mlatom 2.0.0__py3-none-any.whl

MLatom/doc.py

@@ -0,0 +1,620 @@
+#!/usr/bin/env python3
+'''
+  !---------------------------------------------------------------------------! 
+  ! doc: handling help of MLatom                                              ! 
+  ! Implementations and documentation by:                                     !
+  ! Fuchun Ge, Pavlo O. Dral, Bao-Xin Xue                                     ! 
+  !---------------------------------------------------------------------------! 
+'''
+import time, sys
+
+class Doc():
+    @classmethod
+    def printDoc(cls,argdict):
+        mlatom_alias=['mlatomf','mlatom','kreg']
+        gap_alias=[ 'gap', 'gap_fit', 'gapfit']
+        sgdml_alias=['sgdml']
+        deepmd_alias=['dp','deepmd','deepmd-kit']
+        physnet_alias=['physnet']
+        ani_alias=['torchani','ani']
+        overview=True
+        for key, value in argdict.items():
+            for k, v in cls.help_text.items():
+                if key.lower()==k.lower() and value:  
+                    print(v)
+                    overview=False
+            if key.lower() in ['mlmodeltype','mlprog'] and value:
+                if value == True: value='S'
+                if value.lower() in mlatom_alias:
+                    from interface_MLatomF import printHelp
+                    printHelp()
+                    overview=False
+                elif value.lower() in ani_alias:
+                    from interfaces.TorchANI.interface_TorchANI import printHelp
+                    printHelp()
+                    overview=False
+                elif value.lower() in gap_alias:
+                    from interfaces.GAP.interface_GAP import printHelp
+                    printHelp()
+                    overview=False
+                elif value.lower() in sgdml_alias:
+                    from interfaces.sGDML.interface_sGDML import printHelp
+                    printHelp()
+                    overview=False
+                elif value.lower() in deepmd_alias:
+                    from interfaces.DeePMDkit.interface_DeePMDkit import printHelp
+                    printHelp()
+                    overview=False
+                elif value.lower() in physnet_alias:
+                    from interfaces.PhysNet.interface_PhysNet import printHelp
+                    printHelp()
+                    overview=False
+                else:
+                    print(cls.Default_MLprog_type)
+                    overview=False
+        if overview:
+            print(cls.help_text['overview'])
+
+        print(' %s ' % ('='*78))
+        print(time.strftime(" MLatom terminated on %d.%m.%Y at %H:%M:%S", time.localtime()))
+        print(' %s ' % ('='*78))
+        sys.stdout.flush()
+        
+    molDescriptorDoc = '''
+  Optional arguments specifying descriptor:
+    molDescriptor=S            molecular descriptor S
+      RE [default]             vector {Req/R}, where R is internuclear distance
+      CM                       Coulomb matrix
+    molDescrType=S             type S of molecular descriptor
+      sorted                   default for molDescrType=CM
+                               sort by:
+                                 norms of CM matrix (for molDescrType=CM)
+                                 nuclear repulsions (for molDescrType=RE)
+      unsorted                 default for molDescrType=RE
+      permuted                 molecular descriptor with all atom permutations
+  
+  If molDescrType=sorted requested, additional output can be requested:
+    XYZsortedFileOut=S         file S with sorted XYZ coordinates, only works
+                               for molDescrType=RE molDescrType=sorted
+  
+  If molDescrType=permuted requested, at least one of the arguments needed:
+    permInvGroups=S            permutationally invariant groups S
+                               e.g. for water dimer permInvGroups=1,2,3-4,5,6
+                               permute water molecules (atoms 1,2,3 and 5,6,7)
+    permInvNuclei=S            permutationally invariant nuclei S
+                               e.g.permInvNuclei=2-3.5-6
+                               will permute atoms 2,3 and 6,7
