When using the RuNNer code for the validation tests, LAMMPS crashes with the following message:
2021-03-08 10:06:22,758 - pyiron_log - WARNING - Job aborted
2021-03-08 10:06:22,762 - pyiron_log - WARNING - LAMMPS (10 Feb 2021)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.418051 17.682551 26.587360)
1 by 1 by 1 MPI processor grid
reading atoms ...
512 atoms
read_data CPU = 0.004 seconds
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
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WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
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n²p² version : 553e609
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Git branch : HEAD
Git revision : 553e6097553afe442843cc45bce5c974b1ec2f92
Compile date/time : Feb 15 2021 12:43:18
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Please cite the following papers when publishing results obtained with n²p²:
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* General citation for n²p² and the LAMMPS interface:
Singraber, A.; Behler, J.; Dellago, C.
Library-Based LAMMPS Implementation of High-Dimensional
Neural Network Potentials.
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770
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* Additionally, if you use the NNP training features of n²p²:
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
Parallel Multistream Training of High-Dimensional Neural
Network Potentials.
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
https://doi.org/10.1021/acs.jctc.8b01092
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* Additionally, if polynomial symmetry functions are used:
Bircher, M. P.; Singraber, A.; Dellago, C.
Improved Description of Atomic Environments Using Low-Cost
Polynomial Functions with Compact Support.
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
https://arxiv.org/abs/2010.14414
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*** SETUP: SETTINGS FILE ******************************************************
Settings file name: ./input.nn
Read 95 lines.
WARNING: Unknown keyword "calculate_forces" at line 94.
WARNING: Unknown keyword "calculate_stress" at line 95.
WARNING: Unknown keyword "fitting_unit" at line 67.
WARNING: Unknown keyword "force_update_scaling" at line 83.
WARNING: Unknown keyword "mix_all_points" at line 79.
WARNING: Unknown keyword "nn_type_short" at line 24.
WARNING: Unknown keyword "random_number_type" at line 29.
WARNING: Unknown keyword "runner_mode" at line 25.
WARNING: Unknown keyword "use_short_nn" at line 34.
WARNING: 9 problems detected (0 critical).
Found 43 lines with keywords.
This settings file defines a short-range only NNP.
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*** SETUP: NORMALIZATION ******************************************************
Data set normalization is not used.
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*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 1
Element 0: Cu ( 29)
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*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 1
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
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*** SETUP: CUTOFF FUNCTIONS ***************************************************
Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_COS (1)
x := (r - rc * alpha) / (rc - rc * alpha)
f(x) = 1/2 * (cos(pi*x) + 1)
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*** SETUP: SYMMETRY FUNCTIONS *************************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
Short range atomic symmetry functions element Cu :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 Cu 2 ct1 Cu 0.000E+00 0.000E+00 1.200E+01 0.00 48
2 Cu 2 ct1 Cu 6.000E-03 0.000E+00 1.200E+01 0.00 49
3 Cu 2 ct1 Cu 1.600E-02 0.000E+00 1.200E+01 0.00 50
4 Cu 2 ct1 Cu 4.000E-02 0.000E+00 1.200E+01 0.00 51
5 Cu 2 ct1 Cu 1.090E-01 0.000E+00 1.200E+01 0.00 52
6 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 -1 1.0 0.00 58
7 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 1 1.0 0.00 54
8 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 -1 2.0 0.00 59
9 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 1 2.0 0.00 55
10 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 -1 4.0 0.00 60
11 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 1 4.0 0.00 56
12 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 -1 16.0 0.00 61
13 Cu 3 ct1 Cu Cu 0.000E+00 0.000E+00 1.200E+01 1 16.0 0.00 57
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element Cu: 12.000000
Maximum cutoff radius (global) : 12.000000
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*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element Cu :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- Cu: 13 of 13 (100.0 %)
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*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element Cu: in total 2 caches, used 13.00 times on average.
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*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.
