Commit 61cc62b2 authored by Yury Lysogorski's avatar Yury Lysogorski
Browse files

remove old renamed files

parent d7d2323d
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,id,status,chemicalformula,job,subjob,project,timestart,timestop,totalcputime,computer,hamilton,hamversion,parentid,masterid
0,0,finished,,df1_A1_A2_A3_EV_elast_phon,/df1_A1_A2_A3_EV_elast_phon,Cu_training_archive/Cu_database,2021-02-08 10:33:52.341472,,,zora@cmti001#1,GenericJob,0.4,,
1,1,finished,,df3_10k,/df3_10k,Cu_training_archive/Cu_database,2021-02-08 10:33:53.993230,,,zora@cmti001#1,GenericJob,0.4,,
2,2,finished,,df2_1k,/df2_1k,Cu_training_archive/Cu_database,2021-02-08 10:33:54.435308,,,zora@cmti001#1,GenericJob,0.4,,
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### ####################################################################################################################
### This is the input file for the RuNNer tutorial (POTENTIALS WORKSHOP 2021-03-10)
### This input file is intended for release version 1.2
### RuNNer is hosted at www.gitlab.com. The most recent version can only be found in this repository.
### For access please contact Prof. Jörg Behler, joerg.behler@uni-goettingen.de
###
### ####################################################################################################################
### General remarks:
### - commands can be switched off by using the # character at the BEGINNING of the line
### - the input file can be structured by blank lines and comment lines
### - the order of the keywords is arbitrary
### - if keywords are missing, default values will be used and written to runner.out
### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message
###
########################################################################################################################
########################################################################################################################
### The following keywords just represent a subset of the keywords offered by RuNNer
########################################################################################################################
########################################################################################################################
########################################################################################################################
### general keywords
########################################################################################################################
nn_type_short 1 # 1=Behler-Parrinello
runner_mode 2 # 1=calculate symmetry functions, 2=fitting mode, 3=predicition mode
number_of_elements 1 # number of elements
elements Cu # specification of elements
random_seed 20 # integer seed for random number generator
random_number_type 6 # 6 recommended
########################################################################################################################
### NN structure of the short-range NN
########################################################################################################################
use_short_nn # use NN for short range interactions
global_hidden_layers_short 2 # number of hidden layers
global_nodes_short 15 15 # number of nodes in hidden layers
global_activation_short t t l # activation functions (t = hyperbolic tangent, l = linear)
########################################################################################################################
### symmetry function generation ( mode 1):
########################################################################################################################
test_fraction 0.10000 # threshold for splitting between fitting and test set
########################################################################################################################
### symmetry function definitions (all modes):
########################################################################################################################
cutoff_type 1
symfunction_short Cu 2 Cu 0.000000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.006000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.016000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.040000 0.000000 12.000000
symfunction_short Cu 2 Cu 0.109000 0.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 1.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 2.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 4.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 1.000000 16.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 1.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 2.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 4.000000 12.000000
symfunction_short Cu 3 Cu Cu 0.00000 -1.000000 16.000000 12.000000
########################################################################################################################
### fitting (mode 2):general inputs for short range AND electrostatic part:
########################################################################################################################
epochs 10 # number of epochs
fitting_unit eV # unit for error output in mode 2 (eV or Ha)
precondition_weights # optional precondition initial weights
########################################################################################################################
### fitting options ( mode 2): short range part only:
########################################################################################################################
short_energy_error_threshold 0.10000 # threshold of adaptive Kalman filter short E
short_force_error_threshold 1.00000 # threshold of adaptive Kalman filter short F
kalman_lambda_short 0.98000 # Kalman parameter short E/F, do not change
kalman_nue_short 0.99870 # Kalman parameter short E/F, do not change
use_short_forces # use forces for fitting
repeated_energy_update # optional: repeat energy update for each force update
mix_all_points # do not change
scale_symmetry_functions # optional
center_symmetry_functions # optional
short_force_fraction 0.01 #
force_update_scaling -1.0 #
########################################################################################################################
### output options for mode 2 (fitting):
########################################################################################################################
write_trainpoints # write trainpoints.out and testpoints.out files
write_trainforces # write trainforces.out and testforces.out files
########################################################################################################################
### output options for mode 3 (prediction):
########################################################################################################################
calculate_forces # calculate forces
calculate_stress # calculate stress tensor
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-------------------------------------------------------------
---------------------- Welcome to the -----------------------
RuNNer Neural Network Energy Representation - RuNNer
---------- (c) 2008-2020 Prof. Dr. Joerg Behler ----------
---------- Georg-August-Universitaet Goettingen ----------
---------- Theoretische Chemie ----------
---------- Tammannstr. 6 ----------
---------- 37077 Goettingen, Germany ----------
-------------------------------------------------------------
-------------------------------------------------------------
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License along
with this program. If not, see http://www.gnu.org/licenses.
