Merge branch 'develop' into plumed-plugin
This commit is contained in:
Axel Kohlmeyer
@ -1,629 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
||||
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
||||
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
||||
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
||||
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
||||
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
||||
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
||||
Other | | 0.001615 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
||||
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
||||
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
||||
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
||||
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
||||
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
||||
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
||||
Other | | 0.001596 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
||||
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
||||
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
||||
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
||||
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
||||
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
||||
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
||||
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
||||
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98839e-06
|
||||
12 1.08 8.84111e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168383
|
||||
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
||||
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
||||
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
||||
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
||||
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
||||
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
||||
Other | | 0.001731 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,629 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 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 | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
|
||||
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
|
||||
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
|
||||
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
|
||||
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
|
||||
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
|
||||
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
|
||||
Other | | 0.001141 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
|
||||
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 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 | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
|
||||
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
|
||||
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
|
||||
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
|
||||
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
|
||||
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
|
||||
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
|
||||
Other | | 0.001623 | | | 0.28
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
||||
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
||||
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
||||
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
||||
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
||||
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
||||
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
||||
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
||||
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98838e-06
|
||||
12 1.08 8.84113e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168382
|
||||
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
||||
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
||||
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
||||
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
||||
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
||||
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
||||
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
||||
Other | | 0.001705 | | | 0.29
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 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 | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
||||
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
||||
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
||||
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
||||
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
||||
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
||||
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
||||
Other | | 0.001465 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
|
||||
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
|
||||
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
|
||||
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
|
||||
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
|
||||
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
|
||||
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
|
||||
Other | | 0.001264 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/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 | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
|
||||
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
|
||||
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
|
||||
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
|
||||
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
|
||||
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
|
||||
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
|
||||
Other | | 0.001613 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:02
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
|
||||
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
|
||||
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
|
||||
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
|
||||
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
|
||||
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
|
||||
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
|
||||
Other | | 0.001274 | | | 0.21
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/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 | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
|
||||
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
|
||||
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
|
||||
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
|
||||
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
|
||||
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
|
||||
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
|
||||
Other | | 0.001546 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:02
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
|
||||
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
|
||||
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
|
||||
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
|
||||
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
|
||||
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
|
||||
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
|
||||
Other | | 0.001239 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47
|
||||
Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14
|
||||
Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60
|
||||
Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23
|
||||
Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37
|
||||
Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02
|
||||
Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11
|
||||
Other | | 0.0004941 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15
|
||||
Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15
|
||||
Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01
|
||||
Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14
|
||||
Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34
|
||||
Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02
|
||||
Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488
|
||||
220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387
|
||||
230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815
|
||||
250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023
|
||||
260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102
|
||||
270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492
|
||||
290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70
|
||||
Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15
|
||||
Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79
|
||||
Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82
|
||||
Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35
|
||||
Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02
|
||||
Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42
|
||||
Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18
|
||||
Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30
|
||||
Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07
|
||||
Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38
|
||||
Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06
|
||||
Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44
|
||||
Other | | 0.0003631 | | | 0.15
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036
|
||||
190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 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 | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32
|
||||
Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19
|
||||
Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43
|
||||
Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88
|
||||
Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33
|
||||
Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06
|
||||
Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63
|
||||
Other | | 0.0004069 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488
|
||||
220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387
|
||||
230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815
|
||||
250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023
|
||||
260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104
|
||||
270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
|
||||
290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90
|
||||
Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20
|
||||
Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42
|
||||
Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02
|
||||
Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46
|
||||
Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06
|
||||
Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74
|
||||
Other | | 0.0004738 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
|
||||
Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
|
||||
Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
|
||||
Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
|
||||
Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
|
||||
Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
|
||||
Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
|
||||
Other | | 0.0004888 | | | 0.05
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.253421 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76
|
||||
Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22
|
||||
Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46
|
||||
Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01
|
||||
Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57
|
||||
Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05
|
||||
Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74
|
||||
Other | | 0.0004667 | | | 0.18
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58
|
||||
Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14
|
||||
Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69
|
||||
Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03
|
||||
Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37
|
||||
Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02
|
||||
Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11
|
||||
Other | | 0.0005014 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
|
||||
Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
|
||||
Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
|
||||
Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
|
||||
Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
|
||||
Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
|
||||
Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
|
||||
Other | | 0.0004289 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/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 | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77
|
||||
Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14
|
||||
Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66
|
||||
Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82
|
||||
Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40
|
||||
Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02
|
||||
Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13
|
||||
Other | | 0.0005695 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35
|
||||
Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18
|
||||
Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44
|
||||
Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35
|
||||
Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34
|
||||
Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06
|
||||
Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12
|
||||
Other | | 0.0004197 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 200
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00127732034965e+01
|
||||
x 10.012773203962
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.62235997490241e+00
|
||||
x 9.6223599748448
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00136989326255e+01
|
||||
x 10.013698932648
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 1.00648830006091e+01
|
||||
x 10.064883000604
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -13,191 +13,191 @@
|
||||
11 1.01744058364969e+01 8.66916428851601e+00
|
||||
12 1.01894584969823e+01 8.75011341291751e+00
|
||||
13 1.02015949657517e+01 8.81261373358815e+00
|
||||
14 1.02107634786499e+01 8.86010572643564e+00
|
||||
14 1.02107634786498e+01 8.86010572643564e+00
|
||||
15 1.02172802335367e+01 8.89996164389908e+00
|
||||
16 1.02217586687617e+01 8.94046117354318e+00
|
||||
17 1.02249400729821e+01 8.98764357480963e+00
|
||||
18 1.02274821194763e+01 9.04385418276306e+00
|
||||
19 1.02297694921722e+01 9.10767828090644e+00
|
||||
20 1.02317948794015e+01 9.17521818721732e+00
|
||||
20 1.02317948794015e+01 9.17521818721733e+00
|
||||
21 1.02331324174422e+01 9.24256921345538e+00
|
||||
22 1.02330115052436e+01 9.30670040650459e+00
|
||||
22 1.02330115052436e+01 9.30670040650458e+00
|
||||
23 1.02304888847637e+01 9.36477739916766e+00
|
||||
24 1.02246905091409e+01 9.41471338314027e+00
|
||||
25 1.02150557312054e+01 9.45578119421866e+00
|
||||
26 1.02015018849614e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880334e+00
|
||||
26 1.02015018849613e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880333e+00
|
||||
28 1.01647618536435e+01 9.53348342780342e+00
|
||||
29 1.01435075836914e+01 9.54736918677922e+00
|
||||
30 1.01218448127414e+01 9.55679294480281e+00
|
||||
30 1.01218448127414e+01 9.55679294480282e+00
|
||||
31 1.01008234685872e+01 9.56289707955055e+00
|
||||
32 1.00812605992407e+01 9.56689852729787e+00
|
||||
33 1.00636482078211e+01 9.57008522470066e+00
|
||||
34 1.00481219532447e+01 9.57404682801174e+00
|
||||
35 1.00345149123742e+01 9.58097344406653e+00
|
||||
32 1.00812605992407e+01 9.56689852729789e+00
|
||||
33 1.00636482078211e+01 9.57008522470067e+00
|
||||
34 1.00481219532447e+01 9.57404682801176e+00
|
||||
35 1.00345149123742e+01 9.58097344406654e+00
|
||||
36 1.00224896192326e+01 9.59352147402459e+00
|
||||
37 1.00117065902086e+01 9.61412496221624e+00
|
||||
38 1.00019625883763e+01 9.64369256665448e+00
|
||||
39 9.99324045988116e+00 9.68100279483232e+00
|
||||
40 9.98566198277188e+00 9.72340741886406e+00
|
||||
41 9.97939087537504e+00 9.76737558060000e+00
|
||||
42 9.97455220189940e+00 9.80830263552738e+00
|
||||
43 9.97120052013341e+00 9.84185625268822e+00
|
||||
44 9.96933202180119e+00 9.86623764187619e+00
|
||||
45 9.96891976615505e+00 9.88235950966856e+00
|
||||
46 9.96994868341340e+00 9.89287033859050e+00
|
||||
47 9.97242707411381e+00 9.90111363064262e+00
|
||||
48 9.97636549450466e+00 9.91016536955268e+00
|
||||
49 9.98173560597232e+00 9.92197275407224e+00
|
||||
50 9.98843048433684e+00 9.93674029911159e+00
|
||||
39 9.99324045988117e+00 9.68100279483232e+00
|
||||
40 9.98566198277187e+00 9.72340741886405e+00
|
||||
41 9.97939087537503e+00 9.76737558059998e+00
|
||||
42 9.97455220189941e+00 9.80830263552736e+00
|
||||
43 9.97120052013341e+00 9.84185625268820e+00
|
||||
44 9.96933202180119e+00 9.86623764187617e+00
|
||||
45 9.96891976615505e+00 9.88235950966853e+00
|
||||
46 9.96994868341340e+00 9.89287033859049e+00
|
||||
47 9.97242707411382e+00 9.90111363064261e+00
|
||||
48 9.97636549450467e+00 9.91016536955268e+00
|
||||
49 9.98173560597233e+00 9.92197275407223e+00
|
||||
50 9.98843048433685e+00 9.93674029911158e+00
|
||||
51 9.99624064138588e+00 9.95286099036568e+00
|
||||
52 1.00048525916104e+01 9.96759873289121e+00
|
||||
53 1.00138780764319e+01 9.97821328789638e+00
|
||||
53 1.00138780764319e+01 9.97821328789637e+00
|
||||
54 1.00229204333232e+01 9.98289434996108e+00
|
||||
55 1.00316676518615e+01 9.98113328544968e+00
|
||||
56 1.00399758142293e+01 9.97358294450079e+00
|
||||
57 1.00479031641095e+01 9.96154574170506e+00
|
||||
58 1.00556838347250e+01 9.94624156425743e+00
|
||||
59 1.00636555959318e+01 9.92816580065099e+00
|
||||
60 1.00721640105110e+01 9.90692505955277e+00
|
||||
56 1.00399758142293e+01 9.97358294450078e+00
|
||||
57 1.00479031641095e+01 9.96154574170507e+00
|
||||
58 1.00556838347250e+01 9.94624156425742e+00
|
||||
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177 1.00027910151196e+01 9.75024496660445e+00
|
||||
178 1.00065753987481e+01 9.75188677811518e+00
|
||||
179 1.00099096788152e+01 9.74652424221370e+00
|
||||
180 1.00127256286803e+01 9.73825559920752e+00
|
||||
181 1.00150707365928e+01 9.73120003464725e+00
|
||||
182 1.00170870688102e+01 9.72835139174119e+00
|
||||
183 1.00189588750915e+01 9.73088543078432e+00
|
||||
184 1.00208370578559e+01 9.73798856175907e+00
|
||||
185 1.00227676225361e+01 9.74722631009118e+00
|
||||
186 1.00246552850623e+01 9.75544014363497e+00
|
||||
187 1.00262844441069e+01 9.75985860295140e+00
|
||||
188 1.00273887692830e+01 9.75895346064793e+00
|
||||
189 1.00277400469004e+01 9.75275536661271e+00
|
||||
190 1.00272200717913e+01 9.74261383198996e+00
|
||||
191 1.00258549677417e+01 9.73056754639127e+00
|
||||
192 1.00238089554369e+01 9.71853980943337e+00
|
||||
193 1.00213474450786e+01 9.70762044056817e+00
|
||||
194 1.00187805216026e+01 9.69773175201182e+00
|
||||
195 1.00164016141049e+01 9.68784935170505e+00
|
||||
196 1.00144402663323e+01 9.67667426952134e+00
|
||||
197 1.00130444566844e+01 9.66343938641739e+00
|
||||
198 1.00122912603524e+01 9.64854739402150e+00
|
||||
199 1.00122066751424e+01 9.63383866285097e+00
|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 300
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 9.95315918568411e+00
|
||||
x 9.9531592295885
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.79318883680258e+00
