update documents

Author: mohanchen

docs/advanced/input_files/input-main.md

@@ -539,7 +539,7 @@ These variables are used to control general system parameters.
 - **Description**: The accuracy for symmetry analysis. Typically, the default value is good enough, but if the lattice parameters or atom positions in STRU file are not accurate enough, this value should be enlarged.
   > Note: if *[calculation](#calculation)==cell_relax*, this value can be dynamically changed corresponding to the variation of accuracy of the lattice parameters and atom positions during the relaxation. The new value will be printed in `OUT.${suffix}/running_cell-relax.log` in that case.
 - **Default**: 1.0e-6
-- **Unit**:  Bohr
+- **Unit**: Bohr
 
 ### symmetry_autoclose
 
@@ -574,7 +574,7 @@ These variables are used to control general system parameters.
   - bcc: body-centered cubic
   - hexagonal: hexagonal
   - trigonal: trigonal
-  - st: simple tetragona
+  - st: simple tetragonal
   - bct: body-centered tetragonal
   - so: orthorhombic
   - baco: base-centered orthorhombic
@@ -771,15 +771,17 @@ These variables are used to control the plane wave related parameters.
 ### ecutwfc
 
 - **Type**: Real
-- **Description**: Energy cutoff for plane wave functions, the unit is **Rydberg**. Note that even for localized orbitals basis, you still need to setup an energy cutoff for this system. Because our local pseudopotential parts and the related force are calculated from plane wave basis set, etc. Also, because our orbitals are generated by matching localized orbitals to a chosen set of wave functions from a certain energy cutoff, this set of localize orbitals is most accurate under this same plane wave energy cutoff.
+- **Description**: Energy cutoff for plane wave functions. Note that even for localized orbitals basis, you still need to setup an energy cutoff for this system. Because our local pseudopotential parts and the related force are calculated from plane wave basis set, etc. Also, because our orbitals are generated by matching localized orbitals to a chosen set of wave functions from a certain energy cutoff, this set of localize orbitals is most accurate under this same plane wave energy cutoff.
 > `ecutwfc` and `ecutrho` can be set simultaneously. Besides, if only one parameter is set, abacus will automatically set another parameter based on the 4-time relationship. If both parameters are not set, the default values will be employed.
-- **Default**: 50 Ry (PW basis), 100 Ry (LCAO basis)
+- **Default**: 50 for PW basis, 100 for LCAO basis
+- **Unit**: Ry
 
 ### ecutrho
 
 - **Type**: Real
-- **Description**: Energy cutoff for charge density and potential, the unit is **Rydberg**. For norm-conserving pseudopotential you should stick to the default value, you can reduce it by a little but it will introduce noise especially on forces and stress. For ultrasoft pseudopotential a larger value than the default is often desirable (`ecutrho` = 8 to 12 times `ecutwfc`, typically). The use of gradient-corrected functional, especially in cells with vacuum, or for pseudopotential without non-linear core correction, usually requires an higher values of `ecutrho` to be accurately converged.
+- **Description**: Energy cutoff for charge density and potential. For norm-conserving pseudopotential you should stick to the default value, you can reduce it by a little but it will introduce noise especially on forces and stress. For ultrasoft pseudopotential a larger value than the default is often desirable (`ecutrho` = 8 to 12 times `ecutwfc`, typically). The use of gradient-corrected functional, especially in cells with vacuum, or for pseudopotential without non-linear core correction, usually requires an higher values of `ecutrho` to be accurately converged.
 - **Default**: 4*ecutwfc
+- **Unit**: Ry
 
 ### nx, ny, nz
 
@@ -897,20 +899,23 @@ These variables are used to control the numerical atomic orbitals related parame
 ### lcao_dk
 
 - **Type**: Real
-- **Description**: k spacing (in Bohr${}^{-1}$) for two-center integrals. The two-center integration table are obtained via a k space integral on a uniform grid with spacing `lcao_dk`.
+- **Description**: the interval of k points for two-center integrals. The two-center integration table are obtained via a k space integral on a uniform grid with spacing `lcao_dk`.
 - **Default**: 0.01
+- **Unit**: Bohr${}^{-1}$
 
 ### lcao_dr
 
 - **Type**: Real
-- **Description**: r spacing (in Bohr) of the integration table of two-center integrals.
+- **Description**: r spacing of the integration table of two-center integrals.
 - **Default**: 0.01
+- **Unit**: Bohr
 
 ### lcao_rmax
 
 - **Type**: Real
-- **Description**: Maximum distance (in Bohr) for the two-center integration table.
+- **Description**: Maximum distance for the two-center integration table.
 - **Default**: 30
+- **Unit**: Bohr
 
 ### search_radius
 
@@ -984,8 +989,8 @@ calculations.
 
