690 lines
36 KiB
Groff
690 lines
36 KiB
Groff
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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###############################################################################
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# MD simulation for HDNNP water
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###############################################################################
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###############################################################################
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# VARIABLES
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###############################################################################
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Configuration files
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variable cfgFile string "data.H2O-360mol"
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# Timesteps
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variable numSteps equal 10
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variable dt equal 0.0005
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# HDNNP
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variable hdnnpCutoff equal 6.36
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variable hdnnpDir string "hdnnp-data"
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###############################################################################
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# GENERAL SETUP
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###############################################################################
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units metal
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boundary p p p
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atom_style atomic
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region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
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create_box 3 box
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Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
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2 by 2 by 1 MPI processor grid
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mass 1 1.0
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read_data ${cfgFile} add append offset 1 0 0 0 0
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read_data data.H2O-360mol add append offset 1 0 0 0 0
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Reading data file ...
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orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1080 atoms
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read_data CPU = 0.007 seconds
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timestep ${dt}
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timestep 0.0005
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thermo 1
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###############################################################################
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# HDNNP
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###############################################################################
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pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
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pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
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pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
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pair_coeff * * hdnnp NULL H O
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pair_coeff 1 * lj/cut 0.1 3.0
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###############################################################################
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# INTEGRATOR
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###############################################################################
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fix INT all nve
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###############################################################################
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# OUTPUT
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###############################################################################
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#dump 1 all atom 1 dump.hdnnp
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###############################################################################
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# SIMULATION
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###############################################################################
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run ${numSteps}
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run 10
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
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@Article{Singraber19,
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author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
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title = {Library-Based {LAMMPS} Implementation of High-Dimensional
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Neural Network Potentials},
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year = {2019},
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month = mar,
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volume = {15},
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pages = {1827--1840},
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doi = {10.1021/acs.jctc.8b00770},
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journal = {J.~Chem.\ Theory Comput.},
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number = {3}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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*******************************************************************************
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WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
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------------------------------------------------------------------
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n²p² version (from git): patch_2Aug2023-264-g174825fe8c
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(version.h): v2.2.0
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------------------------------------------------------------
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Git branch : collected-small-changes
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Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
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Compile date/time : Aug 23 2023 08:43:11
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------------------------------------------------------------
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Features/Flags:
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------------------------------------------------------------
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Symmetry function groups : enabled
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Symmetry function cache : enabled
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Timing function available : available
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Asymmetric polynomial SFs : available
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SF low neighbor number check : enabled
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SF derivative memory layout : reduced
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MPI explicitly disabled : no
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------------------------------------------------------------
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Please cite the following papers when publishing results obtained with n²p²:
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-------------------------------------------------------------------------------
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* General citation for n²p² and the LAMMPS interface:
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Singraber, A.; Behler, J.; Dellago, C.
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Library-Based LAMMPS Implementation of High-Dimensional
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Neural Network Potentials.
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J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
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https://doi.org/10.1021/acs.jctc.8b00770
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-------------------------------------------------------------------------------
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* Additionally, if you use the NNP training features of n²p²:
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Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
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Parallel Multistream Training of High-Dimensional Neural
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Network Potentials.
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J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
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https://doi.org/10.1021/acs.jctc.8b01092
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-------------------------------------------------------------------------------
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* Additionally, if polynomial symmetry functions are used:
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Bircher, M. P.; Singraber, A.; Dellago, C.
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Improved Description of Atomic Environments Using Low-Cost
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Polynomial Functions with Compact Support.
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arXiv:2010.14414 [cond-mat, physics:physics] 2020.
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https://arxiv.org/abs/2010.14414
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*******************************************************************************
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*** SETUP: SETTINGS FILE ******************************************************
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Settings file name: hdnnp-data/input.nn
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Read 120 lines.
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Found 70 lines with keywords.
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This settings file defines a short-range only NNP.
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*******************************************************************************
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*** SETUP: NORMALIZATION ******************************************************
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Data set normalization is used.
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Mean energy per atom : -2.5521343547039809E+01
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Conversion factor energy : 2.4265748255366972E+02
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Conversion factor length : 5.8038448995319847E+00
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*******************************************************************************
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*** SETUP: ELEMENT MAP ********************************************************
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Number of element strings found: 2
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Element 0: H ( 1)
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Element 1: O ( 8)
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*******************************************************************************
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*** SETUP: ELEMENTS ***********************************************************
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Number of elements is consistent: 2
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Atomic energy offsets per element:
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Element 0: 0.00000000E+00
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Element 1: 0.00000000E+00
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Energy offsets are automatically subtracted from reference energies.
