Additional explanations to the example files and fixing result.ref file in examples/bsse/water

examples/band/lcao_Si2/run.sh

@@ -19,10 +19,10 @@ if [[ ! -f scf.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_nscf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi
 

examples/band/pw_Al/run.sh

@@ -19,9 +19,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_nscf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/berryphase/lcao_PbTiO3/run.sh

@@ -21,9 +21,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_nscf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/berryphase/pw_PbTiO3/run.sh

@@ -19,9 +19,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_nscf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/bravais_lattice/fcc_SiO2/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/bravais_lattice/hexagonal_MoS2/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/bravais_lattice/so_SnTe/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/bsse/water/INPUT

@@ -1,17 +1,21 @@
+#this is the input of using counterpoise to correct the BSSE error
+#
 INPUT_PARAMETERS
 #Parameters	(General)
 pseudo_dir		../../../tests/PP_ORB
 orbital_dir		../../../tests/PP_ORB
 #Parameters (Accuracy)
-ecutwfc			 60 ### Please refer to orbital files[1] to set ecutwfc for LCAO basis.
+ecutwfc			 60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_nmax		100
 scf_thr                 1e-6
 basis_type		lcao
 
-gamma_only 1 ### Abacus will generate KPT file when gamma_only=1.
+gamma_only 1 ### Abacus will generate/overwrite a KPT file when gamma_only is set to 1.
 
 smearing_method gauss
-smearing_sigma 0.02
+smearing_sigma 0.015
 
 
-### [1]The energy cutoff of a LCAO basis can be found in lines starting with "Energy Cutoff" of a .orb file.
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.

examples/bsse/water/KPT

@@ -2,3 +2,4 @@ K_POINTS
 0
 Gamma
 1 1 1 0 0 0
+###This file will be overwritten by Abacus because either kspacing is used or gamma_only is set to 1

examples/bsse/water/README

@@ -1,12 +1,12 @@
 example showcasing how to use BSSE correction to calculate formation energy of water
 STRU_0 : used along with ntype = 2;normal calculation of water molecule (E_h2o)
-	 obtained total energy of -466.4838149140513 eV
+	 obtained total energy of -466.1225988776397 eV
 STRU_1 : used along with ntype = 2;calculation of single O atom (E_o)
-	 obtained total energy of -427.9084406198214 eV
+	 obtained total energy of -427.6271689751553 eV
 STRU_2 : used along with ntype = 3;calculation of 1st H atom (E_h1)
-         obtained total energy of -12.59853381731160 eV
+         obtained total energy of -12.58872469295076 eV
 STRU_3 : used along with ntype = 3;calculation of 2nd H atom (E_h2)
-         obtained total energy of -12.59853378720844 eV
+         obtained total energy of -12.58872446212924 eV
 
 Thus, the formation energy is given by:
-E_h2o - (E_o + E_h1 + E_h2) ~ -13.38 eV
+E_h2o - (E_o + E_h1 + E_h2) ~ -13.32 eV

examples/bsse/water/result.ref

@@ -1,5 +1,5 @@
--13.31774791420906
-E_H2O: -466.1219344619547
-E_O: -427.6267373722137
-E_H1: -12.58872471938786
-E_H2: -12.58872445614408
+-13.31798074740440
+E_H2O: -466.1225988776397
+E_O: -427.6271689751553
+E_H1: -12.58872469295076
+E_H2: -12.58872446212924

examples/bsse/water/run.sh

@@ -51,9 +51,9 @@ if [[ ! -f H2O_scf.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf_H2.log)" == " Total  Time  :"* ) ]] ||
    [ $(echo "$abs_difference < 0.00001" | bc) -ne 1 ]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/charge_density/lcao_nspin1_Si2/INPUT

@@ -8,11 +8,13 @@ nbands                          8
 basis_type                      lcao
 symmetry                        0       
 #Parameters (Accuracy)
-ecutwfc                          60 ### Please refer to orbital files[1] to set ecutwfc for LCAO basis.
+ecutwfc                          60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                         1.0e-7  // about iteration
 scf_nmax			100
 #Parameters (File)
 out_chg                         1
 
 
-### [1]The energy cutoff of a LCAO basis can be found in lines starting with "Energy Cutoff" of a .orb file.
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.

examples/charge_density/lcao_nspin1_Si2/run.sh

@@ -11,9 +11,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/SPIN1_CHG.cube ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/charge_density/pw_nspin1_Al/INPUT

@@ -9,7 +9,7 @@ ecutwfc                          60 ###Energy cutoff needs to be tested to ensur
 scf_thr                         1.0e-8  // about iteration
 scf_nmax			100
 smearing_method         	gauss
-smearing_sigma          	0.015
+smearing_sigma          	0.01
 #Parameters (File)
 out_chg                         1
 

examples/charge_density/pw_nspin1_Al/run.sh

@@ -11,9 +11,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/SPIN1_CHG.cube ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/charge_density/pw_nspin2_Fe/INPUT

