Additional explanations to the example files and fixing result.ref file in examples/bsse/water (#5484)

* fixing sigma value in input files and adding comments to ecutwfc keyword

* fixing comments in examples using LCAO basis

* fixing comments in examples using LCAO basis

* futher change of additional information in example files and change of result.ref in examples/bsse/water/

* adding more explanations in example INPUT and KPT files

* minor change of English

* fixing file name error

* minor fix of a file (I do not tell you which one)

Author: BariumOxide13716

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