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add example for using fix controller with a moving wall to adjust pressure

This commit is contained in:
Axel Kohlmeyer 2018-12-11 05:31:12 -05:00
parent 264dd59c75
commit eeaeab0832
5 changed files with 284 additions and 0 deletions
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examples/controller/in.controller → examples/controller/in.controller.temp
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examples/controller/log.27Nov18.controller.g++.1 → examples/controller/log.27Nov18.controller.temp.g++.1
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examples/controller/log.27Nov18.controller.g++.4 → examples/controller/log.27Nov18.controller.temp.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt, thermostatted by fix controller
units lj
atom_style atomic
boundary p p m
processors * * 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 -4 14
region slab block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
1 by 1 by 1 MPI processor grid
create_atoms 1 region slab
Created 4200 atoms
Time spent = 0.000752687 secs
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 2 every 2 check yes
fix 1 all nve
fix 3 all langevin 1.5 1.5 0.5 412513
variable zhi internal $(10.5*zlat)
variable zhi internal 17.635760009516324942
variable kwall equal 20.0
fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
variable pzz equal pzz
fix ave all ave/time 10 10 100 v_pzz
# equilibrate
thermo_style custom step temp pxx pyy pzz f_ave v_zhi
thermo 500
run 2500
Neighbor list info ...
update every 2 steps, delay 2 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 = 12 12 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) = 3.639 | 3.639 | 3.639 Mbytes
Step Temp Pxx Pyy Pzz f_ave v_zhi
0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
500 1.4850596 3.1161377 2.9246345 2.9122136 2.9795403 17.63576
1000 1.4706875 2.4918963 2.4698964 2.3538419 2.5181301 17.63576
1500 1.4978967 1.9196563 2.0442863 1.978316 1.9215971 17.63576
2000 1.4738152 1.6424128 1.5875245 1.7098788 1.6222172 17.63576
2500 1.5012535 1.3324666 1.3078613 1.30772 1.3830807 17.63576
Loop time of 9.88972 on 1 procs for 2500 steps with 4200 atoms
Performance: 109204.308 tau/day, 252.788 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9583 | 5.9583 | 5.9583 | 0.0 | 60.25
Neigh | 3.0444 | 3.0444 | 3.0444 | 0.0 | 30.78
Comm | 0.095146 | 0.095146 | 0.095146 | 0.0 | 0.96
Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00
Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 7.45
Other | | 0.05447 | | | 0.55
Nlocal: 4200 ave 4200 max 4200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3278 ave 3278 max 3278 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 125488 ave 125488 max 125488 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 125488
Ave neighs/atom = 29.8781
Neighbor list builds = 414
Dangerous builds = 0
# use time averaged pressure for control
#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
# use instantaneous pressure for control
fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
# run with controller
run 5000
Per MPI rank memory allocation (min/avg/max) = 3.645 | 3.645 | 3.645 Mbytes
Step Temp Pxx Pyy Pzz f_ave v_zhi
2500 1.5012535 1.332723 1.3081129 1.3079716 1.3830807 17.63576
3000 1.4976659 1.2148748 1.2873541 1.4929784 1.337029 17.052206
3500 1.5099561 1.2602054 1.2429245 1.3566909 1.2922544 15.926241
4000 1.4993048 1.3600782 1.2700229 1.441161 1.3958688 15.38517
4500 1.5361306 1.4939463 1.4981484 1.6511208 1.4778535 15.14012
5000 1.4858931 1.3755603 1.4202936 1.3321859 1.4463033 14.710626
5500 1.495093 1.5412773 1.3726815 1.3337702 1.4661477 14.551062
6000 1.4867063 1.4204076 1.4972286 1.5325972 1.5125403 14.727292
6500 1.5036424 1.4449136 1.5290335 1.5163832 1.4974 14.866821
7000 1.5376638 1.4409843 1.4434687 1.3927467 1.5097986 14.730925
7500 1.4880255 1.4006281 1.4538957 1.4700911 1.4904586 14.531748
Loop time of 18.1541 on 1 procs for 5000 steps with 4200 atoms
Performance: 118981.600 tau/day, 275.420 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 | 10.685 | 10.685 | 10.685 | 0.0 | 58.86
Neigh | 5.6863 | 5.6863 | 5.6863 | 0.0 | 31.32
Comm | 0.19485 | 0.19485 | 0.19485 | 0.0 | 1.07
Output | 0.0003798 | 0.0003798 | 0.0003798 | 0.0 | 0.00
Modify | 1.479 | 1.479 | 1.479 | 0.0 | 8.15
Other | | 0.1086 | | | 0.60
Nlocal: 4200 ave 4200 max 4200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3252 ave 3252 max 3252 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 126902 ave 126902 max 126902 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126902
Ave neighs/atom = 30.2148
Neighbor list builds = 815
Dangerous builds = 0
Total wall time: 0:00:28

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt, thermostatted by fix controller
units lj
atom_style atomic
boundary p p m
processors * * 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 -4 14
region slab block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
2 by 1 by 1 MPI processor grid
create_atoms 1 region slab
Created 4200 atoms
Time spent = 0.00055027 secs
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 2 every 2 check yes
fix 1 all nve
fix 3 all langevin 1.5 1.5 0.5 412513
variable zhi internal $(10.5*zlat)
variable zhi internal 17.635760009516324942
variable kwall equal 20.0
fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
variable pzz equal pzz
fix ave all ave/time 10 10 100 v_pzz
# equilibrate
thermo_style custom step temp pxx pyy pzz f_ave v_zhi
thermo 500
run 2500
Neighbor list info ...
