Merge branch 'master' of github.com:lammps/lammps
This commit is contained in:
jstewa
@ -14,3 +14,6 @@ use of the `extra/special/per/atom` keyword
|
||||
* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
|
||||
damping)
|
||||
|
||||
* `ethylene_glycol` -- simulation in NpT ensemble with Thole
|
||||
and Tang-Toennies damping and with Nosé-Hoover thermostat
|
||||
|
||||
|
||||
11259
examples/USER/drude/ethylene_glycol/data.ethylene_glycol
Normal file
11259
examples/USER/drude/ethylene_glycol/data.ethylene_glycol
Normal file
File diff suppressed because it is too large
Load Diff
80
examples/USER/drude/ethylene_glycol/in.ethylene_glycol
Normal file
80
examples/USER/drude/ethylene_glycol/in.ethylene_glycol
Normal file
@ -0,0 +1,80 @@
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
|
||||
pair_coeff 1 5 thole 1.662
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||||
pair_coeff 1 6 thole 1.561
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||||
pair_coeff 2 2 thole 1.467
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||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
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||||
pair_coeff 5 5 thole 1.662
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||||
pair_coeff 5 6 thole 1.561
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||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
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||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
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||||
group CORES type 1 2
|
||||
group DRUDES type 5 6
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||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong &
|
||||
press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
|
||||
@ -0,0 +1,200 @@
|
||||
LAMMPS (24 Aug 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
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Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (35.000000 35.000000 35.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2800 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2600 bonds
|
||||
reading angles ...
|
||||
2800 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
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||||
special bond factors lj: 0.0 0.0 0.5
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||||
special bond factors coul: 0.0 0.0 0.5
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5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
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10 = max # of 1-4 neighbors
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||||
13 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
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read_data CPU = 0.023 seconds
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||||
|
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pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
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||||
pair_coeff 1 5 thole 1.662
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||||
pair_coeff 1 6 thole 1.561
|
||||
pair_coeff 2 2 thole 1.467
|
||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
|
||||
pair_coeff 5 5 thole 1.662
|
||||
pair_coeff 5 6 thole 1.561
|
||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1 2
|
||||
800 atoms in group CORES
|
||||
group DRUDES type 5 6
|
||||
800 atoms in group DRUDES
|
||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
400 = # of size 2 clusters
|
||||
400 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 298 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1428)
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 1 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.41206781
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0040479865
|
||||
estimated relative force accuracy = 1.2190391e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 250047 157464
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 13
|
||||
New max number of 1-2 to 1-4 neighbors: 13 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 7 7 7
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair coul/tt, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 39.43 | 39.43 | 39.43 Mbytes
|
||||
Step TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
0 2707.9246 1420.362 1287.5627 1474.8647 30.734202 -461.31379 540022.21 -539778.93 -9408.4231 42875 0.48077588 298 294.34401 6.9394757
|
||||
50 1418.4664 1249.502 168.96443 309.99547 480.01554 -495.04808 539716.53 -540017.02 3344.2851 42776.949 0.48187789 252.07241 255.56807 12.841403
|
||||
100 1391.631 1287.2692 104.36186 333.86636 427.43215 -456.38003 539638.17 -540023.61 -3962.1786 42668.283 0.48310512 265.74273 268.23371 3.3477444
|
||||
150 1404.7861 1334.1949 70.591169 285.69315 480.49154 -340.69071 539518.01 -540045.75 -2082.9182 42395.713 0.48621109 274.19438 278.9463 1.6008228
|
||||
200 1425.8199 1378.4982 47.321668 460.35813 459.3409 -415.44782 539411.67 -540044.6 6205.8012 42117.045 0.48942811 284.32248 288.46225 1.1474711
|
||||
250 1451.5312 1408.0791 43.452124 376.36315 598.2256 -302.5574 539235.03 -540053.8 -3523.5224 41843.302 0.49263001 290.29735 294.90585 0.66499891
|
||||
300 1460.3317 1532.45 -72.118296 394.63946 561.19451 -334.56109 539192.83 -540050.12 4984.7253 41569.486 0.49587493 316.03909 320.8862 0.85911251
|
||||
350 1465.3219 1564.1529 -98.830958 418.42916 585.9688 -296.62501 539077.24 -540036.78 740.62275 41386.895 0.49806264 322.55774 327.69261 0.54088355
|
||||
400 1446.0613 1528.77 -82.708678 414.47172 582.41623 -279.89537 539064.81 -540045.35 -1758.0709 41241.935 0.49981326 314.95112 320.11103 0.86624717
|
||||
450 1411.6647 1569.3338 -157.66914 380.54196 668.12309 -290.80881 538968.32 -540032.63 3122.7219 41154.153 0.50087936 323.38401 328.46391 1.1709084
|
||||
500 1366.0173 1653.6398 -287.62246 433.22615 598.36853 -281.95956 538837.44 -540025.77 -2920.9274 41080.823 0.50177344 340.53461 346.03932 1.3737011
|
||||
Loop time of 21.2526 on 1 procs for 500 steps with 2800 atoms
|
||||
|
||||
Performance: 2.033 ns/day, 11.807 hours/ns, 23.526 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 | 5.0143 | 5.0143 | 5.0143 | 0.0 | 23.59
|
||||
Bond | 0.34285 | 0.34285 | 0.34285 | 0.0 | 1.61
|
||||
Kspace | 7.6454 | 7.6454 | 7.6454 | 0.0 | 35.97
|
||||
Neigh | 0.36282 | 0.36282 | 0.36282 | 0.0 | 1.71
|
||||
Comm | 0.035159 | 0.035159 | 0.035159 | 0.0 | 0.17
|
||||
Output | 0.00068069 | 0.00068069 | 0.00068069 | 0.0 | 0.00
|
||||
Modify | 7.8451 | 7.8451 | 7.8451 | 0.0 | 36.91
|
||||
Other | | 0.006337 | | | 0.03
|
||||
|
||||
Nlocal: 2800.00 ave 2800 max 2800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6816.00 ave 6816 max 6816 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 446966.0 ave 446966 max 446966 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 446966
|
||||
Ave neighs/atom = 159.63071
|
||||
Ave special neighs/atom = 11.714286
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -0,0 +1,200 @@
|
||||
LAMMPS (24 Aug 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (35.000000 35.000000 35.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2800 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2600 bonds
|
||||
reading angles ...
