diff --git a/examples/PACKAGES/hdnnp/in.hdnnp b/examples/PACKAGES/hdnnp/in.hdnnp index 79edc605be..ccf399a0a0 100644 --- a/examples/PACKAGES/hdnnp/in.hdnnp +++ b/examples/PACKAGES/hdnnp/in.hdnnp @@ -39,7 +39,7 @@ fix INT all nve ############################################################################### # OUTPUT ############################################################################### -dump 1 all atom 1 dump.hdnnp +# dump 1 all atom 1 dump.hdnnp ############################################################################### # SIMULATION diff --git a/examples/PACKAGES/hdnnp/in.hybrid b/examples/PACKAGES/hdnnp/in.hybrid new file mode 100644 index 0000000000..bfce2e4cde --- /dev/null +++ b/examples/PACKAGES/hdnnp/in.hybrid @@ -0,0 +1,53 @@ +############################################################################### +# 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} diff --git a/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1 b/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1 new file mode 100644 index 0000000000..600e7033f0 --- /dev/null +++ b/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1 @@ -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) + 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 diff --git a/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4 b/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4 new file mode 100644 index 0000000000..b65970628b --- /dev/null +++ b/examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4 @@ -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 diff --git a/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1 b/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1 new file mode 100644 index 0000000000..40c8578a0b --- /dev/null +++ b/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1 @@ -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 diff --git a/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4 b/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4 new file mode 100644 index 0000000000..4caae1a778 --- /dev/null +++ b/examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4 @@ -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