├── README.md ├── blyp-nnp-potential ├── blyp-reference │ ├── H.cell │ └── H.param ├── input.nn ├── scaling.data └── weights.001.data ├── input-PBE-DFT-aimd ├── dos.in ├── input.xml ├── pseudo │ └── H.pbe-kjpaw.UPF ├── qe-h128.in ├── rs1.26-init.xyz └── single.run ├── input-nnp-WTmetaD ├── A-data.h64-metalunits ├── in.lmp ├── plumed.dat └── submit.sh ├── input-nnp-enthalpy-solid-phases ├── H-H-C2c-24-I.res ├── H-H-C2c-24-II.res ├── H-H-C2c-24-II.xyze ├── H-H-Cmce-12-II.res ├── H-H-Cmce-4-II.res ├── H-H-Fmmm-2-I.res ├── H-H-P21c-8-I.res ├── H-H-P6122-36-I.res ├── H-H-P63m-16-I.res ├── res2lmpin.sh ├── runall.sh └── workdir │ ├── H.in │ ├── H.pp │ └── singlerun.sh ├── input-nnp-md-npt ├── A-data.h64-metalunits ├── M-data.h64-metalunits ├── in.lmp ├── plumed.dat └── submit.sh ├── input-nnp-rss ├── H.cell ├── H.pp └── runrss.sh ├── pbe-nnp-cooling-heating-nst-1728 ├── .ipynb_checkpoints │ └── cooling-heating-analysis-checkpoint.ipynb ├── input │ ├── cooling-nst-template │ │ ├── A-data.h64-metalunits │ │ ├── M-data.h64-metalunits │ │ ├── in.lmp │ │ ├── input.nn │ │ ├── scaling.data │ │ ├── submit.sh │ │ └── weights.001.data │ ├── heating-nst-template │ │ ├── in.lmp │ │ ├── input.nn │ │ ├── scaling.data │ │ ├── submit.sh │ │ └── weights.001.data │ ├── runcool.sh │ └── runheat.sh └── solid-structures.zip ├── pbe-nnp-potential ├── README.md ├── pbe-reference │ ├── H.cell │ └── H.param ├── v1 │ ├── input.nn │ ├── scaling.data │ └── weights.001.data └── v2 │ ├── input.nn │ ├── scaling.data │ └── weights.001.data ├── pbe-training-set ├── H512-rerun-LLT-region-1-WTmetaD.tar.gz ├── H512-rerun-LLT-region-2-WTmetaD.tar.gz ├── H512-rerun-LLT-region-3-WTmetaD.tar.gz ├── H512-rerun-LLT-region-4-WTmetaD.tar.gz ├── H512-rerun-LLT-region-5-WTmetaD.tar.gz ├── H512-rerun-LLT-region-Redmer.tar.gz ├── H512-rerun-LLT-region-more-Redmer.tar.gz ├── airss-fps-n-10000-natom-12.tar.gz ├── airss-fps-n-10000-natom-24.tar.gz ├── airss-fps-n-10000-natom-8.tar.gz ├── all-rerun-P21c.tar.gz ├── old-train-set-fps-n-5000.tar.gz ├── rerun-H-highP-liquid.tar.gz ├── rerun-H-highP-solid-rss-rscan.tar.gz ├── rerun-H-nnp-gen5-nvt-traj.tar.gz ├── rerun-PBE-nnp-gen7-nvt.tar.gz ├── rerun-h-nnp-gen8-nvt-traj.tar.gz ├── rerun-rss-gen15-highP.tar.gz ├── rerun-rss-gen15-more.tar.gz ├── rerun-rss-gen15.tar.gz ├── rerun-rss-gen17.tar.gz ├── rss-highP-fps-n-5000.tar.gz ├── rss-nnpgen3-fps-n-9950.tar.gz ├── rss-nnpgen4-fps-n-9900.tar.gz ├── shake-fps-n-8000.tar.gz └── shake-highP-solid.tar.gz └── vmc-nnp-potential ├── input.nn ├── scaling.data └── weights.001.data /README.md: -------------------------------------------------------------------------------- 1 | # Data repository of "Evidence for supercritical behaviour of high-pressure liquid hydrogen" 2 | 3 | Bingqing Cheng, Guglielmo Mazzola, Chris J. Pickard, and Michele Ceriotti 4 | 5 | Contains three sets of neural network potentials (NNPs) of high-pressure hydrogen, based on PBE, BLYP, and variational Quantum Monte Carlo (QMC) reference calculations. 6 | 7 | Input files for running molecule dynamic simulations using the NNPs are also provided. 8 | 9 | ========================= 10 | 11 | * ./pbe-training-set/: the training set of the PBE NNP, following the N2P2/RuNNer format (see https://github.com/CompPhysVienna/n2p2). Contains energy, forces, and coordinates of atoms. All in atomic units. Redmer.data are from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.82.195107. The production version of the NNP was not trained on this set, although we did try training on this set and did not notice any significant difference. 12 | 13 | * ./pbe-nnp-potential/: the neural network potential (NNP) for high pressure H based on PBE-DFT. Two versions (v1 and v2) are included. v2 is the version used to generate the results reported in the manuscript. v1 is an earlier version, which is almost as accurate! The subdirectory /pbe-reference/ contains the CASTEP input files for the PBE DFT reference calculations. 14 | 15 | * ./blyp-nnp-potential/: the neural network potential for high pressure H based on BLYP-DFT. The subdirectory /blyp-reference/ contains the CASTEP input files for the BLYP DFT reference calculations. 16 | 17 | * ./vmc-nnp-potential/: the neural network potential for high pressure H based on variational Quantum Monte Carlo. 18 | 19 | * ./input-nnp-md-npt/: NPT MD simulations performed using NNP. MD simulations using NNPs are in general performed using LAMMPS+n2p2 library. Copy and paste the three N2P2 files (input.nn scaling.data weight.001.data) in the selected *-nnp-potential folder to the same directory to run the simulations. 20 | 21 | * ./input-nnp-WTmetaD/: Well-tempered MD simulations performed using a NNP, using LAMMPS+n2p2 library+PLUMED plugin. 22 | 23 | * ./input-nnp-rss/: Input for running random structure searches using a NNP, using AIRSS package. 24 | 25 | * ./input-nnp-enthalpy-solid-phases/: Input for computing enthalpies of solid phases using a NNP, using AIRSS package and LAMMPS+n2p2 library. 26 | 27 | * ./pbe-nnp-cooling-heating-nst-1728/: Inputs for running cooling and heating MD simulations using the MLP based on PBE DFT. solid-structures.zip contains the solid structures obtained at the end of the cooling simulations. 28 | 29 | * ./simulations-PBE-DFT-aimd/: Direct AIMD simulations using DFT with PBE functional. We use quantum expresso/6.2.0 for the DFT calculations. 30 | 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /blyp-nnp-potential/blyp-reference/H.cell: -------------------------------------------------------------------------------- 1 | %BLOCK LATTICE_CART 2 | 2.154433 0 0 3 | 0 2.154433 0 4 | 0 0 2.154433 5 | %ENDBLOCK LATTICE_CART 6 | 7 | #VARVOL=10 8 | 9 | %BLOCK POSITIONS_FRAC 10 | H 0.0 0.0 0.0 # H1 % NUM=1 11 | %ENDBLOCK POSITIONS_FRAC 12 | 13 | ##SPECIES=H 14 | ##NATOM=3-9 15 | ##FOCUS=1 16 | 17 | #SYMMOPS=2-4 18 | ##SGRANK=20 19 | #NFORM=1 20 | ##ADJGEN=0-1 21 | ##SLACK=0.25 22 | ##OVERLAP=0.1 23 | #MINSEP=1-3 AUTO 24 | #COMPACT 25 | ##SYSTEM={Rhom,Tric,Mono,Cubi,Hexa,Orth,Tetra} 26 | 27 | KPOINTS_MP_SPACING 0.03 28 | 29 | SYMMETRY_GENERATE 30 | SNAP_TO_SYMMETRY 31 | 32 | %BLOCK SPECIES_POT 33 | %ENDBLOCK SPECIES_POT 34 | 35 | %BLOCK EXTERNAL_PRESSURE 36 | 0 0 0 37 | 0 0 38 | 0 39 | %ENDBLOCK EXTERNAL_PRESSURE 40 | -------------------------------------------------------------------------------- /blyp-nnp-potential/blyp-reference/H.param: -------------------------------------------------------------------------------- 1 | #task : geometryoptimization 2 | xc_functional : BLYP 3 | spin_polarized : false 4 | fix_occupancy : false 5 | metals_method : dm 6 | mixing_scheme : pulay 7 | max_scf_cycles : 1000 8 | cut_off_energy : 700 eV 9 | grid_scale : 2 10 | fine_grid_scale : 3 11 | opt_strategy : speed 12 | page_wvfns : 0 13 | num_dump_cycles : 0 14 | backup_interval : 0 15 | geom_method : LBFGS 16 | geom_max_iter : 20 17 | mix_history_length : 20 18 | finite_basis_corr : 0 19 | fixed_npw : true 20 | write_cell_structure : true 21 | write_checkpoint : none 22 | write_bib : false 23 | write_otfg : false 24 | #write_cst_esp : false # Requires Castep 17 and above 25 | #write_bands : false # Requires Castep 17 and above 26 | #write_geom : false # Requires Castep 17 and above 27 | #bs_write_eigenvalues : false 28 | calculate_stress : true 29 | -------------------------------------------------------------------------------- /blyp-nnp-potential/input.nn: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # GENERAL NNP SETTINGS 3 | ############################################################################### 4 | number_of_elements 1 # Number of elements. 5 | elements H # Specification of elements. 6 | #atom_energy H -0.45890771 # Free atom reference energy (H). 7 | cutoff_type 2 # Cutoff type. 8 | scale_symmetry_functions # Scale all symmetry functions with min/max values. 9 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 10 | scale_min_short 0.0 # Minimum value for scaling. 11 | scale_max_short 1.0 # Maximum value for scaling. 12 | center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 13 | global_hidden_layers_short 3 # Number of hidden layers. 14 | global_nodes_short 20 20 20 # Number of nodes in each hidden layer. 15 | global_activation_short t t t l # Activation function for each hidden layer and output layer. 16 | #normalize_nodes # Normalize input of nodes. 17 | 18 | ############################################################################### 19 | # ADDITIONAL SETTINGS FOR TRAINING 20 | ############################################################################### 21 | epochs 50 # Number of training epochs. 22 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 23 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 24 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 25 | selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 26 | #memorize_symfunc_results # Keep symmetry function results in memory. 27 | random_seed 12216635 28 | test_fraction 0.1 # Fraction of structures kept for testing. 29 | use_short_forces # Use forces for training. 30 | force_weight 5.0 # Weight of force updates relative to energy updates. 31 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 32 | short_force_fraction 0.01 # Fraction of force updates per epoch. 33 | short_energy_error_threshold 1.00 # RMSE threshold for energy update candidates. 34 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 35 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 36 | #repeated_energy_update # After force update perform energy update for corresponding structure. 37 | #use_old_weights_short # Restart fitting with old weight parameters. 38 | weights_min -1.0 # Minimum value for initial random weights. 39 | weights_max 1.0 # Maximum value for initial random weights. 40 | #precondition_weights # Precondition weights with initial energies. 41 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 42 | write_trainpoints 5 # Write energy comparison. 43 | write_trainforces 5 # Write force comparison. 44 | write_weights_epoch # Write weights. 45 | #write_neuronstats 5 10 # Write neuron statistics. 46 | #write_trainlog # Write training log file. 47 | #################### 48 | # GRADIENT DESCENT # 49 | #################### 50 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 51 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 52 | ############################ 53 | # KALMAN FILTER (STANDARD) # 54 | ############################ 55 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 56 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 57 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 58 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 59 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 60 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 61 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 62 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 63 | ################################# 64 | # KALMAN FILTER (FADING MEMORY) # 65 | ################################# 66 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 67 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 68 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 69 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 70 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 71 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 72 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 73 | 74 | ############################################################################### 75 | # SYMMETRY FUNCTIONS 76 | ############################################################################### 77 | 78 | # Radial symmetry function (type 2): 79 | #symfunction_short 2 80 | 81 | # Narrow Angular symmetry function (type 3): 82 | #symfunction_short 3 83 | 84 | # Wide Angular symmetry function (type 9): 85 | #symfunction_short 9 86 | 87 | symfunction_short H 2 H 57.776 0.814 2.000 88 | symfunction_short H 2 H 34.647 1.051 3.000 89 | symfunction_short H 2 H 25.678 1.221 3.000 90 | symfunction_short H 2 H 5.078 2.746 5.000 91 | symfunction_short H 2 H 9.244 2.035 5.000 92 | symfunction_short H 2 H 19.489 1.402 4.000 93 | symfunction_short H 2 H 6.851 2.364 5.000 94 | symfunction_short H 2 H 14.444 1.628 4.000 95 | symfunction_short H 2 H 3.763 3.190 5.000 96 | symfunction_short H 2 H 49.892 0.876 2.500 97 | symfunction_short H 2 H 77.956 0.701 2.000 98 | symfunction_short H 2 H 1.435 5.165 6.000 99 | symfunction_short H 2 H 1.055 6.026 7.000 100 | symfunction_short H 2 H 42.820 0.946 2.000 101 | symfunction_short H 2 H 1.089 5.929 8.000 102 | symfunction_short H 2 H 2.613 3.828 6.000 103 | symfunction_short H 2 H 22.708 1.299 5.000 104 | symfunction_short H 2 H 0.807 6.887 8.000 105 | symfunction_short H 2 H 16.830 1.509 5.000 106 | symfunction_short H 2 H 1.470 5.104 8.000 107 | symfunction_short H 2 H 30.639 1.118 5.000 108 | symfunction_short H 2 H 1.984 4.394 8.000 109 | symfunction_short H 2 H 10.705 1.891 4.000 110 | symfunction_short H 2 H 12.473 1.752 5.000 111 | symfunction_short H 2 H 2.591 3.845 7.000 112 | symfunction_short H 2 H 4.716 2.850 7.000 113 | symfunction_short H 2 H 6.364 2.453 7.000 114 | symfunction_short H 2 H 3.495 3.310 7.000 115 | symfunction_short H 2 H 7.934 2.197 4.000 116 | symfunction_short H 3 H H 0.111 1.000 1.000 3.000 117 | symfunction_short H 3 H H 0.062 -1.000 1.000 4.000 118 | symfunction_short H 3 H H 0.062 1.000 1.000 4.000 119 | symfunction_short H 3 H H 0.062 1.000 16.000 4.000 120 | symfunction_short H 3 H H 0.040 1.000 4.000 5.000 121 | symfunction_short H 3 H H 0.040 -1.000 1.000 5.000 122 | symfunction_short H 3 H H 0.040 -1.000 4.000 5.000 123 | symfunction_short H 3 H H 0.016 1.000 1.000 8.000 124 | symfunction_short H 3 H H 0.016 -1.000 1.000 8.000 125 | symfunction_short H 3 H H 0.020 1.000 1.000 7.000 126 | symfunction_short H 3 H H 0.028 1.000 1.000 6.000 127 | symfunction_short H 3 H H 0.016 1.000 16.000 8.000 128 | symfunction_short H 3 H H 0.016 1.000 4.000 8.000 129 | symfunction_short H 3 H H 0.016 -1.000 16.000 8.000 130 | symfunction_short H 3 H H 0.028 1.000 16.000 6.000 131 | symfunction_short H 3 H H 0.028 -1.000 16.000 6.000 132 | symfunction_short H 3 H H 0.020 -1.000 1.000 7.000 133 | symfunction_short H 3 H H 0.016 -1.000 4.000 8.000 134 | symfunction_short H 3 H H 0.020 1.000 4.000 7.000 135 | -------------------------------------------------------------------------------- /blyp-nnp-potential/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 0.0000000000000000E+00 1.2786864788554039E-01 2.0148701465623242E-04 3.1524761950806630E-03 17 | 1 2 0.0000000000000000E+00 1.5324159403424931E-01 2.6312649631626648E-05 1.2049201618322630E-03 18 | 1 3 0.0000000000000000E+00 1.8779883931284078E-01 2.4100609615632932E-06 4.1087787492401478E-04 19 | 1 4 0.0000000000000000E+00 1.8833496692166160E-01 1.1923536362419721E-04 3.0001964292893754E-03 20 | 1 5 0.0000000000000000E+00 3.5955730712772588E-01 1.4892814158897155E-02 2.6012376022955513E-02 21 | 1 6 0.0000000000000000E+00 3.5929588979511018E-01 1.8674770931646589E-03 1.2590160121393355E-02 22 | 1 7 0.0000000000000000E+00 7.9425620447436296E-01 2.1254143820593810E-01 1.1525862384997716E-01 23 | 1 8 0.0000000000000000E+00 8.7467201947800743E-01 1.7074128934272059E-01 1.1708692558764941E-01 24 | 1 9 0.0000000000000000E+00 7.4811605665701719E-01 1.5519435107662793E-01 7.1275316047969300E-02 25 | 1 10 0.0000000000000000E+00 6.7333285542477783E-01 1.0759055403395651E-01 6.3297413723034684E-02 26 | 1 11 3.5910379683328059E-05 9.7073274581664104E-01 5.0623959362231108E-01 1.2736879346446944E-01 27 | 1 12 1.4651415281849498E-07 1.2321718127446848E+00 5.6452836615588087E-01 1.8262446467122168E-01 28 | 1 13 8.4577697438719571E-13 1.4747184327154994E+00 4.5721468960237244E-01 2.0131653962487583E-01 29 | 1 14 2.1065196719838351E-21 1.3840249655512706E+00 3.1399515618091239E-01 1.9540171709333165E-01 30 | 1 15 8.6972539370641714E-35 1.1709787371985103E+00 2.2399339888890113E-01 1.3937389170540587E-01 31 | 1 16 6.8849742194674013E-55 9.8648969012214727E-01 1.9013342869196725E-01 8.6985029880464221E-02 32 | 1 17 1.9097564541503356E-84 7.1287053045711446E-01 7.0423033342822558E-02 6.1097607892459958E-02 33 | 1 18 3.9041233430555061E-127 5.7910474297282288E-01 7.7979762674756370E-03 3.0001123143202617E-02 34 | 1 19 1.9549728427461759E-02 3.8930917832271078E-01 2.0171598260484119E-01 5.1727433306469041E-02 35 | 1 20 2.2793198416896789E-02 1.4386575716282468E+00 7.6525110162075216E-01 1.4141446941085739E-01 36 | 1 21 4.7646427383803432E-02 5.6115606300904231E-01 3.5202359290322310E-01 8.5427371422089546E-02 37 | 1 22 5.7114363278535099E-02 2.5545080234003468E+00 1.3538612523590432E+00 2.5072471847758254E-01 38 | 1 23 2.4940663697200689E-03 2.7522145071418831E+00 1.4697299433055526E+00 3.2622023343195683E-01 39 | 1 24 7.8682802555547335E-06 2.5944753464285428E+00 1.3058387226565509E+00 3.6913521804174371E-01 40 | 1 25 3.8919161034755070E-10 2.4797469425290117E+00 9.2442605075510287E-01 3.6754562234387905E-01 41 | 1 26 9.2619930581806134E-02 8.1664587623323914E-01 5.0966407948897452E-01 9.9151195954948784E-02 42 | 1 27 1.8318498196390448E-01 1.9153034470475108E+00 1.2247793247301280E+00 2.7230852284979107E-01 43 | 1 28 2.7507711080804348E-01 3.0256562654161572E+00 1.7844962674328060E+00 4.5679177013995692E-01 44 | 1 29 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1.2870123862469087E-03 54 | 1 39 6.2262684617804945E-07 1.0573409296829014E-01 2.4663201317918649E-02 1.2324985639637898E-02 55 | 1 40 3.0303734433414090E-05 8.0480865506783472E-01 1.9705844281684351E-01 9.4076893600784375E-02 56 | 1 41 2.9602459953219584E-04 1.9365314536570741E+00 5.2281410288197383E-01 2.4440723530575639E-01 57 | 1 42 2.3033250210999353E-04 1.0600999125841739E+00 2.9064562025332846E-01 1.3628090064970649E-01 58 | 1 43 4.4156751616116266E-04 1.8181725546180594E+00 5.0504793045530760E-01 2.2653438009689736E-01 59 | 1 44 3.7271975785887314E-03 4.3394225551846519E+00 1.3292398624644119E+00 5.8667197578105734E-01 60 | 1 45 8.0581351847887373E-06 4.0158809640046172E-01 9.7520506174563842E-02 4.6421184682890214E-02 61 | 1 46 2.8285538602087893E-03 2.4132319079528153E+00 7.5095290878482479E-01 3.3351584311932420E-01 62 | 1 47 1.3040678584439959E-09 9.3788161160613240E-02 1.9338171364423416E-02 1.0081020289092305E-02 63 | 1 48 1.1896132844293479E-03 8.2190114793389346E-01 2.5033325307694210E-01 1.1236226432368290E-01 64 | -------------------------------------------------------------------------------- /input-PBE-DFT-aimd/dos.in: -------------------------------------------------------------------------------- 1 | &dos 2 | prefix='pbe' 3 | fildos='pbe.dos' 4 | Emin=-25.0, Emax=25.0, DeltaE=0.1 5 | ngauss = 0 6 | degauss = 0.03 7 | / 8 | -------------------------------------------------------------------------------- /input-PBE-DFT-aimd/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, temperature{kelvin}, conserved{electronvolt}, pot_component_raw(0), pressure_md{megapascal}] 4 | positions 5 | velocities 6 | forces 7 | 8 | 2000000 9 | 840000 10 | 99415 11 | 12 |
HOST
