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n2p2 training size #21

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7a7697c
Wrote function for creating training datasets.
Apr 9, 2019
dffd507
Wrote class NNTSSD with methods on selecting, training, analysing and…
Apr 11, 2019
4252501
Wrote class NNTSSD with methods on selecting, training, analysing and…
Apr 11, 2019
5e588e5
Wrote docstrings for NNTSSD.py
Apr 11, 2019
e503014
Added error messages to code. Created Python 3 version.
Apr 12, 2019
da545d4
Made training, analysing and plotting parts autoread the present dire…
Apr 16, 2019
db8d4e8
Written first version of tests and example.
Apr 17, 2019
477c9db
Added function for writing submission script for VSC, user option for…
Apr 25, 2019
b17148e
Reworked input of NNTSSD parameters, changes on VSC parameters
Apr 26, 2019
7f0d9e1
Changes in analyse and plotting. Added plot of learning curves.
Apr 30, 2019
44a087f
Added module for analysing learning curves/training performance.
MadlenReiner May 6, 2019
0e4df6f
Updated sphinx documentation and new code documentation.
MadlenReiner May 22, 2019
d35e871
Added tools for validation datasets and external testsets.
MadlenReiner Oct 9, 2019
9ea3008
Updated NNTSSD example.
MadlenReiner Oct 9, 2019
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12 changes: 12 additions & 0 deletions .gitignore
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/tools/python/NNTSSD/RPBE-D3_1_split_data
/tools/python/NNTSSD/RPBE-D3_2_selected_13_each
/tools/python/NNTSSD/RPBE-D3_val_1_selected_6_each
/tools/python/NNTSSD/RPBE-D3_val_2_Trainiert_von_VSC
/tools/python/NNTSSD/RPBE-D3_val_3_Trainiert_prep4val
/tools/python/NNTSSD/Z_vonVSC_ext-test_predict_teil
/tools/python/NNTSSD/Z_water_RPBE-D3_70_700_7000
/tools/python/NNTSSD/Z_water_RPBE-D3_testing
/tools/python/NNTSSD/Z_water_RPBE-D3_trainiert_ext-test
__pycache__/
Output/
submit.slrm
35 changes: 35 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/energy.comp
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################################################################################
# Energy comparison.
################################################################################
# Col Name Description
################################################################################
# 1 index Structure index.
# 2 N Number of atoms in structure.
# 3 Eref_phys Reference potential energy (physical units, atomic energy offsets added).
# 4 Ennp_phys NNP potential energy (physical units, atomic energy offsets added).
# 5 Eref_int Reference potential energy (internal units).
# 6 Ennp_int NNP potential energy (internal units).
#########################################################################################
# 1 2 3 4 5 6
# index N Eref_phys Ennp_phys Eref_int Ennp_int
#########################################################################################