|
||||
2800 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
13 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
|
||||
pair_coeff 1 5 thole 1.662
|
||||
pair_coeff 1 6 thole 1.561
|
||||
pair_coeff 2 2 thole 1.467
|
||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
|
||||
pair_coeff 5 5 thole 1.662
|
||||
pair_coeff 5 6 thole 1.561
|
||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1 2
|
||||
800 atoms in group CORES
|
||||
group DRUDES type 5 6
|
||||
800 atoms in group DRUDES
|
||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
400 = # of size 2 clusters
|
||||
400 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 298 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1428)
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 1 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.41206781
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0040479865
|
||||
estimated relative force accuracy = 1.2190391e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 81648 40824
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 13
|
||||
New max number of 1-2 to 1-4 neighbors: 13 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 7 7 7
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair coul/tt, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.28 | 21.36 | 21.43 Mbytes
|
||||
Step TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
0 2707.9246 1420.362 1287.5627 1474.8647 30.734202 -461.31379 540022.21 -539778.93 -9408.4231 42875 0.48077588 298 294.34401 6.9394757
|
||||
50 1418.4665 1249.502 168.96445 309.99547 480.01554 -495.04808 539716.53 -540017.02 3344.2849 42776.949 0.48187789 252.07241 255.56807 12.841403
|
||||
100 1391.631 1287.2692 104.36189 333.86638 427.43215 -456.38003 539638.17 -540023.61 -3962.1786 42668.283 0.48310512 265.74272 268.23371 3.3477454
|
||||
150 1404.786 1334.1949 70.59104 285.69317 480.49154 -340.6907 539518.01 -540045.75 -2082.9181 42395.713 0.48621109 274.19439 278.9463 1.6008224
|
||||
200 1425.8201 1378.4982 47.32185 460.35819 459.34089 -415.44783 539411.67 -540044.6 6205.8014 42117.045 0.48942811 284.32247 288.46225 1.1474763
|
||||
250 1451.5312 1408.0791 43.45212 376.3631 598.22557 -302.55737 539235.03 -540053.8 -3523.5218 41843.302 0.49263001 290.29734 294.90584 0.66500219
|
||||
300 1460.3316 1532.4498 -72.118238 394.63949 561.1946 -334.56112 539192.83 -540050.12 4984.7226 41569.486 0.49587493 316.03906 320.88617 0.85911374
|
||||
350 1465.322 1564.1496 -98.827597 418.43029 585.96947 -296.62447 539077.24 -540036.78 740.63702 41386.895 0.49806264 322.55705 327.69192 0.54088385
|
||||
400 1446.0613 1528.7739 -82.712576 414.46626 582.41806 -279.89551 539064.81 -540045.35 -1758.0964 41241.935 0.49981326 314.95192 320.11185 0.86625313
|
||||
450 1411.6627 1569.3001 -157.63739 380.53709 668.13885 -290.80678 538968.36 -540032.62 3122.8773 41154.153 0.50087936 323.37686 328.45689 1.170821
|
||||
500 1366.0164 1653.6078 -287.59139 433.23854 598.39638 -281.95272 538837.43 -540025.77 -2921.1108 41080.827 0.50177339 340.52802 346.03257 1.3738053
|
||||
Loop time of 8.54338 on 4 procs for 500 steps with 2800 atoms
|
||||
|
||||
Performance: 5.057 ns/day, 4.746 hours/ns, 58.525 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1432 | 1.2405 | 1.3019 | 5.3 | 14.52
|
||||
Bond | 0.085337 | 0.091544 | 0.097553 | 1.4 | 1.07
|
||||
Kspace | 4.3889 | 4.4519 | 4.5415 | 2.6 | 52.11
|
||||
Neigh | 0.098468 | 0.098565 | 0.098639 | 0.0 | 1.15
|
||||
Comm | 0.090891 | 0.096061 | 0.102 | 1.3 | 1.12
|
||||
Output | 0.00051045 | 0.00081128 | 0.0016632 | 0.0 | 0.01
|
||||
Modify | 2.549 | 2.5525 | 2.5554 | 0.1 | 29.88
|
||||
Other | | 0.01154 | | | 0.14
|
||||
|
||||
Nlocal: 700.000 ave 721 max 665 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4229.75 ave 4342 max 4122 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 111742.0 ave 117831 max 101992 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 446967
|
||||
Ave neighs/atom = 159.63107
|
||||
Ave special neighs/atom = 11.714286
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:08
|
||||
Reference in New Issue
Block a user