Fix: update the example of vdwd3 acoording to the latest impl. (#5418)

Author: kirk0830

examples/vdw/si2/INPUT1 renamed to examples/vdw/si2-vdwd2/INPUT1

@@ -1,5 +1,6 @@
-#INPUT file for applying D3(BJ) correction
-#with default VdW parameters
+#INPUT file for applying D2 correction
+#where I chose to manually set the C6 parameter
+#in file c6.txt
 #in pw basis
 
 INPUT_PARAMETERS
@@ -12,4 +13,5 @@ ecutwfc			50
 scf_nmax		100
 scf_thr                 1e-6
 basis_type		pw
-vdw_method 		d3_bj
+vdw_method 		d2
+vdw_C6_file		c6.txt

examples/vdw/si2/INPUT2 renamed to examples/vdw/si2-vdwd2/INPUT2

@@ -0,0 +1,15 @@
+#INPUT file for applying D3(BJ) correction
+#in lcao basis
+
+INPUT_PARAMETERS
+#Parameters    (General)
+pseudo_dir      ../../../tests/PP_ORB
+orbital_dir     ../../../tests/PP_ORB
+ntype           1    
+#Parameters (Accuracy)
+ecutwfc         50
+scf_nmax        100
+scf_thr         1e-6
+basis_type      lcao
+vdw_method      d3_bj
+dft_functional  MGGA_X_SCAN+MGGA_C_SCAN

examples/vdw/si2/KPT renamed to examples/vdw/si2-vdwd2/KPT

@@ -0,0 +1,15 @@
+#INPUT file for applying D3(BJ) correction
+#in pw basis
+
+INPUT_PARAMETERS
+#Parameters    (General)
+pseudo_dir      ../../../tests/PP_ORB
+orbital_dir     ../../../tests/PP_ORB
+ntype           1    
+#Parameters (Accuracy)
+ecutwfc         50
+scf_nmax        100
+scf_thr         1e-6
+basis_type      pw
+vdw_method      d3_bj
+dft_functional  pbe

examples/vdw/si2/STRU renamed to examples/vdw/si2-vdwd2/STRU

@@ -0,0 +1,21 @@
+#INPUT file for applying D3(BJ) correction
+#in lcao basis. This example illustrates 
+#the manually setting on vdw parameters
+
+INPUT_PARAMETERS
+#Parameters    (General)
+pseudo_dir      ../../../tests/PP_ORB
+orbital_dir     ../../../tests/PP_ORB
+ntype           1    
+#Parameters (Accuracy)
+ecutwfc         50
+scf_nmax        100
+scf_thr         1e-6
+basis_type      lcao
+vdw_method      d3_bj
+dft_functional  pbe
+vdw_s6          1.000
+vdw_s8          0.722
+vdw_a1          1.217
+vdw_a2          1.000
+

examples/vdw/si2/c6.txt renamed to examples/vdw/si2-vdwd2/c6.txt

@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+4 4 4 0 0 0