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yaff.log
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yaff.log
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_____/\\\________/\\\___/\\\\\\\\\______/\\\\\\\\\\\\\\\__/\\\\\\\\\\\\\\\______
_____\///\\\____/\\\/__/\\\\\\\\\\\\\___\ \\\///////////__\ \\\///////////______
________\///\\\/\\\/___/\\\/////////\\\__\ \\\_____________\ \\\________________
___________\///\\\/____\ \\\_______\ \\\__\ \\\\\\\\\\\_____\ \\\\\\\\\\\_______
______________\ \\\_____\ \\\\\\\\\\\\\\\__\ \\\///////______\ \\\///////_______
_______________\ \\\_____\ \\\/////////\\\__\ \\\_____________\ \\\_____________
________________\ \\\_____\ \\\_______\ \\\__\ \\\_____________\ \\\____________
_________________\ \\\_____\ \\\_______\ \\\__\ \\\_____________\ \\\___________
__________________\///______\///________\///___\///______________\///___________
Welcome to Yaff 1.6.0 - Yet another force field
Written by
Toon Verstraelen(1)*, Louis Vanduyfhuys(1) and Steven Vandenbrande(1)
(1) Center for Molecular Modeling, Ghent University Belgium.
* mailto: Toon.Verstraelen@UGent.be
In a not-too-distant future, this program will be renamed to NINJAFF, which
stands for 'NINJAFF is not just another force field code'. Please, bear with us.
ENV User: vsc41947
ENV Platform: Linux-3.10.0-1062.9.1.el7.ug.x86_64-x86_64-with-centos-7
ENV .7.1908-Core
ENV Time: 2020-03-20T15:16:09.901357
ENV Python version: 3.7.2 (default, Apr 9 2019, 14:23:44) [GCC 8.2.0]
ENV YAFF version: 1.6.0
ENV Current Dir: /kyukon/scratch/gent/vo/000/gvo00003/vsc41947/pyiron/pro
ENV jects/testing_notebooks/yaff_tests/metadynamics_hdf5/met
ENV adynamics
ENV Command line: yscript.py
UNITS The following units will be used below:
UNITS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UNITS Kind Conversion Format Notation
UNITS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UNITS energy 3.808799176039228e-04 %10.1f kJ/mol
UNITS temperature 1.000000000000000e+00 %10.1f K
UNITS length 1.889726133921252e+00 %10.4f A
UNITS invlength 5.291772082999999e-01 %10.5f A^-1
UNITS area 3.571064861224962e+00 %10.3f A^2
UNITS volume 6.748334594184680e+00 %10.3f A^3
UNITS time 4.134137333664683e+01 %10.1f fs
UNITS mass 1.822888627353289e+03 %10.5f amu
UNITS charge 1.000000000000000e+00 %10.5f e
UNITS force 2.015529714951779e-04 %10.1f kJ/mol/A
UNITS forceconst 1.066572387803877e-04 %10.1f kJ/mol/A**2
UNITS velocity 4.571028926719556e-02 %10.5f A/fs
UNITS acceleration 1.105679022682005e-03 %10.5f A/fs**2
UNITS angle 1.745329251994330e-02 %10.5f deg
UNITS c6 1.000000000000000e+00 %10.5f E_h*a_0**6
UNITS c8 1.000000000000000e+00 %10.5f E_h*a_0**6
UNITS c12 1.000000000000000e+00 %10.5f E_h*a_0**12
UNITS diffconst 8.637992821731958e-05 %10.5f A**2/ps
UNITS density 1.626726283270276e+02 %10.3f g/cm^3
UNITS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UNITS The internal data is divided by the corresponding conversion factor
UNITS before it gets printed on screen.
SYS Unit cell
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Number of periodic dimensions: 0
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Analysis of the bonds:
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS First Second Count
SYS 1 7 3
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Analysis of the neighbors:
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Number of first neighbors: 3
SYS Number of second neighbors: 3
SYS Number of third neighbors: 0
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Element Neighboring elements Count
SYS 1 7 3
SYS 7 1,1,1 1
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS The following atom types are present in the system:
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS Atom type ID Number of atoms
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SYS N3 0 1
SYS H1_n 1 3
SYS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GEN Generating force field from pars.txt
FPINIT Force part: valence
FPINIT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FPINIT Force part: pair_ei
FPINIT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FPINIT scalings: 1.000 1.000 1.000
FPINIT real space cutoff: 15.0000
FPINIT truncation: switch3 4.0000
FPINIT alpha: 0.00000
FPINIT relative permittivity: 1.000
FPINIT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FFINIT Force field with 2 parts: valence, pair_ei.
FFINIT Neighborlist present: True
WARNING!! When using PLUMED as a hook for your integrator and PLUMED
adds time-dependent forces (for instance when performing
metadynamics), there is no energy conservation. The conserved
quantity reported by YAFF is irrelevant in this case.
ENSEM Temperature coupling achieved through NHC thermostat
VERLET WARNING!! You are using PLUMED as a hook for your integrator. If PLUMED
VERLET adds time-dependent forces (for instance when performing
VERLET metadynamics) there is no energy conservation. The conserved
VERLET quantity reported by YAFF is irrelevant in this case.
VERLET ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VERLET Cons.Err. = the root of the ratio of the variance on the conserved
VERLET quantity and the variance on the kinetic energy.
VERLET d-rmsd = the root-mean-square displacement of the atoms.
VERLET g-rmsd = the root-mean-square gradient of the energy.
VERLET counter Cons.Err. Temp d-RMSD g-RMSD Walltime
VERLET ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VERLET 0 0.00000 237.0 0.0000 19.5 0.0
VERLET 1000 1.99480 293.2 0.0055 56.4 9.2
VERLET ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ENV User: vsc41947
ENV Platform: Linux-3.10.0-1062.9.1.el7.ug.x86_64-x86_64-with-centos-7
ENV .7.1908-Core
ENV Time: 2020-03-20T15:16:19.957509
ENV Python version: 3.7.2 (default, Apr 9 2019, 14:23:44) [GCC 8.2.0]
ENV YAFF version: 1.6.0
ENV Current Dir: /kyukon/scratch/gent/vo/000/gvo00003/vsc41947/pyiron/pro
ENV jects/testing_notebooks/yaff_tests/metadynamics_hdf5/met
ENV adynamics
ENV Command line: yscript.py
TIMER Overview of CPU time usage.
TIMER ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TIMER Label Total Own
TIMER ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TIMER Generator 0.0 0.0
TIMER Nlists 0.1 0.1
TIMER PLUMED 0.3 0.2 W
TIMER PP ei 0.0 0.0
TIMER Total 10.0 0.8 WWW
TIMER VERLET 9.2 0.4 WW
TIMER VERLET hooks 8.2 8.0 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
TIMER VERLET special hooks 0.3 0.3 W
TIMER Valence 0.1 0.1
TIMER ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__/\\\__________________________________________________________________/\\\____
\ \\\ \ \\\
\ \\\ End of file. Thanks for using Yaff! Come back soon!! \ \\\
____\///__________________________________________________________________\///__