|
||||
x 9.7931889789213
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,102 +1,102 @@
|
||||
# step one two
|
||||
200 1.00127732034965e+01 9.62235997490241e+00
|
||||
201 1.00139198864982e+01 9.61766167925624e+00
|
||||
202 1.00155004339120e+01 9.62284272858813e+00
|
||||
203 1.00172741972246e+01 9.63964899323068e+00
|
||||
204 1.00189052021826e+01 9.66786718571673e+00
|
||||
205 1.00199887119842e+01 9.70521202056400e+00
|
||||
206 1.00201070660155e+01 9.74782380666112e+00
|
||||
207 1.00189089093749e+01 9.79114913038349e+00
|
||||
208 1.00162005540278e+01 9.83091553260188e+00
|
||||
209 1.00120316562035e+01 9.86409994884863e+00
|
||||
210 1.00067394529596e+01 9.88955328455197e+00
|
||||
211 1.00009200584653e+01 9.90798080826055e+00
|
||||
212 9.99531475905311e+00 9.92127385542524e+00
|
||||
213 9.99063400342297e+00 9.93157198661852e+00
|
||||
214 9.98737188807678e+00 9.94051482696048e+00
|
||||
215 9.98567127567181e+00 9.94885527957784e+00
|
||||
216 9.98528704043382e+00 9.95646746111755e+00
|
||||
217 9.98565832937415e+00 9.96275739929720e+00
|
||||
218 9.98606724184677e+00 9.96730423246689e+00
|
||||
219 9.98583582550472e+00 9.97036378703713e+00
|
||||
220 9.98451001643477e+00 9.97292736129215e+00
|
||||
221 9.98198434901656e+00 9.97627439806637e+00
|
||||
222 9.97853678731273e+00 9.98127100659218e+00
|
||||
223 9.97475984191141e+00 9.98785371236258e+00
|
||||
224 9.97140286510626e+00 9.99492286335624e+00
|
||||
225 9.96917137580259e+00 1.00005443231922e+01
|
||||
226 9.96854523900174e+00 1.00023222923235e+01
|
||||
227 9.96967375964547e+00 9.99790273206806e+00
|
||||
228 9.97237636771905e+00 9.98555960216881e+00
|
||||
229 9.97624253505807e+00 9.96473792067690e+00
|
||||
230 9.98078777310055e+00 9.93636511602182e+00
|
||||
231 9.98560846780419e+00 9.90275990393703e+00
|
||||
232 9.99048787217569e+00 9.86710855077386e+00
|
||||
233 9.99543040822038e+00 9.83269539984149e+00
|
||||
234 1.00006246021103e+01 9.80221208335553e+00
|
||||
235 1.00063530848982e+01 9.77738136586701e+00
|
||||
236 1.00128741709083e+01 9.75887400813685e+00
|
||||
237 1.00203106975850e+01 9.74632163179798e+00
|
||||
238 1.00285805371730e+01 9.73844350416337e+00
|
||||
239 1.00373945897865e+01 9.73349215182819e+00
|
||||
240 1.00463194539327e+01 9.72980720779576e+00
|
||||
241 1.00548770491533e+01 9.72611599020063e+00
|
||||
242 1.00626421174965e+01 9.72152572108181e+00
|
||||
243 1.00693109823863e+01 9.71531423107737e+00
|
||||
244 1.00747300690509e+01 9.70668632474813e+00
|
||||
245 1.00788811512303e+01 9.69472082245661e+00
|
||||
246 1.00818281591535e+01 9.67872530149764e+00
|
||||
247 1.00836382918008e+01 9.65899116363609e+00
|
||||
248 1.00843077585461e+01 9.63702967428387e+00
|
||||
249 1.00837304601058e+01 9.61431312359133e+00
|
||||
250 1.00817369874724e+01 9.59193249256670e+00
|
||||
251 1.00781951382998e+01 9.57162234547176e+00
|
||||
252 1.00731274409141e+01 9.55557274350384e+00
|
||||
253 1.00667870632608e+01 9.54560001126946e+00
|
||||
254 1.00596598859158e+01 9.54253147668434e+00
|
||||
255 1.00523956909045e+01 9.54593692832520e+00
|
||||
256 1.00457028282132e+01 9.55423082330650e+00
|
||||
257 1.00402418669526e+01 9.56514761944992e+00
|
||||
258 1.00365397691695e+01 9.57641296971103e+00
|
||||
259 1.00349276270394e+01 9.58620624196598e+00
|
||||
260 1.00355019919770e+01 9.59332346959128e+00
|
||||
261 1.00381137097146e+01 9.59732188686984e+00
|
||||
262 1.00423905760179e+01 9.59837618250971e+00
|
||||
263 1.00477959188736e+01 9.59679324477687e+00
|
||||
264 1.00537068007149e+01 9.59269523141530e+00
|
||||
265 1.00594937260641e+01 9.58610120816249e+00
|
||||
266 1.00645870781682e+01 9.57722117048002e+00
|
||||
267 1.00685316571224e+01 9.56668493985151e+00
|
||||
268 1.00710357823615e+01 9.55556251047062e+00
|
||||
269 1.00720144042107e+01 9.54520978473172e+00
|
||||
270 1.00716144493745e+01 9.53703781183182e+00
|
||||
271 1.00701992199135e+01 9.53227489206590e+00
|
||||
272 1.00682808706064e+01 9.53173333554826e+00
|
||||
273 1.00663988075209e+01 9.53554943194497e+00
|
||||
274 1.00649733063520e+01 9.54299862049767e+00
|
||||
275 1.00641836485840e+01 9.55262143610080e+00
|
||||
276 1.00639178664285e+01 9.56271517955029e+00
|
||||
277 1.00638153921535e+01 9.57192148747872e+00
|
||||
278 1.00633853985923e+01 9.57957875475062e+00
|
||||
279 1.00621626720543e+01 9.58572327394556e+00
|
||||
280 1.00598570838615e+01 9.59085686511578e+00
|
||||
281 1.00564566071967e+01 9.59567423393283e+00
|
||||
282 1.00522576614697e+01 9.60085550637412e+00
|
||||
283 1.00478091897332e+01 9.60690040068280e+00
|
||||
284 1.00437767664032e+01 9.61396708331890e+00
|
||||
285 1.00407546813490e+01 9.62178118810825e+00
|
||||
286 1.00390773261870e+01 9.62975547860500e+00
|
||||
287 1.00386906040191e+01 9.63733595704590e+00
|
||||
288 1.00391292740982e+01 9.64435229335154e+00
|
||||
289 1.00396077171765e+01 9.65114124926381e+00
|
||||
290 1.00391967746350e+01 9.65843904962787e+00
|
||||
291 1.00370409303829e+01 9.66713735495098e+00
|
||||
292 1.00325613495850e+01 9.67798035621834e+00
|
||||
293 1.00255913568518e+01 9.69130440474672e+00
|
||||
294 1.00164044158125e+01 9.70689841022156e+00
|
||||
295 1.00056261321876e+01 9.72399810930261e+00
|
||||
296 9.99406221883501e+00 9.74140402524052e+00
|
||||
297 9.98250803362175e+00 9.75776438941627e+00
|
||||
298 9.97160202027972e+00 9.77203069297329e+00
|
||||
299 9.96175637151037e+00 9.78379375044905e+00
|
||||
300 9.95315918568411e+00 9.79318883680258e+00
|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
201 1.00139198873142e+01 9.61766167960114e+00
|
||||
202 1.00155004349735e+01 9.62284272927993e+00
|
||||
203 1.00172741984288e+01 9.63964899413135e+00
|
||||
204 1.00189052034286e+01 9.66786718668113e+00
|
||||
205 1.00199887131237e+01 9.70521202139326e+00
|
||||
206 1.00201070669505e+01 9.74782380717117e+00
|
||||
207 1.00189089099933e+01 9.79114913037297e+00
|
||||
208 1.00162005542527e+01 9.83091553193592e+00
|
||||
209 1.00120316559893e+01 9.86409994753053e+00
|
||||
210 1.00067394522266e+01 9.88955328278264e+00
|
||||
211 1.00009200570685e+01 9.90798080630807e+00
|
||||
212 9.99531475670037e+00 9.92127385350745e+00
|
||||
213 9.99063399978946e+00 9.93157198491364e+00
|
||||
214 9.98737188290188e+00 9.94051482558046e+00
|
||||
215 9.98567126870035e+00 9.94885527853167e+00
|
||||
216 9.98528703143402e+00 9.95646746044078e+00
|
||||
217 9.98565831825084e+00 9.96275739920543e+00
|
||||
218 9.98606722850532e+00 9.96730423316541e+00
|
||||
219 9.98583581006681e+00 9.97036378874527e+00
|
||||
220 9.98450999905139e+00 9.97292736402649e+00
|
||||
221 9.98198432974296e+00 9.97627440161597e+00
|
||||
222 9.97853676608100e+00 9.98127101043889e+00
|
||||
223 9.97475981847134e+00 9.98785371579891e+00
|
||||
224 9.97140283904510e+00 9.99492286559338e+00
|
||||
225 9.96917134637541e+00 1.00005443234936e+01
|
||||
226 9.96854520536988e+00 1.00023222900809e+01
|
||||
227 9.96967372102824e+00 9.99790272698630e+00
|
||||
228 9.97237632329275e+00 9.98555959429830e+00
|
||||
229 9.97624248419111e+00 9.96473791046628e+00
|
||||
230 9.98078771543058e+00 9.93636510426670e+00
|
||||
231 9.98560840329183e+00 9.90275989164257e+00
|
||||
232 9.99048780094848e+00 9.86710853890991e+00
|
||||
233 9.99543033063032e+00 9.83269538913306e+00
|
||||
234 1.00006245185513e+01 9.80221207423406e+00
|
||||
235 1.00063529959328e+01 9.77738135842695e+00
|
||||
236 1.00128740773079e+01 9.75887400220566e+00
|
||||
237 1.00203106003782e+01 9.74632162713091e+00
|
||||
238 1.00285804376080e+01 9.73844350045589e+00
|
||||
239 1.00373944894039e+01 9.73349214878674e+00
|
||||
240 1.00463193546284e+01 9.72980720512224e+00
|
||||
241 1.00548769529672e+01 9.72611598750665e+00
|
||||
242 1.00626420263492e+01 9.72152571786963e+00
|
||||
243 1.00693108979996e+01 9.71531422666390e+00
|
||||
244 1.00747299927796e+01 9.70668631833486e+00
|
||||
245 1.00788810840328e+01 9.69472081315003e+00
|
||||
246 1.00818281015229e+01 9.67872528846535e+00
|
||||
247 1.00836382438846e+01 9.65899114629446e+00
|
||||
248 1.00843077202414e+01 9.63702965268533e+00
|
||||
249 1.00837304312378e+01 9.61431309843794e+00
|
||||
250 1.00817369677632e+01 9.59193246490958e+00
|
||||
251 1.00781951275561e+01 9.57162231665577e+00
|
||||
252 1.00731274389447e+01 9.55557271498134e+00
|
||||
253 1.00667870699195e+01 9.54559998431332e+00
|
||||
254 1.00596599010604e+01 9.54253145213164e+00
|
||||
255 1.00523957143832e+01 9.54593690642836e+00
|
||||
256 1.00457028598538e+01 9.55423080384305e+00
|
||||
257 1.00402419064054e+01 9.56514760196478e+00
|
||||
258 1.00365398159221e+01 9.57641295373454e+00
|
||||
259 1.00349276804438e+01 9.58620622717253e+00
|
||||
260 1.00355020510841e+01 9.59332345585722e+00
|
||||
261 1.00381137733017e+01 9.59732187421620e+00
|
||||
262 1.00423906427137e+01 9.59837617102817e+00
|
||||
263 1.00477959872900e+01 9.59679323453788e+00
|
||||
264 1.00537068694862e+01 9.59269522224878e+00
|
||||
265 1.00594937939774e+01 9.58610119961332e+00
|
||||
266 1.00645871442695e+01 9.57722116190429e+00
|
||||
267 1.00685317208695e+01 9.56668493059359e+00
|
||||
268 1.00710358435525e+01 9.55556250017823e+00
|
||||
269 1.00720144628669e+01 9.54520977349603e+00
|
||||
270 1.00716145056864e+01 9.53703780013997e+00
|
||||
271 1.00701992741473e+01 9.53227488069496e+00
|
||||
272 1.00682809229059e+01 9.53173332532930e+00
|
||||
273 1.00663988579612e+01 9.53554942356440e+00
|
||||
274 1.00649733547668e+01 9.54299861430164e+00
|
||||
275 1.00641836945973e+01 9.55262143202964e+00
|
||||
276 1.00639179095174e+01 9.56271517715327e+00
|
||||
277 1.00638154316074e+01 9.57192148613520e+00
|
||||
278 1.00633854335686e+01 9.57957875400668e+00
|
||||
279 1.00621627016565e+01 9.58572327370357e+00
|
||||
280 1.00598571070638e+01 9.59085686592320e+00
|
||||
281 1.00564566229803e+01 9.59567423699651e+00
|
||||
282 1.00522576689401e+01 9.60085551333600e+00
|
||||
283 1.00478091881844e+01 9.60690041329352e+00