+'''
+
+    Default_MLprog_type='''
+  Use of interfaces to ML programs
+  
+  Arguments:
+    MLprog=S                   ML program S
+      or
+    MLmodelType=S              ML model type S
+
+  Supported ML model types and default programs:
+
+  +-------------+----------------+ 
+  | MLmodelType | default MLprog | 
+  +-------------+----------------+ 
+  | KREG        | MLatomF        | 
+  +-------------+----------------+ 
+  | sGDML       | sGDML          | 
+  +-------------+----------- ----+ 
+  | GAP-SOAP    | GAP            | 
+  +-------------+----------------+ 
+  | PhysNet     | PhysNet        | 
+  +-------------+----------------+ 
+  | DeepPot-SE  | DeePMD-kit     | 
+  +-------------+----------------+ 
+  | ANI         | TorchANI       | 
+  +-------------+----------------+ 
+  
+  Supported interfaces with default and tested ML model types:
+  
+  +------------+----------------------+
+  | MLprog     | MLmodelType          |
+  +------------+----------------------+
+  | MLatomF    | KREG [default]       |
+  |            | see                  |
+  |            | MLatom.py KRR help   |
+  +------------+----------------------+
+  | sGDML      | sGDML [default]      |
+  |            | GDML                 |
+  +------------+----------------------+
+  | GAP        | GAP-SOAP             |
+  +------------+----------------------+
+  | PhysNet    | PhysNet              |
+  +------------+----------------------+
+  | DeePMD-kit | DeepPot-SE [default] |
+  |            | DPMD                 |
+  +------------+----------------------+
+  | TorchANI   | ANI [default]        |
+  +------------+----------------------+
+  
+  See interface's help for more details, e.g.
+    MLatom.py MLprog=TorchANI help
+'''
+
+    help_text={
+    'overview':'''
+  Usage:
+    MLatom.py [options]
+
+  Getting help:
+    MLatom.py help             print this help and exit
+    MLatom.py [option] help    print help for [option] and exit
+                               e.g. MLatom.py useMLmodel help
+
+  Options:
+    ML tasks:
+      useMLmodel               use existing ML model    
+      createMLmodel            create and save ML model 
+      estAccMLmodel            estimate accuracy of ML model
+      deltaLearn               use delta-learning
+      selfCorrect              use self-correcting ML
+      learningCurve            generate learning curve
+      crossSection             simulate absorption spectrum
+
+    Data set tasks:
+      XYZ2X                    convert XYZ coordinates into descriptor X
+      analyze                  analyze data sets
+      sample                   sample data points from a data set
+      slice                    slice data set
+      sampleFromSlices         sample from each slice
+      mergeSlices              merge indices from slices
+
+    Multithreading:
+      nthreads=N               set number of threads (N)
+ 
+  Example:
+    MLatom.py createMLmodel XYZfile=CH3Cl.xyz Yfile=en.dat MLmodelOut=CH3Cl.unf
+''',
+  'useMLmodel':'''
+  Use existing ML model
+  
+  Usage: MLatom.py useMLmodel [arguments]
+
+  Arguments:
+    Input file options:
+      MLmodelIn=S              file S with ML model
+      MLprog=S                 only required for third-party programs. See
+                               MLatom.py MLprog help
+      
+      XYZfile=S                file S with XYZ coordinates
+          or
+      XfileIn=S                file S with input vectors X
+
+    Output file options (at least one of these arguments is required):
+      YestFile=S               file S with estimated Y values
+      YgradEstFile=S           file S with estimated gradients
+      YgradXYZestFile=S        file S with estimated XYZ gradients
+      
+  Example:
+    MLatom.py useMLmodel MLmodelIn=CH3Cl.unf XYZfile=CH3Cl.xyz YestFile=MLen.dat  
+''',
+  'createMLmodel':'''
+  Create and save ML model
+  
+  Usage: MLatom.py createMLmodel [arguments]
+
+  Required arguments:
+    Input files:
+      XYZfile=S                file S with XYZ coordinates
+          or
+      XfileIn=S                file S with input vectors X
+      