0 192 -4.90037328E+03 -4.90037247E+03 -6.68092585E+01 -6.66125046E+01
1 48 -1.22507199E+03 -1.22507011E+03 -1.15272744E+01 -1.10694394E+01
2 48 -1.22506986E+03 -1.22507022E+03 -1.10081378E+01 -1.10965350E+01
3 48 -1.22502203E+03 -1.22502119E+03 5.95827955E-01 8.01478245E-01
4 48 -1.22505218E+03 -1.22505220E+03 -6.71902847E+00 -6.72310934E+00
5 48 -1.22506198E+03 -1.22506140E+03 -9.09775124E+00 -8.95720185E+00
6 48 -1.22503158E+03 -1.22502838E+03 -1.72088369E+00 -9.43022153E-01
7 48 -1.22500423E+03 -1.22500324E+03 4.91709424E+00 5.15686403E+00
8 48 -1.22496473E+03 -1.22496515E+03 1.45013635E+01 1.44003183E+01
9 48 -1.22495153E+03 -1.22495439E+03 1.77048257E+01 1.70098142E+01
10 48 -1.22494069E+03 -1.22493883E+03 2.03344660E+01 2.07854856E+01
11 48 -1.22496274E+03 -1.22496063E+03 1.49838564E+01 1.54963594E+01
12 96 -2.45009917E+03 -2.45009678E+03 -1.21796134E+01 -1.15977362E+01
13 192 -4.90020436E+03 -4.90020013E+03 -2.58195517E+01 -2.47915608E+01
14 192 -4.90003217E+03 -4.90003007E+03 1.59636306E+01 1.64751870E+01
15 96 -2.45009730E+03 -2.45009937E+03 -1.17257032E+01 -1.22270407E+01
16 192 -4.90039158E+03 -4.90039010E+03 -7.12491576E+01 -7.08887079E+01
17 192 -4.89966762E+03 -4.89966767E+03 1.04425112E+02 1.04412480E+02
18 192 -4.89968758E+03 -4.89969068E+03 9.95831661E+01 9.88296431E+01
19 192 -4.90014395E+03 -4.90014767E+03 -1.11601885E+01 -1.20623448E+01
6,207 changes: 6,207 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/forces.comp
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458 changes: 458 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/nnp-dataset.log.0000
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2,224 changes: 2,224 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/output.data
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43 changes: 43 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/sensitivity.001.out
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################################################################################
# Sensitivity analysis for element H.
################################################################################
# Col Name Description
################################################################################
# 1 index Symmetry function index.
# 2 sens_msa_norm Mean square average sensitivity (normalized, sum = 100%).
# 3 sens_max_norm Maximum sensitivity (normalized, sum = 100%).
# 4 sens_msa_phys Mean square average sensitivity (physical energy units).
# 5 sens_max_phys Maximum sensitivity (physical energy units).
# 6 sens_msa_int Mean square average sensitivity (internal units).
# 7 sens_max_int Maximum sensitivity (internal units).
################################################################################################################