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*******************************************************************************
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*** SETUP: CUTOFF FUNCTIONS ***************************************************
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Parameter alpha for inner cutoff: 0.000000
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Inner cutoff = Symmetry function cutoff * alpha
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Equal cutoff function type for all symmetry functions:
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CutoffFunction::CT_TANHU (2)
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f(r) = tanh^3(1 - r/rc)
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*******************************************************************************
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*** SETUP: SYMMETRY FUNCTIONS *************************************************
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Abbreviations:
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--------------
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ind .... Symmetry function index.
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ec ..... Central atom element.
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tp ..... Symmetry function type.
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sbtp ... Symmetry function subtype (e.g. cutoff type).
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e1 ..... Neighbor 1 element.
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e2 ..... Neighbor 2 element.
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eta .... Gaussian width eta.
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rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
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angl.... Left cutoff angle for polynomial.
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angr.... Right cutoff angle for polynomial.
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la ..... Angle prefactor lambda.
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zeta ... Angle term exponent zeta.
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rc ..... Cutoff radius / right cutoff radius for polynomial.
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a ...... Free parameter alpha (e.g. cutoff alpha).
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ln ..... Line number in settings file.
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Short range atomic symmetry functions element H :
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-------------------------------------------------------------------------------------------------
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ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
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-------------------------------------------------------------------------------------------------
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1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
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2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
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3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
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4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
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5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
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6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
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7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
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8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
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9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
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10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
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11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
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12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
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13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
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14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
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15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
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16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
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17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
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18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
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19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
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20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
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21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
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22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
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23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
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24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
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25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
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26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
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27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
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-------------------------------------------------------------------------------------------------
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Short range atomic symmetry functions element O :
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-------------------------------------------------------------------------------------------------
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ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
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-------------------------------------------------------------------------------------------------
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1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
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2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
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3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
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4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
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5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
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6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
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7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
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8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
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9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
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10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
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11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
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12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
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13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
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14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
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15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
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16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
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17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
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18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
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19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
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20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
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21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
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22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
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23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
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24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
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25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
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26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
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27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
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28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
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29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
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30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
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-------------------------------------------------------------------------------------------------
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Minimum cutoff radius for element H: 12.000000
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Minimum cutoff radius for element O: 12.000000
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Maximum cutoff radius (global) : 12.000000
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*******************************************************************************
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*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
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Symmetry function derivatives memory table for element H :
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-------------------------------------------------------------------------------
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Relevant symmetry functions for neighbors with element:
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- H: 15 of 27 ( 55.6 %)
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- O: 19 of 27 ( 70.4 %)
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-------------------------------------------------------------------------------
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Symmetry function derivatives memory table for element O :
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-------------------------------------------------------------------------------
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Relevant symmetry functions for neighbors with element:
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- H: 18 of 30 ( 60.0 %)
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- O: 16 of 30 ( 53.3 %)
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-------------------------------------------------------------------------------
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*******************************************************************************
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*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
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Element H: in total 4 caches, used 17.00 times on average.
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Element O: in total 4 caches, used 17.00 times on average.
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*******************************************************************************
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*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
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Abbreviations:
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--------------
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ind .... Symmetry function index.
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ec ..... Central atom element.
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tp ..... Symmetry function type.
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sbtp ... Symmetry function subtype (e.g. cutoff type).
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e1 ..... Neighbor 1 element.
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e2 ..... Neighbor 2 element.
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eta .... Gaussian width eta.
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rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
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angl.... Left cutoff angle for polynomial.
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angr.... Right cutoff angle for polynomial.
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la ..... Angle prefactor lambda.
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zeta ... Angle term exponent zeta.
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rc ..... Cutoff radius / right cutoff radius for polynomial.
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a ...... Free parameter alpha (e.g. cutoff alpha).
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ln ..... Line number in settings file.
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mi ..... Member index.
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sfi .... Symmetry function index.
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e ...... Recalculate exponential term.