-------------------------------------------------------------
-------------------------------------------------------------
When using RuNNer, please cite the following papers:
J. Behler, Angew. Chem. Int. Ed. 56, 12828 (2017).
J. Behler, Int. J. Quant. Chem. 115, 1032 (2015).
-------------------------------------------------------------
Whenever using high-dimensional NNPs irrespective of the Code please cite:
J. Behler and M. Parrinello, Phys. Rev. Lett. 98, 146401 (2007).
-------------------------------------------------------------
The reference for the atom-centered symmetry functions is:
J. Behler, J. Chem. Phys. 134, 074106 (2011).
-------------------------------------------------------------
For high-dimensional NNs including electrostatics:
N. Artrith, T. Morawietz, and J. Behler, Phys. Rev. B 83, 153101 (2011).
-------------------------------------------------------------
-------------------------------------------------------------
RuNNer has been written by Joerg Behler
*** with contributions from some friends ***
Tobias Morawietz - Nguyen Widrow weights and electrostatic screening
Jovan Jose Kochumannil Varghese - Pair symmetry functions and pair NNPs
Michael Gastegger and Philipp Marquetand - element decoupled Kalman filter
Andreas Singraber - more efficient symmetry function type 3 implementation
Sinja Klees and Mariana Rossi - some infrastructure for i-Pi compatibility
Emir Kocer - Symmetry function groups
Fenfei Wei and Emir Kocer - Hessian, frequencies and normal modes
-------------------------------------------------------------
-------------------------------------------------------------
General job information:
-------------------------------------------------------------
Executing host : tc-pc16.uni-pc.gwdg.
User name : mherbold
Starting date : 28. 2.2021
Starting time : 15 h 19 min
Working directory : /scratch2/tmp/mherbold-onPC16SSD/df4/2
-------------------------------------------------------------
-------------------------------------------------------------
Serial run requested
-------------------------------------------------------------
Reading control parameters from input.nn
=============================================================
-------------------------------------------------------------
=============================================================
General input parameters:
-------------------------------------------------------------
Short range NN is on
Electrostatic NN is off
vdW corrections switched off
-------------------------------------------------------------
RuNNer nn_type_short 1
RuNNer is started in mode for fitting (2)
debugging mode is F
parallelization mode 1
enable detailed time measurement F
using symmetry function groups F
enable detailed time measurement at epoch level F
silent mode F
NN force check F
number of elements 1
elements (sorted):
29 Cu
seed for random number generator 20
random number generator type 6
remove free atom reference energies F
shortest allowed bond in structure 0.500
Cutoff_type for symmetry function is 1
Cutoff_alpha for inner cutoff radius is 0.000
-------------------------------------------------------------
Short range NN specifications:
-------------------------------------------------------------
global hidden layers short range NN 2
global nodes hidden layers short NN 15 15
global activation functions short ttl
-------------------------------------------------------------
General fitting parameters:
-------------------------------------------------------------
number of fitting epochs 10
print date and time for each epoch F
number of data sets in memory 200
Fitting mode 1 (online learning) selected
Randomly mixing all points in training set T
save Kalman filter data F
restart from old Kalman filter data F
rescale symmetry functions T
min value of scaled short range symmetry functions 0.000
max value of scaled short range symmetry functions 1.000
remove CMS from symmetry functions T
calculate symmetry function correlation F
weight analysis F
environment analysis F
find contradictions F
fix some weights F
using growth mode for fitting F
global fit of short and charge NN (not implemented) F
error unit for fitting eV
Reading formatted files
Writing formatted files
Resetting Kalman filter matrices each epoch F
Preconditioning of weights is switched on
-------------------------------------------------------------
Fitting parameters short range part:
-------------------------------------------------------------
using forces for fitting T
using Kalman filter optimization (1) for short range energy
using Kalman filter optimization (1) for short range forces
short energy error threshold 0.10000000
short force error threshold 1.00000000
Kalman lambda (short) 0.98000000
Kalman nue (short) 0.99870000
use_noisematrix F
Kalman damp (short energy) 1.00000000
Kalman damp (short force) 1.00000000
restart fit with old weights (short) F
automatic scaling factor for force update selected
grouping energies in blocks of 1
fraction of energies used for update 1.000
grouping forces in blocks of 1
fraction of forces used for update 0.010
weights_min -1.000
weights_max 1.000
Using repeated energy updates after each force update
max_energy 10000.000
max force component used for fitting 10000.000 Ha/Bohr
noise energy threshold 0.00000000 Ha/atom
noise force threshold 0.00000000 Ha/Bohr
restart fit with old weights (charge) F
