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Merge branch 'lammps:develop' into ml-uf3

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This commit is contained in:
Ajinkya Hire
2024-04-13 18:56:07 -04:00
committed by GitHub
parent c502dd4033 1346be4168
commit 01b1d047a2
476 changed files with 16747 additions and 14762 deletions
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38
examples/PACKAGES/pedone/in.pedone.melt Normal file
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# Ca-O melt with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
region box block 0 4 0 4 0 4
create_box 2 box
create_atoms 1 box
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
create_atoms 2 box
mass 1 40.078
mass 2 15.999
set type 1 charge 1.2
set type 2 charge -1.2
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
velocity all create 6000.0 98347
fix 1 all nvt temp 3000.0 3000.0 0.1
# dump 1 all atom 500 Ca-O-melt.lammpstrj
thermo 100
run 1000

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examples/PACKAGES/pedone/in.pedone.relax Normal file
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# Ca-O crystal with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
region box block 0 4 0 4 0 4
create_box 2 box
create_atoms 1 box
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
create_atoms 2 box
mass 1 40.078
mass 2 15.999
displace_atoms all random 0.01 0.01 0.01 9084544
set type 1 charge 1.2
set type 2 charge -1.2
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
variable len equal lx*0.25
thermo_style custom step v_len lx pe press
thermo 100
fix 1 all box/relax iso 0.0
minimize 0.0 0.0 1000 10000
print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)"

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examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.1 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd)
using 1 OpenMP thread(s) per MPI task
# Ca-O melt with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (19.242 19.242 19.242)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
create_atoms 2 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
mass 1 40.078
mass 2 15.999
set type 1 charge 1.2
Setting atom values ...
256 settings made for charge
set type 2 charge -1.2
Setting atom values ...
256 settings made for charge
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
velocity all create 6000.0 98347
fix 1 all nvt temp 3000.0 3000.0 0.1
# dump 1 all atom 500 Ca-O-melt.lammpstrj
thermo 100
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23676226
grid = 24 24 24
stencil order = 5
estimated absolute RMS force accuracy = 1.3089053e-05
estimated relative force accuracy = 9.089844e-07
using double precision FFTW3
3d grid and FFT values/proc = 29791 13824
Generated 0 of 1 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 = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pedone, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.239 | 9.239 | 9.239 Mbytes
Step Temp E_pair E_mol TotEng Press
0 6000 -3771.5568 0 -3375.2452 34213.185
100 2894.1756 -3562.491 0 -3371.3251 114640.32
200 2980.3531 -3570.2657 0 -3373.4076 123673.56
300 2783.0437 -3574.5809 0 -3390.7554 119791.27
400 3021.6581 -3568.2149 0 -3368.6285 116032.29
500 3112.0438 -3580.0178 0 -3374.4613 114798.18
600 2973.4609 -3577.0582 0 -3380.6553 111843.46
700 3180.1687 -3568.4542 0 -3358.3979 121008.83
800 2923.7803 -3573.3023 0 -3380.181 111459.55
900 2940.3133 -3572.1322 0 -3377.9188 118177.36
1000 3070.2584 -3575.5655 0 -3372.769 114175.52
Loop time of 13.683 on 1 procs for 1000 steps with 512 atoms
Performance: 12.629 ns/day, 1.900 hours/ns, 73.084 timesteps/s, 37.419 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.545 | 11.545 | 11.545 | 0.0 | 84.37
Kspace | 1.4121 | 1.4121 | 1.4121 | 0.0 | 10.32
Neigh | 0.65265 | 0.65265 | 0.65265 | 0.0 | 4.77
Comm | 0.056036 | 0.056036 | 0.056036 | 0.0 | 0.41
Output | 0.00022945 | 0.00022945 | 0.00022945 | 0.0 | 0.00
Modify | 0.0090252 | 0.0090252 | 0.0090252 | 0.0 | 0.07
Other | | 0.00801 | | | 0.06
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10901 ave 10901 max 10901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 374419 ave 374419 max 374419 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 374419
Ave neighs/atom = 731.28711
Neighbor list builds = 71
Dangerous builds = 0
Total wall time: 0:00:13

