673091 -0.382802
152 13.1 0 0 0 -0.0693832 -0.0673091 -0.382802
153 13.2 0 0 0 -0.0693832 -0.0673091 -0.382802
154 13.3 0 0 0 -0.0693832 -0.0673091 -0.382802
155 13.4 0 0 0 -0.0693832 -0.0673091 -0.382802
156 13.5 0 0 0 -0.000502433 0.000137492 -0.227425
157 13.6 0 0 0 -0.000502433 0.000137492 -0.227425
158 13.7 0 0 0 -0.000502433 0.000137492 -0.227425
159 13.8 0 0 0 -0.000502433 0.000137492 -0.227425
160 13.9 0 0 0 -0.000502433 0.000137492 -0.227425
161 14 0 0 0 -0.000502433 0.000137492 -0.227425
162 14.1 0 0 0 -0.000502433 0.000137492 -0.227425
163 14.2 0 0 0 -0.000502433 0.000137492 -0.227425
164 14.3 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
165 14.4 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
166 14.5 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
167 14.6 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
168 14.7 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
169 14.8 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
170 14.9 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
171 15 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
172 15.1 0 0 0 0 0 0
173 15.2 0 0 0 0 0 0
174 15.3 0 0 0 0 0 0
175 15.4 0 0 0 0 0 0
176 15.5 0 0 0 0 0 0
177 15.6 0 0 0 0 0 0
178 15.7 0 0 0 0 0 0
179 15.8 0 0 0 0 0 0
180 15.9 0 0 0 0 0 0
181 16 0 0 0 0 0 0

3
examples/USER/misc/mop/mopz0.time.reference Normal file
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@ -0,0 +1,3 @@
# Time-averaged data for fix mopz0t
# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394

25
examples/USER/scafacos/data.NaCl Normal file
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@ -0,0 +1,25 @@
LAMMPS Description
8 atoms
2 atom types
0 1 xlo xhi
0 1 ylo yhi
0 1 zlo zhi
Masses
1 22.98976928
2 35.45
Atoms
1 2 1 0.25 0.25 0.25
2 1 -1 0.75 0.25 0.25
3 1 -1 0.25 0.75 0.25
4 2 1 0.75 0.75 0.25
5 1 -1 0.25 0.25 0.75
6 2 1 0.75 0.25 0.75
7 2 1 0.25 0.75 0.75
8 1 -1 0.75 0.75 0.75

