ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
3ebdc04aacd111c82f658fd1bc654565624f3ad1
lammps/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Axel Kohlmeyer e5957ccc19 recreate example logs with new colvars version
2024-08-05 22:12:30 -04:00

733 lines
31 KiB
Groff
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

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
Reference in New Issue View Git Blame Copy Permalink