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