316
examples/USER/scafacos/data.cloud_wall Normal file
View File

@ -0,0 +1,316 @@
LAMMPS Description
300 atoms
1 atom types
0 10 xlo xhi
0 10 ylo yhi
0 10 zlo zhi
Masses
1 1.0
Atoms
1 1 1 0 0 4.5
2 1 -1 0 0 5.5
3 1 1 0 1 4.5
4 1 -1 0 1 5.5
5 1 1 0 2 4.5
6 1 -1 0 2 5.5
7 1 1 0 3 4.5
8 1 -1 0 3 5.5
9 1 1 0 4 4.5
10 1 -1 0 4 5.5
11 1 1 0 5 4.5
12 1 -1 0 5 5.5
13 1 1 0 6 4.5
14 1 -1 0 6 5.5
15 1 1 0 7 4.5
16 1 -1 0 7 5.5
17 1 1 0 8 4.5
18 1 -1 0 8 5.5
19 1 1 0 9 4.5
20 1 -1 0 9 5.5
21 1 1 1 0 4.5
22 1 -1 1 0 5.5
23 1 1 1 1 4.5
24 1 -1 1 1 5.5
25 1 1 1 2 4.5
26 1 -1 1 2 5.5
27 1 1 1 3 4.5
28 1 -1 1 3 5.5
29 1 1 1 4 4.5
30 1 -1 1 4 5.5
31 1 1 1 5 4.5
32 1 -1 1 5 5.5
33 1 1 1 6 4.5
34 1 -1 1 6 5.5
35 1 1 1 7 4.5
36 1 -1 1 7 5.5
37 1 1 1 8 4.5
38 1 -1 1 8 5.5
39 1 1 1 9 4.5
40 1 -1 1 9 5.5
41 1 1 2 0 4.5
42 1 -1 2 0 5.5
43 1 1 2 1 4.5
44 1 -1 2 1 5.5
45 1 1 2 2 4.5
46 1 -1 2 2 5.5
47 1 1 2 3 4.5
48 1 -1 2 3 5.5
49 1 1 2 4 4.5
50 1 -1 2 4 5.5
51 1 1 2 5 4.5
52 1 -1 2 5 5.5
53 1 1 2 6 4.5
54 1 -1 2 6 5.5
55 1 1 2 7 4.5
56 1 -1 2 7 5.5
57 1 1 2 8 4.5
58 1 -1 2 8 5.5
59 1 1 2 9 4.5
60 1 -1 2 9 5.5
61 1 1 3 0 4.5
62 1 -1 3 0 5.5
63 1 1 3 1 4.5
64 1 -1 3 1 5.5
65 1 1 3 2 4.5
66 1 -1 3 2 5.5
67 1 1 3 3 4.5
68 1 -1 3 3 5.5
69 1 1 3 4 4.5
70 1 -1 3 4 5.5
71 1 1 3 5 4.5
72 1 -1 3 5 5.5
73 1 1 3 6 4.5
74 1 -1 3 6 5.5
75 1 1 3 7 4.5
76 1 -1 3 7 5.5
77 1 1 3 8 4.5
78 1 -1 3 8 5.5
79 1 1 3 9 4.5
80 1 -1 3 9 5.5
81 1 1 4 0 4.5
82 1 -1 4 0 5.5
83 1 1 4 1 4.5
84 1 -1 4 1 5.5
85 1 1 4 2 4.5
86 1 -1 4 2 5.5
87 1 1 4 3 4.5
88 1 -1 4 3 5.5
89 1 1 4 4 4.5
90 1 -1 4 4 5.5
91 1 1 4 5 4.5
92 1 -1 4 5 5.5
93 1 1 4 6 4.5
94 1 -1 4 6 5.5
95 1 1 4 7 4.5
96 1 -1 4 7 5.5
97 1 1 4 8 4.5
98 1 -1 4 8 5.5
99 1 1 4 9 4.5
100 1 -1 4 9 5.5
101 1 1 5 0 4.5
102 1 -1 5 0 5.5
103 1 1 5 1 4.5
104 1 -1 5 1 5.5
105 1 1 5 2 4.5
106 1 -1 5 2 5.5
107 1 1 5 3 4.5
108 1 -1 5 3 5.5
109 1 1 5 4 4.5
110 1 -1 5 4 5.5
111 1 1 5 5 4.5
112 1 -1 5 5 5.5
113 1 1 5 6 4.5
114 1 -1 5 6 5.5
115 1 1 5 7 4.5
116 1 -1 5 7 5.5
117 1 1 5 8 4.5
118 1 -1 5 8 5.5
119 1 1 5 9 4.5
120 1 -1 5 9 5.5
121 1 1 6 0 4.5
122 1 -1 6 0 5.5
123 1 1 6 1 4.5
124 1 -1 6 1 5.5
125 1 1 6 2 4.5
126 1 -1 6 2 5.5
127 1 1 6 3 4.5
128 1 -1 6 3 5.5
129 1 1 6 4 4.5
130 1 -1 6 4 5.5
131 1 1 6 5 4.5
132 1 -1 6 5 5.5
133 1 1 6 6 4.5
134 1 -1 6 6 5.5
135 1 1 6 7 4.5
136 1 -1 6 7 5.5
137 1 1 6 8 4.5
138 1 -1 6 8 5.5
139 1 1 6 9 4.5
140 1 -1 6 9 5.5
141 1 1 7 0 4.5
142 1 -1 7 0 5.5
143 1 1 7 1 4.5
144 1 -1 7 1 5.5
145 1 1 7 2 4.5
146 1 -1 7 2 5.5
147 1 1 7 3 4.5
148 1 -1 7 3 5.5
149 1 1 7 4 4.5
150 1 -1 7 4 5.5
151 1 1 7 5 4.5
152 1 -1 7 5 5.5
153 1 1 7 6 4.5
154 1 -1 7 6 5.5
155 1 1 7 7 4.5
156 1 -1 7 7 5.5
157 1 1 7 8 4.5
158 1 -1 7 8 5.5
159 1 1 7 9 4.5
160 1 -1 7 9 5.5
161 1 1 8 0 4.5
162 1 -1 8 0 5.5
163 1 1 8 1 4.5
164 1 -1 8 1 5.5
165 1 1 8 2 4.5
166 1 -1 8 2 5.5
167 1 1 8 3 4.5
168 1 -1 8 3 5.5
169 1 1 8 4 4.5
170 1 -1 8 4 5.5
171 1 1 8 5 4.5
172 1 -1 8 5 5.5
173 1 1 8 6 4.5
174 1 -1 8 6 5.5
175 1 1 8 7 4.5
176 1 -1 8 7 5.5
177 1 1 8 8 4.5
178 1 -1 8 8 5.5
179 1 1 8 9 4.5
180 1 -1 8 9 5.5
181 1 1 9 0 4.5
182 1 -1 9 0 5.5
183 1 1 9 1 4.5
184 1 -1 9 1 5.5
185 1 1 9 2 4.5
186 1 -1 9 2 5.5
187 1 1 9 3 4.5
188 1 -1 9 3 5.5
189 1 1 9 4 4.5
190 1 -1 9 4 5.5
191 1 1 9 5 4.5
192 1 -1 9 5 5.5
193 1 1 9 6 4.5
194 1 -1 9 6 5.5
195 1 1 9 7 4.5
196 1 -1 9 7 5.5
