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make fix rhok examples more consistent with LAMMPS conventions:

Browse Source 
- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
This commit is contained in:
Axel Kohlmeyer
2017-10-03 10:08:38 -04:00
parent 5f527091b8
commit f07719e924
10 changed files with 1040 additions and 9 deletions
Download Patch File Download Diff File Expand all files Collapse all files

0
examples/USER/pinning/readme.md → examples/USER/misc/pinning/README.md
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7
examples/USER/pinning/in.crystal → examples/USER/misc/pinning/in.crystal
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@ -29,7 +29,8 @@ fix bias all rhok 16 0 0 0.0 0.0
# output
thermo 50
thermo_style custom step temp press density f_bias[3]
dump dumpXYZ all xyz 2000 traj.xyz
# dump dumpXYZ all xyz 2000 traj.xyz
# run
run 100000
# NOTE: this is cut short to 5000 steps for demonstration purposes
# run 100000
run 5000

7
examples/USER/pinning/in.pinning → examples/USER/misc/pinning/in.pinning
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@ -26,7 +26,8 @@ fix bias all rhok 16 0 0 4.0 26.00
# output U_bias rho_k_RE rho_k_IM |rho_k|
thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
thermo 50
dump dumpXYZ all xyz 500 traj.xyz
# dump dumpXYZ all xyz 500 traj.xyz
# run
run 50000
# NOTE: run reduced for demonstration purposes
# run 50000
run 5000

7
examples/USER/pinning/in.setup → examples/USER/misc/pinning/in.setup
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@ -33,8 +33,9 @@ fix langevin left langevin 3.0 0.8 100.0 2017
# outout
thermo_style custom step temp pzz pe lz
thermo 100
dump dumpXYZ all xyz 100 traj.xyz
# dump dumpXYZ all xyz 100 traj.xyz
# run
run 10000
# run reduced for demonstration purposes
# run 10000
run 5000
write_data data.halfhalf

187
examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1 Normal file
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@ -0,0 +1,187 @@
LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
lattice fcc 0.9731
Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
region my_box block 0 8.0 0 8.0 0 20.0
create_box 1 my_box
Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
1 by 1 by 1 MPI processor grid
region particles block 0 8.0 0 8.0 0 20.0
create_atoms 1 region particles
Created 5120 atoms
pair_coeff 1 1 1.0 1.0 2.5
pair_modify tail no
pair_modify shift yes
mass 1 1.0
velocity all create 1.6 1 mom yes rot yes
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
# computing long-range order (no bias is added since k=0)
fix bias all rhok 16 0 0 0.0 0.0
# output
thermo 50
thermo_style custom step temp press density f_bias[3]
# dump dumpXYZ all xyz 2000 traj.xyz
# NOTE: this is cut short to 5000 steps for demonstration purposes
# run 100000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.523 | 4.523 | 4.523 Mbytes
Step Temp Press Density f_bias[3]
0 1.6 -2.7568106 0.9731 71.554175
50 0.78457786 3.1029192 0.97362639 54.327705
100 0.85528971 2.4670259 0.97213457 55.189308
150 0.85241818 2.3210306 0.9698027 56.138125
200 0.82301385 2.3448692 0.96708227 55.735326
250 0.83076383 2.0890816 0.96425763 55.320625
300 0.81602823 2.0118796 0.96173925 54.095736
350 0.81084006 1.9122192 0.95979392 54.526429
400 0.80776593 1.8502174 0.95869117 54.434901
450 0.80694697 1.8435873 0.95851085 53.20809
500 0.81384248 1.8111331 0.95917305 53.419395
550 0.81027072 1.9222272 0.96056019 54.36723
600 0.81199582 2.0291945 0.96248486 54.888582
650 0.82507964 2.0706462 0.96467227 55.807137
700 0.832562 2.1471442 0.9668913 56.721267
750 0.83358138 2.2674672 0.968984 56.723838
800 0.83477542 2.3658275 0.97072603 56.234689
850 0.84722921 2.3506233 0.97189674 56.262424
900 0.83526965 2.4532068 0.97248856 56.219103
950 0.83174583 2.4763958 0.97249527 56.409813
1000 0.83022557 2.4334341 0.97194093 55.890858
1050 0.83208978 2.3478416 0.97092452 54.934691
1100 0.82789545 2.272404 0.9696152 54.90894
1150 0.82678617 2.1798046 0.96819776 54.927782
1200 0.8088841 2.1960256 0.96687735 54.914327
1250 0.81512784 2.0736261 0.96579008 53.927291
1300 0.81271067 2.0297138 0.96504188 54.289698
1350 0.8201767 1.9493976 0.96464115 55.342131
1400 0.80880489 2.0016987 0.96468463 55.757758
1450 0.8114196 2.0282699 0.96514115 55.865676
1500 0.81085664 2.0838361 0.96591869 56.553425
1550 0.81257075 2.1283157 0.96694549 56.921544
1600 0.82617645 2.1017986 0.96817075 56.858808
1650 0.82616141 2.1885582 0.96941073 56.717917
1700 0.81634174 2.2996967 0.97047447 56.453745
1750 0.82447573 2.2924266 0.97128663 56.916813
1800 0.83610432 2.236456 0.97178453 56.400752
1850 0.82479203 2.3103493 0.97197318 55.891368
1900 0.82298992 2.3059289 0.97181084 55.680563
1950 0.82098556 2.2801003 0.97138609 55.754406
2000 0.8181203 2.2480175 0.97078591 55.801363
2050 0.82822293 2.1208884 0.97004107 55.687
2100 0.7976818 2.2711199 0.96930169 55.459844
2150 0.81817848 2.0680351 0.96860201 56.514731
2200 0.80707457 2.1112141 0.96810519 55.504308
2250 0.81651111 2.0077603 0.96781161 55.635702
2300 0.80634534 2.0662241 0.96777177 56.051086
2350 0.80892831 2.0619333 0.96799037 56.548711
2400 0.82454203 1.9585394 0.9684672 56.695235
2450 0.81517178 2.075283 0.96921622 56.613082
2500 0.80969595 2.1624581 0.97010528 56.57516
2550 0.80862964 2.2088622 0.97100774 57.072594
2600 0.81468816 2.2293973 0.97192868 56.879212
2650 0.82063107 2.2244887 0.97269715 55.454502
2700 0.81691618 2.2789954 0.97319841 54.421943
2750 0.8141787 2.2981247 0.97340453 54.469921