13 | PORT 14 | 15 | 16 | 17 | rsDENSITY-init.xyz 18 | TEMPERATURE 19 | 20 | 21 | 22 | 23 | 24 | 25 | 0.2 26 | 27 | 0.50 28 | 100 29 | 30 | 31 | 32 | 33 | TEMPERATURE 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /input-PBE-DFT-aimd/qe-h128.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | title="replay" 3 | calculation='scf', 4 | restart_mode = 'from_scratch', 5 | prefix='pbe', 6 | pseudo_dir='../pseudo' 7 | tstress=.true. 8 | tprnfor=.true. 9 | etot_conv_thr=1.0D-4 10 | forc_conv_thr=1.0D-3 11 | / 12 | &SYSTEM 13 | ibrav = 1, 14 | celldm(1) = CELLSIZE, 15 | nat = 128, 16 | ntyp = 1, 17 | ecutwfc = 80.0 , 18 | occupations = 'smearing' 19 | degauss = 2.000000000000000E-003 20 | / 21 | &ELECTRONS 22 | conv_thr = 1.D-4, 23 | / 24 | &IONS 25 | / 26 | 27 | ATOMIC_SPECIES 28 | 29 | H 1.0000 H.pbe-kjpaw.UPF 30 | 31 | ATOMIC_POSITIONS bohr 32 | H 11.13358 2.563068 -0.9476479 33 | H 12.23845 16.49569 0.6573598 34 | H 4.166445 7.65369 2.817332 35 | H 14.92572 10.7435 -0.5460996 36 | H 16.09931 9.254275 1.385941 37 | H 13.06753 5.799679 -1.316391 38 | H 15.28746 11.20087 4.011162 39 | H 8.046665 11.61112 -16.48944 40 | H 16.20998 6.870582 1.873627 41 | H 11.49788 3.928777 -7.93971 42 | H 7.396416 8.436429 -6.907402 43 | H 10.39602 11.33808 6.42911 44 | H 4.56168 11.25525 -3.081696 45 | H 15.13689 9.858018 4.986384 46 | H 12.89499 12.09686 2.734979 47 | H 17.27692 15.86016 3.482419 48 | H 5.465702 10.15866 2.702443 49 | H 13.58582 10.40799 3.11036 50 | H 6.717968 11.95855 -0.5022352 51 | H 11.39545 9.289434 0.08878013 52 | H 10.39529 7.948069 -9.228843 53 | H 12.22276 11.02394 -10.8961 54 | H 18.31347 4.735957 -5.352116 55 | H 15.5288 7.98828 -5.901859 56 | H 7.920832 8.05947 -1.641675 57 | H 11.77887 8.619972 -2.843172 58 | H 14.16036 16.15471 -4.505226 59 | H 12.34719 12.10204 0.2735512 60 | H 20.17894 3.671077 1.206223 61 | H 9.302746 11.92616 -10.23935 62 | H 19.00634 8.227783 -9.469759 63 | H 21.33967 11.0891 -1.880694 64 | H 9.046382 16.55835 -7.831665 65 | H 6.756915 7.291242 6.923915 66 | H 16.20607 15.47899 -9.322768 67 | H 13.53097 -5.341613 -7.82348 68 | H 16.95197 3.081507 4.406432 69 | H 8.623371 6.009048 -3.289637 70 | H 12.68508 8.457955 -5.159179 71 | H 4.67192 8.333303 -2.838324 72 | H 12.95254 10.57221 -2.365275 73 | H 9.281719 8.282655 -5.582768 74 | H 11.54142 2.91342 -3.617911 75 | H 16.09435 2.107987 1.481427 76 | H 6.36226 2.54781 -1.896769 77 | H 13.94807 1.747594 -2.366465 78 | H 13.07873 6.977726 -6.642425 79 | H 7.850728 1.840354 -7.864013 80 | H 13.35193 13.64138 0.6256301 81 | H 12.63976 3.348917 5.084029 82 | H 9.239234 4.935159 -5.209153 83 | H 10.50648 5.420138 -7.449035 84 | H 10.59883 7.098132 -5.530383 85 | H 14.89787 13.40389 -4.236424 86 | H 19.90099 10.00436 -4.640319 87 | H 11.86709 10.57985 -5.330145 88 | H 8.196292 13.77643 -0.1620325 89 | H 6.177739 9.061378 -6.211158 90 | H 5.105328 12.8786 -7.372071 91 | H 12.53206 8.01398 -0.3238021 92 | H 14.19334 3.354735 -0.7413135 93 | H 15.70845 4.037544 4.08539 94 | H 9.552799 9.846935 -1.223584 95 | H 14.76189 11.91173 1.188867 96 | H 9.494167 6.327264 -10.11591 97 | H 18.2736 11.05707 2.955075 98 | H 13.96907 6.874306 -1.908911 99 | H 16.63882 12.31787 -4.105854 100 | H 5.881734 6.580196 -5.393278 101 | H 18.15059 9.831662 -3.639459 102 | H 9.974396 3.929601 -3.846964 103 | H 18.03518 3.208465 1.358709 104 | H 15.5636 8.73758 -0.5087384 105 | H 14.40409 4.555543 -9.478571 106 | H 6.908387 -0.175953 0.5106229 107 | H 19.26154 9.938878 1.043473 108 | H 9.46263 -0.9724763 -6.962131 109 | H 12.99679 8.791749 -8.435996 110 | H 12.07925 12.18172 -2.926845 111 | H 19.13086 15.19394 -2.292279 112 | H 9.197898 7.578761 -3.283622 113 | H 10.74234 10.16235 -9.255426 114 | H 11.24082 4.26654 -1.629718 115 | H 5.495684 9.351312 6.949149 116 | H 11.50246 9.250808 -6.570507 117 | H 9.190495 12.73979 -1.488982 118 | H 17.35708 7.805506 0.3917696 119 | H 16.69937 11.04702 -1.763673 120 | H 6.340758 7.751109 -1.425245 121 | H 3.090429 3.016995 2.56834 122 | H 13.55212 4.112664 -3.01687 123 | H 9.96044 15.59894 -0.1825631 124 | H 13.6818 9.126515 -1.885449 125 | H 13.99668 8.692113 -10.12784 126 | H 7.83756 6.532343 4.66537 127 | H 7.191633 14.04763 -4.433793 128 | H 13.99813 10.21578 6.801008 129 | H 10.71258 -1.649313 -3.730893 130 | H 14.52981 5.630681 -6.33831 131 | H 9.715895 1.997804 -4.832611 132 | H 11.63832 14.37466 1.336194 133 | H 10.61319 11.05388 -7.029488 134 | H 10.24819 -3.070283 -1.243382 135 | H 8.272265 1.965863 -3.213168 136 | H 11.83489 4.490048 -5.888237 137 | H 7.314965 5.203703 -1.044796 138 | H 21.21968 12.34942 -9.379779 139 | H 11.31212 1.825608 -6.16807 140 | H 5.408049 5.184617 -3.538815 141 | H 11.92069 6.340829 1.873496 142 | H 18.15183 5.378427 0.5225778 143 | H 14.07475 7.502005 -4.163108 144 | H 22.102 7.91792 -7.910808 145 | H 11.43027 5.568214 -3.332864 146 | H 15.96805 3.310197 -1.120458 147 | H 15.60517 4.976072 -0.1103528 148 | H 11.63908 6.723319 -4.002038 149 | H 16.01648 3.817935 -4.302932 150 | H 7.894936 10.14594 -2.036063 151 | H 14.90388 6.911483 -0.1012358 152 | H 13.32417 11.62627 -5.276684 153 | H 9.568202 13.46927 3.777002 154 | H 5.284547 16.72934 -2.179463 155 | H 10.60061 6.218772 -1.197599 156 | H 7.229533 17.81176 2.603475 157 | H 13.96055 13.19568 4.856079 158 | H 8.000329 14.44853 3.424628 159 | H 6.404381 11.2447 -5.265838 160 | 161 | 162 | K_POINTS automatic 163 | 4 4 4 1 1 1 164 | -------------------------------------------------------------------------------- /input-PBE-DFT-aimd/rs1.26-init.xyz: -------------------------------------------------------------------------------- 1 | 128 2 | # CELL(abcABC): 10.23614 10.23614 10.23614 90.00000 90.00000 90.00000 Step: 7091 Bead: 0 positions{atomic_unit} cell{atomic_unit} 3 | H 10.2042 -12.9404 3.48808 4 | H 5.26808 15.9162 5.84579 5 | H 11.3809 6.33922 4.01972 6 | H 16.2718 6.29078 -10.0094 7 | H -8.28956 1.49091 -16.4033 8 | H 21.4726 -0.555977 6.75902 9 | H 21.3189 14.4894 13.1945 10 | H 10.659 2.14997 -16.1945 11 | H 14.9263 11.6146 1.32873 12 | H -8.85039 -1.74489 0.726008 13 | H 9.32811 4.54653 -0.619928 14 | H 8.92975 2.7305 6.62874 15 | H -6.25184 -4.17381 4.05946 16 | H 13.0468 8.47736 0.843278 17 | H 22.2024 26.4668 -7.80677 18 | H 17.8929 22.4005 9.57865 19 | H 16.7657 12.3202 22.768 20 | H 8.86948 12.91 -17.5873 21 | H 7.77798 5.93016 -26.4724 22 | H 18.8855 -1.80987 -27.2849 23 | H 3.43956 8.27026 -22.5141 24 | H 2.62125 18.2545 -3.67384 25 | H 18.6375 -4.5363 -8.86872 26 | H 14.694 21.5245 -2.844 27 | H 3.15563 9.12752 3.1228 28 | H 0.0161681 4.16627 7.6132 29 | H -2.70353 21.5366 6.03594 30 | H 8.3758 1.11936 1.90612 31 | H 13.2068 -16.7407 13.4222 32 | H 29.2037 13.9783 -15.5015 33 | H 13.9746 13.6206 -3.7295 34 | H 14.804 15.8924 2.45903 35 | H -4.69615 28.4463 -18.8771 36 | H 6.04582 1.08851 -1.90544 37 | H 0.971198 9.19042 -7.90736 38 | H 10.8257 3.23986 -18.5815 39 | H 21.9678 -7.03881 5.61249 40 | H 1.16685 -0.326758 13.9111 41 | H 11.0448 17.0523 -11.6309 42 | H 13.0529 21.5465 -10.8604 43 | H 16.3 14.4851 -8.28552 44 | H 2.25594 7.55628 -16.9198 45 | H 6.77734 9.09985 1.45633 46 | H 8.6041 14.1409 -18.3597 47 | H 18.2064 -5.67718 16.3314 48 | H 11.1674 -3.40058 -9.26501 49 | H -2.07733 9.93413 -11.9054 50 | H 4.23561 -0.908762 11.8345 51 | H 23.5371 0.270225 17.1819 52 | H 17.116 5.58141 -1.3886 53 | H 6.62183 7.30827 -38.6662 54 | H 19.4525 18.2702 -10.3167 55 | H 16.3183 1.94859 -3.7618 56 | H 22.887 9.84777 5.58861 57 | H 18.7474 -6.91805 0.41936 58 | H 16.0631 18.2393 -16.6169 59 | H -1.31286 18.1085 -1.88118 60 | H 3.88012 0.883472 15.1355 61 | H 2.77574 24.5149 -5.56912 62 | H 13.153 8.6971 15.6217 63 | H 25.2959 13.0643 0.398068 64 | H 10.991 -4.3961 6.07905 65 | H 30.1085 11.7904 0.583045 66 | H 12.6792 5.48813 15.7605 67 | H 15.5578 3.7698 -5.64389 68 | H 9.64256 6.23498 -8.1111 69 | H 17.5298 3.95768 -11.4165 70 | H 13.831 20.8028 -1.70181 71 | H 5.47604 5.00551 11.1425 72 | H 8.76021 1.42463 -2.77364 73 | H 6.63701 9.90757 -12.7803 74 | H 24.721 10.6108 -7.4923 75 | H 19.5173 -0.905965 7.80662 76 | H 14.6757 12.4208 -4.87001 77 | H 13.2641 -4.33685 1.21826 78 | H 48.8883 -3.76129 -10.035 79 | H 14.1112 3.68927 -2.18449 80 | H 2.496 5.78527 -2.62524 81 | H -3.11165 16.571 -3.48636 82 | H 27.2689 23.7277 -23.4719 83 | H 6.26096 0.608876 -16.5623 84 | H -4.00004 5.40538 -16.9595 85 | H 10.3495 1.87478 -1.02977 86 | H 1.99833 4.42432 8.19461 87 | H 10.3491 25.6604 4.96984 88 | H 0.982112 11.3048 0.319495 89 | H 21.6354 12.0878 2.22323 90 | H 9.35943 9.85029 -4.72683 91 | H 29.5136 -4.69251 7.18372 92 | H -6.82084 12.6811 12.9776 93 | H -0.721701 10.3035 12.4058 94 | H 17.2819 20.1031 3.20304 95 | H 15.3601 -6.16696 -3.16663 96 | H 11.8514 -0.818127 8.1565 97 | H -6.19473 -14.832 9.44297 98 | H 25.4785 8.51485 9.92289 99 | H 22.8129 2.45704 -12.6366 100 | H 6.5805 -7.53818 11.3948 101 | H 7.09549 -12.4297 -11.3081 102 | H 11.3923 1.40609 -2.21356 103 | H -13.6667 20.9124 0.191344 104 | H 4.69016 9.86415 -24.9027 105 | H 6.43357 -1.52709 6.70174 106 | H -1.05992 5.46145 -6.40895 107 | H -3.75649 2.94222 4.49352 108 | H 18.741 1.65797 5.00856 109 | H 39.2523 18.6642 -29.624 110 | H -0.423567 -3.83438 -0.752308 111 | H 12.5182 11.652 -9.04258 112 | H 7.05954 -2.61682 4.35763 113 | H 15.3357 23.2277 9.08253 114 | H 9.57107 8.15935 -4.72624 115 | H 20.2949 11.4349 5.38644 116 | H 21.0873 13.4327 6.85238 117 | H 5.39554 9.09848 -5.39825 118 | H 24.7863 -4.45658 -13.1186 119 | H 22.8219 6.95663 -11.4754 120 | H 22.6521 13.4166 10.3708 121 | H 5.16715 20.545 10.1478 122 | H 41.0915 -0.691703 -0.399971 123 | H 11.265 24.7368 -20.8412 124 | H 4.16518 27.7237 -0.472764 125 | H -4.16089 17.5715 7.9091 126 | H 7.91629 28.8819 -14.3249 127 | H 10.7003 7.66584 -3.81379 128 | H 14.6933 6.88451 -4.91076 129 | H 2.67461 14.9676 0.616289 130 | H 14.7758 8.21931 -3.02357 131 | -------------------------------------------------------------------------------- /input-PBE-DFT-aimd/single.run: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | # i-PI on deneb 3 | # set --ntasks-per-core=1 for 512 tasks, 64 nodes, 8 cores/node, 4 Gb/task 4 | # Use less cores per node if you need more memory per MPI task, e.g.: 5 | # set --ntasks-per-node=4 for 512 tasks with 8 Gb/task on 128 nodes 6 | # 7 | #SBATCH --job-name=sf-1 8 | #SBATCH --time=02:00:00 9 | #SBATCH --ntasks=28 10 | #SBATCH --mem 32000 11 | 12 | set +e 13 | 14 | module load intel/18.0.2 intel-mkl/2018.2.199 intel-mpi/2018.2.199 15 | module load quantum-espresso/6.2.0-mpi 16 | module load python/2.7.14 17 | 18 | den=$1 19 | temp=$2 20 | port=$3 21 | 22 | sed -i "s/TEMPERATURE/${temp}/" input.xml 23 | sed -i "s/DENSITY/${den}/" input.xml 24 | sed -i "s/HOST/${HOSTNAME}/" input.xml 25 | sed -i "s/PORT/${port}/" input.xml 26 | python ~/programlist/i-pi-dev/bin/i-pi input.xml &> log.i-pi & 27 | 28 | sleep 5 29 | 30 | 31 | srun -n 28 --exclusive --mem=30000 pw.x < qe-h128.in >> qe.log --ipi ${HOSTNAME}:${port} 32 | 33 | 34 | wait 35 | -------------------------------------------------------------------------------- /input-nnp-WTmetaD/A-data.h64-metalunits: -------------------------------------------------------------------------------- 1 | MMPS Description 2 | 3 | 64 atoms 4 | 1 atom types 5 | 6 | 0 4.5722377 xlo xhi 7 | 0 4.5722377 ylo yhi 8 | 0 4.5722377 zlo zhi 9 | 10 | Masses 11 | 12 | 1 1.0080 13 | 14 | Atoms 15 | 16 | 1 1 2.80468 9.05783 3.56515 17 | 2 1 -1.12248 11.7725 7.7413 18 | 3 1 0.474428 13.5625 8.12582 19 | 4 1 1.19709 6.81138 4.79682 20 | 5 1 0.354778 14.613 8.67389 21 | 6 1 1.01507 10.4112 8.19445 22 | 7 1 3.18743 10.0978 9.91765 23 | 8 1 2.08409 14.4695 8.92267 24 | 9 1 1.82822 9.43984 5.30971 25 | 10 1 -0.913583 6.11878 4.3159 26 | 11 1 -1.33047 15.9906 4.79571 27 | 12 1 -1.2317 16.5263 10.6824 28 | 13 1 4.00821 12.7781 2.2602 29 | 14 1 -1.36715 12.5402 7.44908 30 | 15 1 -2.6324 16.0738 4.24019 31 | 16 1 -1.7896 11.855 8.40655 32 | 17 1 0.909716 10.3659 6.91076 33 | 18 1 -2.37958 12.1803 5.51685 34 | 19 1 1.59971 17.9346 8.47342 35 | 20 1 -1.37482 14.3437 6.77938 36 | 21 1 2.45321 11.4794 6.76317 37 | 22 1 -0.497476 14.1066 7.50457 38 | 23 1 -4.03507 11.1688 4.88891 39 | 24 1 -3.61797 16.5761 6.13122 40 | 25 1 4.17887 11.5763 6.73951 41 | 26 1 4.16326 10.7853 10.4224 42 | 27 1 -0.0763934 14.9466 9.99505 43 | 28 1 -6.01566 15.2056 7.75634 44 | 29 1 -0.617758 13.6048 5.34656 45 | 30 1 -0.558425 10.8773 7.19426 46 | 31 1 5.85112 17.0642 6.89691 47 | 32 1 -2.82011 10.4384 10.4583 48 | 33 1 4.82964 7.84902 7.0175 49 | 34 1 -1.45178 13.0286 10.987 50 | 35 1 -2.36476 15.1512 8.26188 51 | 36 1 -0.350904 11.8365 8.56327 52 | 37 1 -0.622479 8.90155 8.10136 53 | 38 1 -3.97245 11.9894 8.01623 54 | 39 1 1.1176 14.0922 7.43119 55 | 40 1 -2.95579 12.7719 9.52661 56 | 41 1 -0.0301719 9.94275 6.68688 57 | 42 1 -2.67299 11.1113 7.25289 58 | 43 1 1.38039 13.3127 10.7629 59 | 44 1 6.46931 14.5325 6.86052 60 | 45 1 3.40082 18.9158 9.08896 61 | 46 1 -1.67316 13.0473 8.98222 62 | 47 1 -2.41444 6.8618 14.5355 63 | 48 1 -2.32612 8.25206 6.82988 64 | 49 1 1.87255 12.2583 8.14794 65 | 50 1 0.0166736 10.6846 8.25914 66 | 51 1 -0.0419478 12.7078 8.62414 67 | 52 1 2.54677 13.5979 10.3582 68 | 53 1 0.90012 12.8892 9.0479 69 | 54 1 -2.29291 13.8687 7.38465 70 | 55 1 1.17625 10.9734 10.447 71 | 56 1 -0.565371 7.38279 10.0902 72 | 57 1 -1.35916 12.9135 5.12032 73 | 58 1 0.195113 7.97121 10.1318 74 | 59 1 1.07255 14.4891 9.57345 75 | 60 1 -4.18428 9.1829 4.79076 76 | 61 1 0.689618 13.9175 10.6256 77 | 62 1 -3.6328 11.2419 2.72905 78 | 63 1 -0.154814 8.87707 6.17939 79 | 64 1 2.70594 10.557 10.7417 80 | -------------------------------------------------------------------------------- /input-nnp-WTmetaD/in.lmp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | clear 9 | variable dt equal 0.0002 # timestep (ps) 10 | variable intThermo equal 1 # screen output interval (timesteps) 11 | variable numSteps equal 2000000 # total number of simulation timesteps (timesteps) 12 | variable runnerCutoff equal 4.24 # largest symmetry function cutoff (Angstrom) 13 | variable nameStartCfg string "A-data.h64-metalunits" # name of the starting configuration file 14 | variable runnerDir string "." # directory containing RuNNer files 15 | # set initial velocity distribution 16 | variable initTemp equal TEMPERATURE # initial temperature (K) 17 | variable velSeed equal 49RANDOM9 # seed for random number generator 18 | # NVT integrator (Nose-Hoover) 19 | variable startTemp equal TEMPERATURE # starting temperature for thermostat (K) 20 | variable stopTemp equal TEMPERATURE # final temperature for thermostat (K) 21 | variable tDamp equal 0.02 # thermostat damping factor (ps) 22 | # set pressure 23 | variable Press equal 10000*PRESSURE # units in bar. 1 gpa= 10,000 bar 24 | variable pDamp equal 0.2 25 | # dump thermodynamic properties (temperature, pressure, potential energy, kinetic energy, integrator quantity) 26 | variable intTD equal 10 # thermodynamics dump file interval (timesteps) 27 | variable nameTD string "traj/td" # thermodynamics file name 28 | variable varVolume equal vol # variable required to print volume 29 | variable varKE equal ke # variable required to print kinetic energy 30 | ############################################################################### 31 | # SETUP 32 | ############################################################################### 33 | units metal # define unit system (metal = Angstrom, eV, ps, g/mol) 34 | boundary p p p # set periodic boundary conditions 35 | atom_style atomic # set atomic style for particles 36 | read_data ${nameStartCfg} # read start configuration 37 | 38 | replicate 2 2 2 39 | 40 | change_box all x scale 1.1 y scale 1.1 z scale 1.1 remap 41 | 42 | #pair_style runner dir ${runnerDir} showew no resetew yes maxew 1000000 # set up pair style runner 43 | pair_style nnp dir ${runnerDir} showew no showewsum 1000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 44 | 45 | pair_coeff * * ${runnerCutoff} # set up pair style coefficients 46 | timestep ${dt} # set timestep 47 | 48 | neighbor 2.0 bin # neighbor list skin width 49 | neigh_modify every 1 delay 0 check yes # frequency to update neighor list 50 | 51 | velocity all create ${initTemp} ${velSeed} # create initial velocities 52 | 53 | thermo ${intThermo} # set screen output 54 | thermo_style custom step time temp pe etotal press vol lx ly lz 55 | thermo_modify format 4 %20.15g 56 | 57 | fix eq all npt temp ${startTemp} ${startTemp} ${tDamp} iso ${Press} ${Press} ${pDamp} 58 | 59 | run 50000 60 | 61 | unfix eq 62 | 63 | write_restart equal.restart 64 | 65 | fix 3 all plumed plumedfile plumed.dat outfile p.log 66 | ############################################################################### 67 | # SIMULATION 68 | ############################################################################### 69 | fix 1 all npt temp ${startTemp} ${stopTemp} ${tDamp} iso ${Press} ${Press} ${pDamp} # set up integrator 70 | #fix 1 all nvt temp ${startTemp} ${stopTemp} ${tDamp} 71 | 72 | dump 1 all custom 10000 A.lammpstrj id type x y z # dump configuration into a trajectory file 73 | 74 | run ${numSteps} 75 | #fix 1 all ipi driver.01 32346 unix 76 | #run 10000000 77 | # 78 | ############################################################################### 79 | # CLEAN UP 80 | ############################################################################### 81 | #undump XYZ 82 | #unfix AVE_TD 83 | #unfix INT 84 | ############################################################################### 85 | -------------------------------------------------------------------------------- /input-nnp-WTmetaD/plumed.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A TIME=ps 2 | 3 | COORDINATIONNUMBER ... 4 | LABEL=cn 5 | SPECIES=1-512 6 | SWITCH={CUBIC D_0=0.8 D_MAX=1.1} 7 | MEAN 8 | MORE_THAN1={SMAP R_0=0.5 D_0=0.5 A=8 B=8} 9 | BETWEEN1={GAUSSIAN UPPER=1.2 LOWER=0.8 SMEAR=0.2} 10 | LOWMEM 11 | ... COORDINATIONNUMBER 12 | 13 | DUMPMULTICOLVAR STRIDE=1000 DATA=cn FILE=cn.xyz 14 | 15 | METAD ... 16 | LABEL=metad 17 | ARG=cn.between-1 18 | PACE=400 HEIGHT=2.0 SIGMA=2.0 FILE=HILLS 19 | TEMP=TEMPERATURE BIASFACTOR=200 20 | ... METAD 21 | 22 | PRINT STRIDE=1 ARG=cn.*,metad.bias FILE=COLVAR 23 | FLUSH STRIDE=100 24 | 25 | ENDPLUMED 26 | 27 | -------------------------------------------------------------------------------- /input-nnp-WTmetaD/submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH --job-name=NNP-mpi 4 | #SBATCH --get-user-env 5 | #SBATCH --nodes=1 6 | #SBATCH --ntasks 28 7 | #SBATCH --time=24:00:00 8 | 9 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/programlist/n2p2/lib/ 10 | 11 | module load intel intel-mpi 12 | module load python gsl fftw 13 | 14 | export OMP_NUM_THREADS=1 15 | 16 | temp=$1 17 | press=$2 18 | 19 | sed -i "s/TEMPERATURE/${temp}/g" in.lmp 20 | sed -i "s/TEMPERATURE/${temp}/g" plumed.dat 21 | sed -i "s/PRESSURE/${press}/g" in.lmp 22 | sed -i "s/RANDOM/$RANDOM/" in.lmp 23 | srun -n 28 lmp_fidis_plumed_n2p2 < in.lmp > lmplog & 24 | 25 | wait 26 | cd .. 