+      Yfile=S                  file S with reference values
+         and/or
+      YgradXYZfile=S           file S with reference XYZ gradients
+
+    Output files:
+      MLmodelOut=S             file S with ML model
+    
+  Optional output files:
+    XfileOut=S                 file S with X values
+    XYZsortedFileOut=S         file S with sorted XYZ coordinates
+                               only works for
+                               molDescrType=RE molDescrType=sorted
+    YestFile=S                 file S with estimated Y values
+    YgradEstFile=S             file S with estimated gradients
+    YgradXYZestFile=S          file S with estimated XYZ gradients
+    
+  KREG model with unsorted RE descriptor is trained by default
+  Default hyperparameters sigma=100.0 and lambda=0.0 are used
+    
+  To train ML model with third-party program, see:
+    MLatom.py MLprog help      to list available interfaces and 
+                               default ML models
+           and
+    MLatom.py MLprog=S help    for specific help of interface S
+    
+  To train another KRR model with MLatomF, see:
+    MLatom.py KRR help
+
+  Any hyperparameters can be optimized with the hyperopt package, see:
+    MLatom.py hyperopt help
+      
+  To optimize hyperparameters, the training set should be split into the
+  sub-training and validation sets, see:
+    MLatom.py sample help
+  Additional optional arguments:
+    sampling=user-defined      reads in indices for the sub-training and
+                               validation sets from files defined by arguments
+      iSubtrainIn=S            file S with indices of sub-training points
+      iValidateIn=S            file S with indices of validation points
+      iCVoptPrefIn=S           prefix S of files with indices for CVopt
+    
+  Example:
+    MLatom.py createMLmodel XYZfile=CH3Cl.xyz Yfile=en.dat MLmodelOut=CH3Cl.unf
+''',
+  "estAccMLmodel":'''
+  Estimate accuracy of ML model
+  
+  Usage: MLatom.py estAccMLmodel [arguments]
+
+  estAccMLmodel task estimates accuracy of created ML models, thus it can
+  take the same arguments as createMLmodel task, see:
+    MLatom.py createMLmodel help
+  with exception that MLmodelOut=S argument is optional
+  
+  To estimate accuracy, the data set should be split into the
+  training and validation sets, see:
+    MLatom.py sample help
+  Additional optional arguments:
+    sampling=user-defined      reads in indices for the training and test sets
+                               from files defined by arguments
+      iTrainIn=S               file S with indices of training points
+      iTestIn=S                file S with indices of test points
+      iCVtestPrefIn=S          prefix S of files with indices for CVtest
+    MLmodelIn=S                file S with ML model
+    
+  Example:
+    MLatom.py estAccMLmodel XYZfile=CH3Cl.xyz Yfile=en.dat
+''',
+  'deltaLearn':'''
+  Use delta-learning
+  
+  Usage: MLatom.py deltaLearn [arguments]
+
+  Arguments:
+      Yb=S                     file with data obtained with baseline method
+      Yt=S                     file with data obtained with target   method
+      YestT=S                  file with ML estimations of  target   method
+      YestFile=S               file with ML corrections to  baseline method
+
+  delta-learning should be used with one of the following tasks, see:
+    MLatom.py useMLmodel    help
+    MLatom.py createMLmodel help
+    MLatom.py estAccMLmodel help
+
+  Example:
+    MLatom.py estAccMLmodel deltaLearn XfileIn=x.dat Yb=UHF.dat \\
+    Yt=FCI.dat YestT=D-ML.dat YestFile=corr_ML.dat
+''',
+  'selfCorrect':'''
+  Use self-correcting ML
+  
+  Usage: MLatom.py selfCorrect [arguments]
+
+  Currently works only with four layers and MLatomF
+  Self-correction should be used with one of the following tasks, see:
+    MLatom.py useMLmodel    help
+    MLatom.py createMLmodel help
+    MLatom.py estAccMLmodel help
+
+  Example:
+    MLatom.py estAccMLmodel selfcorrect XYZfile=xyz.dat Yfile=y.dat 
+''',
+  "learningCurve":'''
+  Generate learning curve
+  
+  Usage: MLatom.py learningCurve [arguments]
+
+  Required arguments:
+      lcNtrains=N,N,N,...,N    training set sizes
+  Optional arguments:
+      lcNrepeats=N,N,N,...,N   numbers of repeats for each Ntrain
+                 or
+                =N             number  of repeats for all  Ntrains
+                               [3 repeats default]
+
+  Output files in directory learningCurve:
+    results.json               JSON database file with all results
+    lcy.csv                    CSV  database file with results for values
+    lcygradxyz.csv             CSV  database file with results for XYZ gradients
+    lctimetrain.csv            CSV  database file with training   timings
+    lctimepredict.csv          CSV  database file with prediction timings
+    
+  learningCurve task also requires arguments used in estAccMLmodel task, see:
+    MLatom.py estAccMLmodel help
+
+  Example:
+    MLatom.py learningCurve XYZfile=xyz.dat Yfile=en.dat \\ 
+    lcNtrains=100,1000,10000 lcNrepeats=32
+''',
+  'crossSection':'''
+  Simulate absorption cross-section using ML-NEA (nuclear ensemble approach)
+      
+  Usage:
+    MLatom.py crossSection [arguments]
+
+  Optional arguments:
+    nExcitations=N             number of excited states [3 by default]
+    nQMpoints=N                number of QM calculations
+                               [determined iteratively by default]
+    plotQCNEA                  plot QC-NEA cross section
+    deltaQCNEA=float           set broadening parameter of QC-NEA cross section
+    plotQCSPC                  plot single point convolution cross section
+  
+    Advanced arguments:
+      nMaxPoints=N             maximum number of QC calculations
+                               in the iterative procedure [10000 by default]
+      nNEpoints=N              number of nuclear ensemble points
+                               [50000 by default]
+
+  Environment settings:
+    $NX                        Newton-X environment
+    In addition, Gaussian program environment should be setup
+  
+  Required input and data set files
+    gaussian_optfreq.com       input file for optimization and frequency
+                               calculations with Gaussian program
+    gaussian_ef.com            template input file for excited-state QC
+                               calculations with Gaussian program
+        or
+    eq.xyz                     file with optimized geometry
+    nea_geoms.xyz              file with all geometries in nuclear ensemble
+    
+  Optional input data files:
+    E[i].dat                   files with excitation energies  for excitation i
+    f[i].dat                   files with oscillator strengths for excitation i
+    cross-section_ref.dat      reference cross section spectrum
+  
+  Output files in directory cross-section:
+    cross-section_ml-nea.dat   ML-NEA cross section
+    cross-section_qc-nea.dat   QC-NEA cross section
+    cross-section_spc.dat      single point convolution cross section
+    plot.png                   cross section plots
+  
+  Cite ML-NEA:
+    B.-X. Xue, M. Barbatti, P. O. Dral, J. Phys. Chem. A 2020, 124, 7199.
+    DOI: 10.1021/acs.jpca.0c05310
+  
+  Please also cite Newton-X (and Gaussian)
+''',
+  'XYZ2X':('''
+  Convert XYZ coordinates into descriptor X
+  
+  Usage:
+    MLatom.py XYZ2X [arguments]
+
+  Required arguments:
+    MLmodelIn=S                file S with ML model
+    XYZfile=S                  file S with XYZ coordinates
+    XfileOut=S                 file S with X values
+''' +
+    molDescriptorDoc
+    +
+'''
+  Example:
+    MLatom.py XYZ2X XYZfile=CH3Cl.xyz XfileOut=CH3Cl.x
+'''),
+  'analyze':'''
+  Analyze data sets
+  
+  Usage: MLatom.py analyze [arguments]
+
+  Arguments:
+    For reference data (at least one of these arguments is required):
+      Yfile=S                  file S with values
+      Ygrad=S                  file S with gradients
+      YgradXYZfile=S           file S with gradients in XYZ coordinates
+
+    For estimated data:
+      YestFile=S               file S with estimated Y values
+      YgradEstFile=S           file S with estimated gradients
+      YgradXYZestFile=S        file S with estimated XYZ gradients
+    
+  Example: 