197 1 1 9 8 4.5
198 1 -1 9 8 5.5
199 1 1 9 9 4.5
200 1 -1 9 9 5.5
201 1 -1 9.28495 2.13839 8.88019
202 1 1 4.99281 4.17459 9.83905
203 1 -1 4.91265 6.89408 2.39989
204 1 1 4.43647 3.68895 8.86086
205 1 -1 0.659075 7.07271 0.179131
206 1 1 7.791 3.40021 0.969703
207 1 -1 1.18008 3.63874 7.28751
208 1 1 8.51522 5.24681 6.37702
209 1 -1 4.24226 9.60726 3.16084
210 1 1 8.43745 8.23344 9.2883
211 1 -1 8.48509 8.84988 9.43407
212 1 1 2.81127 8.9903 0.00909212
213 1 -1 6.38283 6.20858 9.92482
214 1 1 4.59962 5.7925 7.52571
215 1 -1 7.03797 7.09336 8.15957
216 1 1 6.68103 8.04734 7.95661
217 1 -1 2.531 8.47145 1.6209
218 1 1 6.71915 8.79876 9.59581
219 1 -1 4.96758 0.0381298 0.827927
220 1 1 9.22955 1.04572 0.84722
221 1 -1 2.3224 2.57084 8.07306
222 1 1 1.94283 3.17375 3.92051
223 1 -1 2.34735 1.91295 1.29127
224 1 1 3.33928 3.30688 0.892089
225 1 -1 1.19738 4.40402 8.70835
226 1 1 7.44541 4.94803 8.28211
227 1 -1 5.93272 1.18886 1.56518
228 1 1 8.50709 8.70343 1.24939
229 1 -1 5.54016 3.38865 8.61698
230 1 1 9.47644 0.573085 3.05941
231 1 -1 9.39695 4.46542 1.84205
232 1 1 3.52268 5.60212 0.333999
233 1 -1 3.69009 9.40954 6.10446
234 1 1 3.96836 6.15307 7.57803
235 1 -1 2.02535 0.0418407 3.21642
236 1 1 2.97488 8.79711 8.33242
237 1 -1 2.4122 1.79458 3.04173
238 1 1 9.72355 3.67773 1.52435
239 1 -1 8.55216 6.1623 1.53201
240 1 1 4.98973 2.41459 9.84381
241 1 -1 8.8901 5.9006 1.97649
242 1 1 9.09932 2.23783 1.42554
243 1 -1 6.70722 8.21769 1.21953
244 1 1 6.83768 0.84508 3.25165
245 1 -1 0.222115 3.07945 0.51825
246 1 1 0.503918 9.34932 6.25278
247 1 -1 0.803159 8.7017 9.46211
248 1 1 4.88636 5.00147 9.65639
249 1 -1 1.62258 0.767285 9.63596
250 1 1 2.70143 3.01111 7.74859
251 1 -1 4.41574 5.31824 0.538729
252 1 1 1.64724 5.18097 3.59205
253 1 -1 2.33672 3.21408 6.6081
254 1 1 7.46603 1.53668 9.09844
255 1 -1 3.61269 8.44556 6.99789
256 1 1 6.95465 6.83045 9.31002
257 1 -1 5.91831 9.01549 3.4626
258 1 1 6.56503 8.42229 3.27105
259 1 -1 4.50822 9.59753 3.47025
260 1 1 4.17357 5.27384 7.34774
261 1 -1 7.70968 6.5292 3.54779
262 1 1 4.7977 4.94239 6.24947
263 1 -1 9.24016 9.36994 6.71263
264 1 1 7.36888 8.75922 0.52403
265 1 -1 9.92895 5.87551 6.21586
266 1 1 3.86308 6.71601 9.69083
267 1 -1 8.90048 0.298719 0.573852
268 1 1 6.58753 6.67768 1.83984
269 1 -1 8.672 0.367497 2.21864
270 1 1 3.44519 3.30359 6.52249
271 1 -1 7.24717 3.25113 3.41567
272 1 1 9.53447 5.81336 1.79208
273 1 -1 1.01722 6.42534 0.715
274 1 1 3.58808 4.92392 7.00979
275 1 -1 1.21399 3.56951 6.34505
276 1 1 3.50336 0.942722 2.76989
277 1 -1 9.45475 6.06299 0.659023
278 1 1 3.44464 4.03075 6.20179
279 1 -1 0.949331 5.40183 8.51385
280 1 1 6.41118 2.62135 2.31132
281 1 -1 3.58837 9.78355 7.04966
282 1 1 9.2267 3.19593 2.10384
283 1 -1 1.83092 2.35627 3.93061
284 1 1 4.97203 4.92287 1.8049
285 1 -1 7.4097 4.757 8.604
286 1 1 0.746575 7.69038 0.89134
287 1 -1 8.54862 6.59135 2.18888
288 1 1 2.18747 4.82994 0.761718
289 1 -1 5.71622 2.51116 6.85522
290 1 1 6.95554 1.83187 8.31157
291 1 -1 7.31818 6.60081 2.63208
292 1 1 0.744495 2.73429 9.86022
293 1 -1 5.1573 8.70962 2.53418
294 1 1 2.40385 1.54057 1.9297
295 1 -1 3.42609 2.25856 2.28437
296 1 1 6.66173 3.70851 9.70052
297 1 -1 7.88966 1.4343 8.91223
298 1 1 3.91118 5.22253 6.29642
299 1 -1 9.17618 3.98313 9.82158
300 1 1 4.95424 5.93521 1.3652