27 | 28 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-C2c-24-I.res: -------------------------------------------------------------------------------- 1 | TITL H-H-C2c-24-I 250.0000 39.013779 -2.82601252E+002 0 0 24 (C2/c) n - 1 2 | REM 3 | REM Run started: Thu, 21 Nov 2019 21:32:23 +0000 in /home/cjp20/work/RUNS/H-Bingqing/Collection-250GPa-NN 4 | REM CASTEP 20.1 from code version 09c4a41f4b97+ Fri, 27 Sep 2019 13:14:09 +0100 5 | REM Functional BLYP Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 800.0000 eV Grid scale 2.0000 Gmax 43.4715 1/A FBSC automatic 7 | REM Offset 0.000 0.000 0.000 No. kpts 322 Spacing 0.03 8 | REM Total runtime: 41.23 s 9 | REM Overall efficiency: 93 % 10 | REM 11 | REM H.cell (59d69ee0e7cddc0fb58bfe5f937484e2) 12 | REM 13 | REM 14 | REM 15 | REM cmdline: crud.pl -mpinp 32 16 | REM 17 | REM 18 | REM H 1|0.6|13|15|17|10(qc=8) 19 | REM 20 | CELL 1.54180 3.13185 3.13185 4.99389 104.21125 104.21125 56.01509 21 | LATT -1 22 | SFAC H 23 | H 1 0.3294736315465 0.9016466644928 0.3492380601248 1.0 24 | H 1 0.7659889057159 0.4829357879674 0.2070924283555 1.0 25 | H 1 0.7469058272244 0.9737447513399 0.2926532683650 1.0 26 | H 1 0.5630529980648 0.1910315696278 0.9202978732037 1.0 27 | H 1 0.0983533355072 0.6705263684535 0.1507619398752 1.0 28 | H 1 0.7120379644307 0.5464054565966 0.4512863275629 1.0 29 | H 1 0.2340110942841 0.5170642120326 0.7929075716445 1.0 30 | H 1 0.9466900387933 0.8093436093736 0.0321098395389 1.0 31 | H 1 0.1910315696278 0.5630529980648 0.4202978732037 1.0 32 | H 1 0.4535945434034 0.2879620355693 0.0487136724371 1.0 33 | H 1 0.5170642120326 0.2340110942841 0.2929075716445 1.0 34 | H 1 0.0533099612067 0.1906563906264 0.9678901604611 1.0 35 | H 1 0.8093436093736 0.9466900387933 0.5321098395389 1.0 36 | H 1 0.6705263684535 0.0983533355072 0.6507619398752 1.0 37 | H 1 0.9737447513399 0.7469058272244 0.7926532683650 1.0 38 | H 1 0.1906563906264 0.0533099612067 0.4678901604611 1.0 39 | H 1 0.2530941727756 0.0262552486601 0.7073467316350 1.0 40 | H 1 0.8089684303722 0.4369470019352 0.5797021267963 1.0 41 | H 1 0.2879620355693 0.4535945434034 0.5487136724371 1.0 42 | H 1 0.5464054565966 0.7120379644307 0.9512863275629 1.0 43 | H 1 0.4369470019352 0.8089684303722 0.0797021267963 1.0 44 | H 1 0.4829357879674 0.7659889057159 0.7070924283555 1.0 45 | H 1 0.0262552486601 0.2530941727756 0.2073467316350 1.0 46 | H 1 0.9016466644928 0.3294736315465 0.8492380601248 1.0 47 | END 48 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-C2c-24-II.res: -------------------------------------------------------------------------------- 1 | TITL H-H-C2c-24-II 400.0193 30.601855 -2.54452333E+002 0 0 24 (C2/c) n - 1 2 | REM 3 | REM Run started: Tue, 02 Jul 2019 15:06:33 +0100 in /home/cjp20/work/RUNS/H-Bingqing/Collection-400GPa 4 | REM CASTEP 19.1 from code version c8d46cc1791f+ Fri, 02 Nov 2018 15:03:39 +0000 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 500.0000 eV Grid scale 2.0000 Gmax 34.3673 1/A FBSC none 7 | REM MP grid 9 9 5 Offset 0.000 0.000 0.000 No. kpts 115 Spacing 0.05 8 | REM 9 | REM H.cell (64aa2a3819804d7fab852ebf16f73635) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 2b12898f19dc+ Mon, 17 Jun 2019 10:04:37 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 2.71666 2.71162 4.79980 90.04084 90.08153 59.93845 18 | LATT -1 19 | SFAC H 20 | H 1 0.7566529031275 0.0575660416527 -0.1261983054605 1.0 21 | H 1 0.6160874622782 -0.1164166876012 -0.3775526901825 1.0 22 | H 1 0.9516555441908 -0.6724251523596 -0.1259256067884 1.0 23 | H 1 0.8386666924609 -0.7897425789396 -0.6249505709135 1.0 24 | H 1 0.1111592981234 0.4060263453566 -0.6138662324338 1.0 25 | H 1 0.5713583719892 -0.3528891333887 -0.6367161017911 1.0 26 | H 1 0.1857810552199 0.0575660416527 -0.3738016945395 1.0 27 | H 1 0.5003292253231 -0.1164166876012 -0.1224473098175 1.0 28 | H 1 0.7207696081689 -0.6724251523596 -0.3740743932116 1.0 29 | H 1 0.9510758864788 -0.7897425789396 -0.8750494290865 1.0 30 | H 1 0.4828143565201 0.4060263453566 -0.8861337675662 1.0 31 | H 1 0.7815307613996 -0.3528891333887 -0.8632838982089 1.0 32 | H 1 0.2433470968725 -0.0575660416525 -0.8738016945395 1.0 33 | H 1 0.3839125377218 0.1164166876014 -0.6224473098175 1.0 34 | H 1 0.0483444558093 0.6724251523598 -0.8740743932116 1.0 35 | H 1 0.1613333075391 0.7897425789398 -0.3750494290865 1.0 36 | H 1 0.8888407018766 -0.4060263453564 -0.3861337675662 1.0 37 | H 1 0.4286416280108 0.3528891333889 -0.3632838982089 1.0 38 | H 1 0.8142189447801 -0.0575660416525 -0.6261983054605 1.0 39 | H 1 0.4996707746769 0.1164166876014 -0.8775526901825 1.0 40 | H 1 0.2792303918310 0.6724251523598 -0.6259256067884 1.0 41 | H 1 0.0489241135212 0.7897425789398 -0.1249505709135 1.0 42 | H 1 0.5171856434799 -0.4060263453564 -0.1138662324338 1.0 43 | H 1 0.2184692386004 0.3528891333889 -0.1367161017911 1.0 44 | END 45 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-C2c-24-II.xyze: -------------------------------------------------------------------------------- 1 | 24 2 | Lattice=" 2.716660 0.000000 0.000000 1.358332 2.346874 0.000000 -0.006830 0.000000 4.799795" Properties=species:S:1:pos:R:3 3 | H 2.1346243959657 0.1351002348372 -0.6057260133012 4 | H 1.5181463309584 -0.2732153238011 -1.8121755676582 5 | H 1.6728080732751 -1.5780970978549 -0.6044171155400 6 | H 1.2099080926132 -1.8534263521121 -2.9996347133855 7 | H 0.8576932396411 0.9528926132240 -2.9464321594139 8 | H 1.0771946051595 -0.8281863722805 -3.0561068513184 9 | H 0.5854508014881 0.1351002152863 -1.7941715569986 10 | H 1.2019282008344 -0.2732153036579 -0.5877220026415 11 | H 1.0472643312200 -1.5780971174489 -1.7954804547598 12 | H 1.5169938174331 -1.8534263718601 -4.2000579975138 13 | H 1.8692132454372 0.9528925917256 -4.2532605514854 14 | H 1.6497089762954 -0.8281863901704 -4.1435858595809 15 | H 0.5888655584442 -0.1351003137973 -4.1940691272983 16 | H 1.2053436234515 0.2732152448411 -2.9876195729413 17 | H 1.0506818811350 1.5780970188949 -4.1953780250595 18 | H 1.5135818617967 1.8534262731521 -1.8001604272140 19 | H 1.8657967147688 -0.9528926921840 -1.8533629811856 20 | H 1.6462953492504 0.8281862933205 -1.7436882892811 21 | H 2.1380391529218 -0.1351002942464 -3.0056235836010 22 | H 1.5215617535754 0.2732152246978 -4.2120731379580 23 | H 1.6762256231897 1.5780970384888 -3.0043146858398 24 | H 1.2064961369768 1.8534262929000 -0.5997371430858 25 | H 0.8542767089726 -0.9528926706856 -0.5465345891141 26 | H 1.0737809781145 0.8281863112104 -0.6562092810186 27 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-Cmce-12-II.res: -------------------------------------------------------------------------------- 1 | TITL H-H-Cmce-12-II 399.9821 15.243991 -1.27283455E+002 0 0 12 (Cmce) n - 1 2 | REM 3 | REM Run started: Tue, 02 Jul 2019 15:06:34 +0100 in /home/cjp20/work/RUNS/H-Bingqing/Collection-400GPa 4 | REM CASTEP 19.1 from code version c8d46cc1791f+ Fri, 02 Nov 2018 15:03:39 +0000 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 500.0000 eV Grid scale 2.0000 Gmax 34.3673 1/A FBSC none 7 | REM Offset 0.000 0.000 0.000 No. kpts 180 Spacing 0.05 8 | REM 9 | REM H.cell (64aa2a3819804d7fab852ebf16f73635) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 2b12898f19dc+ Mon, 17 Jun 2019 10:04:37 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 2.43295 2.57269 2.76395 90.00000 90.00000 118.21909 18 | LATT -1 19 | SFAC H 20 | H 1 -0.0079519133627 0.9840961732747 0.8571001802926 1.0 21 | H 1 -0.1314241290127 0.7371517419747 0.5462609806293 1.0 22 | H 1 -0.2770549647915 0.4458900704171 0.6891275134941 1.0 23 | H 1 -0.4920480866375 0.0159038267251 0.3571001802926 1.0 24 | H 1 -0.3685758709875 0.2628482580251 0.0462609806293 1.0 25 | H 1 -0.2229450352087 0.5541099295827 0.1891275134941 1.0 26 | H 1 -0.5079519133627 -0.0159038267253 0.6428998197074 1.0 27 | H 1 -0.6314241290127 -0.2628482580253 0.9537390193707 1.0 28 | H 1 -0.7770549647915 -0.5541099295829 0.8108724865059 1.0 29 | H 1 -0.9920480866375 -0.9840961732749 0.1428998197074 1.0 30 | H 1 -0.8685758709875 -0.7371517419749 0.4537390193707 1.0 31 | H 1 -0.7229450352087 -0.4458900704173 0.3108724865059 1.0 32 | END 33 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-Cmce-4-II.res: -------------------------------------------------------------------------------- 1 | TITL H-H-Cmce-4-II 400.0291 5.060319 -4.24509444E+001 0 0 4 (Cmce) n - 1 2 | REM 3 | REM Run started: Tue, 02 Jul 2019 15:06:32 +0100 in /home/cjp20/work/RUNS/H-Bingqing/Collection-400GPa 4 | REM CASTEP 19.1 from code version c8d46cc1791f+ Fri, 02 Nov 2018 15:03:39 +0000 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 500.0000 eV Grid scale 2.0000 Gmax 34.3673 1/A FBSC none 7 | REM Offset 0.000 0.000 0.000 No. kpts 320 Spacing 0.05 8 | REM 9 | REM H.cell (64aa2a3819804d7fab852ebf16f73635) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 2b12898f19dc+ Mon, 17 Jun 2019 10:04:37 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 1.54447 1.57190 2.39305 90.00000 90.00000 119.42411 18 | LATT -1 19 | SFAC H 20 | H 1 -0.1338880094884 0.7322239810235 0.9390192113820 1.0 21 | H 1 -0.6338880094884 -0.2677760189765 0.5609807886180 1.0 22 | H 1 -0.3661119905121 0.2677760189761 0.4390192113820 1.0 23 | H 1 -0.8661119905121 -0.7322239810239 0.0609807886180 1.0 24 | END 25 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-Fmmm-2-I.res: -------------------------------------------------------------------------------- 1 | TITL H-H-Fmmm-2-I 250.0381 3.073864 -2.38403233E+001 0 0 2 (Fmmm) n - 1 2 | REM 3 | REM Run started: Tue, 02 Jul 2019 14:36:48 +0100 in /home/cjp20/work/RUNS/H-III/Collection-250GPa 4 | REM CASTEP 19.1 from code version c8d46cc1791f+ Fri, 02 Nov 2018 15:03:39 +0000 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 500.0000 eV Grid scale 2.0000 Gmax 34.3673 1/A FBSC none 7 | REM Offset 0.000 0.000 0.000 No. kpts 4368 Spacing 0.03 8 | REM 9 | REM H.cell (59d69ee0e7cddc0fb58bfe5f937484e2) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 2b12898f19dc+ Mon, 17 Jun 2019 10:04:37 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 1.53275 1.53275 1.65772 105.92222 105.92239 113.99117 18 | LATT -1 19 | SFAC H 20 | H 1 0.6373421100000 -0.3626578900000 -0.7253157800000 1.0 21 | H 1 0.3626578900000 -0.6373421100000 -1.2746842200000 1.0 22 | END 23 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-P21c-8-I.res: -------------------------------------------------------------------------------- 1 | TITL H-H-P21c-8-I 100.0000 18.439446 -1.09591737E+002 0 0 8 (P21/c) n - 1 2 | REM 3 | REM Run started: Fri, 12 Oct 2018 11:58:16 +0100 in /home/cjp20/work/RUNS/H-II/Collection-100GPa 4 | REM CASTEP 19.1 from code version 10fd1d09d1e9+ Thu, 04 Oct 2018 14:12:52 +0100 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 1000.0000 eV Grid scale 2.0000 Gmax 48.6026 1/A FBSC automatic 7 | REM Offset 0.000 0.000 0.000 No. kpts 594 Spacing 0.03 8 | REM 9 | REM H.cell (f746fbe78576123e9b84afe53ed48119) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 46e67c73c3e9+ Thu, 04 Oct 2018 15:09:34 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 2.98132 1.89820 3.25835 90.00000 89.98339 90.00000 18 | LATT -1 19 | SFAC H 20 | H 1 0.2114168844933 0.6537269504572 0.0917996867306 1.0 21 | H 1 0.2895658443285 0.3882547339841 0.2389540926153 1.0 22 | H 1 0.7885831155067 0.1537269504572 0.4082003132694 1.0 23 | H 1 0.7104341556715 -0.1117452660159 0.2610459073847 1.0 24 | H 1 0.7885831155067 0.3462730495428 0.9082003132694 1.0 25 | H 1 0.7104341556715 0.6117452660159 0.7610459073847 1.0 26 | H 1 0.2114168844933 0.8462730495428 0.5917996867306 1.0 27 | H 1 0.2895658443285 1.1117452660159 0.7389540926153 1.0 28 | END 29 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-P6122-36-I.res: -------------------------------------------------------------------------------- 1 | TITL H-H-P6122-36-I 100.0000 82.152749 -4.93129537E+002 0 0 36 (P6122) n - 1 2 | REM 3 | REM Run started: Fri, 12 Oct 2018 11:58:25 +0100 in /home/cjp20/work/RUNS/H-II/Collection-100GPa 4 | REM CASTEP 19.1 from code version 10fd1d09d1e9+ Thu, 04 Oct 2018 14:12:52 +0100 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 1000.0000 eV Grid scale 2.0000 Gmax 48.6026 1/A FBSC automatic 7 | REM Offset 0.000 0.000 0.000 No. kpts 84 Spacing 0.03 8 | REM 9 | REM H.cell (f746fbe78576123e9b84afe53ed48119) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 46e67c73c3e9+ Thu, 04 Oct 2018 15:09:34 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 3.27559 3.27559 8.84124 90.00000 90.00000 120.00000 18 | LATT -1 19 | SFAC H 20 | H 1 0.3305829369007 0.0637245032255 0.6596763439469 1.0 21 | H 1 0.8416454493293 0.3387655139623 0.6698405298976 1.0 22 | H 1 0.9362554967747 0.2668484336753 0.9930096772802 1.0 23 | H 1 0.6612144860379 0.5028699353671 0.0031738632310 1.0 24 | H 1 0.7331315663249 0.6693970630995 0.3263430106135 1.0 25 | H 1 0.4971100646331 0.1583345506709 0.3365071965643 1.0 26 | H 1 0.6693970630995 0.9362554967747 0.1596763439469 1.0 27 | H 1 0.1583345506709 0.6612144860379 0.1698405298976 1.0 28 | H 1 0.0637245032255 0.7331315663249 0.4930096772802 1.0 29 | H 1 0.3387655139623 0.4971100646331 0.5031738632310 1.0 30 | H 1 0.2668484336753 0.3305829369007 0.8263430106135 1.0 31 | H 1 0.5028699353671 0.8416454493293 0.8365071965643 1.0 32 | H 1 0.0637245032255 0.3305829369007 0.6736569893865 1.0 33 | H 1 0.3387655139623 0.8416454493293 0.6634928034357 1.0 34 | H 1 0.2668484336753 0.9362554967747 0.3403236560531 1.0 35 | H 1 0.5028699353671 0.6612144860379 0.3301594701024 1.0 36 | H 1 0.6693970630995 0.7331315663249 0.0069903227198 1.0 37 | H 1 0.1583345506709 0.4971100646331 0.9968261367690 1.0 38 | H 1 0.9362554967747 0.6693970630995 0.1736569893865 1.0 39 | H 1 0.6612144860379 0.1583345506709 0.1634928034357 1.0 40 | H 1 0.7331315663249 0.0637245032255 0.8403236560531 1.0 41 | H 1 0.4971100646331 0.3387655139623 0.8301594701024 1.0 42 | H 1 0.3305829369007 0.2668484336753 0.5069903227198 1.0 43 | H 1 0.8416454493293 0.5028699353671 0.4968261367690 1.0 44 | H 1 0.8228722415382 -0.0000099999999 0.5000000000000 1.0 45 | H 1 0.5976913882421 -0.0000099999999 0.5000000000000 1.0 46 | H 1 -0.0000099999999 0.8228722415382 0.8333333333333 1.0 47 | H 1 -0.0000099999999 0.5976913882421 0.8333333333333 1.0 48 | H 1 0.1771077584620 0.1771077584620 0.1666666666667 1.0 49 | H 1 0.4022886117581 0.4022886117581 0.1666666666667 1.0 50 | H 1 0.1771077584620 -0.0000099999999 -0.0000000000000 1.0 51 | H 1 0.4022886117581 -0.0000099999999 -0.0000000000000 1.0 52 | H 1 -0.0000099999999 0.1771077584620 0.3333333333333 1.0 53 | H 1 -0.0000099999999 0.4022886117581 0.3333333333333 1.0 54 | H 1 0.8228722415382 0.8228722415382 0.6666666666667 1.0 55 | H 1 0.5976913882421 0.5976913882421 0.6666666666667 1.0 56 | END 57 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/H-H-P63m-16-I.res: -------------------------------------------------------------------------------- 1 | TITL H-H-P63m-16-I 100.0000 36.926752 -2.19194806E+002 0 0 16 (P63/m) n - 1 2 | REM 3 | REM Run started: Fri, 12 Oct 2018 11:58:26 +0100 in /home/cjp20/work/RUNS/H-II/Collection-100GPa 4 | REM CASTEP 19.1 from code version 10fd1d09d1e9+ Thu, 04 Oct 2018 14:12:52 +0100 5 | REM Functional Perdew Burke Ernzerhof Relativity Koelling-Harmon Dispersion off 6 | REM Cut-off 1000.0000 eV Grid scale 2.0000 Gmax 48.6026 1/A FBSC automatic 7 | REM Offset 0.000 0.000 0.000 No. kpts 126 Spacing 0.03 8 | REM 9 | REM H.cell (f746fbe78576123e9b84afe53ed48119) 10 | REM AIRSS Version 0.9.2 xxxx 2019 build 46e67c73c3e9+ Thu, 04 Oct 2018 15:09:34 +0100 11 | REM 12 | REM 13 | REM 14 | REM 15 | REM H 1|0.6|13|15|17|10(qc=8) 16 | REM 17 | CELL 1.54180 3.00064 3.76963 3.76963 120.00000 90.00000 90.00000 18 | LATT -1 19 | SFAC H 20 | H 1 0.7500000000000 0.0984939298220 0.3900959071482 1.0 21 | H 1 0.7500000000000 0.1983729342203 0.2659361129082 1.0 22 | H 1 0.2500000000000 0.9324368213121 0.1983729342203 1.0 23 | H 1 0.2500000000000 0.7083980226738 0.0984939298220 1.0 24 | H 1 0.6279207941052 0.6666666666666 0.3333333333332 1.0 25 | H 1 0.8720792058948 0.6666666666666 0.3333333333332 1.0 26 | H 1 0.2500000000000 0.3900959071482 0.2916019773260 1.0 27 | H 1 0.2500000000000 0.2659361129082 0.0675631786877 1.0 28 | H 1 0.2500000000000 0.8016270657795 0.7340638870916 1.0 29 | H 1 0.2500000000000 0.9015060701778 0.6099040928516 1.0 30 | H 1 0.1279207941052 0.3333333333332 0.6666666666666 1.0 31 | H 1 0.3720792058948 0.3333333333332 0.6666666666666 1.0 32 | H 1 0.7500000000000 0.0675631786877 0.8016270657795 1.0 33 | H 1 0.7500000000000 0.2916019773260 0.9015060701778 1.0 34 | H 1 0.7500000000000 0.6099040928516 0.7083980226738 1.0 35 | H 1 0.7500000000000 0.7340638870916 0.9324368213121 1.0 36 | END 37 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/res2lmpin.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | resfile=$1 4 | seed=${resfile%.*} 5 | #echo ${seed} 6 | 7 | info=$(grep 'TITL' ${seed}.res) 8 | 9 | l1=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$3}') 10 | l2=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$4}') 11 | l3=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$5}') 12 | a1=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$6}') 13 | a2=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$7}') 14 | a3=$(grep 'CELL' ${seed}.res | awk '{printf "% 12.6f",$8}') 15 | 16 | v1x=$(echo "$l1" | awk '{printf "% 12.6f",$1}') 17 | v1y=$(echo "0.0" | awk '{printf "% 12.6f",$1}') 18 | v1z=$(echo "0.0" | awk '{printf "% 12.6f",$1}') 19 | v2x=$(echo "$l2 $a3" | awk '{printf "% 12.6f",$1*cos($2*3.1415926/180)}') 20 | v2y=$(echo "$l2 $a3" | awk '{printf "% 12.6f",$1*sin($2*3.1415926/180)}') 21 | v2z=$(echo "0.0" | awk '{printf "% 12.6f",$1}') 22 | v3x=$(echo "$l3 $a2" | awk '{printf "% 12.6f",$1*cos($2*3.1415926/180)}') 23 | v3y=$(echo "$l3 $a1 $a2 $a3" | awk '{printf "% 12.6f",$1*( cos($2*3.1415926/180) - cos($3*3.1415926/180)*cos($4*3.1415926/180) )/sin($4*3.1415926/180) }') 24 | v3z=$(echo "$l3 $v3x $v3y" | awk '{printf "% 12.6f",sqrt(($1)**2-($2)**2-($3)**2)}') 25 | 26 | xmin=$(echo "$v1x" | awk '{printf "% 12.6f",-($1)/2}') 27 | xmax=$(echo "$v1x" | awk '{printf "% 12.6f",($1)/2}') 28 | ymin=$(echo "$v2y" | awk '{printf "% 12.6f",-($1)/2}') 29 | ymax=$(echo "$v2y" | awk '{printf "% 12.6f",($1)/2}') 30 | zmin=$(echo "$v3z" | awk '{printf "% 12.6f",-($1)/2}') 31 | zmax=$(echo "$v3z" | awk '{printf "% 12.6f",($1)/2}') 32 | 33 | xy=$(echo "$v2x" | awk '{printf "% 12.6f",($1)}') 34 | xz=$(echo "$v3x" | awk '{printf "% 12.6f",($1)}') 35 | yz=$(echo "$v3y" | awk '{printf "% 12.6f",($1)}') 36 | 37 | nat=$(awk '$1=="H"{print $1}' ${seed}.res | wc -l | awk '{print $1}') 38 | 39 | echo "LAMMPS data file. CGCMM style. atom_style full." 40 | echo " # ${info}" 41 | echo " ${nat} atoms" 42 | echo " 1 atom types" 43 | echo "" 44 | echo " ${xmin} ${xmax} xlo xhi" 45 | echo " ${ymin} ${ymax} ylo yhi" 46 | echo " ${zmin} ${zmax} zlo zhi" 47 | echo " ${xy} ${xz} ${yz} xy xz yz" 48 | echo "" 49 | echo " Masses" 50 | echo "" 51 | echo " 1 1.008" 52 | echo "" 53 | echo " Atoms" 54 | echo "" 55 | sed -n '/SFAC/,/END/p' ${seed}.res | awk '{printf "%d % 12.6f % 12.6f % 12.6f\n",$2,$3,$4,$5}' | \ 56 | sed '/SFAC/d' | sed '/END/d' | \ 57 | awk -v v1x="$v1x" -v v1y="$v1y" -v v1z="$v1z" -v v2x="$v2x" -v v2y="$v2y" -v v2z="$v2z" -v v3x="$v3x" -v v3y="$v3y" -v v3z="$v3z" '{printf "%3s % 12.6f % 12.6f % 12.6f\n",$1,($2)*(v1x)+($3)*(v2x)+($4)*(v3x),($2)*(v1y)+($3)*(v2y)+($4)*(v3y),($2)*(v1z)+($3)*(v2z)+($4)*(v3z)}' | \ 58 | awk '$1==1 {printf "%3i %d %12.6f % 12.6f % 12.6f % 12.6f\n",NR-1,$1, 0.0,$2,$3,$4;}' 59 | 60 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/runall.sh: -------------------------------------------------------------------------------- 1 | for a in H-Cmce-12-II H-Cmce-4-II H-C2c-24-II H-Fmmm-2-I H-P21c-8-I H-P6122-36-I H-P63m-16-I; do 2 | for p in `seq 50 50 400`; 3 | do bash singlerun.sh $a $p; wait; 4 | done; done 5 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/workdir/H.in: -------------------------------------------------------------------------------- 1 | # --------------------- Initialisation --------------------- 2 | units metal # distances in A, energies in eV, pressure in Bar, time in ps 3 | dimension 3 4 | boundary p p p # periodic in x, y, z 5 | atom_style charge 6 | 7 | # --------------------- set pressure --------------------- 8 | variable extpress equal 10000.0*PRESSURE # Convert GPa to bar 9 | 10 | # --------------------- Atom definition --------------------- 11 | box tilt large # relax restictions on box tilt factors 12 | read_data NAMENOW-P-PRESSURE.conf 13 | 14 | neigh_modify every 1 delay 0 check yes # update neigbour every step 15 | neighbor 2.0 bin # neighbour list skin 16 | 17 | # --------------------- Potential definition --------------------- 18 | include ./H.pp 19 | 20 | thermo 10 21 | thermo_style custom step temp pe ke enthalpy vol lx press #pxx pyy pzz pxy pyz pxz 22 | 23 | # --------------------- record traj --------------------- 24 | dump mintraj all atom 1 NAMENOW-P-PRESSURE.lammpstrj # dump the trajectory 25 | dump_modify mintraj sort id # sort atoms by numerical label 26 | 27 | # --------------------- initial Relaxation of the structure --------------------- 28 | # min_style sd 29 | min_style cg 30 | min_modify line quadratic 31 | 32 | # Multiple minimisations to prevent trapping 33 | fix minbox all box/relax tri ${extpress} vmax 0.1 34 | minimize 1.0e-8 1.0e-6 10000 1000000 35 | fix minbox all box/relax tri ${extpress} vmax 0.01 36 | minimize 1.0e-8 1.0e-6 10000 1000000 37 | fix minbox all box/relax tri ${extpress} vmax 0.01 38 | minimize 1.0e-10 1.0e-8 10000 100000 39 | fix minbox all box/relax tri ${extpress} vmax 0.001 40 | minimize 1.0e-10 1.0e-8 10000 100000 41 | unfix minbox 42 | 43 | # --------------------- dumping xyz files --------------------- 44 | dump 1 all custom 1 NAMENOW-P-PRESSURE.lammpstrj id type x y z fx fy fz # dump configuration into a trajectory fil 45 | dump_modify 1 sort id 46 | 47 | # --------------------- collect results --------------------- 48 | # Variables defined for printing 49 | variable h equal enthalpy 50 | variable e equal etotal 51 | variable v equal vol 52 | variable p equal press/10000.0 # convert Bar back to GPa 53 | variable a equal cella 54 | variable b equal cellb 55 | variable c equal cellc 56 | variable alp equal cellalpha 57 | variable bet equal cellbeta 58 | variable gam equal cellgamma 59 | # Print AIRSS-specific data in $seed.lammps 60 | print "Lattice parameters: ${a} ${b} ${c} ${alp} ${bet} ${gam}" file NAMENOW-P-PRESSURE.lammps 61 | print "Volume: $v" append NAMENOW-P-PRESSURE.lammps 62 | print "Pressure: $p" append NAMENOW-P-PRESSURE.lammps 63 | print "Enthalpy: $h" append NAMENOW-P-PRESSURE.lammps 64 | 65 | undump 1 66 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/workdir/H.pp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | variable runnerCutoff equal CUTOFF # largest symmetry function cutoff (Angstrom) 9 | variable runnerDir string "../../nnp" # directory containing RuNNer files 10 | ############################################################################### 11 | # SETUP 12 | ############################################################################### 13 | # set up pair style runner 14 | pair_style nnp dir ${runnerDir} showew no showewsum 1000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 15 | # set up pair style coefficients 16 | pair_coeff * * ${runnerCutoff} 17 | -------------------------------------------------------------------------------- /input-nnp-enthalpy-solid-phases/workdir/singlerun.sh: -------------------------------------------------------------------------------- 1 | name=$1 2 | pp=$2 3 | bash ../res2lmpin.sh ../H-${name}.res > $name-P-$pp.conf 4 | sed -e "s/NAMENOW/${name}/g" -e "s/PRESSURE/$pp/" H.in > $name-P-$pp.in 5 | lammps < ${name}-P-$pp.in 6 | wait 7 | 8 | # Construct a fake Castep output file 9 | 10 | grep Pressure: ${name}-P-$pp.lammps | tail -1 | awk '{print " * Pressure: "$2}' > ${name}-P-$pp.castep 11 | grep Enthalpy: ${name}-P-$pp.lammps | tail -1 | awk '{print " PP3: Final Enthalpy = "$2}' >> ${name}-P-$pp.castep 12 | grep Volume: ${name}-P-$pp.lammps | tail -1 | awk '{print "Current cell volume = "$2}' >> ${name}-P-$pp.castep 13 | 14 | # Save the final structure in Castep -out.cell format 15 | 16 | lammps2cell ${name}-P-$pp > ${name}-P-$pp-out.cell 17 | 18 | castep2res ${name}-P-$pp | sed -e "s/${name}-P-$pp/H_${pp}p0-$name/" -e "s/LAMM/H/" -e "s/LAM/H/"> H_${pp}p0-${name}.res 19 | 20 | rm ${name}-P-$pp.castep ${name}-P-$pp.conf ${name}-P-$pp.in ${name}-P-$pp.lammps ${name}-P-$pp.lammpstrj ${name}-P-$pp-out.cell 21 | -------------------------------------------------------------------------------- /input-nnp-md-npt/A-data.h64-metalunits: -------------------------------------------------------------------------------- 1 | MMPS Description 2 | 3 | 64 atoms 4 | 1 atom types 5 | 6 | 0 4.5722377 xlo xhi 7 | 0 4.5722377 ylo yhi 8 | 0 4.5722377 zlo zhi 9 | 10 | Masses 11 | 12 | 1 1.0080 13 | 14 | Atoms 15 | 16 | 1 1 2.80468 9.05783 3.56515 17 | 2 1 -1.12248 11.7725 7.7413 18 | 3 1 0.474428 13.5625 8.12582 19 | 4 1 1.19709 6.81138 4.79682 20 | 5 1 0.354778 14.613 8.67389 21 | 6 1 1.01507 10.4112 8.19445 22 | 7 1 3.18743 10.0978 9.91765 23 | 8 1 2.08409 14.4695 8.92267 24 | 9 1 1.82822 9.43984 5.30971 25 | 10 1 -0.913583 6.11878 4.3159 26 | 11 1 -1.33047 15.9906 4.79571 27 | 12 1 -1.2317 16.5263 10.6824 28 | 13 1 4.00821 12.7781 2.2602 29 | 14 1 -1.36715 12.5402 7.44908 30 | 15 1 -2.6324 16.0738 4.24019 31 | 16 1 -1.7896 11.855 8.40655 32 | 17 1 0.909716 10.3659 6.91076 33 | 18 1 -2.37958 12.1803 5.51685 34 | 19 1 1.59971 17.9346 8.47342 35 | 20 1 -1.37482 14.3437 6.77938 36 | 21 1 2.45321 11.4794 6.76317 37 | 22 1 -0.497476 14.1066 7.50457 38 | 23 1 -4.03507 11.1688 4.88891 39 | 24 1 -3.61797 16.5761 6.13122 40 | 25 1 4.17887 11.5763 6.73951 41 | 26 1 4.16326 10.7853 10.4224 42 | 27 1 -0.0763934 14.9466 9.99505 43 | 28 1 -6.01566 15.2056 7.75634 44 | 29 1 -0.617758 13.6048 5.34656 45 | 30 1 -0.558425 10.8773 7.19426 46 | 31 1 5.85112 17.0642 6.89691 47 | 32 1 -2.82011 10.4384 10.4583 48 | 33 1 4.82964 7.84902 7.0175 49 | 34 1 -1.45178 13.0286 10.987 50 | 35 1 -2.36476 15.1512 8.26188 51 | 36 1 -0.350904 11.8365 8.56327 52 | 37 1 -0.622479 8.90155 8.10136 53 | 38 1 -3.97245 11.9894 8.01623 54 | 39 1 1.1176 14.0922 7.43119 55 | 40 1 -2.95579 12.7719 9.52661 56 | 41 1 -0.0301719 9.94275 6.68688 57 | 42 1 -2.67299 11.1113 7.25289 58 | 43 1 1.38039 13.3127 10.7629 59 | 44 1 6.46931 14.5325 6.86052 60 | 45 1 3.40082 18.9158 9.08896 61 | 46 1 -1.67316 13.0473 8.98222 62 | 47 1 -2.41444 6.8618 14.5355 63 | 48 1 -2.32612 8.25206 6.82988 64 | 49 1 1.87255 12.2583 8.14794 65 | 50 1 0.0166736 10.6846 8.25914 66 | 51 1 -0.0419478 12.7078 8.62414 67 | 52 1 2.54677 13.5979 10.3582 68 | 53 1 0.90012 12.8892 9.0479 69 | 54 1 -2.29291 13.8687 7.38465 70 | 55 1 1.17625 10.9734 10.447 71 | 56 1 -0.565371 7.38279 10.0902 72 | 57 1 -1.35916 12.9135 5.12032 73 | 58 1 0.195113 7.97121 10.1318 74 | 59 1 1.07255 14.4891 9.57345 75 | 60 1 -4.18428 9.1829 4.79076 76 | 61 1 0.689618 13.9175 10.6256 77 | 62 1 -3.6328 11.2419 2.72905 78 | 63 1 -0.154814 8.87707 6.17939 79 | 64 1 2.70594 10.557 10.7417 80 | -------------------------------------------------------------------------------- /input-nnp-md-npt/M-data.h64-metalunits: -------------------------------------------------------------------------------- 1 | MMPS Description 2 | 3 | 64 atoms 4 | 1 atom types 5 | 6 | 0 4.5722377 xlo xhi 7 | 0 4.5722377 ylo yhi 8 | 0 4.5722377 zlo zhi 9 | 10 | Masses 11 | 12 | 1 1.0080 13 | 14 | Atoms 15 | 16 | 1 1 6.86153 16.4078 -2.80109 17 | 2 1 6.74762 15.5882 -4.30334 18 | 3 1 8.27704 18.4794 -2.29308 19 | 4 1 7.01422 18.6357 -4.10526 20 | 5 1 6.92366 17.0085 5.00873 21 | 6 1 7.75606 12.144 -8.16508 22 | 7 1 6.45676 13.8611 -0.0596657 23 | 8 1 5.52877 17.0508 -0.403523 24 | 9 1 11.6263 15.3407 -5.92611 25 | 10 1 5.12781 18.0017 1.67085 26 | 11 1 8.98303 15.3383 0.0555764 27 | 12 1 5.90241 17.2688 -2.01957 28 | 13 1 4.64211 14.0359 -0.116765 29 | 14 1 5.64464 15.3817 -0.568984 30 | 15 1 9.45771 16.1873 -1.14027 31 | 16 1 10.2473 17.6341 -0.685423 32 | 17 1 8.36354 18.3157 0.906605 33 | 18 1 10.2939 15.6486 -2.00499 34 | 19 1 7.86835 18.2767 -4.97022 35 | 20 1 4.33271 14.9549 -1.09609 36 | 21 1 12.1529 13.4684 0.999066 37 | 22 1 8.12234 14.8333 -3.16283 38 | 23 1 6.02094 18.4936 -1.8945 39 | 24 1 9.35956 12.9124 1.4439 40 | 25 1 5.40469 16.3763 1.33489 41 | 26 1 9.29072 13.2653 -1.11346 42 | 27 1 8.15795 18.9589 -0.393464 43 | 28 1 9.16856 19.9168 1.79091 44 | 29 1 12.0061 10.6499 0.390184 45 | 30 1 7.14067 12.585 1.8363 46 | 31 1 8.00559 15.5748 -2.03891 47 | 32 1 5.45363 14.7547 -3.26429 48 | 33 1 9.15585 20.5754 1.6708 49 | 34 1 6.92644 14.3506 -2.50401 50 | 35 1 7.5843 15.791 -2.55017 51 | 36 1 6.92216 14.6461 -1.16512 52 | 37 1 7.10398 17.2267 -0.217374 53 | 38 1 10.9447 16.2484 -0.733715 54 | 39 1 5.01408 15.113 -1.42067 55 | 40 1 8.90489 13.6512 -1.54618 56 | 41 1 8.41589 17.4267 -4.61083 57 | 42 1 5.14727 13.7231 0.439172 58 | 43 1 6.63948 16.4599 -1.44453 59 | 44 1 5.81377 16.5981 -3.86673 60 | 45 1 9.51059 15.8044 0.409404 61 | 46 1 7.65483 16.5267 -0.692898 62 | 47 1 5.71902 15.1629 0.735773 63 | 48 1 5.86317 14.7468 -0.811876 64 | 49 1 8.62098 14.824 0.82615 65 | 50 1 10.9678 20.1071 -2.29221 66 | 51 1 5.52848 18.8891 -2.25857 67 | 52 1 8.37783 17.1216 2.07107 68 | 53 1 7.42359 17.6712 -1.75946 69 | 54 1 6.95778 14.7927 -3.07085 70 | 55 1 3.51209 15.7047 -0.694499 71 | 56 1 6.36483 17.8998 -2.87793 72 | 57 1 11.461 17.91 3.20753 73 | 58 1 8.32269 16.2904 0.905803 74 | 59 1 8.45688 12.2822 2.73521 75 | 60 1 5.27726 16.9564 -1.98326 76 | 61 1 4.5328 21.8956 0.124947 77 | 62 1 8.30246 19.0366 -2.00157 78 | 63 1 6.10065 18.0022 1.05711 79 | 64 1 4.23868 16.4932 -0.746998 80 | -------------------------------------------------------------------------------- /input-nnp-md-npt/in.lmp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | clear 9 | variable dt equal 0.0002 # timestep (ps) 10 | variable intThermo equal 1 # screen output interval (timesteps) 11 | variable numSteps equal 2000000 # total number of simulation timesteps (timesteps) 12 | variable runnerCutoff equal 4.24 # largest symmetry function cutoff (Angstrom) 13 | variable nameStartCfg string "M-data.h64-metalunits" # name of the starting configuration file 14 | variable runnerDir string "." # directory containing RuNNer files 15 | # set initial velocity distribution 16 | variable initTemp equal TEMPERATURE # initial temperature (K) 17 | variable velSeed equal 49284PRESSURE # seed for random number generator 18 | # NVT integrator (Nose-Hoover) 19 | variable startTemp equal TEMPERATURE # starting temperature for thermostat (K) 20 | variable stopTemp equal TEMPERATURE # final temperature for thermostat (K) 21 | variable tDamp equal 0.02 # thermostat damping factor (ps) 22 | # set pressure 23 | variable Press equal 10000*PRESSURE # units in bar. 1 gpa= 10,000 bar 24 | variable PressFinal equal 10000*PRESSURE 25 | variable pDamp equal 0.2 26 | # dump thermodynamic properties (temperature, pressure, potential energy, kinetic energy, integrator quantity) 27 | variable intTD equal 10 # thermodynamics dump file interval (timesteps) 28 | variable nameTD string "traj/td" # thermodynamics file name 29 | variable varVolume equal vol # variable required to print volume 30 | variable varKE equal ke # variable required to print kinetic energy 31 | ############################################################################### 32 | # SETUP 33 | ############################################################################### 34 | units metal # define unit system (metal = Angstrom, eV, ps, g/mol) 35 | boundary p p p # set periodic boundary conditions 36 | atom_style atomic # set atomic style for particles 37 | read_data ${nameStartCfg} # read start configuration 38 | 39 | replicate 3 3 3 40 | 41 | #change_box all x scale 1.1 y scale 1.1 z scale 1.1 remap 42 | 43 | #pair_style runner dir ${runnerDir} showew no resetew yes maxew 1000000 # set up pair style runner 44 | pair_style nnp dir ${runnerDir} showew no showewsum 1000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 45 | 46 | pair_coeff * * ${runnerCutoff} # set up pair style coefficients 47 | timestep ${dt} # set timestep 48 | velocity all create ${initTemp} ${velSeed} # create initial velocities 49 | 50 | thermo ${intThermo} # set screen output 51 | thermo_style custom step time temp pe etotal press vol lx ly lz 52 | thermo_modify format 4 %20.15g 53 | 54 | fix eq all npt temp ${startTemp} ${startTemp} ${tDamp} iso ${Press} ${Press} ${pDamp} 55 | 56 | run 50000 57 | 58 | unfix eq 59 | 60 | fix 3 all plumed plumedfile plumed.dat outfile p.log 61 | ############################################################################### 62 | # SIMULATION 63 | ############################################################################### 64 | fix 1 all npt temp ${startTemp} ${stopTemp} ${tDamp} iso ${Press} ${PressFinal} ${pDamp} # set up integrator 65 | #fix 1 all nvt temp ${startTemp} ${stopTemp} ${tDamp} 66 | 67 | dump 1 all custom 1000 A.lammpstrj id type xu yu zu # dump configuration into a trajectory file 68 | 69 | run ${numSteps} 70 | #fix 1 all ipi driver.01 32346 unix 71 | #run 10000000 72 | # 73 | ############################################################################### 74 | # CLEAN UP 75 | ############################################################################### 76 | #undump XYZ 77 | #unfix AVE_TD 78 | #unfix INT 79 | ############################################################################### 80 | -------------------------------------------------------------------------------- /input-nnp-md-npt/plumed.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A TIME=ps 2 | 3 | COORDINATIONNUMBER ... 4 | LABEL=cn 5 | SPECIES=1-1728 6 | SWITCH={CUBIC D_0=0.8 D_MAX=1.1} 7 | MEAN 8 | BETWEEN1={GAUSSIAN UPPER=1.2 LOWER=0.8 SMEAR=0.2} 9 | LOWMEM 10 | ... COORDINATIONNUMBER 11 | 12 | DUMPMULTICOLVAR STRIDE=1000 DATA=cn FILE=cn.xyz 13 | 14 | PRINT STRIDE=10 ARG=cn.* FILE=COLVAR 15 | FLUSH STRIDE=1000 16 | 17 | ENDPLUMED 18 | 19 | -------------------------------------------------------------------------------- /input-nnp-md-npt/submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH --job-name=NNP-mpi 4 | #SBATCH --get-user-env 5 | #SBATCH --nodes=1 6 | #SBATCH --ntasks 28 7 | #SBATCH --time=24:00:00 8 | 9 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/programlist/n2p2/lib/ 10 | 11 | module load intel intel-mpi 12 | module load python gsl fftw 13 | 14 | export OMP_NUM_THREADS=1 15 | 16 | temp=$1 17 | press=$2 18 | 19 | sed -i "s/TEMPERATURE/${temp}/g" in.lmp 20 | sed -i "s/PRESSURE/${press}/g" in.lmp 21 | 22 | srun -n 28 lmp_fidis_plumed_n2p2 < in.lmp > lmplog & 23 | 24 | wait 25 | cd .. 26 | 27 | -------------------------------------------------------------------------------- /input-nnp-rss/H.cell: -------------------------------------------------------------------------------- 1 | #TARGVOL=2 2 | 3 | %BLOCK POSITIONS_FRAC 4 | H 0.0 0.0 0.0 # H1 % NUM=48 5 | %ENDBLOCK POSITIONS_FRAC 6 | 7 | #SLACK=0.25 8 | #OVERLAP=0.1 9 | #MINSEP=1 10 | #COMPACT 11 | -------------------------------------------------------------------------------- /input-nnp-rss/H.pp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | variable runnerCutoff equal 4.24 # largest symmetry function cutoff (Angstrom) 9 | variable runnerDir string "../nnp" # directory containing RuNNer files 10 | ############################################################################### 11 | # SETUP 12 | ############################################################################### 13 | # set up pair style runner 14 | pair_style nnp dir ${runnerDir} showew no showewsum 1000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 15 | # set up pair style coefficients 16 | pair_coeff * * ${runnerCutoff} 17 | -------------------------------------------------------------------------------- /input-nnp-rss/runrss.sh: -------------------------------------------------------------------------------- 1 | pp=$1 2 | airss.pl -lammps -pressure $pp -max 2000 -seed H 3 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/A-data.h64-metalunits: -------------------------------------------------------------------------------- 1 | MMPS Description 2 | 3 | 64 atoms 4 | 1 atom types 5 | 6 | 0 4.5722377 xlo xhi 7 | 0 4.5722377 ylo yhi 8 | 0 4.5722377 zlo zhi 9 | 10 | Masses 11 | 12 | 1 1.0080 13 | 14 | Atoms 15 | 16 | 1 1 2.80468 9.05783 3.56515 17 | 2 1 -1.12248 11.7725 7.7413 18 | 3 1 0.474428 13.5625 8.12582 19 | 4 1 1.19709 6.81138 4.79682 20 | 5 1 0.354778 14.613 8.67389 21 | 6 1 1.01507 10.4112 8.19445 22 | 7 1 3.18743 10.0978 9.91765 23 | 8 1 2.08409 14.4695 8.92267 24 | 9 1 1.82822 9.43984 5.30971 25 | 10 1 -0.913583 6.11878 4.3159 26 | 11 1 -1.33047 15.9906 4.79571 27 | 12 1 -1.2317 16.5263 10.6824 28 | 13 1 4.00821 12.7781 2.2602 29 | 14 1 -1.36715 12.5402 7.44908 30 | 15 1 -2.6324 16.0738 4.24019 31 | 16 1 -1.7896 11.855 8.40655 32 | 17 1 0.909716 10.3659 6.91076 33 | 18 1 -2.37958 12.1803 5.51685 34 | 19 1 1.59971 17.9346 8.47342 35 | 20 1 -1.37482 14.3437 6.77938 36 | 21 1 2.45321 11.4794 6.76317 37 | 22 1 -0.497476 14.1066 7.50457 38 | 23 1 -4.03507 11.1688 4.88891 39 | 24 1 -3.61797 16.5761 6.13122 40 | 25 1 4.17887 11.5763 6.73951 41 | 26 1 4.16326 10.7853 10.4224 42 | 27 1 -0.0763934 14.9466 9.99505 43 | 28 1 -6.01566 15.2056 7.75634 44 | 29 1 -0.617758 13.6048 5.34656 45 | 30 1 -0.558425 10.8773 7.19426 46 | 31 1 5.85112 17.0642 6.89691 47 | 32 1 -2.82011 10.4384 10.4583 48 | 33 1 4.82964 7.84902 7.0175 49 | 34 1 -1.45178 13.0286 10.987 50 | 35 1 -2.36476 15.1512 8.26188 51 | 36 1 -0.350904 11.8365 8.56327 52 | 37 1 -0.622479 8.90155 8.10136 53 | 38 1 -3.97245 11.9894 8.01623 54 | 39 1 1.1176 14.0922 7.43119 55 | 40 1 -2.95579 12.7719 9.52661 56 | 41 1 -0.0301719 9.94275 6.68688 57 | 42 1 -2.67299 11.1113 7.25289 58 | 43 1 1.38039 13.3127 10.7629 59 | 44 1 6.46931 14.5325 6.86052 60 | 45 1 3.40082 18.9158 9.08896 61 | 46 1 -1.67316 13.0473 8.98222 62 | 47 1 -2.41444 6.8618 14.5355 63 | 48 1 -2.32612 8.25206 6.82988 64 | 49 1 1.87255 12.2583 8.14794 65 | 50 1 0.0166736 10.6846 8.25914 66 | 51 1 -0.0419478 12.7078 8.62414 67 | 52 1 2.54677 13.5979 10.3582 68 | 53 1 0.90012 12.8892 9.0479 69 | 54 1 -2.29291 13.8687 7.38465 70 | 55 1 1.17625 10.9734 10.447 71 | 56 1 -0.565371 7.38279 10.0902 72 | 57 1 -1.35916 12.9135 5.12032 73 | 58 1 0.195113 7.97121 10.1318 74 | 59 1 1.07255 14.4891 9.57345 75 | 60 1 -4.18428 9.1829 4.79076 76 | 61 1 0.689618 13.9175 10.6256 77 | 62 1 -3.6328 11.2419 2.72905 78 | 63 1 -0.154814 8.87707 6.17939 79 | 64 1 2.70594 10.557 10.7417 80 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/M-data.h64-metalunits: -------------------------------------------------------------------------------- 1 | MMPS Description 2 | 3 | 64 atoms 4 | 1 atom types 5 | 6 | 0 4.5722377 xlo xhi 7 | 0 4.5722377 ylo yhi 8 | 0 4.5722377 zlo zhi 9 | 10 | Masses 11 | 12 | 1 1.0080 13 | 14 | Atoms 15 | 16 | 1 1 6.86153 16.4078 -2.80109 17 | 2 1 6.74762 15.5882 -4.30334 18 | 3 1 8.27704 18.4794 -2.29308 19 | 4 1 7.01422 18.6357 -4.10526 20 | 5 1 6.92366 17.0085 5.00873 21 | 6 1 7.75606 12.144 -8.16508 22 | 7 1 6.45676 13.8611 -0.0596657 23 | 8 1 5.52877 17.0508 -0.403523 24 | 9 1 11.6263 15.3407 -5.92611 25 | 10 1 5.12781 18.0017 1.67085 26 | 11 1 8.98303 15.3383 0.0555764 27 | 12 1 5.90241 17.2688 -2.01957 28 | 13 1 4.64211 14.0359 -0.116765 29 | 14 1 5.64464 15.3817 -0.568984 30 | 15 1 9.45771 16.1873 -1.14027 31 | 16 1 10.2473 17.6341 -0.685423 32 | 17 1 8.36354 18.3157 0.906605 33 | 18 1 10.2939 15.6486 -2.00499 34 | 19 1 7.86835 18.2767 -4.97022 35 | 20 1 4.33271 14.9549 -1.09609 36 | 21 1 12.1529 13.4684 0.999066 37 | 22 1 8.12234 14.8333 -3.16283 38 | 23 1 6.02094 18.4936 -1.8945 39 | 24 1 9.35956 12.9124 1.4439 40 | 25 1 5.40469 16.3763 1.33489 41 | 26 1 9.29072 13.2653 -1.11346 42 | 27 1 8.15795 18.9589 -0.393464 43 | 28 1 9.16856 19.9168 1.79091 44 | 29 1 12.0061 10.6499 0.390184 45 | 30 1 7.14067 12.585 1.8363 46 | 31 1 8.00559 15.5748 -2.03891 47 | 32 1 5.45363 14.7547 -3.26429 48 | 33 1 9.15585 20.5754 1.6708 49 | 34 1 6.92644 14.3506 -2.50401 50 | 35 1 7.5843 15.791 -2.55017 51 | 36 1 6.92216 14.6461 -1.16512 52 | 37 1 