+    MLatom.py analyze Yfile=en.dat YestFile=enest.dat
+''',
+  'sample':'''
+  Sample data points from a data set
+  
+  Usage:
+    MLatom.py sample [arguments]
+
+  Required arguments:
+    Data set file
+      XYZfile=S                file S with XYZ coordinates
+          or
+      XfileIn=S                file S with input vectors X
+    
+    Splitting arguments (at least one is required):
+      Splitting the data set into the sub-sets:
+        iTrainOut=S            file S with indices of training points
+        iTestOut=S             file S with indices of test points
+        iSubtrainOut=S         file S with indices of sub-training points
+        iValidateOut=S         file S with indices of validation points
+        
+      Cross-validation for testing:
+        CVtest                 CV task with optional arguments:
+          NcvTestFolds=N       sets number of folds to N [5 by default]
+          LOOtest              leave-one-out cross-validation
+        iCVtestPrefOut=S       prefix S of files with indices for CVtest
+      Cross-validation for hyperparameter optimization:
+        CVopt                  CV task with optional arguments:
+          NcvOptFolds=N        sets number of folds to N [5 by default]
+          LOOopt               leave-one-out cross-validation
+        iCVoptPrefOut=S        prefix S of files with indices for CVopt
+
+  Optional arguments:
+    sampling=S                 type S of data set sampling into splits
+      random [default]         random sampling
+      none                     simply split unshuffled data set into
+                               the training and test sets (in this order)
+                               (and sub-training and validation sets)
+      structure-based          structure-based sampling
+      farthest-point           farthest-point traversal iterative procedure
+    Nuse=N                     N first entries of the data set file to be used
+    Ntrain=R                   number of the training points
+                               [0.8, i.e. 80% of the data set, by default]
+    Ntest=R                    number of the test points
+                               [remainder of data set, by default]
+    Nsubtrain=R                number of the sub-training points
+                               [0.8,    80% of the training set, by default]
+    Nvalidate=R                number of the validation points
+                               [remainder of the training set, by default]
+  Note: Number of indices R can either be positive integer or a fraction of 1.
+        R entries for integer R >= 1
+        fraction of the entire data set for 0<R<1
+  
+  Example:
+    MLatom.py sample sampling=structure-based XYZfile=CH3Cl.xyz Ntrain=1000 \\
+    Ntest=10000 iTrainOut=itrain.dat iTestOut=itest.dat
+''',
+  'slice':'''
+  Slice data set
+  
+  Usage:
+    MLatom.py slice [arguments]
+  
+  Required arguments:
+    XfileIn=S                  file S with input vectors X
+    eqXfileIn=S                file S with input vector for equilibrium geometry
+  
+  Optional arguments:
+    Nslices=N                  number of slices [3 by default]
+  
+  Example:
+    MLatom.py slice Nslices=3 XfileIn=x_sorted.dat eqXfileIn=eq.x
+
+''',
+  'sampleFromSlices':'''
+  Sample from each slice
+  
+  Usage:
+    MLatom.py sampleFromSlices [arguments]
+  
+  Required argument:
+    Ntrain=N                   total integer number N of training points
+                               from all slices
+  
+  Optional argument:
+    Nslices=N                  number of slices [3 by default]
+
+  Example:
+    MLatom.py sampleFromSlices Nslices=3 sampling=structure-based Ntrain=4480
+''',
+  'mergeSlices':'''
+  Merge indices from slices
+  
+  Usage:
+    MLatom.py mergeSlices [arguments]
+  
+  Required argument:
+    Ntrain=N                   total integer number N of training points
+                               from all slices
+  
+  Optional argument:
+    Nslices=N                  number of slices [3 by default]
+
+  Example:
+    MLatom.py mlatom mergeSlices Nslices=3 Ntrain=4480
+''',
+  "KRR":'''