1016
examples/USER/scafacos/data.hammersley_sphere Normal file
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File diff suppressed because it is too large Load Diff

37
examples/USER/scafacos/in.scafacos Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p3m 0.001
#kspace_style scafacos tolerance field
timestep 0.005
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.ewald Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.cw.fmm Normal file
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@ -0,0 +1,37 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.p2nfft Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.p3m Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p3m 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.ewald Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.fmm Normal file
View File

@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100

34
examples/USER/scafacos/in.scafacos.hsph.direct Normal file
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@ -0,0 +1,34 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20

37
examples/USER/scafacos/in.scafacos.hsph.fmm Normal file
View File

@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
timestep 0.005
thermo 1
run 20

36
examples/USER/scafacos/in.scafacos.hsph.p2nfft Normal file
View File

@ -0,0 +1,36 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20

37
examples/USER/scafacos/in.scafacos.p2nfft Normal file
View File

@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.p3m Normal file
View File

@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p3m 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49647271 0 0.49647271 0 0
10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861
20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314
30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679
40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911
50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037
60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302
70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118
80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288
90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364
100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922
Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms
Performance: 102047.913 tau/day, 236.222 timesteps/s
99.2% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01
Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04
Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13
Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54
Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07
Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03
Other | | 0.000758 | | | 0.18
Nlocal: 18.75 ave 39 max 6 min
Histogram: 6 1 1 0 1 2 2 1 1 1
Nghost: 122.812 ave 195 max 63 min
Histogram: 8 0 0 0 0 0 0 1 3 4
Neighs: 160.625 ave 598 max 13 min
Histogram: 8 2 1 1 1 0 0 2 0 1
Total # of neighbors = 2570
Ave neighs/atom = 8.56667
Neighbor list builds = 23
Dangerous builds = 16
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49647271 0 0.49647271 0 0
10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087
20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565
30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608
40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582
50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403
60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376
70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802
80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814
90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175
100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344
Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms
Performance: 74052.598 tau/day, 171.418 timesteps/s
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01
Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17
Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16
Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48
Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04
Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03
Other | | 0.00065 | | | 0.11
Nlocal: 37.5 ave 46 max 31 min
Histogram: 2 0 0 2 1 0 2 0 0 1
Nghost: 203.875 ave 212 max 192 min
Histogram: 1 0 1 0 0 2 1 0 0 3
Neighs: 321.625 ave 599 max 112 min
Histogram: 1 2 0 1 1 0 1 1 0 1
Total # of neighbors = 2573
Ave neighs/atom = 8.57667
Neighbor list builds = 23
Dangerous builds = 16
Total wall time: 0:00:00

