Package: packaging-extrapolation
packaging-extrapolation ManualAboutThis package contains partial extrapolation methods in quantum chemistry, written using the extrapolation method proposed in the literature. Extrapolation to the CBS limit can be done by entering two successive energies.Quickly UsePlease use thepipcommand to install:pip install packaging_extrapolationorpython3 -m pip install packaging_extrapolationPlease make sure the package is the latest:pip install --upgrade packaging_extrapolationAfter installation, test the example insrc/packaging_extrapolation/examples/examples_energy.pyto see if you get results.Extrapolation Method Calls:python  examples_energy.py -m "Klopper_1986" -xe -76.0411795 -ye -76.0603284 -low 2 -high 3 -a 4.25-m: extrapolation method name.-xe: energy for E(X).-ye: energy for E(Y).-low: cardinal number for X.-high: cardinal number for Y.-a: extrapolation parameter alpha/beta.Ten Extrapolation SchemesMethodTwo-point FromNameReferenceKlopper-1986$E_{CBS}=\frac{E(Y)e^{-α\sqrt{X}}-E(X)e^{-α\sqrt{Y}}}{e^{-α\sqrt{X}}-e^{-α\sqrt{Y}}}$Klopper_1986https://doi.org/10.1016/0166-1280(86)80068-9Feller-1992$E_{CBS}=\frac{E(Y)e^{-αX}-E(X)e^{-αY}}{e^{-αX}-e^{-αY}}$Feller_1992https://doi.org/10.1063/1.462652Truhlar-1998 (Hartree-Fock)$E_{CBS}=\frac{E(Y)X^{-\alpha}-E(X)Y^{-\alpha}}{X^{-\alpha}-Y^{-\alpha}}$Truhlar_1998https://doi.org/10.1016/S0009-2614(98)00866-5Jensen-2001$E_{CBS}=\frac{E(Y)(X+1)e^{-α\sqrt{X}}-E(X)(Y+1))e^{-α\sqrt{Y}}}{(X+1)e^{-α\sqrt{X}}-(Y+1)e^{-α\sqrt{Y}}}$Jensen_2001https://doi.org/10.1063/1.1413524Schwenke-2005$E_{CBS}=[E(Y)-E(X)]\alpha+E(X)$Schwenke_2005https://doi.org/10.1063/1.1824880Martin-1996$E_{CBS}=\frac{E(Y)(X+1/2)^{-\beta}-E(X)(Y+1/2)^{-\beta}}{(X+1/2)^{-\beta}-(Y+1/2)^{-\beta}}$Martin_1996https://doi.org/10.1016/0009-2614(96)00898-6Truhlar-1998 (Correlation)$E_{CBS}=\frac{E(Y)X^{-\beta}-E(X)Y^{-\beta}}{X^{-\beta}-Y^{-\beta}}$Truhlar_1998https://doi.org/10.1016/S0009-2614(98)00866-5Huh-2003$E_{CBS}=\frac{E(Y)(X+\beta)^{-3}-E(X)(Y+\beta)^{-3}}{(X+\beta)^{-3}-(Y+\beta)^{-3}}$HuhLee_2003https://doi.org/10.1063/1.1534091Bakowies-2007$E_{CBS}=\frac{E(Y)(X+1)^{-\beta}-E(X)(Y+1)^{-\beta}}{(X+1)^{-\beta}-(Y+1)^{-\beta}}$Bkw_2007https://doi.org/10.1063/1.2749516OAN(C)$E_{CBS}=\frac{3^3E(Y)-\beta^3E(X)}{3^3-\beta^3}$OAN_Chttps://doi.org/10.1002/jcc.23896Another UseIf you need to calculate the extrapolation energy of more systems, please refer to the following examples:frompackaging_extrapolationimportUtilToolsfrompackaging_extrapolation.ExtrapolationimportFitMethodimportpandasaspdimportnumpyasnp"""Calculate more systems."""if__name__=="__main__":# Input file.data=pd.read_csv('../data/hf.CSV')# Extrapolation model.model=FitMethod()# The E(X) and E(Y).x_energy_list,y_energy_list=data['aug-cc-pvdz'],data['aug-cc-pvtz']# Using Klopper-1986 method and alpha=4.25, extrapolate to the CBS limit at the AV {D, T}Z basis set pair.low_card,high_card,alpha,method_name=2,3,4.25,'Klopper_1986'result=UtilTools.train_alpha(model=model,method=method_name,x_energy_list=x_energy_list,y_energy_list=y_energy_list,low_card=low_card,high_card=high_card,alpha=alpha)foriinrange(len(result)):print(result[i],'Eh')df=pd.DataFrame()df['CBS Energy']=result# Output file.df.to_csv('CBS_Energy.csv',index=False)The input file should be in.csvformat and have the following content:mol,aug-cc-pvdz,aug-cc-pvtzHCN,-92.8880397,-92.9100033HCO,-113.2672513,-113.2947633HNO,-129.8114596,-129.8401888HO2,-150.2024221,-150.239531N2O,-183.7105405,-183.7530387NH2,-55.5749363,-55.5878344NH3,-56.1972947,-56.2127423NO2,-204.0664514,-204.1137363FunctionsUtilTools.calc_MAD(y_true, y_pred): Calculate the Mean Absolute Deviation (kcal/mol).UtilTools.calc_max_MAD(y_true, y_pred): Calculate the Maximum Absolute Deviation (kcal/mol).UtilTools.calc_min_MAD(y_true, y_pred): Calculate the Minimum Absolute Deviation (kcal/mol).UtilTools.calc_RMSE(y_true, y_pred): Calculate the Root Mean Square Deviation (kcal/mol).UtilTools.calc_MSD(y_true, y_pred): Calculate the Mean Square Deviation (kcal/mol).UtilTools.calc_MaxPosMAD(y_true, y_pred): Calculate the Maximum Positive Deviation (kcal/mol).UtilTools.train_alpha(*,  model, method, x_energy_list, y_energy_list, alpha, low_card, high_card): Calculate extrapolated energy.UtilLog.extract_energy(input_path, output_path): Extracting energy from many log files.train_all(*, model, method, x_energy_list, y_energy_list, low_card, high_card, limit_list, init_guess=0.001, temp='RMSD'): Optimizing extrapolation parameters withRMSDorMAD.