2800 0.81973871 2.2422136 0.9733278 55.959235
2850 0.82037399 2.201016 0.97302727 56.685826
2900 0.80650164 2.2672955 0.9726128 56.574395
2950 0.81752783 2.1317541 0.97207545 56.809412
3000 0.80836945 2.1461483 0.97151192 57.205206
3050 0.80785109 2.1189056 0.97103049 57.418763
3100 0.79835058 2.146416 0.97069705 57.329383
3150 0.79792089 2.1388267 0.97051679 57.279852
3200 0.79934603 2.1049562 0.97046851 56.351494
3250 0.79523232 2.1549779 0.97063956 56.00356
3300 0.8004458 2.1145975 0.97096375 55.725509
3350 0.79772742 2.166292 0.97143785 55.558075
3400 0.80621087 2.1309217 0.97198456 55.816704
3450 0.80540626 2.1727557 0.97263267 55.671283
3500 0.80867606 2.1905129 0.97321538 55.390086
3550 0.80917896 2.2144872 0.97370472 55.742085
3600 0.80930722 2.2288938 0.974093 56.23064
3650 0.80390523 2.2777327 0.97431886 56.084731
3700 0.79620093 2.3143541 0.97435103 55.942797
3750 0.80252393 2.2564638 0.9741875 56.042055
3800 0.78981264 2.3156481 0.9739121 55.971352
3850 0.80391951 2.1804938 0.97351088 55.855858
3900 0.81268129 2.0855818 0.97308521 56.288315
3950 0.7958182 2.175259 0.97273088 56.140141
4000 0.80054484 2.1163279 0.97243129 56.366818
4050 0.79760187 2.105362 0.97225308 56.684619
4100 0.79283424 2.1357603 0.972206 56.203341
4150 0.79543088 2.1036951 0.97227608 56.606315
4200 0.79410999 2.1402049 0.97253758 56.277478
4250 0.7985469 2.1285154 0.97293622 56.356076
4300 0.79700387 2.1470614 0.97337091 56.722298
4350 0.80479321 2.1403244 0.97384674 57.212574
4400 0.79505512 2.224463 0.97434415 56.561877
4450 0.78346648 2.3347865 0.97478611 56.681362
4500 0.79811284 2.259123 0.97510069 57.365929
4550 0.80015561 2.2345254 0.97523653 57.34799
4600 0.79648318 2.2651869 0.97525975 57.502318
4650 0.80524865 2.1943025 0.97507638 57.702488
4700 0.80397778 2.1758629 0.97478268 57.162107
4750 0.78914913 2.2470191 0.9744625 56.849565
4800 0.79324889 2.2028993 0.97408817 57.572344
4850 0.78993209 2.181763 0.97373372 57.683552
4900 0.79041263 2.1604768 0.97348692 56.922312
4950 0.79741332 2.1105901 0.97332545 57.488932
5000 0.7891178 2.163416 0.97328963 57.365252
Loop time of 33.6467 on 1 procs for 5000 steps with 5120 atoms
Performance: 51357.258 tau/day, 148.603 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 | 24.699 | 24.699 | 24.699 | 0.0 | 73.41
Neigh | 2.8894 | 2.8894 | 2.8894 | 0.0 | 8.59
Comm | 0.34907 | 0.34907 | 0.34907 | 0.0 | 1.04
Output | 0.0056 | 0.0056 | 0.0056 | 0.0 | 0.02
Modify | 5.5718 | 5.5718 | 5.5718 | 0.0 | 16.56
Other | | 0.1319 | | | 0.39
Nlocal: 5120 ave 5120 max 5120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7594 ave 7594 max 7594 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 323081 ave 323081 max 323081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 323081
Ave neighs/atom = 63.1018
Neighbor list builds = 248
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:33

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examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4 Normal file
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@ -0,0 +1,187 @@
LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
lattice fcc 0.9731
Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
region my_box block 0 8.0 0 8.0 0 20.0
create_box 1 my_box
Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
1 by 1 by 4 MPI processor grid
region particles block 0 8.0 0 8.0 0 20.0
create_atoms 1 region particles
Created 5120 atoms
pair_coeff 1 1 1.0 1.0 2.5
pair_modify tail no
pair_modify shift yes
mass 1 1.0
velocity all create 1.6 1 mom yes rot yes
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
# computing long-range order (no bias is added since k=0)
fix bias all rhok 16 0 0 0.0 0.0
# output
thermo 50
thermo_style custom step temp press density f_bias[3]
# dump dumpXYZ all xyz 2000 traj.xyz
# NOTE: this is cut short to 5000 steps for demonstration purposes
# run 100000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.23 | 3.23 | 3.23 Mbytes
Step Temp Press Density f_bias[3]
0 1.6 -2.7568106 0.9731 71.554175
50 0.78457786 3.1029192 0.97362639 54.327705
100 0.85528971 2.4670259 0.97213457 55.189308
150 0.85241818 2.3210306 0.9698027 56.138125
200 0.82301385 2.3448692 0.96708227 55.735326
250 0.83076383 2.0890816 0.96425763 55.320625
300 0.81602823 2.0118796 0.96173925 54.095736
350 0.81084006 1.9122192 0.95979392 54.526429
400 0.80776593 1.8502174 0.95869117 54.434901
450 0.80694697 1.8435873 0.95851085 53.20809
500 0.81384248 1.8111331 0.95917305 53.419395
550 0.81027072 1.9222272 0.96056019 54.36723
600 0.81199582 2.0291945 0.96248486 54.888582
650 0.82507964 2.0706462 0.96467227 55.807137
700 0.832562 2.1471442 0.9668913 56.721267
750 0.83358138 2.2674672 0.968984 56.723838
800 0.83477542 2.3658275 0.97072603 56.234689
850 0.84722921 2.3506233 0.97189674 56.262424
900 0.83526965 2.4532068 0.97248856 56.219103
950 0.83174583 2.4763958 0.97249527 56.409813
1000 0.83022557 2.4334341 0.97194093 55.890858
1050 0.83208978 2.3478416 0.97092452 54.934691
1100 0.82789545 2.272404 0.9696152 54.90894
1150 0.82678617 2.1798046 0.96819776 54.927782
1200 0.8088841 2.1960256 0.96687735 54.914327
1250 0.81512784 2.0736261 0.96579008 53.927291
1300 0.81271067 2.0297138 0.96504188 54.289698
1350 0.8201767 1.9493976 0.96464115 55.342131
1400 0.80880489 2.0016987 0.96468463 55.757758
1450 0.8114196 2.0282699 0.96514115 55.865676
1500 0.81085664 2.0838361 0.96591869 56.553425
1550 0.81257075 2.1283157 0.96694549 56.921544
1600 0.82617645 2.1017986 0.96817075 56.858808
