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add reference log outputs for ML-HDNNP and add input demoing use with hybrid

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This commit is contained in:
Axel Kohlmeyer
2023-08-23 08:58:20 -04:00
parent 174825fe8c
commit 476446d93c
6 changed files with 2766 additions and 1 deletions
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2
examples/PACKAGES/hdnnp/in.hdnnp
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@ -39,7 +39,7 @@ fix INT all nve
############################################################################### ###############################################################################
# OUTPUT # OUTPUT
############################################################################### ###############################################################################
dump 1 all atom 1 dump.hdnnp # dump 1 all atom 1 dump.hdnnp
############################################################################### ###############################################################################
# SIMULATION # SIMULATION

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examples/PACKAGES/hdnnp/in.hybrid Normal file
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###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
timestep ${dt}
thermo 1
###############################################################################
# HDNNP
###############################################################################
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
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}

667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1 Normal file
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LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
read_data ${cfgFile}
read_data data.H2O-360mol
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.004 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * H O
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
# dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** 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_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** 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 H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** 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 H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 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: "1:H,2:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> H ( 1)
2 <-> 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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hdnnp, 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) = 4.021 | 4.021 | 4.021 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 3.2801 on 1 procs for 10 steps with 1080 atoms
Performance: 0.132 ns/day, 182.228 hours/ns, 3.049 timesteps/s, 3.293 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2794 | 3.2794 | 3.2794 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030785 | 0.00030785 | 0.00030785 | 0.0 | 0.01
Output | 0.00018531 | 0.00018531 | 0.00018531 | 0.0 | 0.01
Modify | 0.00013118 | 0.00013118 | 0.00013118 | 0.0 | 0.00
Other | | 9.142e-05 | | | 0.00
Nlocal: 1080 ave 1080 max 1080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 239270 ave 239270 max 239270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 239270
Ave neighs/atom = 221.5463
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4 Normal file
View File

@ -0,0 +1,667 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
read_data ${cfgFile}
read_data data.H2O-360mol
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.007 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * H O
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
# dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** 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_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** 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 H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** 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 H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 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: "1:H,2:O"
CAUTION: Please ensure that this mapping between LAMMPS
atom types and NNP elements is consistent:
---------------------------
LAMMPS type | NNP element
---------------------------
1 <-> H ( 1)
2 <-> 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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hdnnp, 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) = 3.13 | 3.13 | 3.13 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 0.930358 on 4 procs for 10 steps with 1080 atoms
Performance: 0.464 ns/day, 51.687 hours/ns, 10.749 timesteps/s, 11.608 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 | 0.85419 | 0.89495 | 0.92919 | 3.5 | 96.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075831 | 0.035035 | 0.075822 | 17.5 | 3.77
Output | 0.00018471 | 0.00023973 | 0.00031043 | 0.0 | 0.03
Modify | 4.0258e-05 | 4.2308e-05 | 4.4218e-05 | 0.0 | 0.00
Other | | 9.199e-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
FullNghs: 59817.5 ave 61917 max 57577 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 239270
Ave neighs/atom = 221.5463
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1 Normal file
View File

@ -0,0 +1,689 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
read_data data.H2O-360mol add append offset 1 0 0 0 0
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
1 by 1 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.004 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
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
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
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
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** 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_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** 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 H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** 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 H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 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) = 7.06 | 7.06 | 7.06 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 3.32416 on 1 procs for 10 steps with 1080 atoms
Performance: 0.130 ns/day, 184.675 hours/ns, 3.008 timesteps/s, 3.249 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3234 | 3.3234 | 3.3234 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00032742 | 0.00032742 | 0.00032742 | 0.0 | 0.01
Output | 0.00019506 | 0.00019506 | 0.00019506 | 0.0 | 0.01
Modify | 0.00011454 | 0.00011454 | 0.00011454 | 0.0 | 0.00
Other | | 0.0001165 | | | 0.00
Nlocal: 1080 ave 1080 max 1080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 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: 0:00:03

689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4 Normal file
View File

@ -0,0 +1,689 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile string "data.H2O-360mol"
# Timesteps
variable numSteps equal 10
variable dt equal 0.0005
# HDNNP
variable hdnnpCutoff equal 6.36
variable hdnnpDir string "hdnnp-data"
###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
create_box 3 box
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
mass 1 1.0
read_data ${cfgFile} add append offset 1 0 0 0 0
read_data data.H2O-360mol add append offset 1 0 0 0 0
Reading data file ...
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
2 by 2 by 1 MPI processor grid
reading atoms ...
1080 atoms
read_data CPU = 0.007 seconds
timestep ${dt}
timestep 0.0005
thermo 1
###############################################################################
# HDNNP
###############################################################################
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
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
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
pair_coeff * * hdnnp NULL H O
pair_coeff 1 * lj/cut 0.1 3.0
###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve
###############################################################################
# OUTPUT
###############################################################################
#dump 1 all atom 1 dump.hdnnp
###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
@Article{Singraber19,
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
Neural Network Potentials},
year = {2019},
month = mar,
volume = {15},
pages = {1827--1840},
doi = {10.1021/acs.jctc.8b00770},
journal = {J.~Chem.\ Theory Comput.},
number = {3}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
*******************************************************************************
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
(version.h): v2.2.0
------------------------------------------------------------
Git branch : collected-small-changes
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time : Aug 23 2023 08:43:11
------------------------------------------------------------
Features/Flags:
------------------------------------------------------------
Symmetry function groups : enabled
Symmetry function cache : enabled
Timing function available : available
Asymmetric polynomial SFs : available
SF low neighbor number check : enabled
SF derivative memory layout : reduced
MPI explicitly disabled : no
------------------------------------------------------------
Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
-------------------------------------------------------------------------------
* 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
*******************************************************************************
*** SETUP: SETTINGS FILE ******************************************************
Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************
*** SETUP: NORMALIZATION ******************************************************
Data set normalization is used.
Mean energy per atom : -2.5521343547039809E+01
Conversion factor energy : 2.4265748255366972E+02
Conversion factor length : 5.8038448995319847E+00
*******************************************************************************
*** SETUP: ELEMENT MAP ********************************************************
Number of element strings found: 2
Element 0: H ( 1)
Element 1: O ( 8)
*******************************************************************************
*** SETUP: ELEMENTS ***********************************************************
Number of elements is consistent: 2
Atomic energy offsets per element:
Element 0: 0.00000000E+00
Element 1: 0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************
*** 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_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************
*** 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 H :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element O :
-------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
-------------------------------------------------------------------------------------------------
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element H: 12.000000
Minimum cutoff radius for element O: 12.000000
Maximum cutoff radius (global) : 12.000000
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
Symmetry function derivatives memory table for element H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 15 of 27 ( 55.6 %)
- O: 19 of 27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
- H: 18 of 30 ( 60.0 %)
- O: 16 of 30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
Element H: in total 4 caches, used 17.00 times on average.
Element O: in total 4 caches, used 17.00 times on average.
*******************************************************************************
*** 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 H :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element O :
----------------------------------------------------------------------------------------------------------
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
----------------------------------------------------------------------------------------------------------
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
- - - - - 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