# 1 2 3 4 5 6 7
# index sens_msa_norm sens_max_norm sens_msa_phys sens_max_phys sens_msa_int sens_max_int
################################################################################################################
1 1.97170552E+00 3.02857692E+00 1.44013644E-01 4.29300706E-01 3.49459883E+01 1.04173028E+02
2 2.00719606E+00 3.25187967E+00 1.46605878E-01 4.60953866E-01 3.55750133E+01 1.11853905E+02
3 3.61027972E+00 5.52864200E+00 2.63695331E-01 7.83684871E-01 6.39876452E+01 1.90166998E+02
4 2.47220894E+00 4.62013389E+00 1.80570484E-01 6.54903869E-01 4.38167790E+01 1.58917324E+02
5 5.18851575E+00 6.63378652E+00 3.78969909E-01 9.40339081E-01 9.19598842E+01 2.28180314E+02
6 5.34656738E+00 5.80432546E+00 3.90514022E-01 8.22762995E-01 9.47611494E+01 1.99649597E+02
7 1.63881962E+00 3.97255475E+00 1.19699612E-01 5.63109542E-01 2.90460064E+01 1.36642744E+02
8 6.11078301E+00 5.88642162E+00 4.46332438E-01 8.34400124E-01 1.08305906E+02 2.02473433E+02
9 2.80797933E+00 3.04080020E+00 2.05095200E-01 4.31033356E-01 4.97678848E+01 1.04593469E+02
10 9.40951931E-01 2.04243583E+00 6.87272594E-02 2.89515230E-01 1.66771838E+01 7.02530368E+01
11 1.63711285E+00 1.65489411E+00 1.19574949E-01 2.34581200E-01 2.90157562E+01 5.69228835E+01
12 4.26603416E-01 8.26070923E-01 3.11591726E-02 1.17095534E-01 7.56100638E+00 2.84141074E+01
13 1.12319823E+00 9.51965296E-01 8.20385543E-02 1.34941058E-01 1.99072691E+01 3.27444574E+01
14 6.33097437E-01 8.32408066E-01 4.62415245E-02 1.17993824E-01 1.12208519E+01 2.86320842E+01
15 4.83942340E-01 1.40593209E+00 3.53472156E-02 1.99290840E-01 8.57726635E+00 4.83594135E+01
16 2.34792494E-01 6.96284037E-01 1.71492763E-02 9.86982456E-02 4.16140022E+00 2.39498678E+01
17 3.31460159E-01 6.96370054E-01 2.42098960E-02 9.87104386E-02 5.87471241E+00 2.39528265E+01
18 8.80621397E+00 5.66005131E+00 6.43207088E-01 8.02312138E-01 1.56079013E+02 1.94687044E+02
19 2.06707567E-01 4.74240485E-01 1.50979493E-02 6.72235774E-02 3.66363038E+00 1.63123041E+01
20 9.43776502E+00 7.49266845E+00 6.89335665E-01 1.06208557E+00 1.67272457E+02 2.57723012E+02
21 7.84750991E+00 7.25796961E+00 5.73183211E-01 1.02881702E+00 1.39087195E+02 2.49650148E+02
22 3.29975887E+00 4.24187543E+00 2.41014845E-01 6.01285741E-01 5.84840556E+01 1.45906484E+02
23 1.26930715E+01 9.62183105E+00 9.27103702E-01 1.36389432E+00 2.24968651E+02 3.30959163E+02
24 5.50627349E+00 3.69088976E+00 4.02178979E-01 5.23183535E-01 9.75917385E+01 1.26954399E+02
25 6.42521799E+00 4.26905940E+00 4.69298812E-01 6.05139068E-01 1.13878868E+02 1.46841523E+02
26 7.70221206E+00 5.10173610E+00 5.62570636E-01 7.23170970E-01 1.36511974E+02 1.75482847E+02
27 1.11005541E+00 1.31619699E+00 8.10786011E-02 1.86570891E-01 1.96743292E+01 4.52728228E+01
46 changes: 46 additions & 0 deletions examples/nnp-dataset/H2O_RPBE-D3/sensitivity.008.out
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################################################################################
