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Commit 3fe162a4 authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15437 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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examples/README
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......@@ -64,6 +64,7 @@ body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
coreshell: adiabatic core/shell model
comb: models using the COMB potential
controller: use of fix controller as a thermostat
crack: crack propagation in a 2d solid
deposit: deposition of atoms and molecules onto a 3d substrate
dipole: point dipolar particles, 2d system
......
examples/controller/in.controller 0 → 100755
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View file @ 3fe162a4
# 3d Lennard-Jones melt, thermostatted by fix controller
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
variable tcontrol internal 0.5
fix tstat all langevin v_tcontrol 0.5 0.5 2938940
# equilibrate
thermo 50
run 500
# instantaneous temp for control
fix 10 all controller 100 1.0 0.5 0.0 0.0 &
c_thermo_temp 1.5 tcontrol
# time-average temp for control
#fix ave all ave/time 5 20 100 c_thermo_temp
#fix 10 all controller 100 0.5 0.0 0.0 f_ave 1.5 tcontrol
# run with controller
run 2500
examples/controller/log.5Aug16.controller.g++.1 0 → 100644
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− 0
View file @ 3fe162a4
LAMMPS (3 Aug 2016)
# 3d Lennard-Jones melt, thermostatted by fix controller
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
variable tcontrol internal 0.5
fix tstat all langevin v_tcontrol 0.5 0.5 2938940
# equilibrate
thermo 50
run 500
Neighbor list info ...
1 neighbor list requests
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 = 12 12 12
Memory usage per processor = 2.19271 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
50 0.61784238 -5.9328913 0 -5.0063594 -0.8309723
100 0.57393741 -6.0180757 0 -5.1573848 -1.3380428
150 0.54905447 -6.0898673 0 -5.2664915 -1.7190041
200 0.5271069 -6.1123127 0 -5.32185 -1.8901277
250 0.52638254 -6.132576 0 -5.3431996 -1.9925428
300 0.51654993 -6.126029 0 -5.3513979 -1.9515674
350 0.50471169 -6.1316734 0 -5.3747951 -1.9743859
400 0.49885979 -6.157314 0 -5.4092114 -2.1544075
450 0.50261633 -6.1458076 0 -5.3920716 -2.1080502
500 0.51198903 -6.1441158 0 -5.3763242 -2.0677941
Loop time of 1.51807 on 1 procs for 500 steps with 4000 atoms
Performance: 142286.109 tau/day, 329.366 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2134 | 1.2134 | 1.2134 | 0.0 | 79.93
Neigh | 0.16519 | 0.16519 | 0.16519 | 0.0 | 10.88
Comm | 0.022159 | 0.022159 | 0.022159 | 0.0 | 1.46
Output | 0.00021291 | 0.00021291 | 0.00021291 | 0.0 | 0.01
Modify | 0.11073 | 0.11073 | 0.11073 | 0.0 | 7.29
Other | | 0.006378 | | | 0.42
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5825 ave 5825 max 5825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151071 ave 151071 max 151071 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151071
Ave neighs/atom = 37.7677
Neighbor list builds = 25
Dangerous builds not checked
# instantaneous temp for control
fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
# time-average temp for control
#fix ave all ave/time 5 20 100 c_thermo_temp
#fix 10 all controller 100 0.5 0.0 0.0 f_ave 1.5 tcontrol
# run with controller
run 2500
Memory usage per processor = 2.19271 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.51198903 -6.1441158 0 -5.3763242 -2.0677941
550 0.50342035 -6.1446822 0 -5.3897404 -2.0872641
600 0.49843033 -6.135933 0 -5.3884744 -2.0299937
650 0.60345516 -6.052878 0 -5.1479216 -1.5107746
700 0.66771365 -5.9560857 0 -4.9547657 -0.95193456
750 0.77985534 -5.8258115 0 -4.656321 -0.17645361
800 0.85051536 -5.720372 0 -4.4449179 0.42446643
850 0.96826934 -5.6155358 0 -4.1634949 1.0388685
900 1.0301813 -5.5468621 0 -4.0019765 1.5025727
950 1.0974533 -5.4247502 0 -3.7789818 2.1535605
1000 1.1501581 -5.3216796 0 -3.5968738 2.7152011
1050 1.2330225 -5.2247739 0 -3.3757025 3.2650402
1100 1.2383162 -5.147574 0 -3.2905642 3.7029116