|
||||
284 1.00437767554115e+01 9.61396710318380e+00
|
||||
285 1.00407546608873e+01 9.62178121653831e+00
|
||||
286 1.00390772967935e+01 9.62975551670189e+00
|
||||
287 1.00386905666453e+01 9.63733600598964e+00
|
||||
288 1.00391292301728e+01 9.64435235461356e+00
|
||||
289 1.00396076684883e+01 9.65114132457984e+00
|
||||
290 1.00391967232973e+01 9.65843914091158e+00
|
||||
291 1.00370408787737e+01 9.66713746391752e+00
|
||||
292 1.00325613002434e+01 9.67798048381559e+00
|
||||
293 1.00255913122523e+01 9.69130455064462e+00
|
||||
294 1.00164043783898e+01 9.70689857240811e+00
|
||||
295 1.00056261042358e+01 9.72399828398139e+00
|
||||
296 9.99406220236070e+00 9.74140420689973e+00
|
||||
297 9.98250803047048e+00 9.75776457125789e+00
|
||||
298 9.97160203186903e+00 9.77203086770013e+00
|
||||
299 9.96175639897897e+00 9.78379391142304e+00
|
||||
300 9.95315922958854e+00 9.79318897892133e+00
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00387423506482e+01
|
||||
x 10.038742350674
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -20,16 +20,16 @@
|
||||
18 9.41602481112176e+00
|
||||
19 9.44413580740584e+00
|
||||
20 9.49001346044027e+00
|
||||
21 9.55036359015270e+00
|
||||
22 9.62258602486444e+00
|
||||
23 9.70460545744668e+00
|
||||
21 9.55036359015271e+00
|
||||
22 9.62258602486445e+00
|
||||
23 9.70460545744666e+00
|
||||
24 9.79475465622561e+00
|
||||
25 9.89135302429916e+00
|
||||
26 9.99213332770717e+00
|
||||
25 9.89135302429913e+00
|
||||
26 9.99213332770716e+00
|
||||
27 1.00938522423366e+01
|
||||
28 1.01925371414626e+01
|
||||
29 1.02845129002944e+01
|
||||
30 1.03676671987640e+01
|
||||
30 1.03676671987639e+01
|
||||
31 1.04416385355998e+01
|
||||
32 1.05071349561950e+01
|
||||
33 1.05650463398331e+01
|
||||
@ -41,39 +41,39 @@
|
||||
39 1.07331870068021e+01
|
||||
40 1.07158913924701e+01
|
||||
41 1.06789115566470e+01
|
||||
42 1.06198840652253e+01
|
||||
42 1.06198840652254e+01
|
||||
43 1.05380097743725e+01
|
||||
44 1.04346581978275e+01
|
||||
45 1.03132910149185e+01
|
||||
46 1.01792819503691e+01
|
||||
46 1.01792819503692e+01
|
||||
47 1.00398949454818e+01
|
||||
48 9.90373650268307e+00
|
||||
49 9.77934647164350e+00
|
||||
50 9.67343955381284e+00
|
||||
51 9.58957255517495e+00
|
||||
52 9.52771577288560e+00
|
||||
53 9.48463495848957e+00
|
||||
54 9.45495747488851e+00
|
||||
55 9.43277083061229e+00
|
||||
56 9.41329510571902e+00
|
||||
57 9.39417852043035e+00
|
||||
49 9.77934647164349e+00
|
||||
50 9.67343955381283e+00
|
||||
51 9.58957255517494e+00
|
||||
52 9.52771577288559e+00
|
||||
53 9.48463495848955e+00
|
||||
54 9.45495747488850e+00
|
||||
55 9.43277083061230e+00
|
||||
56 9.41329510571900e+00
|
||||
57 9.39417852043034e+00
|
||||
58 9.37607916767444e+00
|
||||
59 9.36243879601093e+00
|
||||
60 9.35853234890725e+00
|
||||
61 9.36993739187210e+00
|
||||
62 9.40084256925489e+00
|
||||
59 9.36243879601092e+00
|
||||
60 9.35853234890724e+00
|
||||
61 9.36993739187209e+00
|
||||
62 9.40084256925487e+00
|
||||
63 9.45286356660258e+00
|
||||
64 9.52464585631223e+00
|
||||
65 9.61230948096192e+00
|
||||
66 9.71074418990813e+00
|
||||
67 9.81507236552599e+00
|
||||
68 9.92117974657176e+00
|
||||
69 1.00244259961919e+01
|
||||
66 9.71074418990814e+00
|
||||
67 9.81507236552600e+00
|
||||
68 9.92117974657179e+00
|
||||
69 1.00244259961920e+01
|
||||
70 1.01178306268727e+01
|
||||
71 1.01986985644537e+01
|
||||
71 1.01986985644538e+01
|
||||
72 1.02671003889995e+01
|
||||
73 1.03213098011429e+01
|
||||
74 1.03597236984298e+01
|
||||
73 1.03213098011430e+01
|
||||
74 1.03597236984299e+01
|
||||
75 1.03817789163109e+01
|
||||
76 1.03880650963390e+01
|
||||
77 1.03809140245635e+01
|
||||
@ -82,21 +82,21 @@
|
||||
80 1.03243676495902e+01
|
||||
81 1.03082131278348e+01
|
||||
82 1.02961310659179e+01
|
||||
83 1.02862115513553e+01
|
||||
83 1.02862115513552e+01
|
||||
84 1.02756073299153e+01
|
||||
85 1.02618115461408e+01
|
||||
86 1.02435127550163e+01
|
||||
87 1.02212112849545e+01
|
||||
88 1.01972788307491e+01
|
||||
89 1.01743918261207e+01
|
||||
89 1.01743918261206e+01
|
||||
90 1.01538328424605e+01
|
||||
91 1.01363005552771e+01
|
||||
92 1.01223066231827e+01
|
||||
93 1.01118037967830e+01
|
||||
92 1.01223066231826e+01
|
||||
93 1.01118037967829e+01
|
||||
94 1.01038502876980e+01
|
||||
95 1.00967012947728e+01
|
||||
96 1.00885779123137e+01
|
||||
97 1.00784256309007e+01
|
||||
98 1.00661429612272e+01
|
||||
99 1.00524913461711e+01
|
||||
100 1.00387423506482e+01
|
||||
95 1.00967012947726e+01
|
||||
96 1.00885779123133e+01
|
||||
97 1.00784256308996e+01
|
||||
98 1.00661429612359e+01
|
||||
99 1.00524913461887e+01
|
||||
100 1.00387423506735e+01
|
||||
|
||||
@ -16,7 +16,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} -0.5 0.5 units box
|
||||
create_box 4 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -14,7 +14,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
region box block -$L $L -$L $L -0.5 0.5 units box
|
||||
create_box 2 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
#dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
|
||||
run 100000
|
||||
run 100000
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
@ -24,8 +24,8 @@ variable erres equal c_energies[4]
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
||||
|
||||
min_style cg
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4_ionized
|
||||
variable sname index ch4_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 5000.0 0 0
|
||||
pair_coeff * *
|
||||
pair_style eff/cut 5000.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# minimize
|
||||
|
||||
@ -20,23 +20,23 @@ min_modify line quadratic
|
||||
minimize 0 1.0e-6 10000 100000
|
||||
|
||||
# dynamics
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# equilibrate
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
# the custom dump includes the radii
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
#dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
#dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
fix 2 all nve/eff
|
||||
fix 2 all nve/eff
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
@ -0,0 +1,266 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, 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) = 5.405 | 5.405 | 5.405 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 1.3464499
|
||||
Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms
|
||||
|
||||
88.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331247 -34.0744796893375 -34.0744796893447
|
||||
Force two-norm initial, final = 10.728716 0.00017815706
|
||||
Force max component initial, final = 6.1727999 8.2675815e-05
|
||||
Final line search alpha, max atom move = 1 8.2675815e-05
|
||||
Iterations, force evaluations = 1000 1943
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40
|
||||
Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.001604 | | | 5.20
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 392.66426
|
||||
2000 -34.065618 583.71716 -618.55027
|
||||
3000 -34.063563 475.54605 661.95076
|
||||
4000 -34.06119 350.76183 -449.64687
|
||||
5000 -34.0652 561.71223 -131.2575
|
||||
6000 -34.065798 593.21728 754.38406
|
||||
7000 -34.067408 677.86019 -409.21139
|
||||
8000 -34.065663 586.03411 446.32573
|
||||
9000 -34.06294 442.71136 414.41408
|
||||
10000 -34.060101 293.33406 -1203.0131
|
||||
11000 -34.064946 548.39598 345.29601
|
||||
12000 -34.067323 673.49043 444.55927
|
||||
13000 -34.063275 460.43973 -854.83884
|
||||
14000 -34.064666 533.57265 1542.0127
|
||||
15000 -34.063343 463.97449 -778.73252
|
||||
16000 -34.064462 522.77625 -1.5339614
|
||||
17000 -34.061203 351.37068 -148.19163
|
||||
18000 -34.066534 631.87837 -237.0746
|
||||
19000 -34.065169 560.16772 1360.7348
|
||||
20000 -34.063042 448.13104 -664.72128
|
||||
21000 -34.060696 324.68723 -167.83333
|
||||
22000 -34.065376 570.90279 -831.73853
|
||||
23000 -34.063127 452.61143 766.59984
|
||||
24000 -34.064572 528.62282 -107.80755
|
||||
25000 -34.06584 595.42175 610.33075
|
||||
26000 -34.066886 650.43579 -894.20521
|
||||
27000 -34.062035 395.20224 1754.7666
|
||||
28000 -34.060696 324.66878 -2622.013
|
||||
29000 -34.066777 644.66282 1551.3147
|
||||
30000 -34.066421 625.94614 -507.44173
|
||||
31000 -34.066163 612.36658 610.11907
|
||||
32000 -34.063109 451.70185 -47.463209
|
||||
33000 -34.062833 437.16794 -607.25848
|
||||
34000 -34.061657 375.30056 -158.28097
|
||||
35000 -34.064937 547.86519 272.75585
|
||||
36000 -34.067509 683.23088 359.91072
|
||||
37000 -34.067582 686.96461 -384.97405
|
||||
38000 -34.063213 457.13191 411.86349
|
||||
39000 -34.06272 431.13187 -594.23723
|
||||
40000 -34.062286 408.41212 456.09079
|
||||
41000 -34.064078 502.64096 -1149.8496
|
||||
42000 -34.066408 625.33334 1403.4937
|
||||
43000 -34.065948 601.03876 -773.40678
|
||||
44000 -34.064113 504.49498 179.93456
|
||||
45000 -34.060573 318.11433 223.38679
|
||||
46000 -34.063614 478.24588 -409.99081
|
||||
47000 -34.064814 541.38544 614.25246
|
||||
48000 -34.065602 582.87984 -743.92184
|
||||
49000 -34.063923 494.52673 474.88127
|
||||
50000 -34.064616 530.94533 288.81199
|
||||
51000 -34.062038 395.2991 -480.07513
|
||||
52000 -34.06497 549.5123 -305.53764
|
||||
53000 -34.065578 581.59919 964.80956
|
||||
54000 -34.06766 691.12707 -437.99603
|
||||
55000 -34.064707 535.85658 1058.6734
|
||||
56000 -34.062481 418.58003 -1011.5341
|
||||
57000 -34.064997 551.06731 -32.91724
|
||||
58000 -34.064281 513.25358 374.91628
|
||||
59000 -34.066177 613.1188 -464.85124
|
||||
60000 -34.064718 536.29803 1011.6698
|
||||
61000 -34.065746 590.46955 -1057.9241
|
||||
62000 -34.063253 459.23293 1526.2698
|
||||
63000 -34.062261 407.08636 -1743.6652
|
||||
64000 -34.063835 489.88286 761.60266
|
||||
65000 -34.069569 791.614 323.26812
|
||||
66000 -34.065557 580.45685 874.52459
|
||||
67000 -34.064917 546.77223 -1349.3606
|
||||
68000 -34.062963 443.96697 1178.4319