# Sensitivity analysis for element O.
################################################################################
# Col Name Description
################################################################################
# 1 index Symmetry function index.
# 2 sens_msa_norm Mean square average sensitivity (normalized, sum = 100%).
# 3 sens_max_norm Maximum sensitivity (normalized, sum = 100%).
# 4 sens_msa_phys Mean square average sensitivity (physical energy units).
# 5 sens_max_phys Maximum sensitivity (physical energy units).
# 6 sens_msa_int Mean square average sensitivity (internal units).
# 7 sens_max_int Maximum sensitivity (internal units).
################################################################################################################
# 1 2 3 4 5 6 7
# index sens_msa_norm sens_max_norm sens_msa_phys sens_max_phys sens_msa_int sens_max_int
################################################################################################################
1 9.11698888E-01 1.25370328E+00 1.40121468E-01 3.45865883E-01 3.40015227E+01 8.39269446E+01
2 2.53192343E+00 4.42258713E+00 3.89138161E-01 1.22008295E+00 9.44272866E+01 2.96062258E+02
3 9.19746784E-01 1.53168651E+00 1.41358371E-01 4.22554614E-01 3.43016665E+01 1.02536039E+02
4 5.36305857E+00 8.27788182E+00 8.24262978E-01 2.28366388E+00 2.00013579E+02 5.54148129E+02
5 2.81855242E+00 3.67673699E+00 4.33190946E-01 1.01432125E+00 1.05117024E+02 2.46132642E+02
6 4.00681946E+00 6.36659805E+00 6.15818922E-01 1.75638773E+00 1.49433069E+02 4.26200624E+02
7 2.27278697E+00 2.58519031E+00 3.49310777E-01 7.13190386E-01 8.47628737E+01 1.73060984E+02
8 4.59989389E+00 6.58409353E+00 7.06970134E-01 1.81638938E+00 1.71551593E+02 4.40760473E+02
9 2.40804685E+00 2.08875161E+00 3.70099234E-01 5.76235166E-01 8.98073484E+01 1.39827775E+02
10 7.42509007E-01 1.41975265E+00 1.14118218E-01 3.91674817E-01 2.76916394E+01 9.50428250E+01
11 2.48569711E-01 5.63032040E-01 3.82033513E-02 1.55326684E-01 9.27032904E+00 3.76911821E+01
12 3.94109241E-01 5.75812932E-01 6.05717153E-02 1.58852618E-01 1.46981799E+01 3.85467763E+01
13 1.71929585E-01 2.94230340E-01 2.64243230E-02 8.11709102E-02 6.41205970E+00 1.96967287E+01
14 9.23585481E-02 3.30866586E-01 1.41948351E-02 9.12779486E-02 3.44448295E+00 2.21492772E+01
15 6.91535987E-01 5.61023153E-01 1.06284036E-01 1.54772482E-01 2.57906167E+01 3.75567008E+01
16 4.31870986E-02 8.99199802E-02 6.63754200E-03 2.48067097E-02 1.61064923E+00 6.01953372E+00
17 5.69708617E+00 4.26935823E+00 8.75600583E-01 1.17781087E+00 2.12471033E+02 2.85804620E+02
18 8.49900871E-01 1.08692545E+00 1.30623564E-01 2.99855983E-01 3.16967851E+01 7.27622980E+01
19 7.08623662E+00 6.15405192E+00 1.08910287E+00 1.69775148E+00 2.64278962E+02 4.11972100E+02
20 5.88298264E+00 4.83563424E+00 9.04171514E-01 1.33403249E+00 2.19403983E+02 3.23712965E+02
21 2.30587503E+00 1.67595287E+00 3.54396170E-01 4.62354153E-01 8.59968826E+01 1.12193695E+02
22 1.67675691E+00 1.52471023E+00 2.57705305E-01 4.20630030E-01 6.25341206E+01 1.02069024E+02
23 7.38305459E+00 5.25579576E+00 1.13472163E+00 1.44994471E+00 2.75348694E+02 3.51839933E+02
24 9.26876276E+00 8.20090766E+00 1.42454122E+00 2.26242861E+00 3.45675586E+02 5.48995230E+02
25 8.41294836E+00 5.77127554E+00 1.29300879E+00 1.59215289E+00 3.13758258E+02 3.86347813E+02
26 1.28350104E+00 1.67511234E+00 1.97264746E-01 4.62122273E-01 4.78677667E+01 1.12137427E+02
27 1.09586030E+01 9.50168287E+00 1.68425734E+00 2.62128048E+00 4.08697645E+02 6.36073322E+02
28 4.49103174E+00 4.74404592E+00 6.90238817E-01 1.30876552E+00 1.67491614E+02 3.17581747E+02
29 3.82582742E+00 2.82248544E+00 5.88001765E-01 7.78654275E-01 1.42683028E+02 1.88946286E+02
30 2.66070642E+00 1.86019462E+00 4.08931167E-01 5.13181917E-01 9.92302076E+01 1.24527432E+02
14 changes: 14 additions & 0 deletions examples/nnp-predict/H2O_RPBE-D3/energy.out
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################################################################################
# Energy comparison.
################################################################################
# Col Name Description
################################################################################
# 1 Ennp Potential energy predicted by NNP.
# 2 Eref Reference potential energy.
# 3 Ediff Difference between reference and NNP prediction.
# 4 E_offset Sum of atomic offset energies (included in column Ennp).
################################################################################
# 1 2 3 4
# Ennp Eref Ediff E_offset
###################################################################
-2.75645473E+04 0.00000000E+00 2.75645473E+04 0.00000000E+00
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