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akohlmeyakohlmey
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update reference for test that includes count of constrained bonds via shake
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tests/examples/deposit/log.16Jul20.linux.8.deposit.molecule.shake renamed to tests/examples/deposit/log.22Oct20.linux.8.deposit.molecule.shake

Lines changed: 23 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
LAMMPS (30 Jun 2020)
1+
LAMMPS (22 Oct 2020)
22
# sample surface deposition script for molecules
33

44
units lj
@@ -61,7 +61,7 @@ fix 6 all shake 0.0001 20 1000 b 1 mol dimer
6161
thermo_style custom step atoms temp epair etotal press
6262
thermo 100
6363
thermo_modify temp add lost/bond ignore lost warn
64-
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:473)
64+
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:472)
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6666
#dump 1 all atom 50 dump.deposit.atom
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@@ -98,7 +98,7 @@ Step Atoms Temp E_pair TotEng Press
9898
800 366 1.0959778 -6.641634 -6.5817445 -0.66410097
9999
900 368 1.1262085 -6.6106217 -6.5417638 -0.64913411
100100
SHAKE stats (type/ave/delta/count) on step 1000
101-
1 1.00000 2.22045e-15 20
101+
1 2.00000 2.22045e-15 10
102102
1000 370 1.2436487 -6.5814109 -6.4973806 -0.69068445
103103
1100 372 0.92307586 -6.5800162 -6.5117781 -0.64585329
104104
1200 374 0.90550736 -6.5699018 -6.4972676 -0.66926013
@@ -110,7 +110,7 @@ SHAKE stats (type/ave/delta/count) on step 1000
110110
1800 386 0.63197742 -6.5657642 -6.4920881 -0.66374389
111111
1900 388 0.8458029 -6.5704267 -6.4668813 -0.68083108
112112
SHAKE stats (type/ave/delta/count) on step 2000
113-
1 1.00000 2.55351e-15 40
113+
1 2.00000 2.55351e-15 20
114114
2000 390 0.75734227 -6.5725884 -6.4754933 -0.68208674
115115
2100 392 0.58637307 -6.5613379 -6.4828058 -0.65602656
116116
2200 394 0.66930831 -6.5696117 -6.4761804 -0.66824775
@@ -122,7 +122,7 @@ SHAKE stats (type/ave/delta/count) on step 2000
122122
2800 406 0.48895409 -6.5905528 -6.5062504 -0.68920893
123123
2900 408 0.46279767 -6.5992355 -6.5169981 -0.66235563
124124
SHAKE stats (type/ave/delta/count) on step 3000
125-
1 1.00000 1.77636e-15 60
125+
1 2.00000 1.77636e-15 30
126126
3000 410 0.43796036 -6.5909919 -6.5108772 -0.63023804
127127
3100 412 0.46363556 -6.5980994 -6.5108864 -0.71980891
128128
3200 414 0.47973251 -6.5996146 -6.5069127 -0.72137978
@@ -134,7 +134,7 @@ SHAKE stats (type/ave/delta/count) on step 3000
134134
3800 426 0.41258442 -6.6097047 -6.5176964 -0.75859328
135135
3900 428 0.34545148 -6.6052651 -6.52657 -0.76695568
136136
SHAKE stats (type/ave/delta/count) on step 4000
137-
1 1.00000 2.66454e-15 80
137+
1 2.00000 2.66454e-15 40
138138
4000 430 0.46525721 -6.6163434 -6.5081441 -0.73292439
139139
4100 432 0.48703468 -6.640156 -6.524598 -0.76779394
140140
4200 434 0.43451203 -6.6361469 -6.531023 -0.74203962
@@ -146,7 +146,7 @@ SHAKE stats (type/ave/delta/count) on step 4000
146146
4800 446 0.35289963 -6.6633021 -6.5683515 -0.75098165
147147
4900 448 0.43097952 -6.6743223 -6.5564764 -0.74558941
148148
SHAKE stats (type/ave/delta/count) on step 5000
149-
1 1.00000 2.44249e-15 100
149+
1 2.00000 2.44249e-15 50
150150
5000 450 0.40243306 -6.6551581 -6.5433711 -0.7639727
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5100 452 0.38542262 -6.6607987 -6.5520788 -0.77666011
152152
5200 454 0.31409975 -6.6574381 -6.5674976 -0.75521244
@@ -158,7 +158,7 @@ SHAKE stats (type/ave/delta/count) on step 5000
158158
5800 466 0.38120009 -6.6664152 -6.5478014 -0.66081689
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5900 468 0.35375424 -6.6640855 -6.5525924 -0.69470639
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SHAKE stats (type/ave/delta/count) on step 6000
161-
1 1.00000 2.99760e-15 120
161+
1 2.00000 2.99760e-15 60
162162
6000 470 0.34675472 -6.6648619 -6.5541955 -0.7568866
163163
6100 472 0.4186521 -6.691767 -6.5565033 -0.72258602
164164
6200 474 0.35652563 -6.6909579 -6.5743726 -0.74683749
@@ -170,7 +170,7 @@ SHAKE stats (type/ave/delta/count) on step 6000
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6800 486 0.32324895 -6.7267785 -6.6137078 -0.75926591
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6900 488 0.35373253 -6.7355635 -6.6105248 -0.70790001
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SHAKE stats (type/ave/delta/count) on step 7000
173-
1 1.00000 3.21965e-15 140
173+
1 2.00000 3.21965e-15 70
174174
7000 490 0.30629065 -6.7228534 -6.6134639 -0.75052345
175175
7100 492 0.29253509 -6.7061978 -6.6006592 -0.78460478
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7200 494 0.34481285 -6.7299026 -6.6042623 -0.80994231
@@ -182,7 +182,7 @@ SHAKE stats (type/ave/delta/count) on step 7000
182182
7800 506 0.33789026 -6.7119188 -6.5817042 -0.85601439
183183
7900 508 0.33379862 -6.7206374 -6.5908633 -0.77567302
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SHAKE stats (type/ave/delta/count) on step 8000
185-
1 1.00000 2.77556e-15 160
185+
1 2.00000 2.77556e-15 80
186186
8000 510 0.34836822 -6.736194 -6.599579 -0.75308642
187187
8100 512 0.30010433 -6.7179554 -6.5992618 -0.72267718
188188
8200 514 0.30103286 -6.7176407 -6.597579 -0.87147822
@@ -194,7 +194,7 @@ SHAKE stats (type/ave/delta/count) on step 8000
194194
8800 526 0.31711574 -6.7093952 -6.5767612 -0.88669301
195195
8900 528 0.33837114 -6.7240254 -6.5814353 -0.83265273
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SHAKE stats (type/ave/delta/count) on step 9000
197-
1 1.00000 2.77556e-15 180
197+
1 2.00000 2.77556e-15 90
198198
9000 530 0.3534816 -6.7238895 -6.5738266 -0.89540183
199199
9100 532 0.3776498 -6.7415309 -6.5800359 -0.78471662
200200
9200 534 0.36008303 -6.7387766 -6.5836846 -0.76983869
@@ -206,23 +206,23 @@ SHAKE stats (type/ave/delta/count) on step 9000
206206
9800 546 0.32822212 -6.7713848 -6.6241057 -0.77810668
207207
9900 548 0.30086363 -6.7699646 -6.6340818 -0.80821877
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SHAKE stats (type/ave/delta/count) on step 10000
209-
1 1.00000 3.21965e-15 200
209+
1 2.00000 3.21965e-15 100
210210
10000 550 0.33257615 -6.7805271 -6.6293562 -0.92925003
211-
Loop time of 2.77687 on 8 procs for 10000 steps with 550 atoms
211+
Loop time of 4.00919 on 8 procs for 10000 steps with 550 atoms
212212