|
||||
69000 -34.063063 449.26418 -1660.686
|
||||
70000 -34.063597 477.39716 1323.13
|
||||
71000 -34.065424 573.47914 -131.55428
|
||||
72000 -34.065211 562.31067 -415.56361
|
||||
73000 -34.06339 466.38097 724.92885
|
||||
74000 -34.062286 408.34027 -1094.3845
|
||||
75000 -34.065545 579.79767 587.58121
|
||||
76000 -34.066774 644.61685 -357.22241
|
||||
77000 -34.064479 523.74831 1545.6628
|
||||
78000 -34.065506 577.88405 -1013.2409
|
||||
79000 -34.062874 439.24856 240.66725
|
||||
80000 -34.06306 449.09678 -799.14252
|
||||
81000 -34.063338 463.66067 1528.3351
|
||||
82000 -34.066812 646.52985 -1351.1758
|
||||
83000 -34.064724 536.65114 1338.595
|
||||
84000 -34.063774 486.67172 -876.0475
|
||||
85000 -34.06156 370.19256 617.89915
|
||||
86000 -34.063628 478.95398 -134.40164
|
||||
87000 -34.065141 558.60424 -758.03942
|
||||
88000 -34.066732 642.27865 1159.5992
|
||||
89000 -34.067349 674.83453 -301.45201
|
||||
90000 -34.063623 478.69626 386.87752
|
||||
91000 -34.061885 387.30728 -774.32296
|
||||
92000 -34.061363 359.77745 500.06117
|
||||
93000 -34.065724 589.32209 -469.10399
|
||||
94000 -34.065006 551.42796 818.92294
|
||||
95000 -34.06541 572.75191 -677.20865
|
||||
96000 -34.062331 410.64868 1383.8935
|
||||
97000 -34.061499 366.95753 -1715.2058
|
||||
98000 -34.061153 348.68703 353.63545
|
||||
99000 -34.066217 615.27816 193.79593
|
||||
100000 -34.067739 695.36238 205.35389
|
||||
101000 -34.067314 672.94727 929.41223
|
||||
Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s
|
||||
85.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28
|
||||
Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62
|
||||
Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80
|
||||
Other | | 0.01755 | | | 0.79
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
@ -0,0 +1,266 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, 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) = 5.385 | 5.385 | 5.385 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 0.39495391
|
||||
Loop time of 0.0230482 on 4 procs for 1000 steps with 15 atoms
|
||||
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331249 -34.0744796901924 -34.0744796901707
|
||||
Force two-norm initial, final = 10.728716 0.00024139276
|
||||
Force max component initial, final = 6.1727999 0.00017091779
|
||||
Final line search alpha, max atom move = 1 0.00017091779
|
||||
Iterations, force evaluations = 1000 1946
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015331 | 0.0032095 | 0.0046681 | 2.0 | 13.93
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0037211 | 0.0053887 | 0.0069902 | 1.6 | 23.38
|
||||
Output | 0.0062087 | 0.0079064 | 0.011172 | 2.2 | 34.30
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006544 | | | 28.39
|
||||
|
||||
Nlocal: 3.75 ave 6 max 3 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 26.25 ave 39 max 12 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 391.71277
|
||||
2000 -34.065618 583.70724 -617.78946
|
||||
3000 -34.063563 475.53779 661.75865
|
||||
4000 -34.06119 350.74901 -449.8917
|
||||
5000 -34.065201 561.76559 -130.73147
|
||||
6000 -34.065798 593.21893 753.94281
|
||||
7000 -34.067408 677.86552 -409.14034
|
||||
8000 -34.065662 586.02658 446.74947
|
||||
9000 -34.062939 442.6953 413.93386
|
||||
10000 -34.060101 293.35262 -1202.4169
|
||||
11000 -34.064946 548.37877 344.89658
|
||||
12000 -34.067324 673.52389 444.40605
|
||||
13000 -34.063275 460.44923 -854.41022
|
||||
14000 -34.064667 533.59655 1541.2922
|
||||
15000 -34.063344 464.01572 -777.83895
|
||||
16000 -34.064461 522.76554 -2.2050586
|
||||
17000 -34.061202 351.31261 -148.09486
|
||||
18000 -34.066534 631.89021 -236.72076
|
||||
19000 -34.065169 560.16576 1359.8928
|
||||
20000 -34.063042 448.14707 -663.76152
|
||||
21000 -34.060695 324.66945 -168.3252
|
||||
22000 -34.065376 570.90677 -831.8481
|
||||
23000 -34.063127 452.62391 767.31463
|
||||
24000 -34.064572 528.62018 -108.63204
|
||||
25000 -34.06584 595.41818 610.87995
|
||||
26000 -34.066885 650.4263 -894.11862
|
||||
27000 -34.062035 395.1876 1754.1737
|
||||
28000 -34.060697 324.71187 -2621.333
|
||||
29000 -34.066777 644.68166 1550.7046
|
||||
30000 -34.066421 625.9368 -507.12512
|
||||
31000 -34.066163 612.3605 610.12993
|
||||
32000 -34.063108 451.66459 -48.049967
|
||||
33000 -34.062834 437.21062 -606.58502
|
||||
34000 -34.061656 375.26971 -158.76936
|
||||
35000 -34.064938 547.90576 273.26572
|
||||
36000 -34.067508 683.20936 360.05973
|
||||
37000 -34.067582 686.96938 -385.62265
|
||||
38000 -34.063213 457.13708 412.74004
|
||||
39000 -34.06272 431.16474 -595.05437
|
||||
40000 -34.062285 408.38247 456.29631
|
||||
41000 -34.064078 502.65934 -1149.196
|
||||
42000 -34.066408 625.33356 1402.5676
|
||||
43000 -34.065948 601.04311 -772.96544
|
||||
44000 -34.064113 504.47553 179.83988
|
||||
45000 -34.060572 318.08821 222.85125
|
||||
46000 -34.063614 478.25613 -409.06152
|
||||
47000 -34.064813 541.37361 613.37159
|
||||
48000 -34.065602 582.88704 -743.72019
|
||||
49000 -34.063922 494.52189 475.22811
|
||||
50000 -34.064616 530.95516 288.46302
|
||||
51000 -34.062038 395.30091 -479.68548
|
||||
52000 -34.06497 549.50477 -305.82851
|
||||
53000 -34.065577 581.56927 964.95886
|
||||
54000 -34.06766 691.14533 -437.95563
|
||||
55000 -34.064707 535.85441 1058.0886
|
||||
56000 -34.062481 418.62259 -1010.5517
|
||||
57000 -34.064996 551.02074 -33.54291
|
||||
58000 -34.064281 513.27818 375.07194
|
||||
59000 -34.066177 613.11494 -464.71576
|
||||
60000 -34.064718 536.306 1010.9545
|
||||
61000 -34.065746 590.47317 -1056.9192
|
||||
62000 -34.063252 459.22005 1525.6789
|
||||
63000 -34.06226 407.05859 -1743.9974
|
||||
64000 -34.063836 489.91026 762.61836
|
||||
65000 -34.069569 791.63831 322.35333
|
||||
66000 -34.065557 580.46799 875.11714
|
||||
67000 -34.064916 546.74052 -1349.5741
|
||||
68000 -34.062962 443.93438 1178.1978
|
||||
69000 -34.063064 449.3052 -1659.8695
|
||||
70000 -34.063596 477.36452 1322.0559
|
||||
71000 -34.065424 573.49586 -131.11749
|
||||
72000 -34.06521 562.24612 -415.25895
|
||||
73000 -34.06339 466.38351 724.08642
|
||||
74000 -34.062286 408.37673 -1093.6751
|
||||
75000 -34.065545 579.81257 586.8907
|
||||
76000 -34.066774 644.62609 -356.7044
|
||||
77000 -34.064479 523.75235 1545.8498
|
||||
78000 -34.065506 577.88123 -1014.0878
|
||||
79000 -34.062875 439.30997 241.55748
|
||||
80000 -34.06306 449.06553 -799.58139
|
||||
81000 -34.063338 463.64261 1528.4412
|
||||
82000 -34.066812 646.55603 -1350.9377
|
||||
83000 -34.064724 536.63793 1338.2148
|
||||
84000 -34.063774 486.717 -875.60363
|
||||
85000 -34.06156 370.19433 617.85579
|
||||
86000 -34.063628 478.9961 -135.13703
|
||||
87000 -34.065141 558.62541 -756.91518
|
||||
88000 -34.066732 642.27743 1158.5797
|
||||
89000 -34.067351 674.92164 -300.79164
|
||||
90000 -34.063624 478.70378 386.44004
|
||||
91000 -34.061884 387.27577 -774.22945
|
||||
92000 -34.061364 359.79856 500.36442
|
||||
93000 -34.065723 589.31234 -469.57015
|
||||
94000 -34.065006 551.46665 819.01826
|
||||
95000 -34.065409 572.7351 -676.74519
|
||||
96000 -34.06233 410.60509 1382.9732
|
||||
97000 -34.0615 366.99019 -1714.2302
|
||||
98000 -34.061152 348.67783 352.89211
|
||||
99000 -34.066217 615.29222 193.8722
|
||||
100000 -34.067739 695.32836 206.03841
|
||||
101000 -34.067313 672.90918 928.0541
|
||||
Loop time of 1.62544 on 4 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 26577371.575 fs/day, 0.000 hours/fs, 61521.693 timesteps/s, 922.825 katom-step/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.066581 | 0.15332 | 0.25928 | 21.7 | 9.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.18521 | 0.29733 | 0.3879 | 16.1 | 18.29
|
||||
Output | 0.66513 | 0.81838 | 1.1333 | 20.4 | 50.35
|
||||
Modify | 0.01285 | 0.014237 | 0.016092 | 1.0 | 0.88
|
||||
Other | | 0.3422 | | | 21.05
|
||||
|
||||
Nlocal: 3.75 ave 5 max 3 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 10 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 26.25 ave 47 max 10 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -3,12 +3,11 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,12 +38,12 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 2 ${sname}.min.xyz
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
|
||||
@ -3,18 +3,17 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6.ang
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_style eff/cut 529.177249 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,21 +38,21 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
#dump 1 all xyz 10 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 2000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
|
||||
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
@ -0,0 +1,185 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, 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) = 6.098 | 6.098 | 6.098 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311526 -15.311526
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.10049441 -0.10049441
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138433 -0.12138433
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175181 -1.2175181
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979907 -0.80979907
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945578 -0.85945578
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534716 -0.95534716
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220676 -0.89220676
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44630696 -0.44630696
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919073 -0.72919073
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056004 -17.440392 0 0 -0.049410442 -0.049410442
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025063323 -0.025063323
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010779864 -0.010779864