7.10398 17.2267 -0.217374 53 | 38 1 10.9447 16.2484 -0.733715 54 | 39 1 5.01408 15.113 -1.42067 55 | 40 1 8.90489 13.6512 -1.54618 56 | 41 1 8.41589 17.4267 -4.61083 57 | 42 1 5.14727 13.7231 0.439172 58 | 43 1 6.63948 16.4599 -1.44453 59 | 44 1 5.81377 16.5981 -3.86673 60 | 45 1 9.51059 15.8044 0.409404 61 | 46 1 7.65483 16.5267 -0.692898 62 | 47 1 5.71902 15.1629 0.735773 63 | 48 1 5.86317 14.7468 -0.811876 64 | 49 1 8.62098 14.824 0.82615 65 | 50 1 10.9678 20.1071 -2.29221 66 | 51 1 5.52848 18.8891 -2.25857 67 | 52 1 8.37783 17.1216 2.07107 68 | 53 1 7.42359 17.6712 -1.75946 69 | 54 1 6.95778 14.7927 -3.07085 70 | 55 1 3.51209 15.7047 -0.694499 71 | 56 1 6.36483 17.8998 -2.87793 72 | 57 1 11.461 17.91 3.20753 73 | 58 1 8.32269 16.2904 0.905803 74 | 59 1 8.45688 12.2822 2.73521 75 | 60 1 5.27726 16.9564 -1.98326 76 | 61 1 4.5328 21.8956 0.124947 77 | 62 1 8.30246 19.0366 -2.00157 78 | 63 1 6.10065 18.0022 1.05711 79 | 64 1 4.23868 16.4932 -0.746998 80 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/in.lmp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | clear 9 | variable dt equal 0.0002 # timestep (ps) 10 | variable intThermo equal 1 # screen output interval (timesteps) 11 | variable numSteps equal 2000000 # total number of simulation timesteps (timesteps) 12 | variable runnerCutoff equal 4.24 # largest symmetry function cutoff (Angstrom) 13 | variable nameStartCfg string "M-data.h64-metalunits" # name of the starting configuration file 14 | variable runnerDir string "." # directory containing RuNNer files 15 | # set initial velocity distribution 16 | variable initTemp equal HIGHT # initial temperature (K) 17 | variable velSeed equal 40RANDOM # seed for random number generator 18 | # NVT integrator (Nose-Hoover) 19 | variable startTemp equal HIGHT # starting temperature for thermostat (K) 20 | variable stopTemp equal 0.1 # final temperature for thermostat (K) 21 | variable tDamp equal 0.02 # thermostat damping factor (ps) 22 | # set pressure 23 | variable Press equal 10000*PRESSURE # units in bar. 1 gpa= 10,000 bar 24 | variable PressFinal equal 10000*PRESSURE 25 | variable pDamp equal 0.2 26 | variable pDamp2 equal 2.0 27 | # dump thermodynamic properties (temperature, pressure, potential energy, kinetic energy, integrator quantity) 28 | variable intTD equal 10 # thermodynamics dump file interval (timesteps) 29 | variable nameTD string "traj/td" # thermodynamics file name 30 | variable varVolume equal vol # variable required to print volume 31 | variable varKE equal ke # variable required to print kinetic energy 32 | ############################################################################### 33 | # SETUP 34 | ############################################################################### 35 | units metal # define unit system (metal = Angstrom, eV, ps, g/mol) 36 | boundary p p p # set periodic boundary conditions 37 | atom_style atomic # set atomic style for particles 38 | read_data ${nameStartCfg} # read start configuration 39 | 40 | replicate 3 3 3 41 | 42 | change_box all triclinic # x scale 1.1 y scale 1.1 z scale 1.1 remap 43 | 44 | #pair_style runner dir ${runnerDir} showew no resetew yes maxew 1000000 # set up pair style runner 45 | pair_style nnp dir ${runnerDir} showew no showewsum 10000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 46 | 47 | pair_coeff * * ${runnerCutoff} # set up pair style coefficients 48 | 49 | neigh_modify every 1 delay 0 check yes 50 | 51 | timestep ${dt} # set timestep 52 | velocity all create ${initTemp} ${velSeed} # create initial velocities 53 | 54 | thermo ${intThermo} # set screen output 55 | thermo_style custom step time temp pe etotal press vol lx ly lz xy xz yz 56 | thermo_modify format 4 %20.15g 57 | 58 | fix eq all npt temp ${startTemp} ${startTemp} ${tDamp} iso ${Press} ${Press} ${pDamp} 59 | 60 | run 10000 61 | 62 | unfix eq 63 | 64 | #fix 3 all plumed plumedfile plumed.dat outfile p.log 65 | ############################################################################### 66 | # SIMULATION 67 | ############################################################################### 68 | fix 1 all npt temp ${startTemp} ${stopTemp} ${tDamp} tri ${Press} ${PressFinal} ${pDamp2} # set up integrator 69 | #fix 1 all nvt temp ${startTemp} ${stopTemp} ${tDamp} 70 | 71 | dump 1 all custom 1000 A.lammpstrj id type x y z # dump configuration into a trajectory file 72 | 73 | run ${numSteps} 74 | 75 | ############################################################################### 76 | # CLEAN UP 77 | ############################################################################### 78 | undump 1 79 | unfix 1 80 | #unfix 3 81 | ############################################################################### 82 | # 83 | # 84 | # 85 | write_data data.solid-P-PRESSURE 86 | write_restart restart.solid-P-PRESSURE 87 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/input.nn: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # GENERAL NNP SETTINGS 3 | ############################################################################### 4 | number_of_elements 1 # Number of elements. 5 | elements H # Specification of elements. 6 | #atom_energy H -0.45890771 # Free atom reference energy (H). 7 | cutoff_type 2 # Cutoff type. 8 | scale_symmetry_functions # Scale all symmetry functions with min/max values. 9 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 10 | scale_min_short 0.0 # Minimum value for scaling. 11 | scale_max_short 1.0 # Maximum value for scaling. 12 | center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 13 | global_hidden_layers_short 3 # Number of hidden layers. 14 | global_nodes_short 20 20 20 # Number of nodes in each hidden layer. 15 | global_activation_short t t t l # Activation function for each hidden layer and output layer. 16 | #normalize_nodes # Normalize input of nodes. 17 | 18 | ############################################################################### 19 | # ADDITIONAL SETTINGS FOR TRAINING 20 | ############################################################################### 21 | epochs 50 # Number of training epochs. 22 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 23 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 24 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 25 | selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 26 | #memorize_symfunc_results # Keep symmetry function results in memory. 27 | random_seed 1210215 28 | test_fraction 0.1 # Fraction of structures kept for testing. 29 | use_short_forces # Use forces for training. 30 | force_weight 5.0 # Weight of force updates relative to energy updates. 31 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 32 | short_force_fraction 0.01 # Fraction of force updates per epoch. 33 | short_energy_error_threshold 1.00 # RMSE threshold for energy update candidates. 34 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 35 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 36 | #repeated_energy_update # After force update perform energy update for corresponding structure. 37 | #use_old_weights_short # Restart fitting with old weight parameters. 38 | weights_min -1.0 # Minimum value for initial random weights. 39 | weights_max 1.0 # Maximum value for initial random weights. 40 | #precondition_weights # Precondition weights with initial energies. 41 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 42 | write_trainpoints 5 # Write energy comparison. 43 | write_trainforces 5 # Write force comparison. 44 | write_weights_epoch # Write weights. 45 | #write_neuronstats 5 10 # Write neuron statistics. 46 | #write_trainlog # Write training log file. 47 | #################### 48 | # GRADIENT DESCENT # 49 | #################### 50 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 51 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 52 | ############################ 53 | # KALMAN FILTER (STANDARD) # 54 | ############################ 55 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 56 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 57 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 58 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 59 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 60 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 61 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 62 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 63 | ################################# 64 | # KALMAN FILTER (FADING MEMORY) # 65 | ################################# 66 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 67 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 68 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 69 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 70 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 71 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 72 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 73 | 74 | ############################################################################### 75 | # SYMMETRY FUNCTIONS 76 | ############################################################################### 77 | 78 | # Radial symmetry function (type 2): 79 | #symfunction_short 2 80 | 81 | # Narrow Angular symmetry function (type 3): 82 | #symfunction_short 3 83 | 84 | # Wide Angular symmetry function (type 9): 85 | #symfunction_short 9 86 | 87 | symfunction_short H 2 H 57.776 0.814 2.000 88 | symfunction_short H 2 H 34.647 1.051 3.000 89 | symfunction_short H 2 H 25.678 1.221 3.000 90 | symfunction_short H 2 H 5.078 2.746 5.000 91 | symfunction_short H 2 H 9.244 2.035 5.000 92 | symfunction_short H 2 H 19.489 1.402 4.000 93 | symfunction_short H 2 H 6.851 2.364 5.000 94 | symfunction_short H 2 H 14.444 1.628 4.000 95 | symfunction_short H 2 H 3.763 3.190 5.000 96 | symfunction_short H 2 H 49.892 0.876 2.500 97 | symfunction_short H 2 H 77.956 0.701 2.000 98 | symfunction_short H 2 H 1.435 5.165 6.000 99 | symfunction_short H 2 H 1.055 6.026 7.000 100 | symfunction_short H 2 H 42.820 0.946 2.000 101 | symfunction_short H 2 H 1.089 5.929 8.000 102 | symfunction_short H 2 H 2.613 3.828 6.000 103 | symfunction_short H 2 H 22.708 1.299 5.000 104 | symfunction_short H 2 H 0.807 6.887 8.000 105 | symfunction_short H 2 H 16.830 1.509 5.000 106 | symfunction_short H 2 H 1.470 5.104 8.000 107 | symfunction_short H 2 H 30.639 1.118 5.000 108 | symfunction_short H 2 H 1.984 4.394 8.000 109 | symfunction_short H 2 H 10.705 1.891 4.000 110 | symfunction_short H 2 H 12.473 1.752 5.000 111 | symfunction_short H 2 H 2.591 3.845 7.000 112 | symfunction_short H 2 H 4.716 2.850 7.000 113 | symfunction_short H 2 H 6.364 2.453 7.000 114 | symfunction_short H 2 H 3.495 3.310 7.000 115 | symfunction_short H 2 H 7.934 2.197 4.000 116 | symfunction_short H 3 H H 0.111 1.000 1.000 3.000 117 | symfunction_short H 3 H H 0.062 -1.000 1.000 4.000 118 | symfunction_short H 3 H H 0.062 1.000 1.000 4.000 119 | symfunction_short H 3 H H 0.062 1.000 16.000 4.000 120 | symfunction_short H 3 H H 0.040 1.000 4.000 5.000 121 | symfunction_short H 3 H H 0.040 -1.000 1.000 5.000 122 | symfunction_short H 3 H H 0.040 -1.000 4.000 5.000 123 | symfunction_short H 3 H H 0.016 1.000 1.000 8.000 124 | symfunction_short H 3 H H 0.016 -1.000 1.000 8.000 125 | symfunction_short H 3 H H 0.020 1.000 1.000 7.000 126 | symfunction_short H 3 H H 0.028 1.000 1.000 6.000 127 | symfunction_short H 3 H H 0.016 1.000 16.000 8.000 128 | symfunction_short H 3 H H 0.016 1.000 4.000 8.000 129 | symfunction_short H 3 H H 0.016 -1.000 16.000 8.000 130 | symfunction_short H 3 H H 0.028 1.000 16.000 6.000 131 | symfunction_short H 3 H H 0.028 -1.000 16.000 6.000 132 | symfunction_short H 3 H H 0.020 -1.000 1.000 7.000 133 | symfunction_short H 3 H H 0.016 -1.000 4.000 8.000 134 | symfunction_short H 3 H H 0.020 1.000 4.000 7.000 135 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 0.0000000000000000E+00 1.2786864788554039E-01 2.0148701465623242E-04 3.1524761950806630E-03 17 | 1 2 0.0000000000000000E+00 1.5324159403424931E-01 2.6312649631626648E-05 1.2049201618322630E-03 18 | 1 3 0.0000000000000000E+00 1.8779883931284078E-01 2.4100609615632932E-06 4.1087787492401478E-04 19 | 1 4 0.0000000000000000E+00 1.8833496692166160E-01 1.1923536362419721E-04 3.0001964292893754E-03 20 | 1 5 0.0000000000000000E+00 3.5955730712772588E-01 1.4892814158897155E-02 2.6012376022955513E-02 21 | 1 6 0.0000000000000000E+00 3.5929588979511018E-01 1.8674770931646589E-03 1.2590160121393355E-02 22 | 1 7 0.0000000000000000E+00 7.9425620447436296E-01 2.1254143820593810E-01 1.1525862384997716E-01 23 | 1 8 0.0000000000000000E+00 8.7467201947800743E-01 1.7074128934272059E-01 1.1708692558764941E-01 24 | 1 9 0.0000000000000000E+00 7.4811605665701719E-01 1.5519435107662793E-01 7.1275316047969300E-02 25 | 1 10 0.0000000000000000E+00 6.7333285542477783E-01 1.0759055403395651E-01 6.3297413723034684E-02 26 | 1 11 3.5910379683328059E-05 9.7073274581664104E-01 5.0623959362231108E-01 1.2736879346446944E-01 27 | 1 12 1.4651415281849498E-07 1.2321718127446848E+00 5.6452836615588087E-01 1.8262446467122168E-01 28 | 1 13 8.4577697438719571E-13 1.4747184327154994E+00 4.5721468960237244E-01 2.0131653962487583E-01 29 | 1 14 2.1065196719838351E-21 1.3840249655512706E+00 3.1399515618091239E-01 1.9540171709333165E-01 30 | 1 15 8.6972539370641714E-35 1.1709787371985103E+00 2.2399339888890113E-01 1.3937389170540587E-01 31 | 1 16 6.8849742194674013E-55 9.8648969012214727E-01 1.9013342869196725E-01 8.6985029880464221E-02 32 | 1 17 1.9097564541503356E-84 7.1287053045711446E-01 7.0423033342822558E-02 6.1097607892459958E-02 33 | 1 18 3.9041233430555061E-127 5.7910474297282288E-01 7.7979762674756370E-03 3.0001123143202617E-02 34 | 1 19 1.9549728427461759E-02 3.8930917832271078E-01 2.0171598260484119E-01 5.1727433306469041E-02 35 | 1 20 2.2793198416896789E-02 1.4386575716282468E+00 7.6525110162075216E-01 1.4141446941085739E-01 36 | 1 21 4.7646427383803432E-02 5.6115606300904231E-01 3.5202359290322310E-01 8.5427371422089546E-02 37 | 1 22 5.7114363278535099E-02 2.5545080234003468E+00 1.3538612523590432E+00 2.5072471847758254E-01 38 | 1 23 2.4940663697200689E-03 2.7522145071418831E+00 1.4697299433055526E+00 3.2622023343195683E-01 39 | 1 24 7.8682802555547335E-06 2.5944753464285428E+00 1.3058387226565509E+00 3.6913521804174371E-01 40 | 1 25 3.8919161034755070E-10 2.4797469425290117E+00 9.2442605075510287E-01 3.6754562234387905E-01 41 | 1 26 9.2619930581806134E-02 8.1664587623323914E-01 5.0966407948897452E-01 9.9151195954948784E-02 42 | 1 27 1.8318498196390448E-01 1.9153034470475108E+00 1.2247793247301280E+00 2.7230852284979107E-01 43 | 1 28 2.7507711080804348E-01 3.0256562654161572E+00 1.7844962674328060E+00 4.5679177013995692E-01 44 | 1 29 2.3897224519634894E-01 3.5897251008363615E+00 1.8969495318285576E+00 4.3720752276638192E-01 45 | 1 30 0.0000000000000000E+00 5.8484982044182780E-03 3.1067262157701329E-05 9.1950833931776768E-05 46 | 1 31 0.0000000000000000E+00 1.8477063440026437E-02 8.7325374281955700E-04 9.3136120974875950E-04 47 | 1 32 0.0000000000000000E+00 3.7336807040497737E-02 2.4086044873246389E-03 2.3750767572766765E-03 48 | 1 33 0.0000000000000000E+00 7.0642814078505202E-03 2.6343707911330927E-04 2.7035108042627745E-04 49 | 1 34 1.5929753547141851E-13 8.0731305223699465E-02 1.1074371843129496E-02 7.3575933441624294E-03 50 | 1 35 5.6325947537878221E-16 2.3003444431839482E-02 1.5884397842508863E-03 1.2498264882277600E-03 51 | 1 36 5.3981986786993238E-13 9.3410838688374118E-02 1.5978972418477580E-02 9.9890378669505991E-03 52 | 1 37 1.9700371500545024E-06 6.8969832554816746E-01 1.5443464421476363E-01 8.0162174550083384E-02 53 | 1 38 6.1657159989202514E-16 2.4749528542932317E-02 1.6229878174756835E-03 1.2870123862469087E-03 54 | 1 39 6.2262684617804945E-07 1.0573409296829014E-01 2.4663201317918649E-02 1.2324985639637898E-02 55 | 1 40 3.0303734433414090E-05 8.0480865506783472E-01 1.9705844281684351E-01 9.4076893600784375E-02 56 | 1 41 2.9602459953219584E-04 1.9365314536570741E+00 5.2281410288197383E-01 2.4440723530575639E-01 57 | 1 42 2.3033250210999353E-04 1.0600999125841739E+00 2.9064562025332846E-01 1.3628090064970649E-01 58 | 1 43 4.4156751616116266E-04 1.8181725546180594E+00 5.0504793045530760E-01 2.2653438009689736E-01 59 | 1 44 3.7271975785887314E-03 4.3394225551846519E+00 1.3292398624644119E+00 5.8667197578105734E-01 60 | 1 45 8.0581351847887373E-06 4.0158809640046172E-01 9.7520506174563842E-02 4.6421184682890214E-02 61 | 1 46 2.8285538602087893E-03 2.4132319079528153E+00 7.5095290878482479E-01 3.3351584311932420E-01 62 | 1 47 1.3040678584439959E-09 9.3788161160613240E-02 1.9338171364423416E-02 1.0081020289092305E-02 63 | 1 48 1.1896132844293479E-03 8.2190114793389346E-01 2.5033325307694210E-01 1.1236226432368290E-01 64 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/cooling-nst-template/submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH --job-name=NNP-mpi 4 | #SBATCH --get-user-env 5 | #SBATCH --nodes=3 6 | #SBATCH --ntasks 84 7 | #SBATCH --time=72:00:00 8 | 9 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/programlist/n2p2/lib/ 10 | 11 | module load intel intel-mpi 12 | module load python gsl fftw 13 | 14 | export OMP_NUM_THREADS=1 15 | 16 | press=$1 17 | 18 | sed -i "s/PRESSURE/${press}/g" in.lmp 19 | 20 | srun -n 84 lmp_fidis < in.lmp > lmplog & 21 | 22 | wait 23 | cd .. 24 | 25 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/heating-nst-template/in.lmp: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # MD simulation for PBE H with NN potential 3 | ############################################################################### 4 | 5 | ############################################################################### 6 | # VARIABLES 7 | ############################################################################### 8 | clear 9 | variable dt equal 0.0002 # timestep (ps) 10 | variable intThermo equal 1 # screen output interval (timesteps) 11 | variable numSteps equal 2000000 # total number of simulation timesteps (timesteps) 12 | variable runnerCutoff equal 4.24 # largest symmetry function cutoff (Angstrom) 13 | variable nameStartCfg string "data.solid-P-PRESSURE" # name of the starting configuration file 14 | variable runnerDir string "." # directory containing RuNNer files 15 | # set initial velocity distribution 16 | variable initTemp equal 100 # initial temperature (K) 17 | variable velSeed equal 979RANDOM # seed for random number generator 18 | # NVT integrator (Nose-Hoover) 19 | variable startTemp equal 100 # starting temperature for thermostat (K) 20 | variable stopTemp equal HIGHT # final temperature for thermostat (K) 21 | variable tDamp equal 0.02 # thermostat damping factor (ps) 22 | # set pressure 23 | variable Press equal 10000*PRESSURE # units in bar. 1 gpa= 10,000 bar 24 | variable PressFinal equal 10000*PRESSURE 25 | variable pDamp equal 0.2 26 | # dump thermodynamic properties (temperature, pressure, potential energy, kinetic energy, integrator quantity) 27 | variable intTD equal 10 # thermodynamics dump file interval (timesteps) 28 | variable nameTD string "traj/td" # thermodynamics file name 29 | variable varVolume equal vol # variable required to print volume 30 | variable varKE equal ke # variable required to print kinetic energy 31 | ############################################################################### 32 | # SETUP 33 | ############################################################################### 34 | units metal # define unit system (metal = Angstrom, eV, ps, g/mol) 35 | boundary p p p # set periodic boundary conditions 36 | atom_style atomic # set atomic style for particles 37 | box tilt large 38 | read_data ${nameStartCfg} # read start configuration 39 | 40 | 41 | #pair_style runner dir ${runnerDir} showew no resetew yes maxew 1000000 # set up pair style runner 42 | pair_style nnp dir ${runnerDir} showew no showewsum 10000 resetew yes maxew 200000000 cflength 1.8897261328 cfenergy 0.0367493254 43 | 44 | pair_coeff * * ${runnerCutoff} # set up pair style coefficients 45 | timestep ${dt} # set timestep 46 | velocity all create ${initTemp} ${velSeed} # create initial velocities 47 | 48 | thermo ${intThermo} # set screen output 49 | thermo_style custom step time temp pe etotal press vol lx ly lz xy xz yz 50 | thermo_modify format 4 %20.15g 51 | 52 | fix eq all npt temp ${startTemp} ${startTemp} ${tDamp} iso ${Press} ${Press} ${pDamp} 53 | 54 | run 10000 55 | 56 | unfix eq 57 | 58 | #fix 3 all plumed plumedfile plumed.dat outfile p.log 59 | ############################################################################### 60 | # SIMULATION 61 | ############################################################################### 62 | fix 1 all npt temp ${startTemp} ${stopTemp} ${tDamp} iso ${Press} ${PressFinal} ${pDamp} # set up integrator 63 | #fix 1 all nvt temp ${startTemp} ${stopTemp} ${tDamp} 64 | 65 | dump 1 all custom 1000 A.lammpstrj id type x y z # dump configuration into a trajectory file 66 | 67 | run ${numSteps} 68 | #fix 1 all ipi driver.01 32346 unix 69 | #run 10000000 70 | # 71 | ############################################################################### 72 | # CLEAN UP 73 | ############################################################################### 74 | undump 1 75 | unfix 1 76 | #unfix 3 77 | ############################################################################### 78 | # 79 | # 80 | # 81 | write_data data.liquid-P-PRESSURE 82 | write_restart restart.liquid-P-PRESSURE 83 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/heating-nst-template/input.nn: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # GENERAL NNP SETTINGS 3 | ############################################################################### 4 | number_of_elements 1 # Number of elements. 