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Short range atomic symmetry function groups element H :
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----------------------------------------------------------------------------------------------------------
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ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
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----------------------------------------------------------------------------------------------------------
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1 H 2 ct2 H * * 1.200E+01 0.00 * * *
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- - - - - 1.000E-03 0.000E+00 - - 51 1 1
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- - - - - 1.000E-02 0.000E+00 - - 52 2 3
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- - - - - 3.000E-02 0.000E+00 - - 53 3 5
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- - - - - 6.000E-02 0.000E+00 - - 54 4 7
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- - - - - 1.500E-01 1.900E+00 - - 55 5 10
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- - - - - 3.000E-01 1.900E+00 - - 56 6 12
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- - - - - 6.000E-01 1.900E+00 - - 57 7 14
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- - - - - 1.500E+00 1.900E+00 - - 58 8 16
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2 H 2 ct2 O * * 1.200E+01 0.00 * * *
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- - - - - 1.000E-03 0.000E+00 - - 61 1 2
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- - - - - 1.000E-02 0.000E+00 - - 62 2 4
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- - - - - 3.000E-02 0.000E+00 - - 63 3 6
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- - - - - 6.000E-02 0.000E+00 - - 64 4 8
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- - - - - 1.500E-01 9.000E-01 - - 65 5 9
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- - - - - 3.000E-01 9.000E-01 - - 66 6 11
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- - - - - 6.000E-01 9.000E-01 - - 67 7 13
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- - - - - 1.500E+00 9.000E-01 - - 68 8 15
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3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
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- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
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- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
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- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
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- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
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- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
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- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
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- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
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4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
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- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
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- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
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- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
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- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
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----------------------------------------------------------------------------------------------------------
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Short range atomic symmetry function groups element O :
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----------------------------------------------------------------------------------------------------------
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ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
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----------------------------------------------------------------------------------------------------------
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1 O 2 ct2 H * * 1.200E+01 0.00 * * *
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- - - - - 1.000E-03 0.000E+00 - - 70 1 1
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- - - - - 1.000E-02 0.000E+00 - - 71 2 3
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- - - - - 3.000E-02 0.000E+00 - - 72 3 5
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- - - - - 6.000E-02 0.000E+00 - - 73 4 7
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- - - - - 1.500E-01 9.000E-01 - - 74 5 9
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- - - - - 3.000E-01 9.000E-01 - - 75 6 11
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- - - - - 6.000E-01 9.000E-01 - - 76 7 13
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- - - - - 1.500E+00 9.000E-01 - - 77 8 15
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2 O 2 ct2 O * * 1.200E+01 0.00 * * *
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- - - - - 1.000E-03 0.000E+00 - - 80 1 2
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- - - - - 1.000E-02 0.000E+00 - - 81 2 4
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- - - - - 3.000E-02 0.000E+00 - - 82 3 6
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- - - - - 6.000E-02 0.000E+00 - - 83 4 8
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- - - - - 1.500E-01 4.000E+00 - - 84 5 10
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- - - - - 3.000E-01 4.000E+00 - - 85 6 12
|
||
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
|
||
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
|
||
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
|
||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
|
||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
|
||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
|
||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
|
||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
|
||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
|
||
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
|
||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
|
||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
|
||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
|
||
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
|
||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
|
||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
|
||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
|
||
----------------------------------------------------------------------------------------------------------
|
||
*******************************************************************************
|
||
|
||
*** SETUP: NEURAL NETWORKS ****************************************************
|
||
|
||
Normalize neurons (all elements): 0
|
||
-------------------------------------------------------------------------------
|
||
Atomic short range NN for element H :
|
||
Number of weights : 1325
|
||
Number of biases : 51
|
||
Number of connections: 1376
|
||
Architecture 27 25 25 1
|
||
-------------------------------------------------------------------------------