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examples/PACKAGES/pedone/log.9Apr24.pedone.melt.g++.4 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd)
using 1 OpenMP thread(s) per MPI task
# Ca-O melt with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (19.242 19.242 19.242)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
create_atoms 2 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
mass 1 40.078
mass 2 15.999
set type 1 charge 1.2
Setting atom values ...
256 settings made for charge
set type 2 charge -1.2
Setting atom values ...
256 settings made for charge
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
velocity all create 6000.0 98347
fix 1 all nvt temp 3000.0 3000.0 0.1
# dump 1 all atom 500 Ca-O-melt.lammpstrj
thermo 100
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23676226
grid = 24 24 24
stencil order = 5
estimated absolute RMS force accuracy = 1.3089053e-05
estimated relative force accuracy = 9.089844e-07
using double precision FFTW3
3d grid and FFT values/proc = 11191 3456
Generated 0 of 1 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 = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pedone, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.315 | 5.315 | 5.315 Mbytes
Step Temp E_pair E_mol TotEng Press
0 6000 -3771.5568 0 -3375.2452 34213.185
100 3050.0106 -3571.4712 0 -3370.0121 118480.04
200 3100.0073 -3571.2534 0 -3366.492 120618.37
300 2959.7127 -3580.0883 0 -3384.5935 109184.72
400 2922.7083 -3563.9803 0 -3370.9298 120165.71
500 3145.0439 -3571.3828 0 -3363.6465 115057.51
600 2741.7439 -3563.5077 0 -3382.4102 115504.31
700 2906.3636 -3567.3604 0 -3375.3895 119518.5
800 2995.3864 -3567.3838 0 -3369.5327 117975.22
900 2965.24 -3565.7983 0 -3369.9385 123362.35
1000 2916.6485 -3578.7471 0 -3386.0968 115624.78
Loop time of 4.50395 on 4 procs for 1000 steps with 512 atoms
Performance: 38.366 ns/day, 0.626 hours/ns, 222.028 timesteps/s, 113.678 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2703 | 3.2983 | 3.3259 | 1.3 | 73.23
Kspace | 0.79815 | 0.82633 | 0.85342 | 2.6 | 18.35
Neigh | 0.18328 | 0.18398 | 0.18472 | 0.1 | 4.08
Comm | 0.17423 | 0.17508 | 0.17592 | 0.2 | 3.89
Output | 0.00019336 | 0.0002167 | 0.00028554 | 0.0 | 0.00
Modify | 0.0089842 | 0.0091093 | 0.0092205 | 0.1 | 0.20
Other | | 0.01096 | | | 0.24
Nlocal: 128 ave 143 max 118 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 7622.75 ave 7651 max 7598 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 93581.8 ave 106456 max 84898 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 374327
Ave neighs/atom = 731.10742
Neighbor list builds = 71
Dangerous builds = 0
Total wall time: 0:00:04

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examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.1 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd)
using 1 OpenMP thread(s) per MPI task
# Ca-O crystal with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (19.242 19.242 19.242)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
create_atoms 2 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
mass 1 40.078
mass 2 15.999
displace_atoms all random 0.01 0.01 0.01 9084544
Displacing atoms ...
set type 1 charge 1.2
Setting atom values ...
256 settings made for charge
set type 2 charge -1.2
Setting atom values ...
256 settings made for charge
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
variable len equal lx*0.25
thermo_style custom step v_len lx pe press
thermo 100
fix 1 all box/relax iso 0.0
minimize 0.0 0.0 1000 10000
Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23676226
grid = 24 24 24
stencil order = 5
estimated absolute RMS force accuracy = 1.3089053e-05
estimated relative force accuracy = 9.089844e-07
using double precision FFTW3
3d grid and FFT values/proc = 29791 13824
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pedone, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes
Step v_len Lx PotEng Press
0 4.8105 19.242 -3765.9116 -21299.914
100 4.7797128 19.118851 -3767.814 -164.13101
200 4.7787507 19.115003 -3769.1366 -373.58797
300 4.7768265 19.107306 -3770.5634 48.944709
400 4.7768265 19.107306 -3770.9879 -258.56116
500 4.7758644 19.103458 -3771.3898 173.91894
600 4.7758644 19.103458 -3771.7586 -91.813678
700 4.7758644 19.103458 -3771.9842 -252.52883
800 4.7749023 19.099609 -3772.3526 216.83318
857 4.7747927 19.099171 -3772.8223 32.586251
Loop time of 18.0592 on 1 procs for 857 steps with 512 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3765.91161156884 -3772.82226663623 -3772.82226663623
Force two-norm initial, final = 284.3967 0.46963871
Force max component initial, final = 284.14458 0.42827677
Final line search alpha, max atom move = 2.8580337e-08 1.2240294e-08
Iterations, force evaluations = 857 894
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.907 | 13.907 | 13.907 | 0.0 | 77.01
Kspace | 1.3809 | 1.3809 | 1.3809 | 0.0 | 7.65
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.045871 | 0.045871 | 0.045871 | 0.0 | 0.25
Output | 0.0002809 | 0.0002809 | 0.0002809 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.726 | | | 15.09
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11655 ave 11655 max 11655 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 372155 ave 372155 max 372155 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 372155
Ave neighs/atom = 726.86523
Neighbor list builds = 0
Dangerous builds = 0
print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)"
Expected lattice parameter: 4.7748, computed: 4.7748
Total wall time: 0:00:18