5 | elements H # Specification of elements. 6 | #atom_energy H -0.45890771 # Free atom reference energy (H). 7 | cutoff_type 2 # Cutoff type. 8 | scale_symmetry_functions # Scale all symmetry functions with min/max values. 9 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 10 | scale_min_short 0.0 # Minimum value for scaling. 11 | scale_max_short 1.0 # Maximum value for scaling. 12 | center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 13 | global_hidden_layers_short 3 # Number of hidden layers. 14 | global_nodes_short 20 20 20 # Number of nodes in each hidden layer. 15 | global_activation_short t t t l # Activation function for each hidden layer and output layer. 16 | #normalize_nodes # Normalize input of nodes. 17 | 18 | ############################################################################### 19 | # ADDITIONAL SETTINGS FOR TRAINING 20 | ############################################################################### 21 | epochs 50 # Number of training epochs. 22 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 23 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 24 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 25 | selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 26 | #memorize_symfunc_results # Keep symmetry function results in memory. 27 | random_seed 1210215 28 | test_fraction 0.1 # Fraction of structures kept for testing. 29 | use_short_forces # Use forces for training. 30 | force_weight 5.0 # Weight of force updates relative to energy updates. 31 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 32 | short_force_fraction 0.01 # Fraction of force updates per epoch. 33 | short_energy_error_threshold 1.00 # RMSE threshold for energy update candidates. 34 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 35 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 36 | #repeated_energy_update # After force update perform energy update for corresponding structure. 37 | #use_old_weights_short # Restart fitting with old weight parameters. 38 | weights_min -1.0 # Minimum value for initial random weights. 39 | weights_max 1.0 # Maximum value for initial random weights. 40 | #precondition_weights # Precondition weights with initial energies. 41 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 42 | write_trainpoints 5 # Write energy comparison. 43 | write_trainforces 5 # Write force comparison. 44 | write_weights_epoch # Write weights. 45 | #write_neuronstats 5 10 # Write neuron statistics. 46 | #write_trainlog # Write training log file. 47 | #################### 48 | # GRADIENT DESCENT # 49 | #################### 50 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 51 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 52 | ############################ 53 | # KALMAN FILTER (STANDARD) # 54 | ############################ 55 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 56 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 57 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 58 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 59 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 60 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 61 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 62 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 63 | ################################# 64 | # KALMAN FILTER (FADING MEMORY) # 65 | ################################# 66 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 67 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 68 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 69 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 70 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 71 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 72 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 73 | 74 | ############################################################################### 75 | # SYMMETRY FUNCTIONS 76 | ############################################################################### 77 | 78 | # Radial symmetry function (type 2): 79 | #symfunction_short 2 80 | 81 | # Narrow Angular symmetry function (type 3): 82 | #symfunction_short 3 83 | 84 | # Wide Angular symmetry function (type 9): 85 | #symfunction_short 9 86 | 87 | symfunction_short H 2 H 57.776 0.814 2.000 88 | symfunction_short H 2 H 34.647 1.051 3.000 89 | symfunction_short H 2 H 25.678 1.221 3.000 90 | symfunction_short H 2 H 5.078 2.746 5.000 91 | symfunction_short H 2 H 9.244 2.035 5.000 92 | symfunction_short H 2 H 19.489 1.402 4.000 93 | symfunction_short H 2 H 6.851 2.364 5.000 94 | symfunction_short H 2 H 14.444 1.628 4.000 95 | symfunction_short H 2 H 3.763 3.190 5.000 96 | symfunction_short H 2 H 49.892 0.876 2.500 97 | symfunction_short H 2 H 77.956 0.701 2.000 98 | symfunction_short H 2 H 1.435 5.165 6.000 99 | symfunction_short H 2 H 1.055 6.026 7.000 100 | symfunction_short H 2 H 42.820 0.946 2.000 101 | symfunction_short H 2 H 1.089 5.929 8.000 102 | symfunction_short H 2 H 2.613 3.828 6.000 103 | symfunction_short H 2 H 22.708 1.299 5.000 104 | symfunction_short H 2 H 0.807 6.887 8.000 105 | symfunction_short H 2 H 16.830 1.509 5.000 106 | symfunction_short H 2 H 1.470 5.104 8.000 107 | symfunction_short H 2 H 30.639 1.118 5.000 108 | symfunction_short H 2 H 1.984 4.394 8.000 109 | symfunction_short H 2 H 10.705 1.891 4.000 110 | symfunction_short H 2 H 12.473 1.752 5.000 111 | symfunction_short H 2 H 2.591 3.845 7.000 112 | symfunction_short H 2 H 4.716 2.850 7.000 113 | symfunction_short H 2 H 6.364 2.453 7.000 114 | symfunction_short H 2 H 3.495 3.310 7.000 115 | symfunction_short H 2 H 7.934 2.197 4.000 116 | symfunction_short H 3 H H 0.111 1.000 1.000 3.000 117 | symfunction_short H 3 H H 0.062 -1.000 1.000 4.000 118 | symfunction_short H 3 H H 0.062 1.000 1.000 4.000 119 | symfunction_short H 3 H H 0.062 1.000 16.000 4.000 120 | symfunction_short H 3 H H 0.040 1.000 4.000 5.000 121 | symfunction_short H 3 H H 0.040 -1.000 1.000 5.000 122 | symfunction_short H 3 H H 0.040 -1.000 4.000 5.000 123 | symfunction_short H 3 H H 0.016 1.000 1.000 8.000 124 | symfunction_short H 3 H H 0.016 -1.000 1.000 8.000 125 | symfunction_short H 3 H H 0.020 1.000 1.000 7.000 126 | symfunction_short H 3 H H 0.028 1.000 1.000 6.000 127 | symfunction_short H 3 H H 0.016 1.000 16.000 8.000 128 | symfunction_short H 3 H H 0.016 1.000 4.000 8.000 129 | symfunction_short H 3 H H 0.016 -1.000 16.000 8.000 130 | symfunction_short H 3 H H 0.028 1.000 16.000 6.000 131 | symfunction_short H 3 H H 0.028 -1.000 16.000 6.000 132 | symfunction_short H 3 H H 0.020 -1.000 1.000 7.000 133 | symfunction_short H 3 H H 0.016 -1.000 4.000 8.000 134 | symfunction_short H 3 H H 0.020 1.000 4.000 7.000 135 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/heating-nst-template/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 0.0000000000000000E+00 1.2786864788554039E-01 2.0148701465623242E-04 3.1524761950806630E-03 17 | 1 2 0.0000000000000000E+00 1.5324159403424931E-01 2.6312649631626648E-05 1.2049201618322630E-03 18 | 1 3 0.0000000000000000E+00 1.8779883931284078E-01 2.4100609615632932E-06 4.1087787492401478E-04 19 | 1 4 0.0000000000000000E+00 1.8833496692166160E-01 1.1923536362419721E-04 3.0001964292893754E-03 20 | 1 5 0.0000000000000000E+00 3.5955730712772588E-01 1.4892814158897155E-02 2.6012376022955513E-02 21 | 1 6 0.0000000000000000E+00 3.5929588979511018E-01 1.8674770931646589E-03 1.2590160121393355E-02 22 | 1 7 0.0000000000000000E+00 7.9425620447436296E-01 2.1254143820593810E-01 1.1525862384997716E-01 23 | 1 8 0.0000000000000000E+00 8.7467201947800743E-01 1.7074128934272059E-01 1.1708692558764941E-01 24 | 1 9 0.0000000000000000E+00 7.4811605665701719E-01 1.5519435107662793E-01 7.1275316047969300E-02 25 | 1 10 0.0000000000000000E+00 6.7333285542477783E-01 1.0759055403395651E-01 6.3297413723034684E-02 26 | 1 11 3.5910379683328059E-05 9.7073274581664104E-01 5.0623959362231108E-01 1.2736879346446944E-01 27 | 1 12 1.4651415281849498E-07 1.2321718127446848E+00 5.6452836615588087E-01 1.8262446467122168E-01 28 | 1 13 8.4577697438719571E-13 1.4747184327154994E+00 4.5721468960237244E-01 2.0131653962487583E-01 29 | 1 14 2.1065196719838351E-21 1.3840249655512706E+00 3.1399515618091239E-01 1.9540171709333165E-01 30 | 1 15 8.6972539370641714E-35 1.1709787371985103E+00 2.2399339888890113E-01 1.3937389170540587E-01 31 | 1 16 6.8849742194674013E-55 9.8648969012214727E-01 1.9013342869196725E-01 8.6985029880464221E-02 32 | 1 17 1.9097564541503356E-84 7.1287053045711446E-01 7.0423033342822558E-02 6.1097607892459958E-02 33 | 1 18 3.9041233430555061E-127 5.7910474297282288E-01 7.7979762674756370E-03 3.0001123143202617E-02 34 | 1 19 1.9549728427461759E-02 3.8930917832271078E-01 2.0171598260484119E-01 5.1727433306469041E-02 35 | 1 20 2.2793198416896789E-02 1.4386575716282468E+00 7.6525110162075216E-01 1.4141446941085739E-01 36 | 1 21 4.7646427383803432E-02 5.6115606300904231E-01 3.5202359290322310E-01 8.5427371422089546E-02 37 | 1 22 5.7114363278535099E-02 2.5545080234003468E+00 1.3538612523590432E+00 2.5072471847758254E-01 38 | 1 23 2.4940663697200689E-03 2.7522145071418831E+00 1.4697299433055526E+00 3.2622023343195683E-01 39 | 1 24 7.8682802555547335E-06 2.5944753464285428E+00 1.3058387226565509E+00 3.6913521804174371E-01 40 | 1 25 3.8919161034755070E-10 2.4797469425290117E+00 9.2442605075510287E-01 3.6754562234387905E-01 41 | 1 26 9.2619930581806134E-02 8.1664587623323914E-01 5.0966407948897452E-01 9.9151195954948784E-02 42 | 1 27 1.8318498196390448E-01 1.9153034470475108E+00 1.2247793247301280E+00 2.7230852284979107E-01 43 | 1 28 2.7507711080804348E-01 3.0256562654161572E+00 1.7844962674328060E+00 4.5679177013995692E-01 44 | 1 29 2.3897224519634894E-01 3.5897251008363615E+00 1.8969495318285576E+00 4.3720752276638192E-01 45 | 1 30 0.0000000000000000E+00 5.8484982044182780E-03 3.1067262157701329E-05 9.1950833931776768E-05 46 | 1 31 0.0000000000000000E+00 1.8477063440026437E-02 8.7325374281955700E-04 9.3136120974875950E-04 47 | 1 32 0.0000000000000000E+00 3.7336807040497737E-02 2.4086044873246389E-03 2.3750767572766765E-03 48 | 1 33 0.0000000000000000E+00 7.0642814078505202E-03 2.6343707911330927E-04 2.7035108042627745E-04 49 | 1 34 1.5929753547141851E-13 8.0731305223699465E-02 1.1074371843129496E-02 7.3575933441624294E-03 50 | 1 35 5.6325947537878221E-16 2.3003444431839482E-02 1.5884397842508863E-03 1.2498264882277600E-03 51 | 1 36 5.3981986786993238E-13 9.3410838688374118E-02 1.5978972418477580E-02 9.9890378669505991E-03 52 | 1 37 1.9700371500545024E-06 6.8969832554816746E-01 1.5443464421476363E-01 8.0162174550083384E-02 53 | 1 38 6.1657159989202514E-16 2.4749528542932317E-02 1.6229878174756835E-03 1.2870123862469087E-03 54 | 1 39 6.2262684617804945E-07 1.0573409296829014E-01 2.4663201317918649E-02 1.2324985639637898E-02 55 | 1 40 3.0303734433414090E-05 8.0480865506783472E-01 1.9705844281684351E-01 9.4076893600784375E-02 56 | 1 41 2.9602459953219584E-04 1.9365314536570741E+00 5.2281410288197383E-01 2.4440723530575639E-01 57 | 1 42 2.3033250210999353E-04 1.0600999125841739E+00 2.9064562025332846E-01 1.3628090064970649E-01 58 | 1 43 4.4156751616116266E-04 1.8181725546180594E+00 5.0504793045530760E-01 2.2653438009689736E-01 59 | 1 44 3.7271975785887314E-03 4.3394225551846519E+00 1.3292398624644119E+00 5.8667197578105734E-01 60 | 1 45 8.0581351847887373E-06 4.0158809640046172E-01 9.7520506174563842E-02 4.6421184682890214E-02 61 | 1 46 2.8285538602087893E-03 2.4132319079528153E+00 7.5095290878482479E-01 3.3351584311932420E-01 62 | 1 47 1.3040678584439959E-09 9.3788161160613240E-02 1.9338171364423416E-02 1.0081020289092305E-02 63 | 1 48 1.1896132844293479E-03 8.2190114793389346E-01 2.5033325307694210E-01 1.1236226432368290E-01 64 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/heating-nst-template/submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH --job-name=NNP-mpi 4 | #SBATCH --get-user-env 5 | #SBATCH --nodes=3 6 | #SBATCH --ntasks 84 7 | #SBATCH --time=72:00:00 8 | 9 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/programlist/n2p2/lib/ 10 | 11 | module load intel intel-mpi 12 | module load python gsl fftw 13 | 14 | export OMP_NUM_THREADS=1 15 | 16 | press=$1 17 | 18 | sed -i "s/PRESSURE/${press}/g" in.lmp 19 | 20 | if [ -e ../cooling-npt-P-${press}/data.solid-P-${press} ]; then 21 | cp ../cooling-npt-P-${press}/data.solid-P-${press} . 22 | fi 23 | 24 | srun -n 84 lmp_fidis < in.lmp > lmplog & 25 | 26 | wait 27 | cd .. 28 | 29 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/runcool.sh: -------------------------------------------------------------------------------- 1 | for p in `seq 50 25 125`; do 2 | cp -r cooling-npt-template cooling-npt-P-$p 3 | cd cooling-npt-P-$p 4 | sed -i -e 's/HIGHT/1200/' -e "s/RANDOM/$RANDOM/" in.lmp 5 | #cp -r heating-npt-template heating-npt-P-$p 6 | #cd heating-npt-P-$p 7 | sbatch submit.sh $p 8 | cd .. 9 | done 10 | 11 | for p in `seq 150 25 275`; do 12 | cp -r cooling-npt-template cooling-npt-P-$p 13 | cd cooling-npt-P-$p 14 | sed -i -e 's/HIGHT/1000/' -e "s/RANDOM/$RANDOM/" in.lmp 15 | #cp -r heating-npt-template heating-npt-P-$p 16 | #cd heating-npt-P-$p 17 | sbatch submit.sh $p 18 | cd .. 19 | done 20 | 21 | for p in `seq 300 25 400`; do 22 | cp -r cooling-npt-template cooling-npt-P-$p 23 | cd cooling-npt-P-$p 24 | sed -i -e 's/HIGHT/700/' -e "s/RANDOM/$RANDOM/" in.lmp 25 | #cp -r heating-npt-template heating-npt-P-$p 26 | #cd heating-npt-P-$p 27 | sbatch submit.sh $p 28 | cd .. 29 | done 30 | 31 | 32 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/input/runheat.sh: -------------------------------------------------------------------------------- 1 | for p in `seq 50 25 125`; do 2 | if [ -e cooling-npt-P-$p/data.solid-P-$p ] && [ ! -e heating-npt-P-$p ] ; then 3 | cp -r heating-npt-template heating-npt-P-$p 4 | cd heating-npt-P-$p 5 | sed -i -e 's/HIGHT/1400/' -e "s/RANDOM/$RANDOM/" in.lmp 6 | sbatch submit.sh $p 7 | cd .. 8 | fi 9 | done 10 | 11 | for p in `seq 150 25 275`; do 12 | if [ -e cooling-npt-P-$p/data.solid-P-$p ] && [ ! -e heating-npt-P-$p ] ; then 13 | cp -r heating-npt-template heating-npt-P-$p 14 | cd heating-npt-P-$p 15 | sed -i -e 's/HIGHT/1200/' -e "s/RANDOM/$RANDOM/" in.lmp 16 | sbatch submit.sh $p 17 | cd .. 18 | fi 19 | done 20 | 21 | for p in `seq 300 25 400`; do 22 | if [ -e cooling-npt-P-$p/data.solid-P-$p ] && [ ! -e heating-npt-P-$p ] ; then 23 | cp -r heating-npt-template heating-npt-P-$p 24 | cd heating-npt-P-$p 25 | sed -i -e 's/HIGHT/1100/' -e "s/RANDOM/$RANDOM/" in.lmp 26 | sbatch submit.sh $p 27 | cd .. 28 | fi 29 | done 30 | 31 | 32 | -------------------------------------------------------------------------------- /pbe-nnp-cooling-heating-nst-1728/solid-structures.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BingqingCheng/MLP-highP-H/b9f6d9d0b077006109d7a1897328b127210afad4/pbe-nnp-cooling-heating-nst-1728/solid-structures.zip -------------------------------------------------------------------------------- /pbe-nnp-potential/README.md: -------------------------------------------------------------------------------- 1 | v2 is the newer, more refined version used for the simulations reported in the main text. 2 | -------------------------------------------------------------------------------- /pbe-nnp-potential/pbe-reference/H.cell: -------------------------------------------------------------------------------- 1 | %BLOCK LATTICE_CART 2 | 2.154433 0 0 3 | 0 2.154433 0 4 | 0 0 2.154433 5 | %ENDBLOCK LATTICE_CART 6 | 7 | #VARVOL=10 8 | 9 | %BLOCK POSITIONS_FRAC 10 | H 0.0 0.0 0.0 # H1 % NUM=1 11 | %ENDBLOCK POSITIONS_FRAC 12 | 13 | ##SPECIES=H 14 | ##NATOM=3-9 15 | ##FOCUS=1 16 | 17 | #SYMMOPS=2-4 18 | ##SGRANK=20 19 | #NFORM=1 20 | ##ADJGEN=0-1 21 | ##SLACK=0.25 22 | ##OVERLAP=0.1 23 | #MINSEP=1-3 AUTO 24 | #COMPACT 25 | ##SYSTEM={Rhom,Tric,Mono,Cubi,Hexa,Orth,Tetra} 26 | 27 | KPOINTS_MP_SPACING 0.03 28 | 29 | SYMMETRY_GENERATE 30 | SNAP_TO_SYMMETRY 31 | 32 | %BLOCK SPECIES_POT 33 | %ENDBLOCK SPECIES_POT 34 | 35 | %BLOCK EXTERNAL_PRESSURE 36 | 0 0 0 37 | 0 0 38 | 0 39 | %ENDBLOCK EXTERNAL_PRESSURE 40 | -------------------------------------------------------------------------------- /pbe-nnp-potential/pbe-reference/H.param: -------------------------------------------------------------------------------- 1 | #task : geometryoptimization 2 | xc_functional : PBE 3 | spin_polarized : false 4 | fix_occupancy : false 5 | metals_method : dm 6 | mixing_scheme : pulay 7 | max_scf_cycles : 1000 8 | cut_off_energy : 700 eV 9 | grid_scale : 2 10 | fine_grid_scale : 3 11 | opt_strategy : speed 12 | page_wvfns : 0 13 | num_dump_cycles : 0 14 | backup_interval : 0 15 | geom_method : LBFGS 16 | geom_max_iter : 20 17 | mix_history_length : 20 18 | finite_basis_corr : 0 19 | fixed_npw : true 20 | write_cell_structure : true 21 | write_checkpoint : none 22 | write_bib : false 23 | write_otfg : false 24 | #write_cst_esp : false # Requires Castep 17 and above 25 | #write_bands : false # Requires Castep 17 and above 26 | #write_geom : false # Requires Castep 17 and above 27 | #bs_write_eigenvalues : false 28 | calculate_stress : true 29 | -------------------------------------------------------------------------------- /pbe-nnp-potential/v1/input.nn: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # GENERAL NNP SETTINGS 3 | ############################################################################### 4 | number_of_elements 1 # Number of elements. 5 | elements H # Specification of elements. 