Short range atomic symmetry function groups element Cu :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 Cu 2 ct1 Cu * * 1.200E+01 0.00 * * *
- - - - - 0.000E+00 0.000E+00 - - 48 1 1
- - - - - 6.000E-03 0.000E+00 - - 49 2 2
- - - - - 1.600E-02 0.000E+00 - - 50 3 3
- - - - - 4.000E-02 0.000E+00 - - 51 4 4
- - - - - 1.090E-01 0.000E+00 - - 52 5 5
2 Cu 3 ct1 Cu Cu * * 1.200E+01 * * 0.00 * * * *
- - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 58 1 6 1
- - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 54 2 7 0
- - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 59 3 8 0
- - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 55 4 9 0
- - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 60 5 10 0
- - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 56 6 11 0
- - - - - - 0.000E+00 0.000E+00 - -1 16.0 - 61 7 12 0
- - - - - - 0.000E+00 0.000E+00 - 1 16.0 - 57 8 13 0
----------------------------------------------------------------------------------------------------------
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*** SETUP: NEURAL NETWORKS ****************************************************
Normalize neurons (all elements): 0
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Atomic short range NN for element Cu :
Number of weights : 435
Number of biases : 31
Number of connections: 466
Architecture 13 15 15 1
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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 t t
15 t t
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*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
WARNING: Keyword "scale_min_short" not found.
Default value for Smin = 0.0.
WARNING: Keyword "scale_max_short" not found.
Default value for Smax = 1.0.
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: ./scaling.data
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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 Cu :
-------------------------------------------------------------------------------
ind min max mean sigma sf Smin Smax t
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1 1.43E+01 1.96E+01 1.66E+01 0.00E+00 1.87E-01 0.00 1.00 3
2 1.08E+01 1.49E+01 1.26E+01 0.00E+00 2.41E-01 0.00 1.00 3
3 7.07E+00 9.94E+00 8.33E+00 0.00E+00 3.48E-01 0.00 1.00 3
4 3.06E+00 4.51E+00 3.70E+00 0.00E+00 6.89E-01 0.00 1.00 3
5 4.43E-01 8.41E-01 6.11E-01 0.00E+00 2.52E+00 0.00 1.00 3
6 1.14E+01 2.33E+01 1.61E+01 0.00E+00 8.36E-02 0.00 1.00 3
7 3.09E+01 6.26E+01 4.35E+01 0.00E+00 3.15E-02 0.00 1.00 3
8 4.75E+00 1.02E+01 6.89E+00 0.00E+00 1.83E-01 0.00 1.00 3
9 2.43E+01 4.95E+01 3.43E+01 0.00E+00 3.97E-02 0.00 1.00 3
10 1.69E+00 3.91E+00 2.56E+00 0.00E+00 4.50E-01 0.00 1.00 3
11 1.65E+01 3.43E+01 2.36E+01 0.00E+00 5.63E-02 0.00 1.00 3
12 2.53E-01 8.21E-01 4.60E-01 0.00E+00 1.76E+00 0.00 1.00 3
13 4.07E+00 9.69E+00 6.25E+00 0.00E+00 1.78E-01 0.00 1.00 3
-------------------------------------------------------------------------------
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*** 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
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*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
Short NN weight file name format: ./weights.%03d.data
Setting short NN weights for element Cu from file: ./weights.029.data
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*** SETUP: LAMMPS INTERFACE ***************************************************
Individual extrapolation warnings will not be shown.
Extrapolation warning summary will not be shown.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
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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) : 1.200E+01
Maximum symmetry function cutoff: 6.350E+00
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
WARNING: Potential length units mismatch!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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Element mapping string from LAMMPS to n2p2: "1:Cu"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> Cu ( 29)
---------------------------
NNP setup for LAMMPS completed.
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Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 3 3 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair nnp, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 0
ERROR on proc 0: Too many extrapolation warnings (src/USER-NNP/pair_nnp.cpp:404)