213-
Performance: 1555705.730 tau/day, 3601.171 timesteps/s
214-
74.9% CPU use with 8 MPI tasks x no OpenMP threads
213+
Performance: 1077523.081 tau/day, 2494.266 timesteps/s
214+
94.3% CPU use with 8 MPI tasks x no OpenMP threads
215215

216216
MPI task timing breakdown:
217217
Section | min time | avg time | max time |%varavg| %total
218218
---------------------------------------------------------------
219-
Pair | 0.00081199 | 0.42944 | 1.0541 | 68.2 | 15.46
220-
Bond | 0.0008288 | 0.0027576 | 0.0070681 | 4.3 | 0.10
221-
Neigh | 0.0022112 | 0.18224 | 0.49431 | 46.3 | 6.56
222-
Comm | 0.68195 | 1.5257 | 2.0724 | 45.8 | 54.94
223-
Output | 0.0034165 | 0.0041669 | 0.0050298 | 1.0 | 0.15
224-
Modify | 0.39408 | 0.50206 | 0.58473 | 9.7 | 18.08
225-
Other | | 0.1305 | | | 4.70
219+
Pair | 0.0019728 | 0.54065 | 1.4471 | 81.1 | 13.49
220+
Bond | 0.00085392 | 0.002565 | 0.0063665 | 4.3 | 0.06
221+
Neigh | 0.0042083 | 0.25821 | 0.75124 | 59.5 | 6.44
222+
Comm | 1.0501 | 2.2797 | 2.9807 | 50.8 | 56.86
223+
Output | 0.0040943 | 0.0050436 | 0.0064785 | 1.3 | 0.13
224+
Modify | 0.56501 | 0.74509 | 0.88271 | 13.8 | 18.58
225+
Other | | 0.1779 | | | 4.44
226226

227227
Nlocal: 68.7500 ave 152 max 0 min
228228
Histogram: 4 0 0 0 0 0 0 2 0 2
@@ -236,4 +236,4 @@ Ave neighs/atom = 66.687273
236236
Ave special neighs/atom = 0.36363636
237237
Neighbor list builds = 837
238238
Dangerous builds = 0
239-
Total wall time: 0:00:02
239+
Total wall time: 0:00:04

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