6 | #atom_energy H -0.45890771 # Free atom reference energy (H). 7 | cutoff_type 2 # Cutoff type. 8 | scale_symmetry_functions # Scale all symmetry functions with min/max values. 9 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 10 | scale_min_short 0.0 # Minimum value for scaling. 11 | scale_max_short 1.0 # Maximum value for scaling. 12 | center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 13 | global_hidden_layers_short 3 # Number of hidden layers. 14 | global_nodes_short 20 20 20 # Number of nodes in each hidden layer. 15 | global_activation_short t t t l # Activation function for each hidden layer and output layer. 16 | #normalize_nodes # Normalize input of nodes. 17 | 18 | ############################################################################### 19 | # ADDITIONAL SETTINGS FOR TRAINING 20 | ############################################################################### 21 | epochs 50 # Number of training epochs. 22 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 23 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 24 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 25 | selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 26 | #memorize_symfunc_results # Keep symmetry function results in memory. 27 | random_seed 1210215 28 | test_fraction 0.1 # Fraction of structures kept for testing. 29 | use_short_forces # Use forces for training. 30 | force_weight 5.0 # Weight of force updates relative to energy updates. 31 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 32 | short_force_fraction 0.01 # Fraction of force updates per epoch. 33 | short_energy_error_threshold 1.00 # RMSE threshold for energy update candidates. 34 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 35 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 36 | #repeated_energy_update # After force update perform energy update for corresponding structure. 37 | #use_old_weights_short # Restart fitting with old weight parameters. 38 | weights_min -1.0 # Minimum value for initial random weights. 39 | weights_max 1.0 # Maximum value for initial random weights. 40 | #precondition_weights # Precondition weights with initial energies. 41 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 42 | write_trainpoints 5 # Write energy comparison. 43 | write_trainforces 5 # Write force comparison. 44 | write_weights_epoch # Write weights. 45 | #write_neuronstats 5 10 # Write neuron statistics. 46 | #write_trainlog # Write training log file. 47 | #################### 48 | # GRADIENT DESCENT # 49 | #################### 50 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 51 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 52 | ############################ 53 | # KALMAN FILTER (STANDARD) # 54 | ############################ 55 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 56 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 57 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 58 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 59 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 60 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 61 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 62 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 63 | ################################# 64 | # KALMAN FILTER (FADING MEMORY) # 65 | ################################# 66 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 67 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 68 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 69 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 70 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 71 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 72 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 73 | 74 | ############################################################################### 75 | # SYMMETRY FUNCTIONS 76 | ############################################################################### 77 | 78 | # Radial symmetry function (type 2): 79 | #symfunction_short 2 80 | 81 | # Narrow Angular symmetry function (type 3): 82 | #symfunction_short 3 83 | 84 | # Wide Angular symmetry function (type 9): 85 | #symfunction_short 9 86 | 87 | symfunction_short H 2 H 57.776 0.814 2.000 88 | symfunction_short H 2 H 34.647 1.051 3.000 89 | symfunction_short H 2 H 25.678 1.221 3.000 90 | symfunction_short H 2 H 5.078 2.746 5.000 91 | symfunction_short H 2 H 9.244 2.035 5.000 92 | symfunction_short H 2 H 19.489 1.402 4.000 93 | symfunction_short H 2 H 6.851 2.364 5.000 94 | symfunction_short H 2 H 14.444 1.628 4.000 95 | symfunction_short H 2 H 3.763 3.190 5.000 96 | symfunction_short H 2 H 49.892 0.876 2.500 97 | symfunction_short H 2 H 77.956 0.701 2.000 98 | symfunction_short H 2 H 1.435 5.165 6.000 99 | symfunction_short H 2 H 1.055 6.026 7.000 100 | symfunction_short H 2 H 42.820 0.946 2.000 101 | symfunction_short H 2 H 1.089 5.929 8.000 102 | symfunction_short H 2 H 2.613 3.828 6.000 103 | symfunction_short H 2 H 22.708 1.299 5.000 104 | symfunction_short H 2 H 0.807 6.887 8.000 105 | symfunction_short H 2 H 16.830 1.509 5.000 106 | symfunction_short H 2 H 1.470 5.104 8.000 107 | symfunction_short H 2 H 30.639 1.118 5.000 108 | symfunction_short H 2 H 1.984 4.394 8.000 109 | symfunction_short H 2 H 10.705 1.891 4.000 110 | symfunction_short H 2 H 12.473 1.752 5.000 111 | symfunction_short H 2 H 2.591 3.845 7.000 112 | symfunction_short H 2 H 4.716 2.850 7.000 113 | symfunction_short H 2 H 6.364 2.453 7.000 114 | symfunction_short H 2 H 3.495 3.310 7.000 115 | symfunction_short H 2 H 7.934 2.197 4.000 116 | symfunction_short H 3 H H 0.111 1.000 1.000 3.000 117 | symfunction_short H 3 H H 0.062 -1.000 1.000 4.000 118 | symfunction_short H 3 H H 0.062 1.000 1.000 4.000 119 | symfunction_short H 3 H H 0.062 1.000 16.000 4.000 120 | symfunction_short H 3 H H 0.040 1.000 4.000 5.000 121 | symfunction_short H 3 H H 0.040 -1.000 1.000 5.000 122 | symfunction_short H 3 H H 0.040 -1.000 4.000 5.000 123 | symfunction_short H 3 H H 0.016 1.000 1.000 8.000 124 | symfunction_short H 3 H H 0.016 -1.000 1.000 8.000 125 | symfunction_short H 3 H H 0.020 1.000 1.000 7.000 126 | symfunction_short H 3 H H 0.028 1.000 1.000 6.000 127 | symfunction_short H 3 H H 0.016 1.000 16.000 8.000 128 | symfunction_short H 3 H H 0.016 1.000 4.000 8.000 129 | symfunction_short H 3 H H 0.016 -1.000 16.000 8.000 130 | symfunction_short H 3 H H 0.028 1.000 16.000 6.000 131 | symfunction_short H 3 H H 0.028 -1.000 16.000 6.000 132 | symfunction_short H 3 H H 0.020 -1.000 1.000 7.000 133 | symfunction_short H 3 H H 0.016 -1.000 4.000 8.000 134 | symfunction_short H 3 H H 0.020 1.000 4.000 7.000 135 | -------------------------------------------------------------------------------- /pbe-nnp-potential/v1/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 0.0000000000000000E+00 1.2786864788554039E-01 2.0148701465623242E-04 3.1524761950806630E-03 17 | 1 2 0.0000000000000000E+00 1.5324159403424931E-01 2.6312649631626648E-05 1.2049201618322630E-03 18 | 1 3 0.0000000000000000E+00 1.8779883931284078E-01 2.4100609615632932E-06 4.1087787492401478E-04 19 | 1 4 0.0000000000000000E+00 1.8833496692166160E-01 1.1923536362419721E-04 3.0001964292893754E-03 20 | 1 5 0.0000000000000000E+00 3.5955730712772588E-01 1.4892814158897155E-02 2.6012376022955513E-02 21 | 1 6 0.0000000000000000E+00 3.5929588979511018E-01 1.8674770931646589E-03 1.2590160121393355E-02 22 | 1 7 0.0000000000000000E+00 7.9425620447436296E-01 2.1254143820593810E-01 1.1525862384997716E-01 23 | 1 8 0.0000000000000000E+00 8.7467201947800743E-01 1.7074128934272059E-01 1.1708692558764941E-01 24 | 1 9 0.0000000000000000E+00 7.4811605665701719E-01 1.5519435107662793E-01 7.1275316047969300E-02 25 | 1 10 0.0000000000000000E+00 6.7333285542477783E-01 1.0759055403395651E-01 6.3297413723034684E-02 26 | 1 11 3.5910379683328059E-05 9.7073274581664104E-01 5.0623959362231108E-01 1.2736879346446944E-01 27 | 1 12 1.4651415281849498E-07 1.2321718127446848E+00 5.6452836615588087E-01 1.8262446467122168E-01 28 | 1 13 8.4577697438719571E-13 1.4747184327154994E+00 4.5721468960237244E-01 2.0131653962487583E-01 29 | 1 14 2.1065196719838351E-21 1.3840249655512706E+00 3.1399515618091239E-01 1.9540171709333165E-01 30 | 1 15 8.6972539370641714E-35 1.1709787371985103E+00 2.2399339888890113E-01 1.3937389170540587E-01 31 | 1 16 6.8849742194674013E-55 9.8648969012214727E-01 1.9013342869196725E-01 8.6985029880464221E-02 32 | 1 17 1.9097564541503356E-84 7.1287053045711446E-01 7.0423033342822558E-02 6.1097607892459958E-02 33 | 1 18 3.9041233430555061E-127 5.7910474297282288E-01 7.7979762674756370E-03 3.0001123143202617E-02 34 | 1 19 1.9549728427461759E-02 3.8930917832271078E-01 2.0171598260484119E-01 5.1727433306469041E-02 35 | 1 20 2.2793198416896789E-02 1.4386575716282468E+00 7.6525110162075216E-01 1.4141446941085739E-01 36 | 1 21 4.7646427383803432E-02 5.6115606300904231E-01 3.5202359290322310E-01 8.5427371422089546E-02 37 | 1 22 5.7114363278535099E-02 2.5545080234003468E+00 1.3538612523590432E+00 2.5072471847758254E-01 38 | 1 23 2.4940663697200689E-03 2.7522145071418831E+00 1.4697299433055526E+00 3.2622023343195683E-01 39 | 1 24 7.8682802555547335E-06 2.5944753464285428E+00 1.3058387226565509E+00 3.6913521804174371E-01 40 | 1 25 3.8919161034755070E-10 2.4797469425290117E+00 9.2442605075510287E-01 3.6754562234387905E-01 41 | 1 26 9.2619930581806134E-02 8.1664587623323914E-01 5.0966407948897452E-01 9.9151195954948784E-02 42 | 1 27 1.8318498196390448E-01 1.9153034470475108E+00 1.2247793247301280E+00 2.7230852284979107E-01 43 | 1 28 2.7507711080804348E-01 3.0256562654161572E+00 1.7844962674328060E+00 4.5679177013995692E-01 44 | 1 29 2.3897224519634894E-01 3.5897251008363615E+00 1.8969495318285576E+00 4.3720752276638192E-01 45 | 1 30 0.0000000000000000E+00 5.8484982044182780E-03 3.1067262157701329E-05 9.1950833931776768E-05 46 | 1 31 0.0000000000000000E+00 1.8477063440026437E-02 8.7325374281955700E-04 9.3136120974875950E-04 47 | 1 32 0.0000000000000000E+00 3.7336807040497737E-02 2.4086044873246389E-03 2.3750767572766765E-03 48 | 1 33 0.0000000000000000E+00 7.0642814078505202E-03 2.6343707911330927E-04 2.7035108042627745E-04 49 | 1 34 1.5929753547141851E-13 8.0731305223699465E-02 1.1074371843129496E-02 7.3575933441624294E-03 50 | 1 35 5.6325947537878221E-16 2.3003444431839482E-02 1.5884397842508863E-03 1.2498264882277600E-03 51 | 1 36 5.3981986786993238E-13 9.3410838688374118E-02 1.5978972418477580E-02 9.9890378669505991E-03 52 | 1 37 1.9700371500545024E-06 6.8969832554816746E-01 1.5443464421476363E-01 8.0162174550083384E-02 53 | 1 38 6.1657159989202514E-16 2.4749528542932317E-02 1.6229878174756835E-03 1.2870123862469087E-03 54 | 1 39 6.2262684617804945E-07 1.0573409296829014E-01 2.4663201317918649E-02 1.2324985639637898E-02 55 | 1 40 3.0303734433414090E-05 8.0480865506783472E-01 1.9705844281684351E-01 9.4076893600784375E-02 56 | 1 41 2.9602459953219584E-04 1.9365314536570741E+00 5.2281410288197383E-01 2.4440723530575639E-01 57 | 1 42 2.3033250210999353E-04 1.0600999125841739E+00 2.9064562025332846E-01 1.3628090064970649E-01 58 | 1 43 4.4156751616116266E-04 1.8181725546180594E+00 5.0504793045530760E-01 2.2653438009689736E-01 59 | 1 44 3.7271975785887314E-03 4.3394225551846519E+00 1.3292398624644119E+00 5.8667197578105734E-01 60 | 1 45 8.0581351847887373E-06 4.0158809640046172E-01 9.7520506174563842E-02 4.6421184682890214E-02 61 | 1 46 2.8285538602087893E-03 2.4132319079528153E+00 7.5095290878482479E-01 3.3351584311932420E-01 62 | 1 47 1.3040678584439959E-09 9.3788161160613240E-02 1.9338171364423416E-02 1.0081020289092305E-02 63 | 1 48 1.1896132844293479E-03 8.2190114793389346E-01 2.5033325307694210E-01 1.1236226432368290E-01 64 | -------------------------------------------------------------------------------- /pbe-nnp-potential/v2/input.nn: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # GENERAL NNP SETTINGS 3 | ############################################################################### 4 | number_of_elements 1 # Number of elements. 5 | elements H # Specification of elements. 6 | #atom_energy H -0.45890771 # Free atom reference energy (H). 7 | cutoff_type 2 # Cutoff type. 8 | scale_symmetry_functions # Scale all symmetry functions with min/max values. 9 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 10 | scale_min_short 0.0 # Minimum value for scaling. 11 | scale_max_short 1.0 # Maximum value for scaling. 12 | center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 13 | global_hidden_layers_short 3 # Number of hidden layers. 14 | global_nodes_short 20 20 10 # Number of nodes in each hidden layer. 15 | global_activation_short t t t l # Activation function for each hidden layer and output layer. 16 | #normalize_nodes # Normalize input of nodes. 17 | 18 | ############################################################################### 19 | # ADDITIONAL SETTINGS FOR TRAINING 20 | ############################################################################### 21 | epochs 50 # Number of training epochs. 22 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 23 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 24 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 25 | selection_mode 0 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 26 | #memorize_symfunc_results # Keep symmetry function results in memory. 27 | random_seed 12025 28 | test_fraction 0.1 # Fraction of structures kept for testing. 29 | use_short_forces # Use forces for training. 30 | force_weight 5.0 # Weight of force updates relative to energy updates. 31 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 32 | short_force_fraction 0.01 # Fraction of force updates per epoch. 33 | short_energy_error_threshold 0.50 # RMSE threshold for energy update candidates. 34 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 35 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 36 | #repeated_energy_update # After force update perform energy update for corresponding structure. 37 | use_old_weights_short # Restart fitting with old weight parameters. 38 | weights_min -1.0 # Minimum value for initial random weights. 39 | weights_max 1.0 # Maximum value for initial random weights. 40 | #precondition_weights # Precondition weights with initial energies. 41 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 42 | write_trainpoints 5 # Write energy comparison. 43 | write_trainforces 5 # Write force comparison. 44 | write_weights_epoch # Write weights. 45 | #write_neuronstats 5 10 # Write neuron statistics. 46 | #write_trainlog # Write training log file. 47 | #################### 48 | # GRADIENT DESCENT # 49 | #################### 50 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 51 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 52 | ############################ 53 | # KALMAN FILTER (STANDARD) # 54 | ############################ 55 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 56 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 57 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 58 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 59 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 60 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 61 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 62 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 63 | ################################# 64 | # KALMAN FILTER (FADING MEMORY) # 65 | ################################# 66 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 67 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 68 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 69 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 70 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 71 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 72 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 73 | 74 | ############################################################################### 75 | # SYMMETRY FUNCTIONS 76 | ############################################################################### 77 | 78 | # Radial symmetry function (type 2): 79 | #symfunction_short 2 80 | 81 | # Narrow Angular symmetry function (type 3): 82 | #symfunction_short 3 83 | 84 | # Wide Angular symmetry function (type 9): 85 | #symfunction_short 9 86 | # 87 | # 88 | symfunction_short H 2 H 34.647 1.051 3.000 89 | symfunction_short H 2 H 49.892 0.876 2.500 90 | symfunction_short H 2 H 25.678 1.221 3.000 91 | symfunction_short H 2 H 63.078 0.779 3.000 92 | symfunction_short H 2 H 16.830 1.509 5.000 93 | symfunction_short H 2 H 12.473 1.752 5.000 94 | symfunction_short H 2 H 19.489 1.402 4.000 95 | symfunction_short H 2 H 22.708 1.299 5.000 96 | symfunction_short H 2 H 14.444 1.628 4.000 97 | symfunction_short H 2 H 36.977 1.018 2.500 98 | symfunction_short H 2 H 1.470 5.104 8.000 99 | symfunction_short H 2 H 9.244 2.035 5.000 100 | symfunction_short H 2 H 1.984 4.394 8.000 101 | symfunction_short H 2 H 0.697 7.411 10.000 102 | symfunction_short H 2 H 0.517 8.609 10.000 103 | symfunction_short H 2 H 2.676 3.783 8.000 104 | symfunction_short H 2 H 0.941 6.380 10.000 105 | symfunction_short H 2 H 2.311 4.071 10.000 106 | symfunction_short H 2 H 6.364 2.453 7.000 107 | symfunction_short H 2 H 3.118 3.505 10.000 108 | symfunction_short H 2 H 1.269 5.493 10.000 109 | symfunction_short H 2 H 10.705 1.891 4.000 110 | symfunction_short H 2 H 3.611 3.257 8.000 111 | symfunction_short H 2 H 4.207 3.017 10.000 112 | symfunction_short H 2 H 4.872 2.804 8.000 113 | symfunction_short H 2 H 5.677 2.597 10.000 114 | symfunction_short H 2 H 1.713 4.729 10.000 115 | symfunction_short H 2 H 0.807 6.887 8.000 116 | symfunction_short H 9 H H 0.160 -1.000 1.000 2.500 117 | symfunction_short H 2 H 7.660 2.236 10.000 118 | symfunction_short H 9 H H 0.111 1.000 1.000 3.000 119 | symfunction_short H 2 H 67.319 0.754 2.500 120 | symfunction_short H 9 H H 0.111 -1.000 1.000 3.000 121 | symfunction_short H 9 H H 0.111 -1.000 16.000 3.000 122 | symfunction_short H 9 H H 0.062 -1.000 1.000 4.000 123 | symfunction_short H 9 H H 0.062 1.000 1.000 4.000 124 | symfunction_short H 9 H H 0.062 -1.000 16.000 4.000 125 | symfunction_short H 9 H H 0.111 -1.000 4.000 3.000 126 | symfunction_short H 9 H H 0.040 -1.000 1.000 5.000 127 | symfunction_short H 9 H H 0.040 1.000 1.000 5.000 128 | symfunction_short H 9 H H 0.062 1.000 4.000 4.000 129 | symfunction_short H 9 H H 0.062 1.000 16.000 4.000 130 | symfunction_short H 9 H H 0.028 -1.000 1.000 6.000 131 | symfunction_short H 9 H H 0.062 -1.000 4.000 4.000 132 | symfunction_short H 9 H H 0.028 1.000 1.000 6.000 133 | symfunction_short H 9 H H 0.040 -1.000 4.000 5.000 134 | symfunction_short H 9 H H 0.020 -1.000 1.000 7.000 135 | symfunction_short H 9 H H 0.040 -1.000 16.000 5.000 136 | symfunction_short H 9 H H 0.020 1.000 1.000 7.000 137 | symfunction_short H 9 H H 0.020 -1.000 16.000 7.000 138 | symfunction_short H 9 H H 0.040 1.000 16.000 5.000 139 | symfunction_short H 9 H H 0.028 -1.000 16.000 6.000 140 | symfunction_short H 9 H H 0.028 1.000 4.000 6.000 141 | symfunction_short H 9 H H 0.020 -1.000 4.000 7.000 142 | symfunction_short H 9 H H 0.020 1.000 4.000 7.000 143 | symfunction_short H 9 H H 0.020 1.000 16.000 7.000 144 | symfunction_short H 9 H H 0.040 1.000 4.000 5.000 145 | symfunction_short H 9 H H 0.179 -1.000 1.000 5.000 146 | symfunction_short H 9 H H 0.068 1.000 1.000 7.000 147 | symfunction_short H 3 H H 0.016 1.000 1.000 8.000 148 | symfunction_short H 9 H H 0.068 -1.000 1.000 7.000 149 | symfunction_short H 3 H H 0.016 1.000 16.000 8.000 150 | symfunction_short H 3 H H 0.028 1.000 1.000 6.000 151 | symfunction_short H 3 H H 0.020 