1650 0.82616141 2.1885582 0.96941073 56.717917
1700 0.81634174 2.2996967 0.97047447 56.453745
1750 0.82447573 2.2924266 0.97128663 56.916813
1800 0.83610432 2.236456 0.97178453 56.400752
1850 0.824792 2.3103491 0.97197318 55.891368
1900 0.82298989 2.3059287 0.97181084 55.680562
1950 0.82098545 2.2801009 0.97138609 55.754404
2000 0.81812031 2.2480166 0.97078591 55.801371
2050 0.82822262 2.1208887 0.97004108 55.687001
2100 0.79768162 2.2711186 0.9693017 55.459852
2150 0.81817874 2.0680317 0.96860202 56.514744
2200 0.80707412 2.1112032 0.96810521 55.504308
2250 0.81650921 2.0077757 0.96781164 55.635717
2300 0.80634656 2.066186 0.96777181 56.051088
2350 0.80893174 2.0619084 0.96799042 56.548711
2400 0.82453783 1.9585503 0.96846727 56.695111
2450 0.81517275 2.0752617 0.96921631 56.614046
2500 0.80969622 2.1624476 0.9701054 56.574846
2550 0.80861922 2.2089505 0.97100787 57.072334
2600 0.81468888 2.2293754 0.97192875 56.879416
2650 0.82061239 2.2245462 0.97269723 55.442015
2700 0.81687473 2.2792015 0.97319852 54.420301
2750 0.81416567 2.2982988 0.97340467 54.469427
2800 0.81978563 2.2418723 0.97332803 55.965451
2850 0.82069759 2.1988948 0.97302752 56.686807
2900 0.80631184 2.2684466 0.97261407 56.585682
2950 0.81759744 2.1312328 0.97207888 56.812431
3000 0.80748056 2.152676 0.97151807 57.178849
3050 0.80789237 2.118162 0.97103728 57.433724
3100 0.79882523 2.1414744 0.97070338 57.34686
3150 0.79803949 2.1359043 0.97052875 57.382544
3200 0.79170386 2.1548392 0.97049349 56.465806
3250 0.78848813 2.1990144 0.97067557 55.929088
3300 0.79820555 2.1304609 0.97101444 55.624487
3350 0.79250565 2.1971235 0.97149233 55.933615
3400 0.80584844 2.1417239 0.97206083 55.85922
3450 0.80685744 2.1640501 0.97266047 55.135963
3500 0.80751888 2.1858277 0.97318703 55.407581
3550 0.79882754 2.2796452 0.97363149 55.392366
3600 0.80219171 2.2715765 0.97392571 55.867887
3650 0.79061794 2.3492866 0.97410985 56.0192
3700 0.8058483 2.2327904 0.97411924 56.491303
3750 0.79460746 2.2941868 0.97397764 55.929912
3800 0.80447478 2.2018009 0.97367627 55.663208
3850 0.80355335 2.17638 0.97333164 55.637261
3900 0.80388417 2.1531434 0.9729647 56.03794
3950 0.79557409 2.1853318 0.9726503 56.132348
4000 0.79547396 2.1457051 0.97235244 55.552675
4050 0.8058384 2.0637678 0.97213346 56.185416
4100 0.7976931 2.1028246 0.97208255 56.050347
4150 0.79555522 2.115473 0.97216375 56.868136
4200 0.79324134 2.1510383 0.97246129 56.462635
4250 0.80788167 2.0534887 0.97287821 55.650788
4300 0.79389865 2.2019815 0.97337765 55.596846
4350 0.79786309 2.1851119 0.97389825 57.000921
4400 0.79986518 2.1997541 0.97443778 57.551564
4450 0.8063901 2.1893874 0.97493151 57.236138
4500 0.80005802 2.250364 0.97533075 57.341358
4550 0.79707443 2.2995576 0.97557554 57.338713
4600 0.79869949 2.2807889 0.97563277 57.084504
4650 0.79694427 2.2673215 0.97544638 57.025663
4700 0.79023986 2.2884131 0.97511483 57.131188
4750 0.79566823 2.2215519 0.97464304 57.045676
4800 0.78936986 2.2268037 0.97410626 57.384178
4850 0.79025913 2.1836718 0.973616 57.78438
4900 0.80138424 2.0657609 0.9732124 57.888266
4950 0.77853735 2.207944 0.97296347 57.312213
5000 0.79115984 2.1035893 0.97285578 57.109472
Loop time of 9.53489 on 4 procs for 5000 steps with 5120 atoms
Performance: 181229.223 tau/day, 524.390 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.312 | 6.4238 | 6.5139 | 3.1 | 67.37
Neigh | 0.72062 | 0.73538 | 0.74531 | 1.1 | 7.71
Comm | 0.52697 | 0.64152 | 0.78688 | 14.1 | 6.73
Output | 0.0028393 | 0.0029888 | 0.0033851 | 0.4 | 0.03
Modify | 1.6249 | 1.669 | 1.7253 | 2.9 | 17.50
Other | | 0.06221 | | | 0.65
Nlocal: 1280 ave 1289 max 1266 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 3346.25 ave 3379 max 3331 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 80701.8 ave 81534 max 79755 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 322807
Ave neighs/atom = 63.0482
Neighbor list builds = 248
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

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LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.halfhalf
orthogonal box = (0 0 0) to (12.8152 12.8152 34)
1 by 1 by 1 MPI processor grid
reading atoms ...
5120 atoms
reading velocities ...
5120 velocities
pair_coeff 1 1 1.0 1.0 2.5
mass 1 1.0
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
velocity all create 0.8 1 mom yes rot yes
fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
fix 100 all momentum 100 linear 1 1 1
# harmonic rho_k bias-field
# nx ny nz k a
fix bias all rhok 16 0 0 4.0 26.00
# output U_bias rho_k_RE rho_k_IM |rho_k|
thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
thermo 50
dump dumpXYZ all xyz 500 traj.xyz
# NOTE: run reduced for demonstration purposes
# run 50000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 5.723 | 5.723 | 5.723 Mbytes
Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
0 0.8 5.1566801 -4.8556711 34 179.52419 35.473155 -0.2832763 35.474286
50 1.072533 3.8158392 -5.2704532 34.024206 0.010596224 25.927135 -0.063106738 25.927212
100 1.1093231 3.6703116 -5.3380965 34.094814 1.8552612 26.958236 -0.51403326 26.963136
150 1.1080721 3.8202601 -5.3568368 34.207473 0.39188605 26.420755 -1.0759575 26.442655
200 1.1435287 3.3445987 -5.4365298 34.354119 3.0758718 27.239465 -0.19115251 27.240135
250 1.1203046 3.4669456 -5.4293867 34.511473 0.8543814 26.652785 -0.20818214 26.653598
300 1.1012709 3.4583154 -5.4281803 34.664509 2.4837156 27.097674 0.9518628 27.114387