-------------------------------------------------------------
Fitting output options:
-------------------------------------------------------------
write weights in every epoch 1
write temporary weights each epoch F
write trainpoints.out and testpoints.out T
write binding energies only F
write trainforces.out and testforces.out T
=============================================================
Element pairs: 1 , shortest distance (Bohr)
pair 1 Cu Cu 2.824
=============================================================
=> short range NN weights type 1 Cu 466
-------------------------------------------------------------
-------------------------------------------------
Atomic short range NN for element: Cu
architecture 13 15 15 1
-------------------------------------------------
1 G t t l
2 G t t
3 G t t
4 G t t
5 G t t
6 G t t
7 G t t
8 G t t
9 G t t
10 G t t
11 G t t
12 G t t
13 G t t
14 t t
15 t t
-------------------------------------------------------------
-------------------------------------------------------------
short range atomic symmetry functions element Cu :
-------------------------------------------------------------
1 Cu 2 Cu 0.000 0.000 12.000
2 Cu 2 Cu 0.006 0.000 12.000
3 Cu 2 Cu 0.016 0.000 12.000
4 Cu 2 Cu 0.040 0.000 12.000
5 Cu 2 Cu 0.109 0.000 12.000
6 Cu 3 Cu Cu 0.000 -1.000 1.000 12.000
7 Cu 3 Cu Cu 0.000 1.000 1.000 12.000
8 Cu 3 Cu Cu 0.000 -1.000 2.000 12.000
9 Cu 3 Cu Cu 0.000 1.000 2.000 12.000
10 Cu 3 Cu Cu 0.000 -1.000 4.000 12.000
11 Cu 3 Cu Cu 0.000 1.000 4.000 12.000
12 Cu 3 Cu Cu 0.000 -1.000 16.000 12.000
13 Cu 3 Cu Cu 0.000 1.000 16.000 12.000
-------------------------------------------------------------
=============================================================
Short range symmetry function values for element Cu
Training set: min max average range stddev range/stddev
1 6.72393532 25.25447208 14.00001115 18.53053676 4.02011080 4.60945921
2 5.03976308 19.37796546 10.59714429 14.33820238 3.11321693 4.60559053
3 3.25577537 13.11073890 6.98744718 9.85496353 2.14525332 4.59384607
4 1.25883453 6.21227127 3.05195579 4.95343674 1.07630994 4.60224009
5 0.06568766 1.53442885 0.48718005 1.46874120 0.26713619 5.49809898
6 2.42989188 42.06637435 12.30898440 39.63648248 7.96564228 4.97593051
7 6.59284339 109.34982696 33.28285935 102.75698358 21.03610544 4.88479124
8 0.78142670 19.11390444 5.22756080 18.33247774 3.61016236 5.07802030
9 5.20079617 86.39735705 26.20143575 81.19656088 16.68008353 4.86787495
10 0.15497639 7.72411752 1.91198556 7.56914113 1.46079520 5.18152107
11 3.59136462 60.38094318 17.95854981 56.78957856 11.72399989 4.84387403
12 0.00059457 1.66933490 0.34750355 1.66874033 0.32743124 5.09646040
13 0.52030958 18.24849080 4.70826264 17.72818122 3.59567219 4.93042198
-------------------------------------------------------------
Energies in training set (Ha/atom):
Emin Emax average stddev range
Eshort -0.135967 -0.091874 -0.118413 0.012680 0.044093
Eelec 0.000000 0.000000 0.000000 0.000000 0.000000
Etot -0.135967 -0.091874 -0.118413 0.012680 0.044093
-------------------------------------------------------------
Energies in training set (eV/atom):
Emin Emax average stddev range
Eshort -3.699790 -2.499974 -3.222125 0.345036 1.199816
Eelec 0.000000 0.000000 0.000000 0.000000 0.000000
Etot -3.699790 -2.499974 -3.222125 0.345036 1.199816
-------------------------------------------------------------
Force vectors in training set (Ha/Bohr):
Fmin Fmax average stddev range
Cu 0.000000 0.873705 0.011256 0.030995 0.873705
-------------------------------------------------------------
Force vectors in training set (eV/Bohr):
Fmin Fmax average stddev range
Cu 0.000000 23.774389 0.306275 0.843406 23.774389
-------------------------------------------------------------
Force components in training set (Ha/Bohr):
Fmin Fmax range
Cu 0.000000 0.873705 0.873705
-------------------------------------------------------------
Force components in training set (eV/Bohr):
Fmin Fmax range
Cu 0.000000 23.774389 23.774389
-------------------------------------------------------------
number of training points 7259
number of training atoms 64729
number of training forces 194187
number of testing points 814
number of testing atoms 7250
number of testing forces 21750
-------------------------------------------------------------
Number of atoms for each element:
training: testing:
1 Cu 64729 7250
=============================================================
Weight Preconditioner:
Warning: Forces are not used for preconditioning
----------------------
-------------------------------------------------------------
Final preconditioning of the output values:
--------------------------------------------
Minimum NN Eshort -3.346222 Ha/atom
Minimum Ref Eshort -0.135967 Ha/atom
Maximum NN Eshort -2.012861 Ha/atom
Maximum Ref Eshort -0.091874 Ha/atom
Average NN Eshort -2.855668 Ha/atom
Average Ref Eshort -0.118413 Ha/atom
Stddev NN Eshort 0.200995 Ha/atom
Stddev Ref Eshort 0.012680 Ha/atom
Factor for connecting short range weights: 0.063086
=============================================================
-------------------------------------------------------------
initialization time (min): 0.05
-------------------------------------------------------------
Did you check your output file for warnings? ;-)
-------------------------------------------------------------
Short range energies below 10000.000 Ha/atom are used for fitting and Eshort RMSE!