|
||
1 G t t l
|
||
2 G t t
|
||
3 G t t
|
||
4 G t t
|
||
5 G t t
|
||
6 G t t
|
||
7 G t t
|
||
8 G t t
|
||
9 G t t
|
||
10 G t t
|
||
11 G t t
|
||
12 G t t
|
||
13 G t t
|
||
14 G t t
|
||
15 G t t
|
||
16 G t t
|
||
17 G t t
|
||
18 G t t
|
||
19 G t t
|
||
20 G t t
|
||
21 G t t
|
||
22 G t t
|
||
23 G t t
|
||
24 G t t
|
||
25 G t t
|
||
26 G
|
||
27 G
|
||
-------------------------------------------------------------------------------
|
||
Atomic short range NN for element O :
|
||
Number of weights : 1400
|
||
Number of biases : 51
|
||
Number of connections: 1451
|
||
Architecture 30 25 25 1
|
||
-------------------------------------------------------------------------------
|
||
1 G t t l
|
||
2 G t t
|
||
3 G t t
|
||
4 G t t
|
||
5 G t t
|
||
6 G t t
|
||
7 G t t
|
||
8 G t t
|
||
9 G t t
|
||
10 G t t
|
||
11 G t t
|
||
12 G t t
|
||
13 G t t
|
||
14 G t t
|
||
15 G t t
|
||
16 G t t
|
||
17 G t t
|
||
18 G t t
|
||
19 G t t
|
||
20 G t t
|
||
21 G t t
|
||
22 G t t
|
||
23 G t t
|
||
24 G t t
|
||
25 G t t
|
||
26 G
|
||
27 G
|
||
28 G
|
||
29 G
|
||
30 G
|
||
-------------------------------------------------------------------------------
|
||
*******************************************************************************
|
||
|
||
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
|
||
|
||
Equal scaling type for all symmetry functions:
|
||
Scaling type::ST_SCALECENTER (3)
|
||
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
|
||
Smin = 0.000000
|
||
Smax = 1.000000
|
||
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
|
||
-------------------------------------------------------------------------------
|
||
|
||
Abbreviations:
|
||
--------------
|
||
ind ..... Symmetry function index.
|
||
min ..... Minimum symmetry function value.
|
||
max ..... Maximum symmetry function value.
|
||
mean .... Mean symmetry function value.
|
||
sigma ... Standard deviation of symmetry function values.
|
||
sf ...... Scaling factor for derivatives.
|
||
Smin .... Desired minimum scaled symmetry function value.
|
||
Smax .... Desired maximum scaled symmetry function value.
|
||
t ....... Scaling type.
|
||
|
||
Scaling data for symmetry functions element H :
|
||
-------------------------------------------------------------------------------
|
||
ind min max mean sigma sf Smin Smax t
|
||
-------------------------------------------------------------------------------
|
||
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
|
||
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
|
||
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
|
||
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
|
||
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
|
||
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
|
||
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
|
||
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
|
||
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
|
||
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
|
||
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
|
||
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
|
||
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
|
||
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
|
||
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
|
||
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
|
||
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
|
||
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
|
||
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
|
||
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
|
||
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
|
||
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
|
||
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
|
||
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
|
||
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
|
||
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
|
||
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
|
||
-------------------------------------------------------------------------------
|
||
Scaling data for symmetry functions element O :
|
||
-------------------------------------------------------------------------------
|
||
ind min max mean sigma sf Smin Smax t
|
||
-------------------------------------------------------------------------------
|
||
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
|
||
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
|
||
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
|
||
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
|
||
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
|
||
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
|
||
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
|
||
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
|
||
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
|
||
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
|
||
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
|
||
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
|
||
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
|
||
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
|
||
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
|
||
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
|
||
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
|
||
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
|
||
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
|
||
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
|
||
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
|
||
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
|
||
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
|
||
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
|
||
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
|
||
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
|
||
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
|
||
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
|
||
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
|
||
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
|
||
-------------------------------------------------------------------------------
|
||
*******************************************************************************
|
||
|
||
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
|
||
|
||
Equal symmetry function statistics for all elements.
|
||
Collect min/max/mean/sigma : 0
|
||
Collect extrapolation warnings : 1
|
||
Write extrapolation warnings immediately to stderr: 0
|
||
Halt on any extrapolation warning : 0
|
||
*******************************************************************************
|
||
|
||
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
|
||
|
||
Short NN weight file name format: hdnnp-data/weights.%03d.data
|
||
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
|
||
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
|
||
*******************************************************************************
|
||
|
||
*** SETUP: LAMMPS INTERFACE ***************************************************
|
||
|
||
Individual extrapolation warnings will not be shown.
|
||
Extrapolation warning summary will be shown every 5 timesteps.
|
||
The simulation will be stopped when 100 extrapolation warnings are exceeded.
|
||
Extrapolation warnings are accumulated over all time steps.