@@ -13,7 +13,7 @@ basis_type    pw
 ks_solver     cg
 
 smearing_method    gaussian
-smearing_sigma       0.07
+smearing_sigma       0.015
 
 mixing_type    broyden 
 mixing_beta    0.5

examples/charge_density/pw_nspin2_Fe/run.sh

@@ -12,9 +12,9 @@ if [[ ! -f output ]] ||
    [[ ! -f OUT.ABACUS/SPIN2_CHG.cube ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/charge_mixing/pw_Al/run.sh

@@ -32,9 +32,9 @@ if [[ ! -f scf1.output ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf3.log)" == " Total  Time  :"* ) ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf4.log)" == " Total  Time  :"* ) ]]
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/compensating_charge/Pt-slab/INPUT

@@ -8,9 +8,9 @@ ecutwfc		  60 ###Energy cutoff needs to be tested to ensure your calculation is
 scf_nmax	  200
 scf_thr		  1.0e-7
 basis_type	  pw
-gamma_only        1 ### Abacus will generate KPT file when gamma_only=1.
+gamma_only        1 ### Abacus will generate/overwrite a KPT file when gamma_only is set to 1.
 smearing_method	  gauss
-smearing_sigma	  0.02
+smearing_sigma	  0.015
 mixing_type       broyden
 mixing_beta       0.1
 

examples/compensating_charge/Pt-slab/run.sh

@@ -12,9 +12,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! -f OUT.ABACUS/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.ABACUS/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/deepks/lcao_CsPbI3/INPUT

@@ -7,17 +7,17 @@ calculation             scf
 symmetry                0
 
 #Parameters (2.Iteration)
-ecutwfc                 100 ### Please refer to orbital files[1] to set ecutwfc for LCAO basis.
+ecutwfc                 100 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                     1e-7
 scf_nmax                   50
 
 #Parameters (3.Basis)
 basis_type             lcao 
-kspacing               0.1 ### Abacus will generate KPT file when kspacing is used.
+kspacing               0.1 ### Abacus will generate/overwrite a KPT file when kspacing is used.
 
 #Parameters (4.Smearing)
 smearing_method                gaussian
-smearing_sigma                   0.015
+smearing_sigma                   0.0015
 
 #Parameters (5.Mixing)
 mixing_type             broyden
@@ -32,4 +32,6 @@ lspinorb 1
 
 
 
-### [1]The energy cutoff of a LCAO basis can be found in lines starting with "Energy Cutoff" of a .orb file.
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.

examples/deepks/lcao_CsPbI3/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! -f OUT.abacus/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.abacus/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/deepks/lcao_H2O/INPUT

@@ -8,7 +8,7 @@ nbands                  16
 symmetry                0
 
 #Parameters (2.Iteration)
-ecutwfc                  60 ### Please refer to orbital files[1] to set ecutwfc for LCAO basis.
+ecutwfc                  60 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr                 1e-8
 scf_nmax                5
 
@@ -18,7 +18,7 @@ gamma_only              0
 
 #Parameters (4.Smearing)
 smearing_method         gaussian
-smearing_sigma          0.02
+smearing_sigma          0.015
 
 #Parameters (5.Mixing)
 mixing_type             broyden
@@ -33,4 +33,6 @@ deepks_model	    model.ptg
 deepks_bandgap      1
 
 
-### [1]The energy cutoff of a LCAO basis can be found in lines starting with "Energy Cutoff" of a .orb file.
+### [1] Energy cutoff determines the quality of numerical quadratures in your calculations.
+###     So it is strongly recommended to test whether your result (such as converged SCF energies) is
+###     converged with respect to the energy cutoff.

examples/deepks/lcao_H2O/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! -f OUT.abacus/running_scf.log ]] ||
    [[ ! ( "$(tail -1 OUT.abacus/running_scf.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi

examples/deepks/pw_H2O/INPUT

@@ -14,11 +14,11 @@ scf_nmax                   50
 
 #Parameters (3.Basis)
 basis_type              pw
-gamma_only              1 ### Abacus will generate KPT file when gamma_only=1.
+gamma_only              1 ### Abacus will generate/overwrite a KPT file when gamma_only is set to 1.
 
 #Parameters (4.Smearing)
 smearing_method                gaussian
-smearing_sigma                   0.1
+smearing_sigma                   0.015
 
 #Parameters (5.Mixing)
 mixing_type             broyden

examples/deepks/pw_H2O/KPT

@@ -2,6 +2,4 @@ K_POINTS
 0
 Gamma
 1 1 1 0 0 0
-### If you are running an energy calculation, please make sure your final energy is
-### converged with respect to the k-point settings, unless you set a loose k-point
-### mesh on purpose.
+###This file will be overwritten by Abacus because either kspacing is used or gamma_only is set to 1

examples/deepks/pw_H2O/run.sh

@@ -10,9 +10,9 @@ if [[ ! -f scf.output ]] ||
    [[ ! -f OUT.abacus/running_gen_bessel.log ]] ||
    [[ ! ( "$(tail -1 OUT.abacus/running_gen_bessel.log)" == " Total  Time  :"* ) ]] 
 then
-	echo "job is failed!"
+	echo "job failed!"
 	exit 1
 else
-	echo "job is successed!"
+	echo "job succeeded!"
 	exit 0
 fi