+  Kernel ridge regression (KRR) calculations with MLatomF
+
+  Optional arguments:  
+    kernel=S                   kernel function type S
+      Gaussian [default]   
+      Laplacian
+      exponential
+      Matern
+    permInvKernel              permutationally invariant kernel, sub-option:
+      Nperm=N                  number of permutations N (with XfileIn argument)
+      molDescrType=permuted    (with XYZfile argument, see below)
+    lambda=R                   regularization hyperparameter R [0 by default]
+      opt                      requests optimization of lambda on a log grid
+        NlgLambda=N            N points on a logarithmic grid
+                               [6 by default]
+        lgLambdaL=R            lowest  value of log2(lambda) [-16.0 by default]
+        lgLambdaH=R            highest value of log2(lambda) [ -6.0 by default]
+    sigma=S                    length scale
+                               [default values: 100 (Gaussian  & Matern)
+                                                800 (Laplacian & exponential)]
+      opt                      requests optimization of sigma on a log grid
+        NlgSigma=N             N points on a logarithmic grid
+                               [11 by default]
+        lgSigmaL=R             lowest  value of log2(lambda)
+                               [default values:  2.0 (Gaussian  & Matern)
+                                                 5.0 (Laplacian & exponential)]
+        lgSigmaH=R             highest value of log2(lambda)
+                               [default values:  9.0 (Gaussian  & Matern)
+                                                12.0 (Laplacian & exponential)]
+    matDecomp=S                type of matrix decomposition
+      Cholesky [default]
+      LU                   
+      Bunch-Kaufman   
+    invMatrix                  invert matrix
+    refine                     refine solution matrix
+    on-the-fly                 on-the-fly calculation of kernel
+                               matrix elements for validation,
+                               by default it is false and those
+                               elements are stored
+    benchmark                  additional output for benchmarking
+    debug                      additional output for debugging
+    
+  Additional arguments for hyperparameter optimization on a log grid:
+    minimizeError=S            type S of error to minimize
+      RMSE                     root-mean-square error [default]
+      MAE                      mean absolute error
+   lgOptDepth=N                depth of log grid optimization N [3 by default]
+''' +
+    molDescriptorDoc +
+'''
+  Example:
+    MLatom.py createMLmodel XYZfile=CH3Cl.xyz Yfile=en.dat \\
+              MLmodelOut=CH3Cl.unf sigma=opt kernel=Matern
+''',
+  "hyperopt":'''
+  Hyperparameter optimization with the hyperopt package
+  For now, only Tree-Structured Parzen Estimator algorithm is supported
+  
+  Usage: substitute numeric value(s) with hyperopt.xx()
+  
+  Arguments for hyperopt.xx():
+    hyperopt.uniform(lb,ub)    linear search space from lb to ub
+    hyperopt.loguniform(lb,ub) logarithmic search space, base 2
+    hyperopt.quniform(lb,ub,q) discrete linear space, rounded by q
+  lb is lower bound, ub is upper bound
+
+  Arguments:
+      hyperopt.max_evals=N     max number of search attempts [8 by default]
+      hyperopt.losstype=S      type of loss used in optimization
+        geomean [default]      geometric mean
+        weighted               weight for gradients, defined by
+          hyperopt.w_grad=R    [0.1 by default]
+
+  Cite hyperopt:
+    J. Bergstra, D. Yamins, D. D. Cox, Making a Science of Model Search:
+    Hyperparameter Optimization in Hundreds of Dimensions for Vision
+    Architectures.
+    Proceedings of the 30th International Conference on Machine Learning
+    (ICML 2013), Vol. 28, JMLR.org, Atlanta, GA, USA, 2013, pp. I-115
+    
+  Cite Tree-Structured Parzen Estimator algorithm:
+    J. Bergstra, R. Bardenet, Y. Bengio, B. Kegl,
+    Algorithms for Hyper-Parameter Optimization.
+    In Advances in Neural Information Processing Systems, Vol. 24.