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087251782 0.087251782
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822668 -0.13822668
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043786214 -0.043786214
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054938 -17.440458 0 0 -0.10833476 -0.10833476
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.04772439 -0.04772439
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055815521 -0.055815521
|
||||
Loop time of 0.00236996 on 1 procs for 88 steps with 22 atoms
|
||||
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620961 -10.4595390706544 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.8001667e-06
|
||||
Force max component initial, final = 1.8019385 2.1391495e-06
|
||||
Final line search alpha, max atom move = 1 2.1391495e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0019013 | 0.0019013 | 0.0019013 | 0.0 | 80.23
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.926e-06 | 7.926e-06 | 7.926e-06 | 0.0 | 0.33
|
||||
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 11.64
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0001848 | | | 7.80
|
||||
|
||||
Nlocal: 22 ave 22 max 22 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 231 ave 231 max 231 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
@ -0,0 +1,185 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, 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) = 6.113 | 6.113 | 6.113 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311525 -15.311525
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.1004938 -0.1004938
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138436 -0.12138436
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175176 -1.2175176
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979946 -0.80979946
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945162 -0.85945162
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534903 -0.95534903
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220297 -0.89220297
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44631358 -0.44631358
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919322 -0.72919322
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056005 -17.440392 0 0 -0.049401694 -0.049401694
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025056381 -0.025056381
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010774653 -0.010774653
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087250755 0.087250755
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822694 -0.13822694
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043784806 -0.043784806
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054937 -17.440458 0 0 -0.10833935 -0.10833935
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.047719128 -0.047719128
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055818341 -0.055818341
|
||||
Loop time of 0.00213866 on 4 procs for 88 steps with 22 atoms
|
||||
|
||||
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620958 -10.4595390706543 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.7997573e-06
|
||||
Force max component initial, final = 1.8019385 2.1386971e-06
|
||||
Final line search alpha, max atom move = 1 2.1386971e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027642 | 0.00052972 | 0.00096856 | 0.0 | 24.77
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00035997 | 0.00081245 | 0.0010746 | 0.0 | 37.99
|
||||
Output | 0.00037064 | 0.00039193 | 0.00045231 | 0.0 | 18.33
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0004046 | | | 18.92
|
||||
|
||||
Nlocal: 5.5 ave 7 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 16.5 ave 19 max 15 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 57.75 ave 109 max 29 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/AlCu.eam.alloy
|
||||
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/SiC.tersoff.zbl
|
||||
@ -12,8 +12,8 @@ region box block -10 10 -10 10 -10 10
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * AlCu.eam.alloy Al Cu
|
||||
|
||||
mass 1 26.982
|
||||
mass 2 63.546
|
||||
|
||||
@ -13,7 +13,7 @@ create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style tersoff/zbl
|
||||
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
|
||||
pair_coeff * * SiC.tersoff.zbl Si
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
|
||||
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/COH.DMC.aip.water.2dm
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -457,9 +457,9 @@ mass *4 ${wheel_mass}
|
||||
variable dx equal 1.0
|
||||
variable density equal 0.001184
|
||||
|
||||
neighbor 0.5 bin
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
comm_modify cutoff 3.0
|
||||
comm_modify cutoff 3.0
|
||||
|
||||
pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
@ -474,7 +474,7 @@ reset_timestep 0
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-653-ge4a654c7cd-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#===========================================================================#
|
||||
# Toy car driving down a system with a floor and ceiling. #
|
||||
# #
|
||||
@ -12,6 +14,7 @@ units cgs
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
processors * 1 *
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Set up the simulation box
|
||||
@ -36,7 +39,7 @@ region mybox block -48 48 -90 630 -9 ${zh}
|
||||
region mybox block -48 48 -90 630 -9 87
|
||||
create_box 14 mybox
|
||||
Created orthogonal box = (-48 -90 -9) to (48 630 87)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
2 by 1 by 2 MPI processor grid
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Creating the regions and filling them with atoms assigned to surge_group
|
||||
@ -647,9 +650,9 @@ fix 2 all nve
|
||||
#restart 100000 ParticleRestart
|
||||
|
||||
run 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5255396
|
||||
ghost atom cutoff = 2.5255396
|
||||
@ -660,53 +663,53 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.245 | 5.007 | 7.291 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29877588 4.6948567e-06 0 3.6195804e-05 3.987621e-12
|
||||
10000 27827776 7.2619763e-06 0 3.6601737e-05 4.407525e-12
|
||||
15000 26336751 8.3045873e-06 0 3.6072311e-05 4.7591238e-12
|
||||
20000 25052655 8.3618019e-06 0 3.477566e-05 5.0138704e-12
|
||||
25000 23854604 8.149944e-06 0 3.3300657e-05 5.1772301e-12
|
||||
30000 21629039 8.0369285e-06 0 3.0841153e-05 5.3056994e-12
|
||||
35000 20550367 7.0527369e-06 0 2.8719681e-05 5.253199e-12
|
||||
40000 18310227 6.4085866e-06 0 2.5713675e-05 5.1263402e-12
|
||||
45000 16963286 5.9460113e-06 0 2.3830975e-05 5.0913287e-12
|
||||
50000 15639408 5.1326227e-06 0 2.1621777e-05 4.8649712e-12
|
||||
55000 14004560 4.550004e-06 0 1.9315483e-05 4.6920784e-12
|
||||
60000 12777371 3.941146e-06 0 1.7412759e-05 4.4574594e-12
|
||||
65000 10919170 3.3361501e-06 0 1.4848599e-05 4.1051819e-12
|
||||
70000 9469421.4 2.7031575e-06 0 1.2687087e-05 3.7302586e-12
|
||||
75000 7926062.4 2.054775e-06 0 1.0411489e-05 3.3099123e-12
|
||||
80000 6314071.7 1.5118865e-06 0 8.169025e-06 2.8050899e-12
|
||||
85000 4847441.7 1.0803078e-06 0 6.1911288e-06 2.3005982e-12
|
||||
90000 3260324.1 6.858841e-07 0 4.1233536e-06 1.7789287e-12
|
||||
95000 1724645.4 3.1351302e-07 0 2.1318647e-06 1.1211538e-12
|
||||
100000 218390.81 4.4631827e-08 0 2.7488861e-07 3.8685559e-13
|
||||
Loop time of 647.752 on 4 procs for 100000 steps with 5092 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.685 | 6.044 | 7.403 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29842261 4.7942025e-06 0 3.6257904e-05 3.9879238e-12
|
||||
10000 28098061 7.2385794e-06 0 3.6863311e-05 4.4347259e-12
|
||||
15000 26888635 8.1191579e-06 0 3.6468752e-05 4.7939026e-12
|
||||
20000 24887991 8.3385518e-06 0 3.4578799e-05 4.9862342e-12
|
||||
25000 23265144 8.3946029e-06 0 3.2923828e-05 5.1750035e-12
|
||||
30000 21711263 7.6172235e-06 0 3.0508139e-05 5.2324506e-12
|
||||
35000 20102910 7.2232838e-06 0 2.8418459e-05 5.2342282e-12
|
||||
40000 18634097 6.5402802e-06 0 2.6186836e-05 5.2128024e-12
|
||||
45000 17486541 5.6292406e-06 0 2.4065889e-05 5.0867315e-12
|
||||
50000 15741195 4.96711e-06 0 2.1563581e-05 4.8546007e-12
|
||||
55000 14195280 4.6806146e-06 0 1.9647177e-05 4.7201162e-12
|
||||
60000 12378448 3.8806954e-06 0 1.693171e-05 4.3985323e-12
|
||||
65000 10976639 3.3069428e-06 0 1.4879983e-05 4.1055737e-12
|
||||
70000 9434340 2.6574414e-06 0 1.2604384e-05 3.703813e-12
|
||||
75000 7827664.3 2.1262358e-06 0 1.0379206e-05 3.3234802e-12
|
||||
80000 6487719.3 1.6234085e-06 0 8.4636294e-06 2.878629e-12
|
||||
85000 4761145.2 1.1556952e-06 0 6.175531e-06 2.3647084e-12
|
||||
90000 3196900 6.7497651e-07 0 4.0455759e-06 1.7461024e-12
|
||||
95000 1711466.2 3.2662861e-07 0 2.1310851e-06 1.1318791e-12
|
||||
100000 217597.05 4.394432e-08 0 2.7336422e-07 3.7619707e-13
|
||||
Loop time of 131.294 on 4 procs for 100000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.036284 | 19.922 | 79.572 | 771.6 | 3.08
|
||||
Neigh | 10.175 | 17.392 | 38.739 | 295.5 | 2.69
|
||||
Comm | 0.97616 | 1.0979 | 1.2312 | 8.6 | 0.17
|
||||
Output | 0.0043794 | 0.098646 | 0.13021 | 17.3 | 0.02
|
||||
Modify | 1.2262 | 132.11 | 524.58 |1971.4 | 20.39
|
||||
Other | | 477.1 | | | 73.66
|
||||
Pair | 0.0045648 | 9.3721 | 18.946 | 306.0 | 7.14
|
||||
Neigh | 2.8643 | 5.951 | 9.063 | 125.7 | 4.53
|
||||
Comm | 0.3616 | 0.90559 | 1.7801 | 61.8 | 0.69
|
||||
Output | 0.00058742 | 0.013642 | 0.026668 | 11.2 | 0.01
|
||||
Modify | 0.17841 | 50.602 | 101.42 | 708.8 | 38.54
|
||||
Other | | 64.45 | | | 49.09
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19856 ave 79424 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2549 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 247 ave 496 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19929 ave 39908 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 79424