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms
Performance: 68029.122 tau/day, 157.475 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01
Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01
Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56
Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16
Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02
Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16
Other | | 0.0004218 | | | 0.07
Nlocal: 300 ave 300 max 300 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 374 ave 374 max 374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2459 ave 2459 max 2459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms
Performance: 183509.107 tau/day, 424.790 timesteps/s
97.9% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02
Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31
Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15
Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97
Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16
Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06
Other | | 0.0007878 | | | 0.33
Nlocal: 18.75 ave 36 max 6 min
Histogram: 4 3 1 0 0 1 2 1 2 2
Nghost: 127 ave 196 max 71 min
Histogram: 8 0 0 0 0 0 0 1 6 1
Neighs: 153.688 ave 491 max 10 min
Histogram: 8 1 1 1 1 1 0 0 0 3
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms
Performance: 110479.760 tau/day, 255.740 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02
Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67
Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50
Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51
Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04
Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13
Other | | 0.0004461 | | | 0.11
Nlocal: 150 ave 159 max 141 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 392 ave 395 max 389 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1229.5 ave 1773 max 686 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms
Performance: 148735.741 tau/day, 344.296 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02
Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41
Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37
Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84
Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09
Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11
Other | | 0.0004706 | | | 0.16
Nlocal: 75 ave 81 max 70 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 282.5 ave 290 max 274 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 614.75 ave 981 max 285 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms
Performance: 147513.337 tau/day, 341.466 timesteps/s
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02
Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25
Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21
Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09
Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11
Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08
Other | | 0.0007486 | | | 0.26
Nlocal: 37.5 ave 45 max 31 min
Histogram: 1 1 1 1 1 0 1 0 1 1
Nghost: 200 ave 209 max 189 min
Histogram: 1 0 0 0 1 4 0 0 0 2
Neighs: 307.375 ave 514 max 115 min
Histogram: 2 1 0 1 1 0 0 0 1 2
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms
Performance: 59891.733 tau/day, 138.638 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01
Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13
Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49
Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14
Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02
Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14
Other | | 0.0004385 | | | 0.06
Nlocal: 300 ave 300 max 300 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 381 ave 381 max 381 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2461 ave 2461 max 2461 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms
Performance: 272716.448 tau/day, 631.288 timesteps/s
99.4% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02
Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74
Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22
Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26
Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21
Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08
Other | | 0.0007506 | | | 0.47
Nlocal: 18.75 ave 33 max 6 min
Histogram: 2 6 0 0 0 0 2 1 2 3
Nghost: 128.875 ave 198 max 71 min
Histogram: 7 1 0 0 0 0 0 1 5 2
Neighs: 153.812 ave 490 max 14 min
Histogram: 8 0 3 0 1 1 0 0 1 2
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms
Performance: 97092.373 tau/day, 224.751 timesteps/s
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02
Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84
Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44
Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45
Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04
Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11
Other | | 0.0004425 | | | 0.10
Nlocal: 150 ave 157 max 143 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 399 ave 402 max 396 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1230.5 ave 1756 max 705 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms
Performance: 153805.254 tau/day, 356.031 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02
Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56
Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39
Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72
Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07
Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10
Other | | 0.0004173 | | | 0.15
Nlocal: 75 ave 81 max 69 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 287 ave 296 max 278 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 615.25 ave 964 max 286 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms
Performance: 216363.074 tau/day, 500.840 timesteps/s
99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02
Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08
Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31
Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12
Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12
Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09
Other | | 0.0005245 | | | 0.26
Nlocal: 37.5 ave 42 max 33 min
Histogram: 2 1 0 1 0 0 1 0 1 2
Nghost: 202.25 ave 212 max 194 min
Histogram: 1 0 2 1 0 2 0 1 0 1
Neighs: 307.625 ave 505 max 129 min
Histogram: 3 0 0 1 1 0 0 0 1 2
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.000498772 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 11.99707
10 1.500011 -1.747529 0 0.50193816 11.997158
20 1.5000023 -1.7475152 0 0.50193898 11.997089
30 1.4999308 -1.747404 0 0.50194285 11.996517
40 1.4997722 -1.7471622 0 0.50194686 11.995248
50 1.4995835 -1.746878 0 0.50194808 11.993739
60 1.4996054 -1.7469114 0 0.50194749 11.993914
70 1.5004341 -1.7481558 0 0.50194592 12.000543
80 1.5033218 -1.7524875 0 0.50194458 12.023638
90 1.5108306 -1.7637462 0 0.50194636 12.083694
100 1.5292479 -1.7913449 0 0.50196695 12.230996
Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms
Performance: 38.530 tau/day, 0.089 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00
Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00
Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00
Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00
Other | | 0.00418 | | | 0.00
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:18:57