1.000 4.000 7.000 152 | -------------------------------------------------------------------------------- /pbe-nnp-potential/v2/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 0.0000000000000000E+00 2.5772856893554319E-01 1.1082741929516208E-03 7.8591954780583544E-03 17 | 1 2 0.0000000000000000E+00 1.8841611202025066E-01 1.3964418531350919E-04 3.5122645824120853E-03 18 | 1 3 0.0000000000000000E+00 2.2093567613105006E-01 1.9131544157244370E-05 1.2790333257117284E-03 19 | 1 4 0.0000000000000000E+00 3.5955730712772588E-01 2.1673642088280355E-02 3.2508390463681272E-02 20 | 1 5 0.0000000000000000E+00 3.5929588979511018E-01 2.5996689310169509E-03 1.2948142631031875E-02 21 | 1 6 0.0000000000000000E+00 2.4864539970870128E-01 3.7187446433503231E-05 1.9777272507283967E-03 22 | 1 7 0.0000000000000000E+00 9.1370552956840267E-01 1.5444986665918758E-01 1.2437621241395309E-01 23 | 1 8 0.0000000000000000E+00 7.4811605665701719E-01 1.4591079651072239E-01 7.2951054361532500E-02 24 | 1 9 0.0000000000000000E+00 6.7333285542477783E-01 1.1201359528405232E-01 6.4614465043590724E-02 25 | 1 10 2.1065196719838351E-21 1.5063379126278071E+00 2.8081032316896953E-01 2.0693259665323069E-01 26 | 1 11 8.6972539370641714E-35 1.1959070131058456E+00 2.0675592641238444E-01 1.4916331218013917E-01 27 | 1 12 6.8849742194674013E-55 9.8648969012214727E-01 1.8312580334830220E-01 8.0136361261278086E-02 28 | 1 13 1.9097564541503356E-84 7.1287053045711446E-01 8.4441609933956122E-02 7.4226435762823936E-02 29 | 1 14 3.8919161034755070E-10 3.0650126879270458E+00 8.6459973544363478E-01 3.8018829666868587E-01 30 | 1 15 9.2619930581806134E-02 9.2276494710527446E-01 5.0026552833035909E-01 1.0222809808912736E-01 31 | 1 16 2.7507711080804348E-01 3.2637298177549106E+00 1.7157126342433082E+00 4.8394223125871588E-01 32 | 1 17 2.3897224519634894E-01 3.8350802443816194E+00 1.8427778241253647E+00 4.7119921504734541E-01 33 | 1 18 7.7598723342890599E-02 3.9457798999266807E+00 1.9266684158704539E+00 3.4928933854921845E-01 34 | 1 19 2.4168276766085468E-03 3.8410721116774735E+00 1.8888998927323468E+00 4.0585177214434348E-01 35 | 1 20 8.5273487568006248E-06 3.9679263629032695E+00 1.5063374660128226E+00 4.5547356593015503E-01 36 | 1 21 1.7574037745037652E-01 1.7100102651357916E+00 9.6549664566193683E-01 2.2667214671302074E-01 37 | 1 22 4.3387341020277759E-01 3.9700302256208859E+00 2.2470851469366000E+00 5.1637930981316660E-01 38 | 1 23 6.5305767253395575E-01 6.2415583317020094E+00 3.4336867447687092E+00 7.1594689216971419E-01 39 | 1 24 6.0415621831100041E-01 7.0133587243352240E+00 3.9678034392114561E+00 9.7042278108852953E-01 40 | 1 25 4.9803783790146117E-01 6.9101934078101905E+00 3.5618479950491393E+00 1.0139525297096224E+00 41 | 1 26 2.9824206953046062E-01 6.2489371408587848E+00 3.0073344501294277E+00 6.6064864747953123E-01 42 | 1 27 3.4955303424036785E-02 5.1986278234357650E+00 2.7531307800542555E+00 5.0284415428463913E-01 43 | 1 28 1.9011422727804585E-04 4.7192347742227172E+00 2.2662433090075664E+00 5.6971284644285092E-01 44 | 1 29 1.1191921646494595E-07 4.8264480450080240E+00 1.5192160946916058E+00 5.6166220338080719E-01 45 | 1 30 5.0045919062327138E-14 3.4232384677653016E+00 8.3725204934333353E-01 4.6368098397362406E-01 46 | 1 31 1.9700371500545024E-06 6.8969832554816746E-01 1.4322579504717267E-01 8.9993220776408353E-02 47 | 1 32 2.3033250210999353E-04 1.0600999125841739E+00 2.7237379337093265E-01 1.5315440455682311E-01 48 | 1 33 3.7271975785887314E-03 4.3394225551846519E+00 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number_of_elements 1 # Number of elements. 14 | elements H # Specification of elements. 15 | #atom_energy H -0.45890771 # Free atom reference energy (H). 16 | cutoff_type 2 # Cutoff type. 17 | #scale_symmetry_functions # Scale all symmetry functions with min/max values. 18 | #scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. 19 | scale_min_short 0.0 # Minimum value for scaling. 20 | scale_max_short 1.0 # Maximum value for scaling. 21 | #center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. 22 | global_hidden_layers_short 2 # Number of hidden layers. 23 | global_nodes_short 20 20 # Number of nodes in each hidden layer. 24 | global_activation_short t t l # Activation function for each hidden layer and output layer. 25 | #normalize_nodes # Normalize input of nodes. 26 | 27 | ############################################################################### 28 | # ADDITIONAL SETTINGS FOR TRAINING 29 | ############################################################################### 30 | epochs 25 # Number of training epochs. 31 | updater_type 1 # Weight update method (0 = Gradient Descent, 1 = Kalman filter). 32 | parallel_mode 4 # Training parallelization used (0 = Serial, 1 = Multi-stream, 2 = MS with PMO). 33 | update_strategy 0 # Update strategy (0 = Combined, 1 = Per-element). 34 | selection_mode 2 # Update candidate selection mode (0 = Random, 1 = Sort, 2 = Threshold). 35 | memorize_symfunc_results # Keep symmetry function results in memory. 36 | random_seed 5 37 | test_fraction 0.1 # Fraction of structures kept for testing. 38 | use_short_forces # Use forces for training. 39 | force_weight 2.0 # Weight of force updates relative to energy updates. 40 | short_energy_fraction 1.000 # Fraction of energy updates per epoch. 41 | short_force_fraction 0.01 # Fraction of force updates per epoch. 42 | short_energy_error_threshold 1.00 # RMSE threshold for energy update candidates. 43 | short_force_error_threshold 1.00 # RMSE threshold for force update candidates. 44 | rmse_threshold_trials 3 # Maximum number of RMSE threshold trials. 45 | #repeated_energy_update # After force update perform energy update for corresponding structure. 46 | #use_old_weights_short # Restart fitting with old weight parameters. 47 | weights_min -1.0 # Minimum value for initial random weights. 48 | weights_max 1.0 # Maximum value for initial random weights. 49 | #precondition_weights # Precondition weights with initial energies. 50 | #nguyen_widrow_weights_short # Initialize neural network weights according to Nguyen-Widrow scheme. 51 | write_trainpoints 25 # Write energy comparison. 52 | write_trainforces 25 # Write force comparison. 53 | write_weights_epoch # Write weights. 54 | write_neuronstats 5 10 # Write neuron statistics. 55 | write_trainlog # Write training log file. 56 | #################### 57 | # GRADIENT DESCENT # 58 | #################### 59 | gradient_type 0 # Gradient descent type (0 = Fixed step size). 60 | gradient_eta 1.0E-4 # Gradient descent parameter eta (fixed step size). 61 | ############################ 62 | # KALMAN FILTER (STANDARD) # 63 | ############################ 64 | kalman_type 0 # Kalman filter type (0 = Standard, 1 = Fading memory). 65 | kalman_epsilon 1.0E-2 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 66 | kalman_q0 0.01 # General Kalman filter parameter q0 ("large"). 67 | kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 68 | kalman_qmin 1.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 69 | kalman_eta 0.01 # Standard Kalman filter parameter eta (0.001-1.0). 70 | kalman_etatau 2.302 # Standard Kalman filter parameter etatau (2.302 => 1 order of magnitude per epoch). 71 | kalman_etamax 1.0 # Standard Kalman filter parameter etamax (1.0+). 72 | ################################# 73 | # KALMAN FILTER (FADING MEMORY) # 74 | ################################# 75 | #kalman_type 1 # Kalman filter type (0 = Standard, 1 = Fading memory). 76 | #kalman_epsilon 1.0E-1 # General Kalman filter parameter epsilon (sigmoidal: 0.01, linear: 0.001). 77 | #kalman_q0 0.00 # General Kalman filter parameter q0 ("large"). 78 | #kalman_qtau 2.302 # General Kalman filter parameter qtau (2.302 => 1 order of magnitude per epoch). 79 | #kalman_qmin 0.0E-6 # General Kalman filter parameter qmin (typ. 1.0E-6). 80 | #kalman_lambda_short 0.96000 # Fading memory Kalman filter parameter lambda (forgetting factor 0.95-0.99). 81 | #kalman_nue_short 0.99950 # Fading memory Kalman filter parameter nu (0.99-0.9995). 82 | 83 | ############################################################################### 84 | # SYMMETRY FUNCTIONS 85 | ############################################################################### 86 | 87 | # Radial symmetry function (type 2): 88 | #symfunction_short 2 89 | 90 | # Narrow Angular symmetry function (type 3): 91 | #symfunction_short 3 92 | 93 | # Wide Angular symmetry function (type 9): 94 | #symfunction_short 9 95 | 96 | symfunction_short H 2 H 38.7368 0.9940 6.0000 97 | symfunction_short H 2 H 10.1773 0.0000 4.0000 98 | symfunction_short H 2 H 16.8296 1.5090 5.0000 99 | symfunction_short H 2 H 26.2963 1.2070 4.0000 100 | symfunction_short H 2 H 6.4196 2.4430 6.0000 101 | symfunction_short H 3 H H 0.8000 -1.0000 1.0000 5.0000 102 | symfunction_short H 2 H 2.0671 4.3040 5.0000 103 | symfunction_short H 3 H H 0.8000 1.0000 16.0000 5.0000 104 | symfunction_short H 3 H H 0.5089 -1.0000 4.0000 4.0000 105 | symfunction_short H 2 H 47.8741 0.8940 4.0000 106 | symfunction_short H 2 H 3.2298 3.4440 4.0000 107 | symfunction_short H 2 H 11.6872 1.8100 6.0000 108 | symfunction_short H 3 H H 0.0843 -1.0000 16.0000 4.0000 109 | symfunction_short H 3 H H 2.6516 1.0000 1.0000 5.0000 110 | symfunction_short H 2 H 18.5284 0.0000 4.0000 111 | symfunction_short H 2 H 7.9338 2.1970 4.0000 112 | symfunction_short H 3 H H 1.4565 -1.0000 4.0000 5.0000 113 | symfunction_short H 3 H H 1.9652 1.0000 16.0000 5.0000 114 | symfunction_short H 2 H 14.4440 1.6280 4.0000 115 | symfunction_short H 2 H 19.4891 1.4020 4.0000 116 | symfunction_short H 3 H H 0.6866 -1.0000 16.0000 4.0000 117 | symfunction_short H 2 H 1.4355 5.1650 6.0000 118 | symfunction_short H 2 H 30.6394 1.1180 5.0000 119 | symfunction_short H 3 H H 0.2795 1.0000 16.0000 4.0000 120 | symfunction_short H 2 H 2.7891 3.7060 5.0000 121 | symfunction_short H 3 H H 0.0400 -1.0000 16.0000 5.0000 122 | symfunction_short H 2 H 55.7810 0.8290 5.0000 123 | symfunction_short H 3 H H 2.6516 1.0000 4.0000 5.0000 124 | symfunction_short H 2 H 5.0776 2.7460 5.0000 125 | symfunction_short H 3 H H 0.9264 -1.0000 4.0000 4.0000 126 | symfunction_short H 3 H H 1.3647 1.0000 16.0000 6.0000 127 | symfunction_short H 2 H 35.4811 1.0390 4.0000 128 | symfunction_short H 3 H H 0.3771 -1.0000 16.0000 4.0000 129 | symfunction_short H 2 H 9.2442 2.0350 5.0000 130 | symfunction_short H 3 H H 1.2500 -1.0000 1.0000 4.0000 131 | symfunction_short H 2 H 0.5929 0.0000 5.0000 132 | symfunction_short H 2 H 75.2644 0.7130 5.0000 133 | symfunction_short H 2 H 1.9368 4.4470 6.0000 134 | symfunction_short H 2 H 15.7694 1.5580 6.0000 135 | symfunction_short H 3 H H 0.5089 1.0000 4.0000 4.0000 136 | symfunction_short H 3 H H 0.9264 -1.0000 16.0000 4.0000 137 | symfunction_short H 2 H 22.7079 1.2990 5.0000 138 | symfunction_short H 2 H 41.3413 0.9630 5.0000 139 | symfunction_short H 2 H 6.8512 2.3640 5.0000 140 | symfunction_short H 3 H H 0.5929 1.0000 16.0000 5.0000 141 | symfunction_short H 3 H H 0.2072 -1.0000 4.0000 4.0000 142 | symfunction_short H 3 H H 1.9652 1.0000 4.0000 5.0000 143 | symfunction_short H 2 H 3.5261 3.2960 6.0000 144 | symfunction_short H 2 H 12.4730 1.7520 5.0000 145 | symfunction_short H 3 H H 0.1326 -1.0000 16.0000 5.0000 146 | symfunction_short H 2 H 52.2669 0.8560 6.0000 147 | symfunction_short H 3 H H 1.3647 -1.0000 4.0000 6.0000 148 | symfunction_short H 3 H H 0.9264 1.0000 16.0000 4.0000 149 | symfunction_short H 2 H 4.7578 2.8370 6.0000 150 | symfunction_short H 2 H 70.5229 0.7370 6.0000 151 | symfunction_short H 3 H H 0.3771 -1.0000 1.0000 4.0000 152 | symfunction_short H 2 H 28.7092 1.1550 6.0000 153 | symfunction_short H 2 H 2.6133 3.8280 6.0000 154 | symfunction_short H 3 H H 2.4845 1.0000 1.0000 6.0000 155 | symfunction_short H 3 H H 0.2072 -1.0000 16.0000 4.0000 156 | symfunction_short H 3 H H 0.1535 1.0000 16.0000 4.0000 157 | symfunction_short H 2 H 21.2774 1.3420 6.0000 158 | symfunction_short H 3 H H 0.6866 -1.0000 4.0000 4.0000 159 | symfunction_short H 3 H H 1.8414 1.0000 16.0000 6.0000 160 | 161 | -------------------------------------------------------------------------------- /vmc-nnp-potential/scaling.data: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Symmetry function scaling data. 3 | ################################################################################ 4 | # Col Name Description 5 | ################################################################################ 6 | # 1 e_index Element index. 7 | # 2 sf_index Symmetry function index. 8 | # 3 sf_min Symmetry function minimum. 9 | # 4 sf_max Symmetry function maximum. 10 | # 5 sf_mean Symmetry function mean. 11 | # 6 sf_sigma Symmetry function sigma. 12 | ######################################################################################################################### 13 | # 1 2 3 4 5 6 14 | # e_index sf_index sf_min sf_max sf_mean sf_sigma 15 | ######################################################################################################################### 16 | 1 1 2.9688498708365843E-08 1.3330328347640785E-01 5.4998280645225155E-02 2.0086568970400343E-02 17 | 1 2 4.2177692108572335E-12 5.9791164704632260E-01 1.2806660862764108E-01 8.0155943277853997E-02 18 | 1 3 2.4006957430383080E-65 3.3266149222590420E-03 1.1712781675202007E-07 7.9542144304493595E-06 19 | 1 4 1.2564647086839161E-31 4.8307648588561219E-01 1.1029073138853877E-01 6.2736854541097120E-02 20 | 1 5 1.5343574577738687E-115 7.9056640262152713E-05 5.4644420611086442E-10 1.3946830094991827E-07 21 | 1 6 1.1582598937358718E-49 4.5879414672651553E-01 1.0084047086884232E-01 7.0590695212115098E-02 22 | 1 7 2.6243305011726404E-76 4.3664522670068168E-01 4.5750349887353332E-02 6.3985826626755990E-02 23 | 1 8 6.0885324958352034E-115 2.5510231665877098E-01 8.4757964241114880E-03 2.8705152662688953E-02 24 | 1 9 3.1610999017030293E-170 2.7613835473954951E-01 8.6775063574762135E-04 9.7105477357799265E-03 25 | 1 10 1.0619647239577898E-05 2.7105391098046705E-01 7.4433265490396902E-02 2.8824205467546091E-02 26 | 1 11 4.0940839848928236E-03 1.8057818459141725E-01 9.9674474833791507E-02 2.3247323461075935E-02 27 | 1 12 2.9613706678806619E-03 4.8079378238366405E-01 2.4970011393498226E-01 6.8765619361559782E-02 28 | 1 13 3.6158396681069808E-06 1.0638969058930783E+00 3.8428959410525970E-01 1.6327033760248277E-01 29 | 1 14 7.0418274644441424E-08 1.1333669297371769E+00 2.8793526669825931E-01 1.5238582990498378E-01 30 | 1 15 7.8087669296307599E-14 9.5101691346412864E-01 1.8564667550754083E-01 1.3003747929143317E-01 31 | 1 16 1.8192411743857230E-23 7.9407558697546188E-01 1.4754058555244570E-01 1.0290362096247503E-01 32 | 1 17 3.0408655309821999E-38 6.4809648344150883E-01 1.4554660348076948E-01 8.0316346312501577E-02 33 | 1 18 2.5199650392461007E-60 4.9720194014049290E-01 9.4015431074584530E-02 9.0420300772976497E-02 34 | 1 19 1.2998459489798217E-92 4.4241779830515082E-01 2.6063026117733909E-02 5.4307924848541335E-02 35 | 1 20 5.4428167499079272E-139 2.9876860862589244E-01 3.2415043225280235E-03 1.9246844177113764E-02 36 | 1 21 5.4806649122035181E-205 3.1854018385747229E-01 3.0044916336584320E-04 6.1521017359889895E-03 37 | 1 22 4.5815619361507372E-298 3.3010570490069463E-01 2.6171098544772173E-05 1.8263239832214740E-03 38 | 1 23 2.1228091075623436E-02 2.7668404515157285E-01 1.5388913056327114E-01 3.5590321050295949E-02 39 | 1 24 4.7420000309323106E-02 6.6794069997786876E-01 3.7307873751944803E-01 7.9117560440823451E-02 40 | 1 25 2.5687619638859367E-02 1.1063471158412221E+00 6.2017214795683995E-01 1.4850999864919304E-01 41 | 1 26 1.7807871504639606E-03 1.6153988129426777E+00 7.5284634519930360E-01 2.3478967486771612E-01 42 | 1 27 4.1200167021593989E-05 1.6829433251595407E+00 6.7208458760168943E-01 2.6651971433146909E-01 43 | 1 28 5.5414298207484993E-08 1.6838422923800382E+00 4.6370699303877078E-01 2.2914196247012980E-01 44 | 1 29 1.6468733997760233E-20 1.0198285146706478E+00 1.8447444065725305E-01 1.3694357711875937E-01 45 | 1 30 4.8761922507899182E-34 7.2458393332769944E-01 1.7341382727776028E-01 9.4399370637167884E-02 46 | 1 31 2.7077133871523426E-54 5.6622178244654564E-01 1.2609784620080222E-01 1.0338405515978598E-01 47 | 1 32 4.5146112798405390E-84 5.3166110181972615E-01 4.1893832731881020E-02 7.1936770039491685E-02 48 | 1 33 4.7226435674078945E-127 3.1863994052618466E-01 5.8504470108667588E-03 2.6699477951704562E-02 49 | 1 34 3.1785987806447766E-188 3.3573880705879922E-01 5.4352182346179229E-04 8.5147987208488481E-03 50 | 1 35 1.4587091537583024E-274 3.4857616994787727E-01 4.8150199571951661E-05 2.5388889683544994E-03 51 | 1 36 0.0000000000000000E+00 1.3555347119400549E-03 3.6211538476777476E-06 1.4778346761596520E-05 52 | 1 37 0.0000000000000000E+00 1.4083579466269130E-03 3.1730017797005334E-05 3.5810728236193283E-05 53 | 1 38 0.0000000000000000E+00 7.2139591916777282E-04 5.0485924317818516E-06 1.0003989155239698E-05 54 | 1 39 0.0000000000000000E+00 3.8938142961171009E-04 5.4085881889493847E-07 2.9894415956025322E-06 55 | 1 40 0.0000000000000000E+00 6.3878615372245308E-04 5.2219150031752276E-06 8.3262632854160041E-06 56 | 1 41 0.0000000000000000E+00 9.0109550357557195E-04 4.2992220844433281E-06 9.5598396399258509E-06 57 | 1 42 0.0000000000000000E+00 7.1030030438731155E-05 4.4324275803407990E-08 3.8688250015798271E-07 58 | 1 43 0.0000000000000000E+00 7.2466993554742148E-05 8.8454747888769982E-08 4.1898321303063191E-07 59 | 1 44 0.0000000000000000E+00 7.3884100506775466E-04 1.2378274834430599E-06 4.2250105322650687E-06 60 | 1 45 0.0000000000000000E+00 2.2848736584137155E-05 1.0591216559367753E-08 8.9564607782379146E-08 61 | 1 46 0.0000000000000000E+00 4.3078072472043977E-06 6.6261486886085156E-10 1.3924851773761680E-08 62 | 1 47 0.0000000000000000E+00 5.5019822636038758E-06 7.9721590728959935E-10 1.4578689750549745E-08 63 | 1 48 0.0000000000000000E+00 4.9549634277124926E-07 3.4236342364240657E-11 1.3577287313324616E-09 64 | 1 49 0.0000000000000000E+00 2.1907028305783108E-05 2.4090105024481063E-09 4.1826386683040246E-08 65 | 1 50 0.0000000000000000E+00 9.4922433944136104E-06 6.9343706236154447E-10 2.3213405451816434E-08 66 | 1 51 3.0196591137080808E-18 7.6501557133235943E-03 1.4053694289031769E-04 2.3068247335897171E-04 67 | 1 52 8.6146839153867392E-20 2.9204613698187126E-03 2.4787754270293622E-05 5.4748379957230817E-05 68 | 1 53 2.0171601670004260E-18 2.3147209406249478E-04 4.3313807339791900E-07 1.2012527330059282E-06 69 | 1 54 2.4292619748571447E-20 1.8416297464526283E-04 1.2935097229291295E-07 8.3211348529264453E-07 70 | 1 55 8.9387767457508200E-22 7.8676864348151108E-05 3.4283461662420020E-08 2.1972956610433107E-07 71 | 1 56 5.8047145538895774E-35 4.7525227289995917E-07 1.7766236989729589E-11 9.7667514339825073E-10 72 | 1 57 7.1918834783165308E-39 6.9537892814357404E-07 1.1310440311868529E-11 1.0835044598655892E-09 73 | 1 58 1.6469205523391053E-40 1.8158834831606716E-07 1.3069024151335231E-12 2.1559950024975644E-10 74 | 1 59 8.3478928513951922E-50 2.7210332634763483E-08 3.1723616039466053E-13 4.8361829016794879E-11 75 | 1 60 3.0306881211218335E-50 1.9451382059457083E-08 1.4680675002412226E-13 2.5659953612250723E-11 76 | 1 61 8.4498846987056394E-32 1.2270222057325745E-06 6.8728831628495082E-11 2.6459226589986910E-09 77 | 1 62 6.3373350245125815E-29 5.9682814874706602E-06 2.1249993742102495E-10 9.0333460239648451E-09 78 | 1 63 6.8382565537696602E-37 4.9786708996744183E-07 4.8850096868257160E-12 6.1819275677875738E-10 79 | 1 64 2.7767636611712372E-45 9.3485426692877917E-08 1.3298537973997382E-12 1.7408004133911231E-10 80 | --------------------------------------------------------------------------------