350 1.0439632 3.8953869 -5.368619 34.810399 0.55385719 26.518391 0.64525272 26.52624
400 1.0083878 4.0523864 -5.3418278 34.957669 0.34806057 26.404011 0.83368604 26.417169
450 0.9675244 4.310087 -5.3089468 35.114208 0.7921285 26.607512 1.077889 26.629336
500 0.94605476 4.1050097 -5.3062273 35.284018 0.87757754 26.639125 1.1140858 26.662411
550 0.92662323 3.9299063 -5.3062927 35.458565 1.3746441 26.773494 1.7256603 26.829049
600 0.89723165 3.7683555 -5.289725 35.629881 0.46692943 26.372973 2.4135502 26.483182
650 0.90612566 3.1098837 -5.3267851 35.788537 0.032662126 25.918784 3.2982102 26.127793
700 0.9152508 2.6527976 -5.3597799 35.923343 0.014621588 25.834591 3.6093492 26.085503
750 0.90156356 2.3474851 -5.3545938 36.031813 0.75225637 26.307204 4.0247215 26.613293
800 0.89748513 1.9825103 -5.3610202 36.113888 0.33402511 26.261326 2.7858039 26.408672
850 0.89496343 1.8906342 -5.3673514 36.169424 0.85431557 26.534648 2.5150347 26.653573
900 0.89463983 1.5654217 -5.3753283 36.20181 1.5689239 26.764737 2.5474794 26.885699
950 0.88663832 1.4399476 -5.3703322 36.209971 0.044436903 25.818418 1.2963356 25.850941
1000 0.87407208 1.485718 -5.3572665 36.195386 1.4405611 26.828072 1.0520795 26.848693
1050 0.87580489 1.163155 -5.3647269 36.160279 0.15319559 26.234791 1.4845964 26.276763
1100 0.86978111 1.3743181 -5.3594907 36.104958 1.1313537 25.19895 1.5711793 25.247885
1150 0.86987861 1.3212927 -5.3628503 36.035486 0.039865678 25.841762 0.93898962 25.858816
1200 0.87142486 1.3293818 -5.3676854 35.954411 0.16827389 25.70952 -0.14639427 25.709936
1250 0.87582265 1.3203803 -5.3764058 35.86575 0.25946652 25.639682 0.082696867 25.639815
1300 0.87371627 1.4680294 -5.375151 35.772824 0.17697069 25.701417 0.2397926 25.702535
1350 0.88617453 1.5923057 -5.3954912 35.681046 0.00049155526 25.973634 -0.74521794 25.984323
1400 0.87809636 1.5821707 -5.3850722 35.594706 0.024050814 26.107395 -0.34393685 26.10966
1450 0.87912192 1.7820174 -5.3885842 35.514722 0.20999914 25.667238 -0.66933655 25.675964
1500 0.88293618 2.0295275 -5.3963602 35.443445 0.60232374 25.376395 -1.9501461 25.451218
1550 0.90012542 1.9476472 -5.4249456 35.382791 0.4488038 26.448928 -1.1452474 26.473711
1600 0.89155063 2.2462603 -5.4153432 35.332095 0.039621687 26.138157 -0.36825239 26.140751
1650 0.8942624 2.343747 -5.4233433 35.294954 0.0089980332 26.064277 0.38189192 26.067075
1700 0.90047841 2.451289 -5.4376312 35.27234 0.86985171 26.646438 0.83408084 26.659489
1750 0.87586052 2.6381221 -5.4067182 35.264564 6.346204 27.652722 2.6699692 27.78132
1800 0.87392582 2.6338176 -5.4109056 35.270073 0.046414129 26.016188 2.6651053 26.152339
1850 0.86540415 2.5434301 -5.4058587 35.285902 0.054615472 26.074279 2.1799787 26.165251
1900 0.87043082 2.5776772 -5.4216997 35.309062 0.68978148 26.38648 3.2614091 26.587274
1950 0.86281992 2.3107762 -5.4188978 35.338501 0.0072672577 25.736893 3.2375012 25.93972
2000 0.85905576 2.2894047 -5.4215995 35.36787 0.095633435 26.072085 2.7685848 26.21867
2050 0.85793751 2.2382039 -5.4279351 35.395213 0.13602344 25.598457 2.6881027 25.739209
2100 0.85585253 2.0765811 -5.4324511 35.418877 0.0059888115 25.754128 3.1436222 25.945279
2150 0.86701057 1.8449875 -5.4562208 35.436124 0.097328618 25.413697 4.3268293 25.7794
2200 0.85168154 1.9024923 -5.4395776 35.44246 0.20764576 25.094788 5.4406104 25.677784
2250 0.8429719 1.870335 -5.4320586 35.438363 0.34419961 24.998478 5.4475709 25.585151
2300 0.84176891 1.7100228 -5.4351472 35.422863 0.76036958 24.697018 5.8629967 25.383409
2350 0.84601588 1.8539039 -5.4456629 35.395979 0.38437531 25.647986 6.4163366 26.438392
2400 0.84637647 1.6299091 -5.4498948 35.36125 0.074236719 24.995872 7.8269968 26.192661
2450 0.85650449 1.6828907 -5.4683101 35.316669 0.3671827 25.280669 7.7040329 26.428476
2500 0.84963707 1.7305222 -5.4605394 35.265508 0.1406965 25.236741 7.2780025 26.265232
2550 0.84084365 1.8758368 -5.4497083 35.208725 0.33937687 24.544376 7.2334512 25.588067
2600 0.85317342 1.7781674 -5.4702734 35.149747 0.60378248 24.046307 8.3370138 25.450554
2650 0.85487644 2.0065374 -5.4747643 35.090431 0.22483651 24.937101 8.4669004 26.335288
2700 0.84550083 1.9363031 -5.4628401 35.034349 0.43442577 24.250196 7.9943738 25.533939
2750 0.85843419 2.0473138 -5.484528 34.980671 0.45959294 24.17438 8.179356 25.520629
2800 0.86047607 2.0754522 -5.4899966 34.932466 0.00038123477 24.619856 8.3153434 25.986194
2850 0.86375793 2.2751324 -5.4977459 34.892337 0.0016455263 24.927259 7.289789 25.971316
2900 0.84438986 2.3790377 -5.4721407 34.863512 1.2372354 25.819445 7.132603 26.786523
2950 0.8551438 2.2721926 -5.4925958 34.84473 1.5405388 25.956466 6.976385 26.87765
3000 0.83737707 2.4009609 -5.4707188 34.834171 0.28507766 25.643879 6.1778846 26.377543
3050 0.84923235 2.4187994 -5.4938573 34.830836 0.036512025 25.139252 7.1457857 26.135115
3100 0.83872396 2.3811576 -5.4838787 34.833673 0.246984 24.21358 8.4588719 25.648586
3150 0.83957817 2.3901421 -5.4913118 34.84163 0.20477984 24.309852 10.088243 26.319984
3200 0.84283033 2.17292 -5.5025459 34.853975 1.3367154 24.581685 10.72011 26.817531
3250 0.84002379 2.1247709 -5.5044955 34.866106 0.11434509 24.463842 9.4874246 26.239108
3300 0.83311101 2.1492058 -5.5000847 34.875625 0.0053284993 23.815298 10.560222 26.051616
3350 0.83216701 1.9587594 -5.5043446 34.881623 0.58985562 23.934253 11.475462 26.543073
3400 0.82396039 2.1914951 -5.4971506 34.881199 0.098206955 23.393402 10.82936 25.778407
3450 0.83483253 1.9783612 -5.5182844 34.877327 7.6571212e-05 23.675355 10.761012 26.006188