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000462294 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms
Performance: 538.132 tau/day, 1.246 timesteps/s
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00
Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01
Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00
Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00
Other | | 0.001511 | | | 0.00
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:22

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.000344753 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 11.99707
10 1.500011 -1.747529 0 0.50193816 11.997158
20 1.5000023 -1.7475152 0 0.50193898 11.997089
30 1.4999308 -1.747404 0 0.50194285 11.996517
40 1.4997722 -1.7471622 0 0.50194686 11.995248
50 1.4995835 -1.746878 0 0.50194808 11.993739
60 1.4996054 -1.7469114 0 0.50194749 11.993914
70 1.5004341 -1.7481558 0 0.50194592 12.000543
80 1.5033218 -1.7524875 0 0.50194458 12.023638
90 1.5108306 -1.7637462 0 0.50194636 12.083694
100 1.5292479 -1.7913449 0 0.50196695 12.230996
Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms
Performance: 76.218 tau/day, 0.176 timesteps/s
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00
Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00
Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00
Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00
Other | | 0.002497 | | | 0.00
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:09:38

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000261068 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms
Performance: 145.948 tau/day, 0.338 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00
Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00
Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00
Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00
Other | | 0.001821 | | | 0.00
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:05:02

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000232935 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms
Performance: 279.720 tau/day, 0.647 timesteps/s
99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00
Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01
Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00
Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00
Other | | 0.001309 | | | 0.00
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:38

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.000518799 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms
Performance: 1244.749 tau/day, 2.881 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00
Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04
Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00
Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03
Other | | 0.004232 | | | 0.01
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000400543 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms
Performance: 10194.102 tau/day, 23.597 timesteps/s
99.6% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01
Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29
Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01
Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02
Other | | 0.002255 | | | 0.05
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.0003407 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms
Performance: 2408.014 tau/day, 5.574 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01
Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10
Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00
Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03
Other | | 0.002716 | | | 0.02
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:19

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000270367 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms
Performance: 4286.533 tau/day, 9.923 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01
Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15
Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00
Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03
Other | | 0.002214 | | | 0.02
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000236988 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms
Performance: 7247.876 tau/day, 16.777 timesteps/s
99.8% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01
Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25
Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01
Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03
Other | | 0.001971 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.00049448 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms
Performance: 2385.257 tau/day, 5.521 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01
Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08
Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00
Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06
Other | | 0.004455 | | | 0.02
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:21

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000361443 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms
Performance: 27571.239 tau/day, 63.822 timesteps/s
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03
Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65
Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02
Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06
Other | | 0.001859 | | | 0.12
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.0003438 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms
Performance: 4600.920 tau/day, 10.650 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01
Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21
Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00
Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06
Other | | 0.002495 | | | 0.03
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000260592 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms
Performance: 8470.643 tau/day, 19.608 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01
Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28
Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01
Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06
Other | | 0.002036 | | | 0.04
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000324488 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms
Performance: 14973.700 tau/day, 34.661 timesteps/s
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02
Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51
Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01
Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06
Other | | 0.001645 | | | 0.06
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

0
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms
Performance: 18547.165 tau/day, 42.933 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05
Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08
Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59
Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03
Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06
Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12
Other | | 0.0003715 | | | 0.08
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 247817 ave 247817 max 247817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