|
||
-------------------------------------------------------------------------------
|
||
CAUTION: If the LAMMPS unit system differs from the one used
|
||
during NN training, appropriate conversion factors
|
||
must be provided (see keywords cflength and cfenergy).
|
||
|
||
Length unit conversion factor: 1.8897261327999999E+00
|
||
Energy unit conversion factor: 3.6749325399999998E-02
|
||
|
||
Checking consistency of cutoff radii (in LAMMPS units):
|
||
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
|
||
Maximum symmetry function cutoff: 6.350E+00
|
||
Cutoff radii are consistent.
|
||
-------------------------------------------------------------------------------
|
||
Element mapping string from LAMMPS to n2p2: "2:H,3:O"
|
||
|
||
CAUTION: Please ensure that this mapping between LAMMPS
|
||
atom types and NNP elements is consistent:
|
||
|
||
---------------------------
|
||
LAMMPS type | NNP element
|
||
---------------------------
|
||
1 <-> --
|
||
2 <-> H ( 1)
|
||
3 <-> O ( 8)
|
||
---------------------------
|
||
|
||
NNP setup for LAMMPS completed.
|
||
*******************************************************************************
|
||
Neighbor list info ...
|
||
update: every = 1 steps, delay = 0 steps, check = yes
|
||
max neighbors/atom: 2000, page size: 100000
|
||
master list distance cutoff = 8.36
|
||
ghost atom cutoff = 8.36
|
||
binsize = 4.18, bins = 6 6 6
|
||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||
(1) pair lj/cut, perpetual, skip from (3)
|
||
attributes: half, newton on, cut 8
|
||
pair build: skip
|
||
stencil: none
|
||
bin: none
|
||
(2) pair hdnnp, perpetual, skip from (4)
|
||
attributes: full, newton on
|
||
pair build: skip
|
||
stencil: none
|
||
bin: none
|
||
(3) neighbor class addition, perpetual, half/full trim from (4)
|
||
attributes: half, newton on, cut 8
|
||
pair build: halffull/newton/trim
|
||
stencil: none
|
||
bin: none
|
||
(4) neighbor class addition, perpetual
|
||
attributes: full, newton on
|
||
pair build: full/bin/atomonly
|
||
stencil: full/bin/3d
|
||
bin: standard
|
||
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
|
||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
||
Step Temp E_pair E_mol TotEng Press
|
||
0 0 -750069.48 0 -750069.48 -5297.5537
|
||
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
|
||
2 30.988787 -750073.91 0 -750069.59 -5023.6945
|
||
3 58.859866 -750077.88 0 -750069.67 -4427.8346
|
||
4 82.576399 -750081.26 0 -750069.74 -3275.4378
|
||
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
|
||
5 94.968097 -750083.01 0 -750069.76 -1511.6733
|
||
6 93.724286 -750082.8 0 -750069.73 709.20465
|
||
7 82.243957 -750081.13 0 -750069.66 3020.5084
|
||
8 68.611429 -750079.14 0 -750069.57 4922.5176
|
||
9 62.314385 -750078.21 0 -750069.51 5933.1543
|
||
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
|
||
10 69.501045 -750079.21 0 -750069.52 5761.8646
|
||
Loop time of 0.936871 on 4 procs for 10 steps with 1080 atoms
|
||
|
||
Performance: 0.461 ns/day, 52.048 hours/ns, 10.674 timesteps/s, 11.528 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 | 0.86567 | 0.89891 | 0.93611 | 3.1 | 95.95
|
||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||
Comm | 0.00035446 | 0.037585 | 0.070835 | 15.3 | 4.01
|
||
Output | 0.00018528 | 0.00023648 | 0.00030553 | 0.0 | 0.03
|
||
Modify | 4.2224e-05 | 4.4078e-05 | 4.6256e-05 | 0.0 | 0.00
|
||
Other | | 9.307e-05 | | | 0.01
|
||
|
||
Nlocal: 270 ave 278 max 262 min
|
||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
Nghost: 2552 ave 2564 max 2541 min
|
||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||
Neighs: 0 ave 0 max 0 min
|
||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||
|
||
Total # of neighbors = 0
|
||
Ave neighs/atom = 0
|
||
Neighbor list builds = 0
|
||
Dangerous builds = 0
|
||
Total wall time: 0:00:01
|