3500 0.82712062 1.9718522 -5.5111818 34.869214 0.014836125 23.314122 11.312845 25.913872
3550 0.8342927 1.9114357 -5.5259968 34.855179 1.4050442 22.442758 11.377192 25.161834
3600 0.82631637 1.9836457 -5.5176244 34.835738 0.084637609 23.413286 10.824194 25.794285
3650 0.82425697 1.9218541 -5.5178548 34.811901 0.11000071 22.788707 12.022258 25.765478
3700 0.82491437 1.9624493 -5.521738 34.782417 0.034984027 23.011433 12.384217 26.132257
3750 0.82758167 2.0856442 -5.5283493 34.748872 0.001362163 23.030662 12.122144 26.026098
3800 0.81891108 1.9858824 -5.5177774 34.714618 0.17075993 23.21344 12.345683 26.292199
3850 0.83392227 2.1631514 -5.5426333 34.681146 0.82106473 22.510204 11.678329 25.359272
3900 0.82230654 2.0017132 -5.5276756 34.650221 0.48735732 23.444809 12.339117 26.493638
3950 0.81929288 2.1749936 -5.5256673 34.61976 0.089219805 23.540062 11.527925 26.211211
4000 0.83415169 2.0446791 -5.5506187 34.591266 0.15593937 23.742282 11.26508 26.279231
4050 0.82362522 2.1998083 -5.5375157 34.563164 0.25405351 23.913834 11.081011 26.356408
4100 0.82589505 2.3074345 -5.543718 34.537763 0.080213125 24.03253 10.435108 26.200266
4150 0.83855297 2.2424199 -5.5658171 34.517758 0.62913338 23.974257 8.5079223 25.439138
4200 0.82522111 2.2622619 -5.5493275 34.502472 1.8756517 25.754617 7.9996898 26.968414
4250 0.82083124 2.4135193 -5.5464932 34.4919 1.1217436 25.8944 6.7070444 26.748914
4300 0.83059704 2.1375109 -5.5653245 34.487366 0.53623038 26.05979 4.9072346 26.517798
4350 0.82755047 2.1159821 -5.5650889 34.484506 0.10017723 25.405936 4.3532342 25.776195
4400 0.83192877 2.180851 -5.5759565 34.480909 0.053664012 25.993034 2.9844338 26.163805
4450 0.81860572 2.2333381 -5.5602138 34.477183 0.037864077 25.792233 1.9038859 25.862406
4500 0.82821762 2.1142023 -5.5788682 34.474784 0.088221344 26.20329 0.59417897 26.210025
4550 0.8205154 2.0896984 -5.5715531 34.472405 0.016076192 26.083166 -0.58187024 26.089655
4600 0.81294948 2.2274108 -5.5642678 34.469014 0.033774986 25.869616 0.14951307 25.870048
4650 0.80890532 2.1556346 -5.5622407 34.465277 0.67402048 25.413229 -0.56341819 25.419474
4700 0.82070227 1.9852605 -5.583747 34.460206 0.052623237 26.158394 -0.44673492 26.162209
4750 0.81451857 2.1097726 -5.5779782 34.451438 0.12221733 25.733718 -0.9911436 25.752798
4800 0.81300453 2.0211325 -5.5790076 34.439504 0.34536082 26.358606 -1.7335167 26.415548
4850 0.82035497 1.9489595 -5.5929886 34.424097 0.70899626 26.575865 -1.0191012 26.595397
4900 0.8127066 2.1312269 -5.584271 34.405998 0.087959314 26.185217 -1.1329105 26.209713
4950 0.81252621 2.1094866 -5.5866296 34.387869 0.79067667 26.564722 -1.8456354 26.628759
5000 0.80575936 2.1875995 -5.579054 34.370679 0.031787364 26.027557 -2.2666774 26.12607
Loop time of 32.2397 on 1 procs for 5000 steps with 5120 atoms
Performance: 53598.557 tau/day, 155.088 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.967 | 22.967 | 22.967 | 0.0 | 71.24
Neigh | 2.9914 | 2.9914 | 2.9914 | 0.0 | 9.28
Comm | 0.37485 | 0.37485 | 0.37485 | 0.0 | 1.16
Output | 0.064337 | 0.064337 | 0.064337 | 0.0 | 0.20
Modify | 5.7143 | 5.7143 | 5.7143 | 0.0 | 17.72
Other | | 0.1281 | | | 0.40
Nlocal: 5120 ave 5120 max 5120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7962 ave 7962 max 7962 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 296101 ave 296101 max 296101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 296101
Ave neighs/atom = 57.8322
Neighbor list builds = 283
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:32

186
examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4 Normal file
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LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.halfhalf
orthogonal box = (0 0 0) to (12.8152 12.8152 34)
1 by 1 by 4 MPI processor grid
reading atoms ...
5120 atoms
reading velocities ...
5120 velocities
pair_coeff 1 1 1.0 1.0 2.5
mass 1 1.0
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
velocity all create 0.8 1 mom yes rot yes
fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
fix 100 all momentum 100 linear 1 1 1
# harmonic rho_k bias-field
# nx ny nz k a
fix bias all rhok 16 0 0 4.0 26.00
# output U_bias rho_k_RE rho_k_IM |rho_k|
thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
thermo 50
dump dumpXYZ all xyz 500 traj.xyz
# NOTE: run reduced for demonstration purposes
# run 50000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.023 | 4.027 | 4.03 Mbytes
Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
0 0.8 5.1872229 -4.8361269 34 152.02869 34.711006 -0.72709593 34.71862
50 1.0819371 3.9250728 -5.2655842 34.02563 0.51385908 26.505979 0.2187864 26.506882
100 1.1182271 3.5397251 -5.3331401 34.100753 2.1059904 27.025883 -0.12127124 27.026156
150 1.1121434 3.7845571 -5.3440494 34.213993 1.7206575 26.894862 -1.3261751 26.927539
200 1.1446439 3.4114364 -5.4199119 34.358914 2.383615 27.054401 -1.4211151 27.091699
250 1.1115073 3.5603047 -5.3988013 34.517397 0.60819391 26.51404 -1.4089688 26.55145
300 1.0828478 3.7411116 -5.3842818 34.673948 0.73987465 26.528178 -2.062382 26.608225
350 1.0342597 3.9206217 -5.3384367 34.825105 0.99965014 26.657737 -1.6211152 26.706983
400 1.0064356 3.9929044 -5.324003 34.97579 0.41927007 26.402623 -1.7087432 26.457859
450 0.96799277 4.2764255 -5.2947175 35.133839 0.77739461 26.503753 -2.5217998 26.623456
500 0.94691076 4.1007962 -5.2922124 35.301893 0.17015805 26.212252 -2.0421698 26.291683
550 0.93675297 3.7404088 -5.3056917 35.474301 0.56247039 26.335926 -3.205722 26.530316
