Merge pull request #855 from caic99/develop

Doc: Format markdown files.

Author: dyzheng

doc/features.md

@@ -1,16 +1,19 @@
 # Features
+
 Here we summarize several features of ABACUS:
-   - [Basis sets](#basis-sets)
-   - [Pseudopotentials](#pseudopotentials)
-   - [Boundary conditions and k-points](#boundary-conditions-and-k-points)
-   - [Kohn-Sham solver](#kohn-sham-solver)
-   - [Exchange-correlation functionals](#exchange-correlation-functionals)
+
+- [Basis sets](#basis-sets)
+- [Pseudopotentials](#pseudopotentials)
+- [Boundary conditions and k-points](#boundary-conditions-and-k-points)
+- [Kohn-Sham solver](#kohn-sham-solver)
+- [Exchange-correlation functionals](#exchange-correlation-functionals)
 
      [back to main page](../README.md)
 
 ## Basis sets
 
 In ABACUS, there are 3 types of basis set choices:
+
 1. PW
 
     Plane wave basis.
@@ -22,15 +25,15 @@ In ABACUS, there are 3 types of basis set choices:
 3. LCAO_in_PW
 
     Expand the atomic basis in terms of plane waves, and use plane-waves techniques to construct the Hamiltonian matrix, but solve the eigenvalue problem within the LCAO basis set.
-    
+
 In the INPUT file, the keyword basis_type controls what basis type to use:
 
    1. PW: basis_type = pw
    2. LCAO: basis_type = lcao
    3. LCAO_in_PW: basis_type = lcao_in_pw
 
 The default value of basis_type is pw. When choosing lcao or lcao_in_pw, the user should prepare atomic orbitals first.
-    
+
 Information on the keyword basis_type can also be found in [the list of input keywords](input-main.md#basis-type).
 
 We also provide a [detailed instruction](generate-basis.md) on generating basis functions.
@@ -88,10 +91,11 @@ Information on the keyword ks_solver is also given in the [list of input variabl
 [back to top](#features)
 
 ## Exchange-correlation functionals
+
 In our package, the XC functional can either be set explicitly using the dft_functional keyword as explained below, or set implicitly according to the XC functional information read from pseudopotential file. The user should ensure that the XC functional set in the INPUT file and the pseudopotential file are consistent. **Currently only LDA and GGA are supported.**
 
 To be specific, we briefly explain the format of the pseudopotential file and the key information it contains. There are a few lines in Si’s GGA pseudopotential file Si_ONCV_PBE-1.0.upf:
-    
+
 ```
 <PP_HEADER
 generated="Generated using ONCVPSP code by D. R. Hamann"
@@ -115,12 +119,13 @@ rho_cutoff=" 6.01000000000E+00"
 ```
 
 The user can set the XC functional type in INPUT file with the parameter, dft_functional:
+
 - none: the functional is specified implicity by the input pseudopotential file
 - lda: Perdew-Zunger local density approximation
 - pbe: Perdew-Burke-Ernzerhof general gradient approximation
-    
+
 If the functional specified by the user is not consistent with the pseudopotential file, the program will stop with an error message.
 
 Information on the keyword ks_solver is also given in the [list of input variables](input-main.md#dft-functional).
 
-[back to top](#features)
+[back to top](#features)

doc/input-kpt.md

@@ -1,40 +1,45 @@
 # KPT file
+
 - [Generate k-mesh automatically](#generate-k-mesh-automatically)
 - [Set k-points explicitly](#set-k-points-explicitly)
 - [Band structure calculations](#band-structure-calculations)
 
-
    [back to main page](../README.md)
 
 ABACUS uses periodic boundary conditions for both crystals and finite systems. For isolated systems, such as atoms, molecules, clusters, etc., one uses the so-called supercell model. Lattice vectors of the supercell are set in the `STRU` file. For the input k-point (`KPT`) file, the file should either contain the k-point coordinates and weights or the mesh size for creating the k-point gird. Both options are allowed in `ABACUS`.
 
-## Generate k-mesh automatically 
+## Generate k-mesh automatically
+
 To generate k-mesh automatically, it requires the input subdivisions of the Brillouin zone
 in each direction and the origin for the k-mesh. ABACUS uses the Monkhorst-Pack
 method to generate k-mesh, and the following is an example input k-point (`KPT`) file used in
 `ABACUS`.
+
 ```
 K_POINTS //keyword for start
 0 //total number of k-point, `0' means generate automatically
 Gamma //which kind of Monkhorst-Pack method, `Gamma' or `MP'
 2 2 2 0 0 0 //first three number: subdivisions along recpri. vectors
-last three number: shift of the mesh
+            //last three number: shift of the mesh
 ```
+
 In the above example, the first line is a keyword, and it can be set as `K_POINTS`, or `KPOINTS` or just `K`.
 The second line is an integer, and its value determines how to get k-points. In this example, `0` means using Monkhorst-Pack (MP) method to generate k-points automatically.
 
-The third line tells the input type of k-points, ‘Gamma’ or ‘MP’, different Monkhorst Pack
+The third line tells the input type of k-points, `Gamma` or `MP`, different Monkhorst Pack
 (MP) method. Monkhorst-Pack (MP) is a method which uses the uniform k-points sampling in
-Brillouin-zone, while ’Gamma’ means the Γ-centered Monkhorst-Pack method.
+Brillouin-zone, while `Gamma` means the Γ-centered Monkhorst-Pack method.
 The first three numbers of the last line are integers, which give the MP k grid dimensions, and
 the rest three are real numbers, which give the offset of the k grid. In this example, the numbers
 `0 0 0` means that there is no offset, and this is the a standard 2by2by2 k grid.
 
 [back to top](#kpt-file)
 
 ## Set k-points explicitly
+
 If the user wants to set up the k-points explicitly, the input k-point file should contain
 the k-point coordinates and weights. An example is given as follows:
+
 ```
 K_POINTS //keyword for start
 8 //total number of k-point
@@ -52,22 +57,25 @@ Direct //`Direct' or `Cartesian' coordinate
 [back to top](#kpt-file)
 
 ## Band structure calculations
+
 ABACUS uses specified high-symmetry directions of the Brillouin zone for band structure
 calculations. The third line of k-point file should start with ‘Line’ or ‘Line_Cartesian’ for
 line mode. ‘Line’ means the positions below are in Direct coordinates, while ‘Line_Cartesian’
 means in Cartesian coordinates:
+
 ```
-K_POINTS # keyword for start
-6 # number of high symmetry lines
-Line # line-mode
-0.5 0.0 0.5 20 # X
-0.0 0.0 0.0 20 # G
-0.5 0.5 0.5 20 # L
-0.5 0.25 0.75 20 # W
-0.375 0.375 0.75 20 # K
-0.0 0.0 0.0 1 # G
+K_POINTS // keyword for start
+6 // number of high symmetry lines
+Line // line-mode
+0.5 0.0 0.5 20 // X
+0.0 0.0 0.0 20 // G
+0.5 0.5 0.5 20 // L
+0.5 0.25 0.75 20 // W
+0.375 0.375 0.75 20 // K
+0.0 0.0 0.0 1 // G
 ```
+
 The fourth line and the following are special k-point coordinates and number of k-points
 between this special k-point and the next.
 
-[back to top](#kpt-file)
+[back to top](#kpt-file)