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Merge pull request #101 from singraber/check-forces
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New tool to check analytic vs. numeric forces
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@singraber
singraber authored Apr 12, 2021
2 parents ca9558d + 7457aee commit 68425bc
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168 changes: 168 additions & 0 deletions examples/nnp-checkf/H2O_RPBE-D3/input.data
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128 changes: 128 additions & 0 deletions examples/nnp-checkf/H2O_RPBE-D3/input.nn
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###############################################################################
# HDNNP for water H2O
###############################################################################
# Length unit : Bohr
# Energy unit : Ha
# Reference method: RPBE-D3
###############################################################################

###############################################################################
# DATA SET NORMALIZATION
###############################################################################
# This section was automatically added by nnp-norm.
mean_energy -2.5521343547039809E+01
conv_energy 2.4265748255366972E+02
conv_length 5.8038448995319847E+00
###############################################################################

###############################################################################
# GENERAL NNP SETTINGS
###############################################################################
# These keywords are (almost) always required.
number_of_elements 2 # Number of elements.
elements H O # Specification of elements.
#atom_energy H -0.45890771 # Free atom reference energy (H).
#atom_energy O -74.94518524 # Free atom reference energy (O).
cutoff_type 2 # Cutoff type.
scale_symmetry_functions # Scale all symmetry functions with min/max values.
#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma.
scale_min_short 0.0 # Minimum value for scaling.
scale_max_short 1.0 # Maximum value for scaling.
center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value.
global_hidden_layers_short 2 # Number of hidden layers.
global_nodes_short 25 25 # Number of nodes in each hidden layer.
global_activation_short t t l # Activation function for each hidden layer and output layer.
#normalize_nodes # Normalize input of nodes.

###############################################################################
# ADDITIONAL SETTINGS FOR DATASET TOOLS
###############################################################################
# These keywords are used only by some tools handling data sets:
# nnp-comp2, nnp-scaling, nnp-dataset, nnp-train.
use_short_forces # Use forces.
random_seed 1234567 # Random number generator seed.

###############################################################################
# SYMMETRY FUNCTIONS
###############################################################################

# Radial symmetry function (type 2):
#symfunction_short <element-central> 2 <element-neighbor> <eta> <rshift> <rcutoff>

# Narrow Angular symmetry function (type 3):
#symfunction_short <element-central> 3 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>

# Wide Angular symmetry function (type 9):
#symfunction_short <element-central> 9 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>

# radial H H
symfunction_short H 2 H 0.001 0.0 12.00
symfunction_short H 2 H 0.01 0.0 12.00
symfunction_short H 2 H 0.03 0.0 12.00
symfunction_short H 2 H 0.06 0.0 12.00
symfunction_short H 2 H 0.15 1.9 12.00
symfunction_short H 2 H 0.30 1.9 12.00
symfunction_short H 2 H 0.60 1.9 12.00
symfunction_short H 2 H 1.50 1.9 12.00

# radial H O / O H
symfunction_short H 2 O 0.001 0.0 12.00
symfunction_short H 2 O 0.01 0.0 12.00
symfunction_short H 2 O 0.03 0.0 12.00
symfunction_short H 2 O 0.06 0.0 12.00
symfunction_short H 2 O 0.15 0.9 12.00
symfunction_short H 2 O 0.30 0.9 12.00
symfunction_short H 2 O 0.60 0.9 12.00
symfunction_short H 2 O 1.50 0.9 12.00

symfunction_short O 2 H 0.001 0.0 12.00
symfunction_short O 2 H 0.01 0.0 12.00
symfunction_short O 2 H 0.03 0.0 12.00
symfunction_short O 2 H 0.06 0.0 12.00
symfunction_short O 2 H 0.15 0.9 12.00
symfunction_short O 2 H 0.30 0.9 12.00
symfunction_short O 2 H 0.60 0.9 12.00
symfunction_short O 2 H 1.50 0.9 12.00

# radial O O
symfunction_short O 2 O 0.001 0.0 12.00
symfunction_short O 2 O 0.01 0.0 12.00
symfunction_short O 2 O 0.03 0.0 12.00
symfunction_short O 2 O 0.06 0.0 12.00
symfunction_short O 2 O 0.15 4.0 12.00
symfunction_short O 2 O 0.30 4.0 12.00
symfunction_short O 2 O 0.60 4.0 12.00
symfunction_short O 2 O 1.50 4.0 12.00