600 0.92707577 3.5439822 -5.3176094 35.641282 0.04054693 25.679461 -3.0301039 25.857615
650 0.91828226 3.1833648 -5.3278237 35.794766 0.8427054 26.4003 -3.6331211 26.649117
700 0.9084826 2.8374306 -5.3327944 35.928138 1.5635222 26.605971 -3.8575939 26.884173
750 0.91219559 2.46172 -5.3548299 36.039156 6.3772911 27.350725 -4.8971146 27.785678
800 0.90000337 2.2187716 -5.3499181 36.126451 4.9080838 27.085156 -5.1291678 27.566538
850 0.9003432 1.8634244 -5.3614648 36.189019 0.0081092188 25.497333 -5.4038153 26.063676
900 0.89741573 1.5697398 -5.3660799 36.226074 0.011155479 25.312724 -6.2574069 26.074684
950 0.88871454 1.4427205 -5.3604669 36.237407 0.3287078 25.659237 -6.232896 26.405406
1000 0.88606353 1.3088636 -5.3626576 36.226015 0.30068168 24.554896 -7.2832017 25.612262
1050 0.88527541 1.3194263 -5.3666773 36.19311 0.10646314 24.514921 -7.9419424 25.76928
1100 0.87522001 1.2852124 -5.3556811 36.143056 0.13675329 24.865981 -8.446822 26.261489
1150 0.8805978 1.246973 -5.3671716 36.0781 0.00043275463 24.187039 -9.4985495 25.98529
1200 0.85711495 1.376588 -5.3346243 36.002427 0.47623639 23.691349 -9.4648541 25.512026
1250 0.88116805 1.3562001 -5.3731036 35.919289 0.32797055 23.322103 -10.54448 25.595049
1300 0.87178482 1.5046564 -5.3610798 35.831278 0.17704849 24.190231 -10.314689 26.29753
1350 0.87022621 1.6830825 -5.3603618 35.743318 0.0052854997 23.731157 -10.747465 26.051408
1400 0.89019669 1.6144812 -5.3921986 35.659687 1.4152796 22.8393 -10.551347 25.158787
1450 0.88852819 1.7587964 -5.3918592 35.580319 0.63560961 23.599033 -12.195 26.563742
1500 0.89029085 1.8772498 -5.3966098 35.509232 0.20895386 23.055083 -12.703366 26.323229
1550 0.88639722 2.2284824 -5.3933288 35.449043 0.44413965 22.448774 -12.156068 25.528757
1600 0.88816451 2.2167704 -5.3994757 35.401661 0.12210235 23.108351 -12.44643 26.247085
1650 0.89154791 2.3397824 -5.4086923 35.365815 0.4820208 23.090699 -12.984179 26.490928
1700 0.88518032 2.5351236 -5.4041601 35.343757 0.080806002 22.749825 -12.99762 26.201005
1750 0.86848721 2.5527491 -5.3851928 35.336433 0.045102165 22.357111 -13.564328 26.15017
1800 0.88501061 2.5215825 -5.4169341 35.340849 0.27488483 22.086584 -14.408273 26.370732
1850 0.8716061 2.5809558 -5.4045854 35.355038 0.042909785 21.270956 -14.695278 25.853525
1900 0.85672517 2.4836326 -5.3902797 35.375469 0.72877764 21.639909 -15.474764 26.603646
1950 0.85133731 2.3141629 -5.3902573 35.398523 0.0016908803 21.106617 -15.132733 25.970924
2000 0.86152109 2.1562002 -5.4132601 35.419851 0.371016 21.325237 -15.614625 26.430706
2050 0.86243551 2.019931 -5.4220349 35.436069 0.017935421 20.4131 -16.255418 26.094698
2100 0.87417672 1.8083823 -5.4464117 35.445091 0.18429432 19.75625 -17.365705 26.303558
2150 0.85872128 1.7608768 -5.4293103 35.44341 0.91209166 20.149648 -17.480387 26.675312
2200 0.86615373 1.8372778 -5.4458315 35.430616 0.10151993 18.559234 -17.885469 25.7747
2250 0.85053605 1.7198437 -5.4272104 35.408688 0.96154548 17.200861 -18.562206 25.306622
2300 0.85400281 1.7939644 -5.4364682 35.377708 0.12283263 18.759325 -18.358539 26.247823
2350 0.85495278 1.5856029 -5.4417321 35.337987 0.20564329 18.967923 -18.248149 26.320658
2400 0.84606771 1.7782708 -5.4315646 35.287411 0.10063977 19.185527 -17.878215 26.224321
2450 0.85210051 1.8190391 -5.4432116 35.232321 0.69988647 19.268861 -18.325448 26.59156
2500 0.85304715 1.7466204 -5.4470889 35.175245 0.0048314937 18.09176 -18.74157 26.04915
2550 0.85401123 1.8601945 -5.4509309 35.115748 0.99467901 17.170045 -18.574587 25.294777
2600 0.85778606 1.974012 -5.4586742 35.058013 0.0026599702 17.438966 -19.333395 26.036469
2650 0.8521239 2.0606329 -5.4526006 35.003616 0.091056354 17.16363 -19.244738 25.786627
2700 0.85918482 2.0766792 -5.4658947 34.954171 0.89590606 15.77108 -19.822153 25.330707
2750 0.85786577 2.225549 -5.4667773 34.911468 0.26577575 15.769018 -21.128817 26.364538
2800 0.86764664 2.2325018 -5.4849414 34.877604 0.47167555 14.950515 -20.675229 25.514369
2850 0.85209564 2.3434319 -5.465734 34.852715 2.7350296 13.51553 -20.829996 24.830592
2900 0.85757283 2.3512971 -5.4786051 34.836138 0.14816492 14.06033 -21.545946 25.727819
2950 0.86098926 2.3480431 -5.4890615 34.826408 0.26401534 13.381395 -22.714827 26.363329
3000 0.85413421 2.3243973 -5.4844129 34.823242 0.024244334 12.739486 -22.538687 25.889899
3050 0.85015323 2.5479266 -5.4844303 34.825228 0.4463147 12.990582 -21.975063 25.527605
3100 0.8530523 2.3643505 -5.495343 34.834883 0.12144265 12.844293 -22.321989 25.753583
3150 0.85098478 2.2521299 -5.4990526 34.848419 0.33194916 12.747856 -23.126671 26.4074
3200 0.84391449 2.2650057 -5.495222 34.862626 0.031888328 12.788845 -22.782174 26.12627
3250 0.84807155 2.1715388 -5.5080873 34.877548 0.082426694 13.316219 -22.09441 25.796989
3300 0.83028242 2.242889 -5.4878846 34.89175 1.1334975 14.326678 -22.593363 26.752827
3350 0.82924001 2.0324002 -5.4924558 34.903232 0.35473989 14.354166 -22.181868 26.421153
3400 0.83032841 2.0003371 -5.4997142 34.908733 0.041677437 14.528378 -21.735998 26.144356
3450 0.82908891 1.8683902 -5.5029185 34.907936 0.02365857 15.069507 -21.053887 25.891237
3500 0.82842914 1.9165344 -5.5064218 34.898681 0.17663531 15.27043 -20.674834 25.702817
3550 0.82735822 1.98221 -5.5088197 34.88272 1.5607134 14.915228 -20.208431 25.116622
3600 0.82642915 1.8422766 -5.5110752 34.8611 1.1861112 15.312314 -20.051953 25.229899
3650 0.82556781 1.9351408 -5.5130349 34.833406 1.018872 16.152478 -19.454871 25.286252