=> Fitted energy range has width of 0.044 Ha/atom = 1.200 eV/atom
=> Number of short range training energies below max_energy: 7259
Force components below 10000.000 Ha/Bohr are used for fitting and Fshort RMSE!
Cu => Fitted force range has width of 0.874 Ha/Bohr = 23.774 eV/Bohr
Cu => Number of short range training force components below max_force: 194187
-------------------------------------------------------------------------------
RMSEs (energies: eV/atom, forces: eV/Bohr):
--- E_short: --- - time -
/atom min
epoch train test
ENERGY 0 0.486020 0.481254 9.86
FORCES 0 0.543702 0.502894
-------------------------------------------------------------------------------
ENERGY 1 0.039459 0.039840 19.05
FORCES 1 0.201312 0.174885
INFORMATION USED FOR UPDATE (E,F) 1 1998 45
-------------------------------------------------------------------------------
ENERGY 2 0.024635 0.026306 19.14
FORCES 2 0.132738 0.123616
INFORMATION USED FOR UPDATE (E,F) 2 5565 112
-------------------------------------------------------------------------------
ENERGY 3 0.022316 0.024581 19.13
FORCES 3 0.120274 0.111427
INFORMATION USED FOR UPDATE (E,F) 3 6033 131
-------------------------------------------------------------------------------
ENERGY 4 0.021333 0.023145 19.16
FORCES 4 0.113496 0.105447
INFORMATION USED FOR UPDATE (E,F) 4 6132 142
-------------------------------------------------------------------------------
ENERGY 5 0.022327 0.023597 19.13
FORCES 5 0.113152 0.102596
INFORMATION USED FOR UPDATE (E,F) 5 6064 137
-------------------------------------------------------------------------------
ENERGY 6 0.021007 0.022555 19.15
FORCES 6 0.102685 0.094464
INFORMATION USED FOR UPDATE (E,F) 6 6094 168
-------------------------------------------------------------------------------
ENERGY 7 0.021018 0.022213 19.15
FORCES 7 0.098023 0.097181
INFORMATION USED FOR UPDATE (E,F) 7 6226 158
-------------------------------------------------------------------------------
ENERGY 8 0.020692 0.022248 19.15
FORCES 8 0.095995 0.097202
INFORMATION USED FOR UPDATE (E,F) 8 6186 183
-------------------------------------------------------------------------------
ENERGY 9 0.020880 0.022219 19.16
FORCES 9 0.094960 0.095833
INFORMATION USED FOR UPDATE (E,F) 9 6122 176
-------------------------------------------------------------------------------
ENERGY 10 0.021217 0.022457 19.41
FORCES 10 0.097554 0.094895
INFORMATION USED FOR UPDATE (E,F) 10 6226 203
=============================================================
Best short range fit has been obtained in epoch 7
--- E_short: --- --- F_short: ---
train test train test
OPTSHORT 0.021018 0.022213 0.098023 0.097181
-------------------------------------------------------------
max Eshort error in last epoch (train set): 0.281291 eV/atom (structure 788 )
max Eshort error in last epoch (test set) : 0.261851 eV/atom (structure 253 )
-------------------------------------------------------------
Total runtime (s) : 12095.013
Total runtime (min): 201.584
Total runtime (h) : 3.360
Normal termination of RuNNer
-------------------------------------------------------------
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