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examples/PACKAGES/pedone/log.9Apr24.pedone.relax.g++.4 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-373-g7ac84e18dd)
using 1 OpenMP thread(s) per MPI task
# Ca-O crystal with Pedone potential
units metal
atom_style charge
lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (19.242 19.242 19.242)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell
Lattice spacing in x,y,z = 4.8105 4.8105 4.8105
create_atoms 2 box
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (19.242 19.242 19.242)
create_atoms CPU = 0.000 seconds
mass 1 40.078
mass 2 15.999
displace_atoms all random 0.01 0.01 0.01 9084544
Displacing atoms ...
set type 1 charge 1.2
Setting atom values ...
256 settings made for charge
set type 2 charge -1.2
Setting atom values ...
256 settings made for charge
timestep 0.002
neigh_modify delay 5 every 1 check yes
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
variable len equal lx*0.25
thermo_style custom step v_len lx pe press
thermo 100
fix 1 all box/relax iso 0.0
minimize 0.0 0.0 1000 10000
Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23676226
grid = 24 24 24
stencil order = 5
estimated absolute RMS force accuracy = 1.3089053e-05
estimated relative force accuracy = 9.089844e-07
using double precision FFTW3
3d grid and FFT values/proc = 11191 3456
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pedone, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 6.44 | 6.44 | 6.44 Mbytes
Step v_len Lx PotEng Press
0 4.8105 19.242 -3765.9116 -21299.914
100 4.7797128 19.118851 -3767.814 -164.13101
200 4.7787507 19.115003 -3769.1367 -373.59489
300 4.7768265 19.107306 -3770.5868 32.046893
400 4.7768265 19.107306 -3771.0322 -290.69703
500 4.7758644 19.103458 -3771.4223 150.34606
600 4.7758644 19.103458 -3771.7941 -117.26938
700 4.7758644 19.103458 -3772.0193 -277.34372
800 4.7749023 19.099609 -3772.42 171.95177
860 4.7748339 19.099336 -3772.8237 1.0976356
Loop time of 5.65601 on 4 procs for 860 steps with 512 atoms
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3765.91161156888 -3772.82365446552 -3772.82365446552
Force two-norm initial, final = 284.3967 0.067746634
Force max component initial, final = 284.14458 0.014426328
Final line search alpha, max atom move = 1.9073486e-06 2.7516038e-08
Iterations, force evaluations = 860 922
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7408 | 3.8442 | 4.0543 | 6.5 | 67.97
Kspace | 0.60187 | 0.81211 | 0.91543 | 14.1 | 14.36
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14969 | 0.15017 | 0.15071 | 0.1 | 2.66
Output | 0.00019203 | 0.00020711 | 0.0002511 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.8494 | | | 15.02
Nlocal: 128 ave 135 max 123 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 8175 ave 8180 max 8168 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 93038.8 ave 98164 max 89373 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 372155
Ave neighs/atom = 726.86523
Neighbor list builds = 0
Dangerous builds = 0
print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)"
Expected lattice parameter: 4.7748, computed: 4.7748
Total wall time: 0:00:05

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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

260
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