3700 0.82360651 1.9791184 -5.5128431 34.802021 0.14080727 16.907104 -19.401616 25.734663
3750 0.83017793 1.9855734 -5.5253254 34.768644 0.15311334 16.969506 -19.331958 25.723311
3800 0.82362926 2.1029656 -5.5179624 34.734178 0.10807487 17.892584 -18.542426 25.76754
3850 0.82313508 2.0781681 -5.5196175 34.70093 0.13343085 19.072706 -17.28778 25.741707
3900 0.83643385 2.0570262 -5.5421224 34.669761 0.00022792038 19.551677 -17.1548 26.010675
3950 0.82346174 2.0842322 -5.5252757 34.640849 0.0093759386 20.892792 -15.590263 26.068469
4000 0.83485868 2.1196669 -5.5451736 34.612396 0.31198053 21.630258 -15.126984 26.394956
4050 0.82729429 2.2033274 -5.5365945 34.585721 0.53752252 21.283533 -14.011497 25.481578
4100 0.82040242 2.1757309 -5.5292269 34.562271 0.36031984 22.047609 -12.961927 25.575548
4150 0.81932521 2.285666 -5.5307807 34.542102 0.84343149 22.486289 -11.70555 25.350604
4200 0.83819319 2.231174 -5.5625532 34.526447 0.47190752 23.311855 -12.57189 26.485751
4250 0.82542274 2.1874789 -5.5472057 34.513795 0.70518398 23.411553 -12.614639 26.593795
4300 0.81971158 2.241167 -5.5424504 34.503969 0.26707612 23.089805 -12.727793 26.365429
4350 0.83255377 2.1295532 -5.5657895 34.496326 0.072548591 23.003138 -12.52181 26.190458
4400 0.8128474 2.3327845 -5.5402264 34.490126 0.0013023434 23.020811 -12.029795 25.974482
4450 0.82013491 2.3069915 -5.5554953 34.488039 0.041123896 23.632908 -11.178674 26.143394
4500 0.81411544 2.2247193 -5.5509183 34.488014 0.54440601 23.010678 -10.938506 25.478269
4550 0.82814624 2.1142779 -5.5763482 34.487885 0.1518945 23.696817 -11.351972 26.275585
4600 0.82929492 2.090881 -5.5823492 34.486698 0.0045520899 23.538527 -10.929741 25.952292
4650 0.81061417 1.9818043 -5.5584018 34.484038 0.012526806 23.993543 -10.219174 26.079142
4700 0.81816105 1.9605811 -5.5735005 34.476764 1.2079835 25.151166 -9.1888856 26.777169
4750 0.81657042 2.0064313 -5.5744795 34.465784 1.2045017 25.487486 -8.2063886 26.776048
4800 0.81789335 2.0838696 -5.5796632 34.451996 0.27642542 24.647157 -7.023095 25.62823
4850 0.80649339 1.9892413 -5.5654796 34.436067 0.024697945 25.09823 -6.3492244 25.888874
4900 0.81673441 2.0125635 -5.5835037 34.416236 0.0011188576 25.446818 -5.2182483 25.976348
4950 0.82250033 1.9770391 -5.5946082 34.394723 0.72696707 26.37002 -3.5122842 26.602896
5000 0.80762758 2.075517 -5.5746076 34.371696 0.12796344 26.102184 -2.8094827 26.252946
Loop time of 10.3394 on 4 procs for 5000 steps with 5120 atoms
Performance: 167127.370 tau/day, 483.586 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 | 5.029 | 6.0128 | 7.1918 | 35.0 | 58.15
Neigh | 0.65673 | 0.75825 | 0.88597 | 10.3 | 7.33
Comm | 0.43982 | 1.5284 | 2.4112 | 60.5 | 14.78
Output | 0.022835 | 0.023039 | 0.023453 | 0.2 | 0.22
Modify | 1.7294 | 1.9472 | 2.5687 | 25.7 | 18.83
Other | | 0.06978 | | | 0.67
Nlocal: 1280 ave 1404 max 1214 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 3521.25 ave 3581 max 3426 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 73872.2 ave 87973 max 64161 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 295489
Ave neighs/atom = 57.7127
Neighbor list builds = 278
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10

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LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
# fcc lattice
lattice fcc 0.9731
Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
region my_box block 0 8.0 0 8.0 0 20.0
create_box 1 my_box
Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
1 by 1 by 1 MPI processor grid
region particles block 0 8.0 0 8.0 0 20.0
create_atoms 1 region particles
Created 5120 atoms
pair_coeff 1 1 1.0 1.0 2.5
mass 1 1.0
change_box all z final 0.0 34 remap units box
orthogonal box = (0 0 0) to (12.8152 12.8152 34)
# select particles in one side of the elongated box
region left plane 0 0 10 0 0 1
group left region left
2688 atoms in group left
velocity left create 6.0 1 mom yes rot yes
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
fix ensemble left nve # Note: only move particle in left-hand side
fix langevin left langevin 3.0 0.8 100.0 2017
# outout
thermo_style custom step temp pzz pe lz
thermo 100
# dump dumpXYZ all xyz 100 traj.xyz
# run reduced for demonstration purposes
# run 10000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.524 | 4.524 | 4.524 Mbytes
Step Temp Pzz PotEng Lz
0 3.1494433 -3.4735106 -6.8707307 34
100 1.7727555 6.5330255 -4.8035477 34
200 1.7462368 7.0070325 -4.7646426 34
300 1.7564888 6.6190123 -4.7894637 34
400 1.7641186 6.609684 -4.8064772 34
500 1.7383511 6.7304936 -4.7708095 34
600 1.731708 6.8574656 -4.7612918 34
700 1.7332167 6.6530919 -4.7670014 34
800 1.7487537 6.5644963 -4.7907458 34
900 1.7353648 6.7115188 -4.7772149 34
1000 1.728878 6.4175719 -4.7797216 34
1100 1.7471488 6.5346083 -4.813376 34
1200 1.7188149 6.2502104 -4.7822235 34
1300 1.7151194 6.792534 -4.7781701 34
1400 1.7406603 6.6639592 -4.8170174 34
1500 1.7090537 6.4677579 -4.770701 34
1600 1.7014954 6.2853535 -4.7679742 34
1700 1.7064354 6.4352857 -4.7812978 34
1800 1.7169971 6.5808758 -4.799426 34
1900 1.6822712 6.3746758 -4.7522464 34
2000 1.7126546 6.534969 -4.8091595 34
2100 1.7086108 6.4679932 -4.8146664 34
2200 1.6974952 6.3802129 -4.8052505 34
2300 1.6868035 6.4009243 -4.7935769 34
2400 1.7107125 6.2318869 -4.8358765 34
2500 1.660241 6.4891487 -4.7661183 34
2600 1.6801816 6.1988356 -4.8024291 34
2700 1.6940298 6.1328187 -4.8290053 34
2800 1.6755061 6.4150693 -4.8145473 34
2900 1.6749928 6.4248792 -4.8213509 34
3000 1.6310737 6.6491291 -4.7673027 34