105
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms
Performance: 30421.778 tau/day, 70.421 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08
Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19
Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84
Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58
Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11
Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10
Other | | 0.0002506 | | | 0.09
Nlocal: 500 ave 516 max 484 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 456.5 ave 475 max 438 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 123908 ave 172139 max 75678 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms
Performance: 53553.228 tau/day, 123.966 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14
Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19
Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62
Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60
Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24
Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10
Other | | 0.0001805 | | | 0.11
Nlocal: 250 ave 259 max 238 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 672.25 ave 683 max 663 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 61954.2 ave 97157 max 25016 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms
Performance: 97743.448 tau/day, 226.258 timesteps/s
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27
Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44
Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15
Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37
Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50
Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10
Other | | 0.0001439 | | | 0.16
Nlocal: 125 ave 133 max 113 min
Histogram: 2 0 0 0 0 1 1 0 2 2
Nghost: 773.625 ave 788 max 764 min
Histogram: 1 1 2 1 1 0 0 0 1 1
Neighs: 30977.1 ave 50690 max 10447 min
Histogram: 1 1 1 0 1 1 0 0 2 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms
Performance: 10836.721 tau/day, 25.085 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03
Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83
Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95
Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03
Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05
Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07
Other | | 0.0003934 | | | 0.05
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 244342 ave 244342 max 244342 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms
Performance: 12321.981 tau/day, 28.523 timesteps/s
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03
Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00
Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55
Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27
Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06
Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05
Other | | 0.0002786 | | | 0.04
Nlocal: 500 ave 509 max 491 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 455.5 ave 467 max 444 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 122171 ave 171834 max 72508 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms
Performance: 12955.555 tau/day, 29.990 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04
Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38
Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00
Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43
Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08
Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03
Other | | 0.0002366 | | | 0.04
Nlocal: 250 ave 259 max 240 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 668.75 ave 679 max 657 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 61085.5 ave 95363 max 24964 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms
Performance: 15174.000 tau/day, 35.125 timesteps/s
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04
Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66
Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57
Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55
Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12
Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02
Other | | 0.0002268 | | | 0.04
Nlocal: 125 ave 137 max 111 min
Histogram: 1 1 0 0 0 2 2 1 0 1
Nghost: 768.875 ave 788 max 761 min
Histogram: 4 0 2 0 0 0 1 0 0 1
Neighs: 30542.8 ave 48077 max 10011 min
Histogram: 1 1 1 0 1 1 0 0 0 3
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

107
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms
Performance: 8150.306 tau/day, 18.866 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02
Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42
Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43
Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01
Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03
Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05
Other | | 0.0003803 | | | 0.04
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 247817 ave 247817 max 247817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

107
examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 Normal file
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@ -0,0 +1,107 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms
Performance: 12320.557 tau/day, 28.520 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03
Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95
Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64
Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24
Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06
Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04
Other | | 0.000288 | | | 0.04
Nlocal: 500 ave 516 max 484 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 456.5 ave 475 max 438 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 123908 ave 172139 max 75678 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

107
examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 Normal file
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@ -0,0 +1,107 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms
Performance: 20210.785 tau/day, 46.784 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05
Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85
Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31
Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60
Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10
Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04
Other | | 0.0002093 | | | 0.05
Nlocal: 250 ave 259 max 238 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 672.25 ave 683 max 663 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 61954.2 ave 97157 max 25016 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

107
examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 Normal file
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@ -0,0 +1,107 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms
Performance: 35681.038 tau/day, 82.595 timesteps/s
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10
Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48
Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81
Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29
Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20
Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04
Other | | 0.0001938 | | | 0.08
Nlocal: 125 ave 133 max 113 min
Histogram: 2 0 0 0 0 1 1 0 2 2
Nghost: 773.625 ave 788 max 764 min
Histogram: 1 1 2 1 1 0 0 0 1 1
Neighs: 30977.1 ave 50690 max 10447 min
Histogram: 1 1 1 0 1 1 0 0 2 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

2
examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
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@ -129,7 +129,7 @@ compute contact_radius all smd/contact/radius
compute S solids smd/tlsph/stress
compute nn water smd/ulsph/num/neighs
compute epl solids smd/plastic/strain
compute vol all smd/volume
compute vol all smd/vol
compute rho all smd/rho
dump dump_id all custom 100 dump.LAMMPS id type x y &