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Updating pair tracker example

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This commit is contained in:
jtclemm
2024-11-04 13:57:54 -07:00
parent 5ce635757f
commit 34113226ae
5 changed files with 20951 additions and 8260 deletions
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28935
examples/tracker/contact_history.dat
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File diff suppressed because it is too large Load Diff

7
examples/tracker/in.track
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@ -11,7 +11,7 @@ mass 1 1.0
mass 2 1.0
velocity all create 2.0 87287 loop geom
pair_style hybrid/overlay lj/cut 2.5 tracker
pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
pair_coeff * * lj/cut 1.0 1.0 2.5
pair_coeff * * tracker 2.5
@ -19,10 +19,9 @@ neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
dump_modify 1 header no
# compute 1 all property/local patom1 patom2

54
examples/tracker/lifetime_hist.dat
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@ -1,4 +1,4 @@
# Histogrammed data for fix 3
# Histogrammed data for fix 2
# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
# Bin Coord Count Count/Total
0 30 0 0 1e+20 -1e+20
@ -32,34 +32,34 @@
28 5.5 0 0
29 5.7 0 0
30 5.9 0 0
1000 30 8122 0 0.5 5
1000 30 528 20285 1 1000
1 0.1 0 0
2 0.3 0 0
3 0.5 910 0.112041
4 0.7 1253 0.154272
5 0.9 953 0.117336
6 1.1 747 0.0919724
7 1.3 559 0.0688254
8 1.5 501 0.0616843
9 1.7 421 0.0518345
10 1.9 356 0.0438316
11 2.1 300 0.0369367
12 2.3 281 0.0345974
13 2.5 242 0.0297956
14 2.7 226 0.0278257
15 2.9 175 0.0215464
16 3.1 168 0.0206846
17 3.3 162 0.0199458
18 3.5 129 0.0158828
19 3.7 151 0.0185915
20 3.9 137 0.0168678
21 4.1 98 0.012066
22 4.3 104 0.0128047
23 4.5 83 0.0102192
24 4.7 77 0.00948042
25 4.9 86 0.0105885
26 5.1 3 0.000369367
3 0.5 0 0
4 0.7 0 0
5 0.9 0 0
6 1.1 17 0.032197
7 1.3 0 0
8 1.5 0 0
9 1.7 0 0
10 1.9 0 0
11 2.1 51 0.0965909
12 2.3 0 0
13 2.5 0 0
14 2.7 0 0
15 2.9 0 0
16 3.1 80 0.151515
17 3.3 0 0
18 3.5 0 0
19 3.7 0 0
20 3.9 0 0
21 4.1 91 0.172348
22 4.3 0 0
23 4.5 0 0
24 4.7 0 0
25 4.9 0 0
26 5.1 117 0.221591
27 5.3 0 0
28 5.5 0 0
29 5.7 0 0
30 5.9 0 0
30 5.9 172 0.325758

108
examples/tracker/log.29Aug24.tracker.g++.1 Normal file
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@ -0,0 +1,108 @@
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-731-g5ce635757f)
# 3d Lennard-Jones melt with tracking
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
create_atoms CPU = 0.000 seconds
mass 1 1.0
mass 2 1.0
velocity all create 2.0 87287 loop geom
pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
pair_coeff * * lj/cut 1.0 1.0 2.5
pair_coeff * * tracker 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
dump_modify 1 header no
# compute 1 all property/local patom1 patom2
# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
# dump 3 all atom 1 atoms.dat
thermo 50
run 1000 #0
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 20 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) pair tracker, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.679 | 8.679 | 8.679 Mbytes
Step Temp E_pair E_mol TotEng Press
0 2 -6.7733681 0 -3.7850868 -4.5535126
50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
250 1.070121 -5.3902744 0 -3.791363 2.4908658
300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
350 1.000601 -5.2859643 0 -3.7909257 2.9065274
400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
450 1.0482542 -5.357452 0 -3.7912128 2.4707397
500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
600 1.0683914 -5.3863229 0 -3.789996 2.3002719
650 1.0130779 -5.303917 0 -3.7902362 2.8726423
700 1.0583333 -5.3737358 0 -3.792437 2.5770307
750 0.98274506 -5.2612464 0 -3.792887 2.9447027
800 1.0294191 -5.332001 0 -3.7939042 2.5293193
850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
950 0.97137182 -5.2424403 0 -3.7910742 3.129989
1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
Loop time of 0.286151 on 1 procs for 1000 steps with 256 atoms
Performance: 1509690.552 tau/day, 3494.654 timesteps/s, 894.631 katom-step/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21578 | 0.21578 | 0.21578 | 0.0 | 75.41
Neigh | 0.020262 | 0.020262 | 0.020262 | 0.0 | 7.08
Comm | 0.0051679 | 0.0051679 | 0.0051679 | 0.0 | 1.81
Output | 0.021204 | 0.021204 | 0.021204 | 0.0 | 7.41
Modify | 0.02307 | 0.02307 | 0.02307 | 0.0 | 8.06
Other | | 0.0006654 | | | 0.23
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1327 ave 1327 max 1327 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9612 ave 9612 max 9612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9612
Ave neighs/atom = 37.546875
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:00

107
examples/tracker/log.8Apr21.tracker.g++.1
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@ -1,107 +0,0 @@
LAMMPS (8 Apr 2021)
# 3d Lennard-Jones melt with tracking
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 256 atoms
create_atoms CPU = 0.001 seconds
mass 1 1.0
mass 2 1.0
velocity all create 2.0 87287 loop geom
pair_style hybrid/overlay lj/cut 2.5 tracker
pair_coeff * * lj/cut 1.0 1.0 2.5
pair_coeff * * tracker 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
dump_modify 1 header no
# compute 1 all property/local patom1 patom2
# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
# dump 3 all atom 1 atoms.dat
thermo 50
run 1000 #0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) pair tracker, perpetual
attributes: half, newton on, history
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes
Step Temp E_pair E_mol TotEng Press
0 2 -6.7733681 0 -3.7850868 -4.5535126
50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
250 1.070121 -5.3902744 0 -3.791363 2.4908658
300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
350 1.000601 -5.2859643 0 -3.7909257 2.9065274
400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
450 1.0482542 -5.357452 0 -3.7912128 2.4707397
500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
600 1.0683914 -5.3863229 0 -3.789996 2.3002719
650 1.0130779 -5.303917 0 -3.7902362 2.8726423
700 1.0583333 -5.3737358 0 -3.792437 2.5770307
750 0.98274506 -5.2612464 0 -3.792887 2.9447027
800 1.0294191 -5.332001 0 -3.7939042 2.5293193
850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
950 0.97137182 -5.2424403 0 -3.7910742 3.129989
1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
Loop time of 0.310363 on 1 procs for 1000 steps with 256 atoms
Performance: 1391918.252 tau/day, 3222.033 timesteps/s
100.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22132 | 0.22132 | 0.22132 | 0.0 | 71.31
Neigh | 0.03458 | 0.03458 | 0.03458 | 0.0 | 11.14
Comm | 0.0087938 | 0.0087938 | 0.0087938 | 0.0 | 2.83
Output | 0.014075 | 0.014075 | 0.014075 | 0.0 | 4.54
Modify | 0.02818 | 0.02818 | 0.02818 | 0.0 | 9.08
Other | | 0.003411 | | | 1.10
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1327.00 ave 1327 max 1327 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9612.00 ave 9612 max 9612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9612
Ave neighs/atom = 37.546875
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:00