1150 1.285211 -5.0594791 0 -3.1321446 4.1344831
1200 1.3429729 -5.0291604 0 -3.0152046 4.3204751
1250 1.3941609 -4.9542149 0 -2.8634963 4.7215049
1300 1.4439999 -4.9789421 0 -2.8134838 4.6347071
1350 1.4355932 -4.9395463 0 -2.7866948 4.8031855
1400 1.439132 -4.9441872 0 -2.7860289 4.8044805
1450 1.4347829 -4.9257577 0 -2.7741214 4.8738569
1500 1.4830328 -4.9473618 0 -2.7233688 4.8394125
1550 1.4178717 -4.9070465 0 -2.7807706 4.9432828
1600 1.4285161 -4.8964176 0 -2.7541792 5.0266343
1650 1.4732357 -4.8997853 0 -2.6904842 5.0366006
1700 1.4859419 -4.9036811 0 -2.6753255 5.0160666
1750 1.4756247 -4.8531762 0 -2.6402926 5.2521218
1800 1.4615868 -4.8508782 0 -2.6590461 5.2722729
1850 1.4555249 -4.8736043 0 -2.6908628 5.158512
1900 1.4839265 -4.8589546 0 -2.6336213 5.260185
1950 1.4698295 -4.8536401 0 -2.649447 5.226069
2000 1.4965555 -4.8785558 0 -2.6342837 5.155282
2050 1.4850569 -4.8496964 0 -2.622668 5.2897546
2100 1.4880052 -4.851961 0 -2.6205112 5.2941813
2150 1.513051 -4.8668802 0 -2.597871 5.217126
2200 1.5018225 -4.8470034 0 -2.5948328 5.3193544
2250 1.5127122 -4.873504 0 -2.6050029 5.1863314
2300 1.5029926 -4.8685751 0 -2.6146498 5.2282438
2350 1.4998902 -4.8487396 0 -2.5994668 5.3001222
2400 1.4902901 -4.8912088 0 -2.6563325 5.0668311
2450 1.4995102 -4.867998 0 -2.6192951 5.1996129
2500 1.5072473 -4.8344452 0 -2.5741395 5.3656649
2550 1.5090398 -4.8658253 0 -2.6028315 5.2128265
2600 1.5004359 -4.8683055 0 -2.6182144 5.2039471
2650 1.5020983 -4.843517 0 -2.5909329 5.2583337
2700 1.5042547 -4.8175886 0 -2.5617707 5.4286382
2750 1.5120477 -4.8269014 0 -2.559397 5.3933663
2800 1.5028865 -4.8445407 0 -2.5907745 5.300129
2850 1.5162767 -4.8464952 0 -2.5726487 5.2917987
2900 1.5287303 -4.8393493 0 -2.546827 5.3276564
2950 1.5175567 -4.8779763 0 -2.6022104 5.1592321
3000 1.5038518 -4.8714664 0 -2.6162526 5.1494048
Loop time of 7.81543 on 1 procs for 2500 steps with 4000 atoms
Performance: 138188.243 tau/day, 319.880 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.2599 | 6.2599 | 6.2599 | 0.0 | 80.10
Neigh | 0.85839 | 0.85839 | 0.85839 | 0.0 | 10.98
Comm | 0.11165 | 0.11165 | 0.11165 | 0.0 | 1.43
Output | 0.0010052 | 0.0010052 | 0.0010052 | 0.0 | 0.01
Modify | 0.55397 | 0.55397 | 0.55397 | 0.0 | 7.09
Other | | 0.03055 | | | 0.39
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5495 ave 5495 max 5495 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151408 ave 151408 max 151408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151408
Ave neighs/atom = 37.852
Neighbor list builds = 125
Dangerous builds not checked
Total wall time: 0:00:09
examples/controller/log.5Aug16.controller.g++.4 0 → 100644
+ 172
− 0
View file @ 3fe162a4
LAMMPS (3 Aug 2016)
# 3d Lennard-Jones melt, thermostatted by fix controller
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
variable tcontrol internal 0.5
fix tstat all langevin v_tcontrol 0.5 0.5 2938940
# equilibrate
thermo 50
run 500
Neighbor list info ...
1 neighbor list requests
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 = 12 12 12
Memory usage per processor = 2.10344 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
50 0.61546984 -5.9273631 0 -5.0043892 -0.80234884
100 0.58816457 -6.0381041 0 -5.1560778 -1.4213766
150 0.54978107 -6.0786179 0 -5.2541524 -1.6676166
200 0.52617482 -6.1036411 0 -5.3145762 -1.8461101
250 0.52287422 -6.1266535 0 -5.3425383 -1.9824146
300 0.5108217 -6.1212898 0 -5.3552488 -1.9340949
350 0.51609466 -6.1301783 0 -5.3562299 -1.9779768
400 0.50869337 -6.1435002 0 -5.3806509 -2.0654599
450 0.50821435 -6.1436659 0 -5.381535 -2.0660991
500 0.51057155 -6.138733 0 -5.3730671 -2.0305015
Loop time of 0.453014 on 4 procs for 500 steps with 4000 atoms
Performance: 476806.251 tau/day, 1103.718 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32365 | 0.32949 | 0.33618 | 1.0 | 72.73
Neigh | 0.043907 | 0.044821 | 0.045741 | 0.3 | 9.89
Comm | 0.037718 | 0.04614 | 0.053796 | 3.2 | 10.19
Output | 0.00033951 | 0.00036806 | 0.00042248 | 0.2 | 0.08
Modify | 0.027845 | 0.028714 | 0.029447 | 0.3 | 6.34