|
||||
Ave neighs/atom = 15.5978
|
||||
Neighbor list builds = 4946
|
||||
Total # of neighbors = 79716
|
||||
Ave neighs/atom = 15.655145
|
||||
Neighbor list builds = 4954
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
@ -743,114 +746,114 @@ fix 3 all langevin 100000.0 5000.0 100.0 5678
|
||||
fix 2 all nve
|
||||
|
||||
run 200000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.179 | 7.463 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 218390.81 0 0 2.3025679e-07 2.3133759e-14
|
||||
105000 103860.18 6.708614e-08 0 1.7658943e-07 6.9220989e-13
|
||||
110000 97287.339 7.0116647e-08 0 1.7268996e-07 7.4104867e-13
|
||||
115000 92211.102 6.7456604e-08 0 1.6467788e-07 7.2196879e-13
|
||||
120000 91577.119 6.8360083e-08 0 1.6491292e-07 7.3664397e-13
|
||||
125000 89670.176 6.7876707e-08 0 1.6241899e-07 7.29547e-13
|
||||
130000 87135.819 6.6698539e-08 0 1.5856877e-07 7.296178e-13
|
||||
135000 84795.008 6.3054439e-08 0 1.5245667e-07 7.1371044e-13
|
||||
140000 81222.266 6.4732255e-08 0 1.5036763e-07 7.2429578e-13
|
||||
145000 78548.301 6.3633278e-08 0 1.464494e-07 7.1795316e-13
|
||||
150000 76597.034 6.3093645e-08 0 1.4385248e-07 7.1457515e-13
|
||||
155000 73820.896 6.0685032e-08 0 1.3851689e-07 7.1093329e-13
|
||||
160000 71360.569 6.2615029e-08 0 1.3785288e-07 7.2019292e-13
|
||||
165000 67879.165 5.9691015e-08 0 1.3125831e-07 7.0403501e-13
|
||||
170000 66641.482 5.9273104e-08 0 1.2953546e-07 7.0719355e-13
|
||||
175000 65623.831 6.011737e-08 0 1.2930679e-07 7.1498836e-13
|
||||
180000 63627.376 5.8380162e-08 0 1.2546465e-07 7.0457247e-13
|
||||
185000 60865.93 5.8039489e-08 0 1.2221249e-07 7.1190327e-13
|
||||
190000 57329.276 5.8432616e-08 0 1.188768e-07 7.1940596e-13
|
||||
195000 54829.503 5.6354458e-08 0 1.1416305e-07 7.0364147e-13
|
||||
200000 52720.064 5.4124289e-08 0 1.0970883e-07 6.935829e-13
|
||||
205000 50368.95 5.4872306e-08 0 1.0797799e-07 7.0426031e-13
|
||||
210000 47452.093 5.3729225e-08 0 1.0375956e-07 6.994635e-13
|
||||
215000 45119.016 5.4481066e-08 0 1.0205156e-07 7.1418206e-13
|
||||
220000 43023.929 5.2752651e-08 0 9.8114229e-08 6.9834508e-13
|
||||
225000 40153.742 5.1097395e-08 0 9.3432837e-08 6.9738856e-13
|
||||
230000 39369.117 5.0504151e-08 0 9.2012337e-08 6.894872e-13
|
||||
235000 36113.296 4.9984145e-08 0 8.8059609e-08 6.9525606e-13
|
||||
240000 33557.343 4.74199e-08 0 8.2800537e-08 6.782253e-13
|
||||
245000 31543.784 4.6897571e-08 0 8.0155245e-08 6.7496202e-13
|
||||
250000 29448.798 4.5972171e-08 0 7.702103e-08 6.6988749e-13
|
||||
255000 26258.805 4.522174e-08 0 7.2907283e-08 6.7773348e-13
|
||||
260000 24024.155 4.4693255e-08 0 7.002273e-08 6.7584518e-13
|
||||
265000 22118.293 4.3984189e-08 0 6.730425e-08 6.7927214e-13
|
||||
270000 20024.409 4.2544987e-08 0 6.3657396e-08 6.8136681e-13
|
||||
275000 17107.549 4.1072236e-08 0 5.9109301e-08 6.666371e-13
|
||||
280000 14749.603 4.0000425e-08 0 5.5551428e-08 6.613669e-13
|
||||
285000 12500.706 4.0279102e-08 0 5.3459018e-08 6.8142024e-13
|
||||
290000 10030.224 3.8370444e-08 0 4.8945647e-08 6.7352743e-13
|
||||
295000 7601.7068 3.723413e-08 0 4.5248866e-08 6.6989317e-13
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
Loop time of 1070.02 on 4 procs for 200000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.325 | 7.684 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 217597.05 0 0 2.294199e-07 2.3049678e-14
|
||||
105000 105542.67 6.5899047e-08 0 1.7717623e-07 6.9064382e-13
|
||||
110000 96801.947 6.6329049e-08 0 1.683906e-07 7.0960381e-13
|
||||
115000 93283.767 6.4052852e-08 0 1.6240507e-07 7.0033324e-13
|
||||
120000 90930.59 6.3799892e-08 0 1.5967108e-07 7.0244972e-13
|
||||
125000 90114.178 6.3511381e-08 0 1.5852179e-07 7.1128852e-13
|
||||
130000 83917.505 6.279089e-08 0 1.5126794e-07 6.9980391e-13
|
||||
135000 84057.326 6.269189e-08 0 1.5131636e-07 7.1046329e-13
|
||||
140000 80989.747 6.2166941e-08 0 1.4755716e-07 7.0822238e-13
|
||||
145000 79082.787 5.999291e-08 0 1.4337256e-07 7.0169908e-13
|
||||
150000 76377.704 6.0983734e-08 0 1.4151132e-07 7.0803269e-13
|
||||
155000 74642.465 5.8016291e-08 0 1.3671435e-07 6.8979034e-13
|
||||
160000 71320.499 5.8203836e-08 0 1.3339944e-07 6.9671842e-13
|
||||
165000 69769.632 5.8523021e-08 0 1.3208349e-07 6.9774909e-13
|
||||
170000 67002.509 5.6265118e-08 0 1.2690812e-07 6.8640935e-13
|
||||
175000 65045.732 5.5231406e-08 0 1.2381131e-07 6.8623008e-13
|
||||
180000 62633.05 5.3858988e-08 0 1.1989512e-07 6.7679278e-13
|
||||
185000 60510.328 5.3138189e-08 0 1.1693627e-07 6.7838603e-13
|
||||
190000 56958.939 5.3092173e-08 0 1.131459e-07 6.7336019e-13
|
||||
195000 55591.155 5.1736031e-08 0 1.1034766e-07 6.6906721e-13
|
||||
200000 53009.069 5.0934685e-08 0 1.0682393e-07 6.7160648e-13
|
||||
205000 50806.268 5.1266492e-08 0 1.0483325e-07 6.7042981e-13
|
||||
210000 47438.734 4.9024426e-08 0 9.9040681e-08 6.6234011e-13
|
||||
215000 45998.084 4.7751227e-08 0 9.6248556e-08 6.5536559e-13
|
||||
220000 43057.946 4.7441717e-08 0 9.2839159e-08 6.6414744e-13
|
||||
225000 41339.318 4.6636471e-08 0 9.0221906e-08 6.5621184e-13
|
||||
230000 37991.695 4.5885529e-08 0 8.5941452e-08 6.5311348e-13
|
||||
235000 36765.626 4.4005371e-08 0 8.2768609e-08 6.4411688e-13
|
||||
240000 33633.564 4.3031845e-08 0 7.8492844e-08 6.411006e-13
|
||||
245000 31441.462 4.186446e-08 0 7.5014252e-08 6.3558893e-13
|
||||
250000 28346.474 4.1330305e-08 0 7.1216947e-08 6.3547167e-13
|
||||
255000 26485.436 4.0303887e-08 0 6.8228374e-08 6.3491378e-13
|
||||
260000 24251.816 3.8404659e-08 0 6.3974165e-08 6.2184492e-13
|
||||
265000 21588.99 3.8470221e-08 0 6.1232221e-08 6.3046737e-13
|
||||
270000 19476.088 3.7190768e-08 0 5.7725063e-08 6.2042977e-13
|
||||
275000 17402.215 3.719862e-08 0 5.5546362e-08 6.3332028e-13
|
||||
280000 14911.078 3.5602533e-08 0 5.1323785e-08 6.2734446e-13
|
||||
285000 12478.751 3.4819713e-08 0 4.7976481e-08 6.2920228e-13
|
||||
290000 10052.548 3.3720905e-08 0 4.4319645e-08 6.2607642e-13
|
||||
295000 7653.5468 3.190337e-08 0 3.9972762e-08 6.210325e-13
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
Loop time of 240.576 on 4 procs for 200000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.057981 | 36.178 | 144.53 |1040.0 | 3.38
|
||||
Neigh | 0.25871 | 0.37261 | 0.69124 | 30.2 | 0.03
|
||||
Comm | 0.47965 | 0.49514 | 0.51697 | 2.1 | 0.05
|
||||
Output | 0.0064233 | 0.16356 | 0.21598 | 22.4 | 0.02
|
||||
Modify | 0.21709 | 229.82 | 918.61 |2623.2 | 21.48
|
||||
Other | | 803 | | | 75.04
|
||||
Pair | 0.0094455 | 19.351 | 39.054 | 439.7 | 8.04
|
||||
Neigh | 0.069968 | 0.11626 | 0.16266 | 13.6 | 0.05
|
||||
Comm | 0.10053 | 0.88025 | 1.9201 | 85.4 | 0.37
|
||||
Output | 0.0012827 | 0.02596 | 0.050595 | 15.3 | 0.01
|
||||
Modify | 0.03084 | 98.954 | 197.96 | 994.4 | 41.13
|
||||
Other | | 121.2 | | | 50.40
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19214.5 ave 76858 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19108 ave 38228 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76858
|
||||
Ave neighs/atom = 15.093873
|
||||
Neighbor list builds = 116
|
||||
Total # of neighbors = 76432
|
||||
Ave neighs/atom = 15.010212
|
||||
Neighbor list builds = 114
|
||||
Dangerous builds = 0
|
||||
|
||||
minimize 0.0 1.0e-8 1000 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.461 | 8.588 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
301000 5231.1956 3.591074e-08 0 4.1426165e-08 6.6674716e-13
|
||||
Loop time of 5.73822 on 4 procs for 1000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.887 | 8.809 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
301000 5240.5437 3.0896022e-08 0 3.6421304e-08 6.2016488e-13
|
||||
Loop time of 1.30229 on 4 procs for 1000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.59175937800124e-08 3.59107465269502e-08 3.59107396814365e-08
|
||||
Force two-norm initial, final = 8.3566626e-08 8.3465615e-08
|
||||
Force max component initial, final = 3.1363101e-09 3.1301201e-09
|
||||
Final line search alpha, max atom move = 1 3.1301201e-09
|
||||
3.09028409031651e-08 3.08960287166428e-08 3.08960219060082e-08
|
||||
Force two-norm initial, final = 8.2667468e-08 8.2568929e-08
|
||||
Force max component initial, final = 2.9188021e-09 2.9146337e-09
|
||||
Final line search alpha, max atom move = 1 2.9146337e-09
|
||||
Iterations, force evaluations = 1000 1000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0003564 | 0.3119 | 1.2465 | 96.6 | 5.44
|
||||
Pair | 5.6358e-05 | 0.14395 | 0.28791 | 37.9 | 11.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0007532 | 0.00080708 | 0.000957 | 0.0 | 0.01
|
||||
Output | 4.88e-05 | 6.4775e-05 | 0.0001121 | 0.0 | 0.00
|
||||
Modify | 0.0004412 | 1.0758 | 4.3017 | 179.6 | 18.75
|
||||
Other | | 4.35 | | | 75.80
|
||||
Comm | 0.00010928 | 0.0035209 | 0.0074675 | 5.8 | 0.27
|
||||
Output | 1.9357e-05 | 2.0372e-05 | 2.2403e-05 | 0.0 | 0.00
|
||||
Modify | 4.6032e-05 | 0.4419 | 0.88539 | 66.5 | 33.93
|
||||
Other | | 0.7129 | | | 54.74
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19216 ave 76864 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19105.5 ave 38227 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76864
|
||||
Ave neighs/atom = 15.095051
|
||||
Total # of neighbors = 76422
|
||||
Ave neighs/atom = 15.008248
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
@ -884,22 +887,25 @@ pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
|
||||
timestep 0.025
|
||||
if "$(is_defined(dump,mydump))" then "undump mydump"
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
#dump mydump all atom 10000 run.lammpstrj
|
||||
#variable total_force equal 0.2
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 # dumpxdmf 1000 sflow 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx ${dx} zwall_velocity 0 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx 1 zwall_velocity 0 0
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 points.