+    Eds.: J. Shawe-Taylor, R. Zemel, P. Bartlett, F. Pereira, K. Q. Weinberger,
+    Curan Associates, Inc., 2011
+
+  Example:
+    MLatom.py estAccMLmodel XYZfile=CH3Cl.xyz Yfile=en.dat \\
+              sigma=hyperopt.loguniform(4,20)
+'''
+    }

MLatom/header.py

@@ -0,0 +1,64 @@
+import json
+import sys,os
+
+def printHeader(args):
+    with open(os.path.dirname(__file__)+'/ref.json','r') as f:
+        refs = json.load(f)
+    refItems = {}
+
+    # ML tasks
+    if args.deltaLearn:  refItems['delta-learning']  = refs['JCTC2015_DeltaLearning']
+    if args.molDescriptor.upper() == 'CM': refItems['Coulomb matrix'] = refs['CM']
+    if args.selfCorrect: refItems['cross-section'] = refs['JCP2017_MLCH3Cl']
+    if (args.MLprog.lower() == 'mlatomf' or args.MLprog == '') and (args.MLmodelType.lower() == 'kreg' or not args.MLmodelType) and (args.createMLmodel or args.estAccMLmodel or args.XYZ2X):
+        if args.XYZfile != '' and (args.molDescriptor.upper() == 'RE' or not args.molDescriptor):
+            if args.kernel.lower() == 'gaussian' or args.kernel == '' and not args.XYZ2X:
+                refItems['KREG model'] = refs['JCP2017_MLCH3Cl']
+            else:
+                refItems['RE descriptor'] = refs['JCP2017_MLCH3Cl']
+    if (args.MLprog.lower() == 'sgdml' or args.MLmodelType.lower() == 'sgdml' or args.MLmodelType.lower() == 'gdml'):
+        refItems['sGDML program'] = refs['sGDMLprog']
+        if (args.MLmodelType.lower() == 'sgdml' or args.MLmodelType.lower() == ''):
+            refItems['sGDML model'] = refs['sGDMLmodel']
+        if (args.MLmodelType.lower() == 'gdml'):
+            refItems['GDML model'] = refs['sGDMLmodel']
+    if (args.MLprog.lower() in ['torchani','ani'] or args.MLmodelType.lower() == 'ani' or args.MLmodelType.lower() == 'ani-aev'):
+        refItems['TorchANI program'] = refs['TorchANI']
+        if (args.MLmodelType.lower() == 'ani' or args.MLmodelType.lower() == 'ani-aev' or args.MLmodelType.lower() == ''):
+            refItems['ANI model'] = refs['ANI']
+    if (args.MLprog.lower() in ['dp','deepmd','deepmd-kit'] or args.MLmodelType.lower() == 'dpmd' or args.MLmodelType.lower() == 'deeppot-se'):
+        refItems['DeePMD-kit program'] = refs['DeePMD-kit']
+        if (args.MLmodelType.lower() == 'deeppot-se' or args.MLmodelType.lower() == ''):
+            refItems['DeepPot-SE model'] = refs['DeepPot-SE']
+        if (args.MLmodelType.lower() == 'dpmd'):
+            refItems['DPMD model'] = refs['DPMD']
+    if (args.MLprog.lower() == 'physnet' or args.MLmodelType.lower() == 'physnet'):
+        refItems['PhysNet model & program'] = refs['PhysNet']
+    if (args.MLprog.lower() in [ 'gap', 'gap_fit', 'gapfit'] or args.MLmodelType.lower() == 'gap-soap'):
+        refItems['GAP model'] = refs['GAP']
+        if (args.MLmodelType.lower() == 'gap-soap' or args.MLmodelType.lower() == ''):
+            refItems['SOAP descriptor'] = refs['SOAP']
+    
+    if args.crossSection:  
+        refItems['ML-NEA']  = refs['ML-NEA']
+        refItems['NEA']  = refs['NEA']
+        refItems['Wigner distribution']  = refs['Wigner']
+        refItems['NEWTON-X']  = refs['NEWTON-X']
+
+    if 'hyperopt' in ' '.join(args.args2pass).lower():
+        refItems['hyperopt program'] = refs['hyperopt']
+        refItems['Tree-Structured Parzen Estimator algorithm'] = refs['TPE']
+    
+    # Data set tasks
+    if args.sampleFromSlices or args.mergeSlices or args.slice: refItems['slicing'] = refs['JCP2017_MLCH3Cl']
+    if args.sampling == 'structure-based': refItems['structure-based sampling'] = refs['JCP2017_MLCH3Cl']
+
+    if len(refItems.keys()) > 0:
+        print('\n %s \n' % ('*'*78))
+        print(' You are going to use feature(s) listed below. \n Please cite corresponding work(s) in your paper:')
+        for key in refItems.keys():
+            print('\n %s:'%key)
+            refstrs = refItems[key].split('\n')
+            for refstr in refstrs:
+                print('   %s' % refstr)
+        print('\n %s ' % ('*'*78))