update every 2 steps, delay 2 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 = 12 12 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) = 3.205 | 3.205 | 3.205 Mbytes
Step Temp Pxx Pyy Pzz f_ave v_zhi
0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
500 1.4685077 2.9959993 2.9101136 2.9557017 2.9691654 17.63576
1000 1.4660014 2.3677693 2.4832805 2.3853443 2.495998 17.63576
1500 1.503875 1.9958194 1.8192177 1.8732779 1.9196618 17.63576
2000 1.508944 1.6772869 1.6171356 1.5363361 1.6221247 17.63576
2500 1.4754205 1.4808824 1.3803411 1.3538329 1.433588 17.63576
Loop time of 5.20209 on 2 procs for 2500 steps with 4200 atoms
Performance: 207608.821 tau/day, 480.576 timesteps/s
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0816 | 3.1008 | 3.1199 | 1.1 | 59.61
Neigh | 1.5272 | 1.5364 | 1.5455 | 0.7 | 29.53
Comm | 0.12968 | 0.15815 | 0.18662 | 7.2 | 3.04
Output | 0.00012827 | 0.00048637 | 0.00084448 | 0.0 | 0.01
Modify | 0.3743 | 0.37516 | 0.37602 | 0.1 | 7.21
Other | | 0.03114 | | | 0.60
Nlocal: 2100 ave 2121 max 2079 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2593 ave 2606 max 2580 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 62766.5 ave 63603 max 61930 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 125533
Ave neighs/atom = 29.8888
Neighbor list builds = 410
Dangerous builds = 0
# use time averaged pressure for control
#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
# use instantaneous pressure for control
fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
# run with controller
run 5000
Per MPI rank memory allocation (min/avg/max) = 3.208 | 3.208 | 3.208 Mbytes
Step Temp Pxx Pyy Pzz f_ave v_zhi
2500 1.4754205 1.482216 1.3815843 1.3550522 1.433588 17.63576
3000 1.4805196 1.4121967 1.3859531 1.4360385 1.3724589 16.755204
3500 1.4909046 1.3658062 1.3441219 1.3839841 1.3998033 15.699356
4000 1.500835 1.4985308 1.4043943 1.3989491 1.4418757 15.030304
4500 1.5371526 1.4614358 1.4941526 1.455191 1.5121676 14.738878
5000 1.4766657 1.4037866 1.2404757 1.3679074 1.4173969 14.670117
5500 1.48302 1.5591058 1.3928461 1.3952178 1.5334476 14.58675
6000 1.5191325 1.4416274 1.5290468 1.5077685 1.5176605 14.560389
6500 1.495773 1.6695592 1.6621934 1.6073908 1.5508856 14.668722
7000 1.5033866 1.48723 1.5054815 1.4755225 1.5024653 14.676533
7500 1.5512429 1.6282941 1.7399228 1.6351273 1.6851571 14.671092
Loop time of 9.76074 on 2 procs for 5000 steps with 4200 atoms
Performance: 221294.755 tau/day, 512.256 timesteps/s
98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5979 | 5.6281 | 5.6583 | 1.3 | 57.66
Neigh | 2.9053 | 2.9335 | 2.9618 | 1.6 | 30.05
Comm | 0.31645 | 0.37703 | 0.43762 | 9.9 | 3.86
Output | 0.00025439 | 0.0009656 | 0.0016768 | 0.0 | 0.01
Modify | 0.75674 | 0.75966 | 0.76258 | 0.3 | 7.78
Other | | 0.06145 | | | 0.63
Nlocal: 2100 ave 2109 max 2091 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2578 ave 2578 max 2578 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 63578.5 ave 64145 max 63012 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 127157
Ave neighs/atom = 30.2755
Neighbor list builds = 816
Dangerous builds = 0
Total wall time: 0:00:14