|
||||
Local Grid Geometry created.
|
||||
First Run initialized
|
||||
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
@ -925,11 +931,11 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
- fix lb/fluid command: doi:10.1016/j.cpc.2022.108318
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
author = {C. Denniston and N. Afrasiabian and M. G. Cole-Andre, F. E. Mackay and S. T. T. Ollila and T. Whitehead},
|
||||
title = {{LAMMPS} lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into {LAMMPS} Through a Lattice-{B}oltzmann Fluid}, journal = {Comput.\ Phys.\ Commun.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
@ -937,9 +943,9 @@ Your simulation uses code contributions which should be cited:
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7
|
||||
ghost atom cutoff = 3
|
||||
@ -950,85 +956,15 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.03 | 14.01 | 16.94 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 -0.62398934 11.636864 -1.4385266
|
||||
200 5092 98.193244 265447.33 -0.0067390379 12.774129 0.77152356
|
||||
300 5092 98.193244 265447.33 -0.016866727 11.816838 0.164604
|
||||
400 5092 98.193244 265447.33 -0.099751559 14.292633 3.5403419
|
||||
500 5092 98.193244 265447.33 0.020826826 12.371064 3.4680188
|
||||
600 5092 98.193244 265447.33 -0.12187023 10.702747 0.7831029
|
||||
700 5092 98.193244 265447.33 -0.075493864 10.829418 0.98211649
|
||||
800 5092 98.193244 265447.33 -0.11468917 12.399304 1.7926202
|
||||
900 5092 98.193244 265447.33 -0.068927619 11.055182 2.4723876
|
||||
1000 5092 98.193244 265447.33 -0.069248548 10.39473 1.5087726
|
||||
1100 5092 98.193244 265447.33 0.065523336 9.4891653 1.3947719
|
||||
1200 5092 98.193244 265447.33 -0.044004235 11.847192 2.5397604
|
||||
1300 5092 98.193244 265447.33 0.040137088 10.997654 2.8832378
|
||||
1400 5092 98.193244 265447.33 0.067812628 10.154351 3.4014094
|
||||
1500 5092 98.193244 265447.33 0.026101525 10.034855 2.5467227
|
||||
1600 5092 98.193244 265447.33 0.023101669 11.834913 2.9961902
|
||||
1700 5092 98.193244 265447.33 -0.016678555 11.057297 1.1303356
|
||||
1800 5092 98.193244 265447.33 0.038804941 9.2005261 3.2383612
|
||||
1900 5092 98.193244 265447.33 0.045475707 8.592855 2.7327399
|
||||
2000 5092 98.193244 265447.33 0.0029052791 11.37239 1.650534
|
||||
2100 5092 98.193244 265447.33 0.0021721335 10.534175 1.4627128
|
||||
2200 5092 98.193244 265447.33 0.033545767 9.6499738 1.7555886
|
||||
2300 5092 98.193244 265447.33 0.037477935 10.604272 2.6811451
|
||||
2400 5092 98.193244 265447.33 0.013734867 9.5032009 3.4535601
|
||||
2500 5092 98.193244 265447.33 -0.074779755 10.655833 2.4798429
|
||||
2600 5092 98.193244 265447.33 -0.03912509 9.9731913 1.3805939
|
||||
2700 5092 98.193244 265447.33 0.084748343 9.6155874 1.9680204
|
||||
2800 5092 98.193244 265447.33 0.004716293 11.060178 2.3097572
|
||||
2900 5092 98.193244 265447.33 -0.01716838 10.851167 1.2315357
|
||||
3000 5092 98.193244 265447.33 0.0089978545 10.101686 1.6655875
|
||||
3100 5092 98.193244 265447.33 0.10214007 9.8489205 1.3991661
|
||||
3200 5092 98.193244 265447.33 0.030416619 10.303674 2.8620249
|
||||
3300 5092 98.193244 265447.33 -0.080891033 10.665193 1.6805084
|
||||
3400 5092 98.193244 265447.33 0.011781712 10.916621 0.79341262
|
||||
3500 5092 98.193244 265447.33 0.050815855 9.5573732 0.40493186
|
||||
3600 5092 98.193244 265447.33 -0.017225395 10.438887 2.303509
|
||||
3700 5092 98.193244 265447.33 0.0042521202 9.8119963 3.1057822
|
||||
3800 5092 98.193244 265447.33 0.037295562 9.3673981 2.2084367
|
||||
3900 5092 98.193244 265447.33 0.053448378 8.9799381 1.9075618
|
||||
4000 5092 98.193244 265447.33 0.039518888 10.999985 2.2441035
|
||||
4100 5092 98.193244 265447.33 -0.022548252 10.07084 1.7986935
|
||||
4200 5092 98.193244 265447.33 0.093070808 8.8837865 1.8491384
|
||||
4300 5092 98.193244 265447.33 0.16605392 10.080625 2.3851261
|
||||
4400 5092 98.193244 265447.33 0.071707012 11.041363 1.3512251
|
||||
4500 5092 98.193244 265447.33 -0.044985642 10.590977 0.89464128
|
||||
4600 5092 98.193244 265447.33 0.010801743 9.745945 1.3254718
|
||||
4700 5092 98.193244 265447.33 0.11301693 9.8629299 1.2450238
|
||||
4800 5092 98.193244 265447.33 0.29083508 10.35163 1.6481913
|
||||
4900 5092 98.193244 265447.33 0.274316 9.7650593 1.6979411
|
||||
5000 5092 98.193244 265447.33 -0.041118665 9.9508487 1.7688687
|
||||
Loop time of 5880.47 on 4 procs for 5000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.8823 | 1.2112 | 1.6656 | 29.1 | 0.02
|
||||
Neigh | 22.261 | 23.161 | 24.045 | 15.0 | 0.39
|
||||
Comm | 1.1838 | 1.3636 | 1.6084 | 14.2 | 0.02
|
||||
Output | 0.99304 | 0.99848 | 1.0061 | 0.5 | 0.02
|
||||
Modify | 5850 | 5851.7 | 5853.1 | 1.6 | 99.51
|
||||
Other | | 2.046 | | | 0.03
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8835 ave 35340 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 35340
|
||||
Ave neighs/atom = 6.9402985
|
||||
Neighbor list builds = 2500
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
Total wall time: 2:06:45
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.67 | 16.66 | 18.64 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 0.42848502 10.910894 -2.3324154
|
||||
200 5092 98.193244 265447.33 -0.02627078 13.323497 0.5134388
|
||||
300 5092 98.193244 265447.33 0.33955198 12.017917 0.07308431
|
||||
400 5092 98.193244 265447.33 0.28511704 14.563626 3.4626969
|
||||
500 5092 98.193244 265447.33 -0.080267505 11.795121 3.266271
|
||||
600 5092 98.193244 265447.33 0.11024837 10.763593 0.68027763
|
||||
700 5092 98.193244 265447.33 0.22058041 10.773118 1.1020572
|
||||
800 5092 98.193244 265447.33 0.26569373 12.841207 1.7015156
|
||||
900 5092
|
||||
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Fe_mm.eam.fs
|
||||
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Cu_mishin1.eam.alloy
|
||||
Reference in New Issue
Block a user