# angular
symfunction_short H 3 O H 0.2 1.0 1.0 12.00000

symfunction_short O 3 H H 0.07 1.0 1.0 12.00000
symfunction_short H 3 O H 0.07 1.0 1.0 12.00000
symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000
symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000

symfunction_short O 3 H H 0.03 1.0 1.0 12.00000
symfunction_short H 3 O H 0.03 1.0 1.0 12.00000
symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000
symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000

symfunction_short O 3 H H 0.01 1.0 4.0 12.00000
symfunction_short H 3 O H 0.01 1.0 4.0 12.00000
symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000
symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000

symfunction_short O 3 O H 0.03 1.0 1.0 12.00000
symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000
symfunction_short O 3 O H 0.001 1.0 4.0 12.00000
symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000

symfunction_short H 3 O O 0.03 1.0 1.0 12.00000
symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000
symfunction_short H 3 O O 0.001 1.0 4.0 12.00000
symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000

symfunction_short O 3 O O 0.03 1.0 1.0 12.00000
symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000
symfunction_short O 3 O O 0.001 1.0 4.0 12.00000
symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000
72 changes: 72 additions & 0 deletions examples/nnp-checkf/H2O_RPBE-D3/scaling.data
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################################################################################
# Symmetry function scaling data.
################################################################################
# Col Name Description
################################################################################
# 1 e_index Element index.
# 2 sf_index Symmetry function index.
# 3 sf_min Symmetry function minimum.
# 4 sf_max Symmetry function maximum.
# 5 sf_mean Symmetry function mean.
# 6 sf_sigma Symmetry function sigma.
#########################################################################################################################
# 1 2 3 4 5 6
# e_index sf_index sf_min sf_max sf_mean sf_sigma
#########################################################################################################################
1 1 1.0882016636170764E+00 9.6166419119419064E+00 2.2691752247542194E+00 6.7883526611658462E-01
1 2 7.3274438904180561E-01 5.0028559321574191E+00 1.3272332317543580E+00 3.3936750181780473E-01
1 3 7.6010783783215696E-01 7.1427942966219815E+00 1.6470726712825305E+00 5.0771115927383836E-01
1 4 5.4842285884800812E-01 3.7661771168267726E+00 1.0163698211361718E+00 2.5362958053787776E-01
1 5 4.0080665126604625E-01 4.1469832401668629E+00 9.0925040981537897E-01 2.9758019277508319E-01
1 6 3.6209352253798227E-01 2.2678239402766054E+00 6.4931154122889623E-01 1.4835420345383032E-01
1 7 1.8919103878435897E-01 2.2292652677252804E+00 4.5693857051003817E-01 1.5976079618578123E-01
1 8 2.6704178695764313E-01 1.3208742362468955E+00 4.2395636902644862E-01 8.0492394978461931E-02
1 9 2.4513099752055156E-01 9.4751160662053002E-01 3.6244199023263673E-01 5.2993540556109331E-02
1 10 2.2248910067848982E-01 2.7596216013647377E+00 5.3891576898130766E-01 2.0137334230483950E-01
1 11 1.4743601726548086E-01 5.5599270746969276E-01 2.6773972195910817E-01 2.6188094566404998E-02
1 12 9.9110926426029380E-02 1.7265405335201480E+00 2.9553976311554875E-01 1.1619768775752932E-01
1 13 6.5093699123904267E-02 3.4521757733971170E-01 1.8521249136783141E-01 1.9741155185936318E-02
1 14 3.1653527247865069E-02 9.1293170125596168E-01 1.5025164684953513E-01 5.3480187368038674E-02
1 15 2.9202821602466694E-03 2.6453981776124141E-01 7.6525296616004684E-02 1.8780956137549487E-02
1 16 3.2145385719803329E-04 2.8696425565429240E-01 4.5792284631233672E-02 2.3263495133568998E-02
1 17 2.4693757528509622E-04 1.3848731138266304E-01 1.7693289653297604E-02 9.7460303038080908E-03