Other | | 0.003484 | | | 0.77
Nlocal: 1000 ave 1027 max 969 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 2885.25 ave 2911 max 2861 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 37772 ave 38810 max 36870 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 151088
Ave neighs/atom = 37.772
Neighbor list builds = 25
Dangerous builds not checked
# instantaneous temp for control
fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
# time-average temp for control
#fix ave all ave/time 5 20 100 c_thermo_temp
#fix 10 all controller 100 0.5 0.0 0.0 f_ave 1.5 tcontrol
# run with controller
run 2500
Memory usage per processor = 2.10344 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.51057155 -6.138733 0 -5.3730671 -2.0305015
550 0.50420106 -6.1501845 0 -5.394072 -2.095219
600 0.5075585 -6.1512444 0 -5.390097 -2.0925064
650 0.61394102 -6.0420986 0 -5.1214173 -1.4274822
700 0.67032315 -5.965645 0 -4.9604117 -0.9694324
750 0.7995115 -5.8169475 0 -4.6179801 -0.13608729
800 0.87610143 -5.7296899 0 -4.4158663 0.40557198
850 0.96383524 -5.5956055 0 -4.1502141 1.1534463
900 1.0207275 -5.5145367 0 -3.9838283 1.6360277
950 1.0984003 -5.4082226 0 -3.7610341 2.2188238
1000 1.139839 -5.3115591 0 -3.6022281 2.7535047
1050 1.2025815 -5.2255494 0 -3.422128 3.2200737
1100 1.2595149 -5.1728043 0 -3.2840043 3.5501607
1150 1.3025925 -5.1191016 0 -3.1657013 3.8402647
1200 1.3678555 -5.0639122 0 -3.0126419 4.1910384
1250 1.3875027 -5.0214839 0 -2.9407501 4.404731
1300 1.3985783 -4.9905716 0 -2.8932285 4.5357644
1350 1.404464 -4.9440099 0 -2.8378405 4.7567965
1400 1.4439169 -4.9177331 0 -2.7523992 4.9211759
1450 1.4567014 -4.9145471 0 -2.7300412 4.9141048
1500 1.4538545 -4.9471549 0 -2.7669183 4.7845287
1550 1.4754919 -4.9216982 0 -2.7090137 4.9066693
1600 1.4836876 -4.9031127 0 -2.6781377 4.9962941
1650 1.4952819 -4.8996673 0 -2.6573052 5.0717102
1700 1.4951735 -4.8997078 0 -2.6575083 5.038247
1750 1.4776262 -4.8819892 0 -2.666104 5.1218618
1800 1.4696068 -4.8977646 0 -2.6939055 5.0316078
1850 1.4826885 -4.8925271 0 -2.6690504 5.0910199
1900 1.5071931 -4.9033121 0 -2.6430877 5.0838357
1950 1.4661426 -4.8827745 0 -2.6841104 5.0760354
2000 1.4767078 -4.9109185 0 -2.6964105 4.9734933
2050 1.4937469 -4.9028545 0 -2.6627943 5.0569847
2100 1.4773117 -4.8404457 0 -2.6250321 5.309595
2150 1.5092661 -4.9133618 0 -2.6500287 4.9779751
2200 1.4704363 -4.8641645 0 -2.6590615 5.1531222
2250 1.4983843 -4.8637168 0 -2.6167023 5.1627163
2300 1.5099457 -4.8616382 0 -2.5972859 5.2308054
2350 1.5175717 -4.8659949 0 -2.5902064 5.2342039
2400 1.4882052 -4.8943652 0 -2.6626154 5.0296201
2450 1.5095317 -4.874837 0 -2.6111055 5.2093244
2500 1.4868645 -4.8498 0 -2.6200609 5.2901738
2550 1.5321845 -4.8990536 0 -2.6013514 5.0684999
2600 1.4471055 -4.8422313 0 -2.6721158 5.2581052
2650 1.5274854 -4.8477035 0 -2.5570481 5.2963179
2700 1.532968 -4.824428 0 -2.5255508 5.4684052
2750 1.5040089 -4.8364477 0 -2.5809983 5.3343669
2800 1.5052109 -4.8374717 0 -2.5802198 5.3150061
2850 1.510141 -4.8485185 0 -2.5838732 5.2705772
2900 1.4994026 -4.8400966 0 -2.591555 5.3231654
2950 1.5057915 -4.8842358 0 -2.6261131 5.1645778
3000 1.5038806 -4.8661399 0 -2.610883 5.2228747
Loop time of 2.26012 on 4 procs for 2500 steps with 4000 atoms
Performance: 477850.096 tau/day, 1106.134 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.625 | 1.654 | 1.6952 | 2.2 | 73.18
Neigh | 0.2238 | 0.22532 | 0.22785 | 0.3 | 9.97
Comm | 0.18091 | 0.22445 | 0.25435 | 6.1 | 9.93
Output | 0.0015404 | 0.0016042 | 0.0017579 | 0.2 | 0.07
Modify | 0.14057 | 0.14187 | 0.14303 | 0.2 | 6.28
Other | | 0.01285 | | | 0.57
Nlocal: 1000 ave 1014 max 988 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 2705.25 ave 2718 max 2687 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 37851.2 ave 39431 max 36724 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 151405
Ave neighs/atom = 37.8513
Neighbor list builds = 125
Dangerous builds not checked
Total wall time: 0:00:02
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