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Steve Plimpton
2024-04-05 09:36:29 -06:00
parent ed0cff92de 2927471892
commit 905ceb98f1
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260
examples/micelle/log.29Mar2019.micelle-rigid.g++.1
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000473022 secs
read_data CPU = 0.0024147 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00022316 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
Performance: 2093802.885 tau/day, 4846.766 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21
Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11
Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86
Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17
Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37
Other | | 0.002726 | | | 2.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3094 ave 3094 max 3094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 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 = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
Performance: 1208012.705 tau/day, 2796.326 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17
Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38
Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92
Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45
Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10
Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34
Other | | 0.00293 | | | 1.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 416 ave 416 max 416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8769 ave 8769 max 8769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.00015378 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
Performance: 1297278.008 tau/day, 3002.958 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51
Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56
Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83
Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44
Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11
Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66
Other | | 0.003141 | | | 1.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8743 ave 8743 max 8743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

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examples/micelle/log.29Mar2019.micelle-rigid.g++.4
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000422001 secs
read_data CPU = 0.00473404 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000183344 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
Performance: 5066547.720 tau/day, 11728.120 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
Other | | 0.002669 | | | 6.26
Nlocal: 300 ave 304 max 292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 103.5 ave 108 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 773.5 ave 792 max 735 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 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 = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
Performance: 2434100.210 tau/day, 5634.491 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
Other | | 0.002938 | | | 3.31
Nlocal: 300 ave 309 max 291 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 218.75 ave 223 max 216 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 2192.25 ave 2251 max 2113 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 7.70092e-05 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
Performance: 3671840.233 tau/day, 8499.630 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
Other | | 0.00224 | | | 3.81
Nlocal: 300 ave 303 max 295 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 219 ave 224 max 215 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2185.75 ave 2244 max 2143 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0365221 on 1 procs for 500 steps with 1200 atoms
Performance: 5914221.123 tau/day, 13690.327 timesteps/s, 16.428 Matom-step/s
89.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022939 | 0.022939 | 0.022939 | 0.0 | 62.81
Bond | 0.00073851 | 0.00073851 | 0.00073851 | 0.0 | 2.02
Neigh | 0.0078339 | 0.0078339 | 0.0078339 | 0.0 | 21.45
Comm | 0.00072134 | 0.00072134 | 0.00072134 | 0.0 | 1.98
Output | 7.1419e-05 | 7.1419e-05 | 7.1419e-05 | 0.0 | 0.20
Modify | 0.0034868 | 0.0034868 | 0.0034868 | 0.0 | 9.55
Other | | 0.0007314 | | | 2.00
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3094 ave 3094 max 3094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3094
Ave neighs/atom = 2.5783333
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 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 = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109
100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772
150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796
200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262
250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445
300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851
350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818
400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566
450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611
500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738
Loop time of 0.0650638 on 1 procs for 500 steps with 1200 atoms
Performance: 3319817.322 tau/day, 7684.762 timesteps/s, 9.222 Matom-step/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 | 0.027565 | 0.027565 | 0.027565 | 0.0 | 42.37
Bond | 0.0007043 | 0.0007043 | 0.0007043 | 0.0 | 1.08
Neigh | 0.012724 | 0.012724 | 0.012724 | 0.0 | 19.56
Comm | 0.00091442 | 0.00091442 | 0.00091442 | 0.0 | 1.41
Output | 6.004e-05 | 6.004e-05 | 6.004e-05 | 0.0 | 0.09
Modify | 0.022329 | 0.022329 | 0.022329 | 0.0 | 34.32
Other | | 0.0007666 | | | 1.18
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 411 ave 411 max 411 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8759 ave 8759 max 8759 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8759
Ave neighs/atom = 7.2991667
Ave special neighs/atom = 0.5
Neighbor list builds = 46
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.000 seconds
150 rigid bodies with 450 atoms
1.3043524 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752
550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662
600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379
650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789
700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082
750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147
800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481
850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703
900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388
950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786
1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630988
Loop time of 0.0592806 on 1 procs for 500 steps with 1200 atoms
Performance: 3643690.276 tau/day, 8434.468 timesteps/s, 10.121 Matom-step/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 | 0.026866 | 0.026866 | 0.026866 | 0.0 | 45.32
Bond | 0.00071863 | 0.00071863 | 0.00071863 | 0.0 | 1.21
Neigh | 0.010927 | 0.010927 | 0.010927 | 0.0 | 18.43
Comm | 0.00084187 | 0.00084187 | 0.00084187 | 0.0 | 1.42
Output | 6.8106e-05 | 6.8106e-05 | 6.8106e-05 | 0.0 | 0.11
Modify | 0.019075 | 0.019075 | 0.019075 | 0.0 | 32.18
Other | | 0.000783 | | | 1.32
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 417 ave 417 max 417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8654 ave 8654 max 8654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8654
Ave neighs/atom = 7.2116667
Ave special neighs/atom = 0.5
Neighbor list builds = 39
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
Reading data file ...
orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
special_bonds fene
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0138659 on 4 procs for 500 steps with 1200 atoms
Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0053896 | 0.0057144 | 0.0060899 | 0.4 | 41.21
Bond | 0.00020074 | 0.00021422 | 0.00022291 | 0.0 | 1.54
Neigh | 0.0025301 | 0.0025401 | 0.0025501 | 0.0 | 18.32
Comm | 0.0031194 | 0.0035074 | 0.0038196 | 0.4 | 25.30
Output | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 | 0.0 | 0.49
Modify | 0.0013391 | 0.0013582 | 0.0013972 | 0.1 | 9.80
Other | | 0.0004638 | | | 3.34
Nlocal: 300 ave 304 max 292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 103.5 ave 108 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 773.5 ave 792 max 735 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 3094
Ave neighs/atom = 2.5783333
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 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 = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109
100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772
150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796
200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262
250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445
300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851
350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818
400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566
450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611
500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738
Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms
Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0059651 | 0.0062314 | 0.0066404 | 0.3 | 16.32
Bond | 0.00021057 | 0.00022477 | 0.0002333 | 0.0 | 0.59
Neigh | 0.0041424 | 0.0041487 | 0.0041512 | 0.0 | 10.87
Comm | 0.004264 | 0.0047244 | 0.0050297 | 0.4 | 12.37
Output | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 | 0.0 | 0.23
Modify | 0.021833 | 0.021946 | 0.022094 | 0.1 | 57.48
Other | | 0.0008157 | | | 2.14
Nlocal: 300 ave 303 max 296 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 216.25 ave 219 max 214 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 2189.75 ave 2205 max 2173 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 8759
Ave neighs/atom = 7.2991667
Ave special neighs/atom = 0.5
Neighbor list builds = 46
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.000 seconds
150 rigid bodies with 450 atoms
1.3043524 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752
550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662
600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379
650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789
700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082
750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147
800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481
850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703
900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388
950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786
1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987
Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms
Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0058656 | 0.0059718 | 0.0061355 | 0.1 | 25.22
Bond | 0.0002083 | 0.00022447 | 0.00023485 | 0.0 | 0.95
Neigh | 0.0035477 | 0.0035644 | 0.0035824 | 0.0 | 15.05
Comm | 0.0041037 | 0.0042227 | 0.0043024 | 0.1 | 17.83
Output | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 | 0.0 | 0.33
Modify | 0.008976 | 0.0090549 | 0.0091663 | 0.1 | 38.24
Other | | 0.0005654 | | | 2.39
Nlocal: 300 ave 306 max 295 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 221 ave 226 max 217 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2163.5 ave 2271 max 2100 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 8654
Ave neighs/atom = 7.2116667
Ave special neighs/atom = 0.5
Neighbor list builds = 39
Dangerous builds = 0
Total wall time: 0:00:00