1 18 5.0992836797990751E-03 5.8319173651547385E-01 2.3851656540978389E-02 3.7790771891778152E-02
1 19 3.2282960174310170E-04 2.1613962298381925E-01 1.7072560754702336E-02 1.4026518665786077E-02
1 20 4.9647513277769700E-02 1.6851617426880194E+00 1.4541325969622534E-01 1.0954306125703028E-01
1 21 3.4073471604482227E-03 3.1637071808861689E-01 1.8422597685566724E-02 2.0125274191649719E-02
1 22 1.3121382132811807E-04 1.0258348935693713E-01 6.3684016949344113E-03 6.6071626858835051E-03
1 23 3.3813162813665906E-02 9.1618560879938926E-01 8.1266384503339575E-02 5.7918502576695730E-02
1 24 4.1708500446352870E-04 1.5785966980407021E-01 4.6646981268568697E-03 9.8630700614506465E-03
1 25 7.3528900917695290E-04 5.9225627251013026E-02 3.7042174075139758E-03 3.3118079036492621E-03
1 26 8.9828333062972592E-03 1.9426085555380754E-01 2.4093377110646338E-02 1.0980657457661532E-02
1 27 2.1228022180417653E-04 8.7777813240869640E-03 2.0550705761547970E-03 5.8802103858137246E-04
2 1 1.5142595331454245E+00 1.0005711988559998E+01 2.6544664635087183E+00 6.7806617585688911E-01
2 2 4.4366445360926199E-01 4.6195409357987076E+00 9.6587051599896101E-01 3.3688559575009042E-01
2 3 1.1907810568758714E+00 7.5323544094345003E+00 2.0327396422723472E+00 5.0607867531004169E-01
2 4 2.7576036468694687E-01 3.3862131032504492E+00 6.5929732667024776E-01 2.5004687333979903E-01
2 5 8.0580777590695674E-01 4.5356481255168557E+00 1.2986230824577940E+00 2.9449908325462404E-01
2 6 1.0517053799863604E-01 1.8909877539194515E+00 3.0673921331641835E-01 1.4198497108573313E-01
2 7 5.6949141690859706E-01 2.6154328621607852E+00 8.4791273805289546E-01 1.5714071578589769E-01
2 8 2.3251646720171416E-02 9.3641034200657891E-01 1.1140979781150941E-01 6.9796654369842781E-02
2 9 5.1354161698115419E-01 1.8545341781448565E+00 7.2488398046527269E-01 9.8011511620611044E-02
2 10 1.1057465545812291E-01 2.9121456897811342E+00 4.7474421797982730E-01 2.3441807910092233E-01
2 11 3.5269317308496489E-01 1.0714592032613128E+00 5.3547944391821678E-01 4.5179661104166338E-02
2 12 3.0424313539726355E-02 2.5277642768509305E+00 3.1652845366685045E-01 2.1026891409654727E-01
2 13 1.5980022688828247E-01 6.6348817066386512E-01 3.7042498273566293E-01 3.0753700953611234E-02
2 14 2.7781847150922931E-03 2.3030057819082539E+00 1.7737800292869690E-01 1.8600239464755819E-01
2 15 9.5641036809349829E-03 3.9085233064570807E-01 1.5305059323200970E-01 2.7862233984302390E-02
2 16 3.7500170432292374E-06 2.0367068825281995E+00 5.4144316535640342E-02 1.4305857218443538E-01
2 17 2.4726232100491033E-03 3.4335400617385042E-01 1.6684597803376652E-02 2.1902951351570905E-02
2 18 1.7405672406959600E-05 5.6319316766205302E-02 9.5478184601751693E-04 3.3588039002222358E-03
2 19 5.4785372164647961E-02 3.0182597583971442E+00 2.0392031625072374E-01 2.0088721011517138E-01
2 20 1.3795234987637416E-03 4.9878800454061323E-01 1.2788265359933434E-02 3.1829452602194934E-02
2 21 6.6852772684814245E-03 2.6739582842775905E-01 3.0851859894574358E-02 1.7089886758420030E-02
2 22 1.7021399438214336E-02 1.4167796508898451E+00 7.6274174813506748E-02 9.2852504206357669E-02
2 23 1.9759831791959857E-02 4.0756378297923890E-01 4.8843503112397949E-02 2.5474332458885439E-02
2 24 5.2768632746659245E-04 2.3324050667069166E-01 7.2057238727819412E-03 1.4495435261027742E-02
2 25 1.1144879740881719E-05 3.5285772934088612E-02 4.2545240948261025E-04 2.0471375111485984E-03
2 26 1.6013752685265073E-02 8.2245409953473059E-01 5.0845479076508403E-02 5.2802834522172923E-02
2 27 3.9898424495541764E-03 7.8557031440100300E-01 3.6926675414383096E-02 5.0474458307624794E-02
2 28 4.0523818189746699E-05 9.8448068666705968E-02 1.2119235889230262E-03 5.7945700128174639E-03
2 29 6.0374649986214514E-03 9.9251766407842473E-02 1.6156539248049700E-02 5.5245068674135743E-03
2 30 2.9595491075765732E-03 1.5478537567691833E-01 1.1641055270110553E-02 8.9415193910804703E-03
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