3100 1.6559915 6.2726719 -4.8109181 34
3200 1.6574579 5.7132029 -4.8189484 34
3300 1.6816136 5.7697439 -4.8652811 34
3400 1.6489483 6.4463349 -4.8247812 34
3500 1.6557974 5.9763333 -4.8383712 34
3600 1.6215459 6.2806534 -4.7954657 34
3700 1.6484987 6.0671609 -4.8470777 34
3800 1.6473922 5.8688108 -4.8555351 34
3900 1.6435957 5.930425 -4.8562076 34
4000 1.6514434 6.1962122 -4.872998 34
4100 1.6138337 6.4808124 -4.8219373 34
4200 1.6215239 5.9467966 -4.8412146 34
4300 1.6129295 5.9377323 -4.8414596 34
4400 1.6020549 6.1104301 -4.8395939 34
4500 1.6047738 6.0816222 -4.8538151 34
4600 1.6053565 6.183466 -4.8686817 34
4700 1.6088152 5.7416542 -4.894114 34
4800 1.5954309 5.694319 -4.8840198 34
4900 1.5582564 6.1199614 -4.8429998 34
5000 1.5786672 5.8813574 -4.8907344 34
Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms
Performance: 60873.483 tau/day, 176.139 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.269 | 22.269 | 22.269 | 0.0 | 78.45
Neigh | 4.7222 | 4.7222 | 4.7222 | 0.0 | 16.64
Comm | 0.40821 | 0.40821 | 0.40821 | 0.0 | 1.44
Output | 0.0042329 | 0.0042329 | 0.0042329 | 0.0 | 0.01
Modify | 0.88231 | 0.88231 | 0.88231 | 0.0 | 3.11
Other | | 0.1005 | | | 0.35
Nlocal: 5120 ave 5120 max 5120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7768 ave 7768 max 7768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297167 ave 297167 max 297167 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297167
Ave neighs/atom = 58.0404
Neighbor list builds = 474
Dangerous builds = 246
write_data data.halfhalf
Total wall time: 0:00:28

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LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
# fcc lattice
lattice fcc 0.9731
Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
region my_box block 0 8.0 0 8.0 0 20.0
create_box 1 my_box
Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
1 by 1 by 4 MPI processor grid
region particles block 0 8.0 0 8.0 0 20.0
create_atoms 1 region particles
Created 5120 atoms
pair_coeff 1 1 1.0 1.0 2.5
mass 1 1.0
change_box all z final 0.0 34 remap units box
orthogonal box = (0 0 0) to (12.8152 12.8152 34)
# select particles in one side of the elongated box
region left plane 0 0 10 0 0 1
group left region left
2688 atoms in group left
velocity left create 6.0 1 mom yes rot yes
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
fix ensemble left nve # Note: only move particle in left-hand side
fix langevin left langevin 3.0 0.8 100.0 2017
# outout
thermo_style custom step temp pzz pe lz
thermo 100
# dump dumpXYZ all xyz 100 traj.xyz
# run reduced for demonstration purposes
# run 10000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.23 | 3.23 | 3.23 Mbytes
Step Temp Pzz PotEng Lz
0 3.1494433 -3.4735106 -6.8707307 34
100 1.7914373 6.4805818 -4.8420353 34
200 1.740256 6.6108149 -4.7672571 34
300 1.7663827 6.5188941 -4.8103672 34
400 1.7440644 6.5156543 -4.7769467 34
500 1.7471724 6.5208992 -4.7843928 34
600 1.7320106 6.6557835 -4.7654637 34
700 1.6839043 6.7689759 -4.7045352 34
800 1.7216746 6.66436 -4.7601673 34
900 1.7342542 6.3242367 -4.7790803 34
1000 1.7338566 6.5803438 -4.7854529 34
1100 1.7328856 6.3846366 -4.7902625 34
1200 1.7546906 6.5048137 -4.8213443 34
1300 1.7163891 6.3903221 -4.7665145 34
1400 1.7011627 6.5782672 -4.7517875 34
1500 1.7105234 6.5811813 -4.7677748 34
1600 1.7334403 6.5032837 -4.8067749 34
1700 1.7252102 6.5443871 -4.8058994 34
1800 1.721958 6.3378188 -4.8150073 34
1900 1.6797892 6.6780506 -4.7538618 34
2000 1.7001774 6.3578192 -4.7894018 34
2100 1.7127784 6.3219105 -4.8161059 34
2200 1.696825 6.536793 -4.7946902 34
2300 1.6704578 6.7186933 -4.7609628 34
2400 1.6772498 6.3432817 -4.7778471 34
2500 1.7073862 6.2153226 -4.8299181 34
2600 1.6951557 6.4397257 -4.8156787 34
2700 1.6845984 6.0123544 -4.8136864 34
2800 1.6550565 6.2489392 -4.7829639 34
2900 1.6892315 6.158499 -4.8423004 34
3000 1.6814436 6.07976 -4.8400696 34
3100 1.6387025 6.330166 -4.7878978 34
3200 1.6747855 6.0767043 -4.8481995 34
3300 1.6508768 6.2749233 -4.8181888 34
3400 1.6426364 6.3934935 -4.8223824 34
3500 1.6576512 6.0638185 -4.8559078 34
3600 1.6444173 6.1376573 -4.8463113 34
3700 1.6480039 5.9943705 -4.8601776 34
3800 1.6467212 6.0556591 -4.8722719 34
3900 1.6271804 6.116738 -4.8547278 34
4000 1.6158134 5.9089534 -4.8477829 34
4100 1.6388157 5.9890465 -4.8920284 34
4200 1.6182368 6.0639887 -4.8724963 34
4300 1.647633 5.6333906 -4.9267536 34
4400 1.5856411 6.2675475 -4.8471239 34
4500 1.5773417 6.1789163 -4.8469057 34
4600 1.6181445 5.7988068 -4.922419 34
4700 1.5876712 5.7398111 -4.8853849 34
4800 1.5708353 6.2204997 -4.8718872 34
4900 1.5514708 5.9782256 -4.8523812 34
5000 1.553347 5.9286523 -4.86582 34
Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms
Performance: 213265.164 tau/day, 617.087 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2964 | 5.6236 | 5.8982 | 9.0 | 69.40
Neigh | 1.0562 | 1.1907 | 1.3257 | 8.7 | 14.70
Comm | 0.43963 | 0.98786 | 1.5968 | 42.5 | 12.19
Output | 0.0023124 | 0.004741 | 0.0090873 | 4.0 | 0.06
Modify | 0.018652 | 0.22213 | 0.39884 | 36.4 | 2.74
Other | | 0.07357 | | | 0.91
Nlocal: 1280 ave 1337 max 1211 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 3416.25 ave 3549 max 3297 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 74269.8 ave 77932 max 69612 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 297079
Ave neighs/atom = 58.0232
Neighbor list builds = 474
Dangerous builds = 247
write_data data.halfhalf
Total wall time: 0:00:08