   Then the user has to correct the input file and restart the calculation.
 - **Default**: 
-  - **PW basis**: cg.
-  - **LCAO basis**:
+  - PW basis: cg.
+  - LCAO basis:
     - genelpa (if compiling option `USE_ELPA` has been set)
     - lapack (if compiling option `ENABLE_MPI` has not been set)
     - scalapack_gvx (if compiling option `USE_ELPA` has not been set and compiling option `ENABLE_MPI` has been set)
@@ -1186,26 +1191,26 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 - **Type**: Boolean
 - **Availability**: Only relevant for meta-GGA calculations.
 - **Description**: Whether to mix the kinetic energy density.
-  - **True**: The kinetic energy density will also be mixed. It seems for general cases, SCF converges fine even without this mixing. However, if there is difficulty in converging SCF for meta-GGA, it might be helpful to turn this on.
-  - **False**: The kinetic energy density will not be mixed.
+  - True: The kinetic energy density will also be mixed. It seems for general cases, SCF converges fine even without this mixing. However, if there is difficulty in converging SCF for meta-GGA, it might be helpful to turn this on.
+  - False: The kinetic energy density will not be mixed.
 - **Default**: False
 
 ### mixing_dftu
 
 - **Type**: Boolean
 - **Availability**: Only relevant for DFT+U calculations.
 - **Description**: Whether to mix the occupation matrices.
-  - **True**: The occupation matrices will also be mixed by plain mixing. From experience this is not very helpful if the +U calculation does not converge.
-  - **False**: The occupation matrices will not be mixed.
+  - True: The occupation matrices will also be mixed by plain mixing. From experience this is not very helpful if the +U calculation does not converge.
+  - False: The occupation matrices will not be mixed.
 - **Default**: False
 
 ### gamma_only
 
 - **Type**: Integer
 - **Availability**: Only used in localized orbitals set
 - **Description**: Whether to use gamma_only algorithm.
-  - **0**: more than one k-point is used and the ABACUS is slower compared to the gamma only algorithm.
-  - **1**: ABACUS uses gamma only, the algorithm is faster and you don't need to specify the k-points file.
+  - 0: more than one k-point is used and the ABACUS is slower compared to the gamma only algorithm.
+  - 1: ABACUS uses gamma only, the algorithm is faster and you don't need to specify the k-points file.
 
   Note: If gamma_only is set to 1, the KPT file will be overwritten. So make sure to turn off gamma_only for multi-k calculations.
 
@@ -1241,8 +1246,8 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 
 - **Type**: Integer
 - **Description**: Choose the calculation method of convergence criterion.
-  - **1**: the criterion is defined as $\Delta\rho_G = \frac{1}{2}\iint{\frac{\Delta\rho(r)\Delta\rho(r')}{|r-r'|}d^3r d^3r'}$, which is used in SCF of PW basis with unit Ry. 
-  - **2**: the criterion is defined as $\Delta\rho_R = \frac{1}{N_e}\int{|\Delta\rho(r)|d^3r}$, where $N_e$ is the number of electron, which is used in SCF of LCAO with unit **dimensionless**.
+  - 1: the criterion is defined as $\Delta\rho_G = \frac{1}{2}\iint{\frac{\Delta\rho(r)\Delta\rho(r')}{|r-r'|}d^3r d^3r'}$, which is used in SCF of PW basis with unit Ry. 
+  - 2: the criterion is defined as $\Delta\rho_R = \frac{1}{N_e}\int{|\Delta\rho(r)|d^3r}$, where $N_e$ is the number of electron, which is used in SCF of LCAO with unit **dimensionless**.
 
 - **Default**: 1 (plane-wave basis), or 2 (localized atomic orbital basis).
 
@@ -1251,8 +1256,8 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 - **Type**: bool
 - **Description**: For systems that are difficult to converge, the SCF process may exhibit oscillations in charge density, preventing further progress toward the specified convergence criteria and resulting in continuous oscillation until the maximum number of steps is reached; this greatly wastes computational resources. To address this issue, this function allows ABACUS to terminate the SCF process early upon detecting oscillations, thus reducing subsequent meaningless calculations. The detection of oscillations is based on the slope of the logarithm of historical drho values.. To this end, Least Squares Method is used to calculate the slope of the logarithmically taken drho for the previous `scf_os_ndim` iterations. If the calculated slope is larger than `scf_os_thr`, stop the SCF.
 
-  - **0**: The SCF will continue to run regardless of whether there is oscillation or not. 
-  - **1**: If the calculated slope is larger than `scf_os_thr`, stop the SCF.
+  - 0: The SCF will continue to run regardless of whether there is oscillation or not. 
+  - 1: If the calculated slope is larger than `scf_os_thr`, stop the SCF.
 
 - **Default**: false
 
@@ -1279,25 +1284,25 @@ Note: In new angle mixing, you should set `mixing_beta_mag >> mixing_beta`. The
 
 - **Type**: String
 - **Description**: Methods to do extrapolation of density when ABACUS is doing geometry relaxations or molecular dynamics.
-  - **atomic**: atomic extrapolation.
-  - **first-order**: first-order extrapolation.
-  - **second-order**: second-order extrapolation.
+  - atomic: atomic extrapolation.
+  - first-order: first-order extrapolation.
+  - second-order: second-order extrapolation.
 - **Default**: first-order (geometry relaxations), second-order (molecular dynamics), else atomic
 
 ### lspinorb
 
 - **Type**: Boolean
 - **Description**: Whether to consider spin-orbital coupling effect in the calculation.
-  - **True**: Consider spin-orbital coupling effect, and `nspin` is also automatically set to 4.
-  - **False**: Do not consider spin-orbital coupling effect.
+  - True: Consider spin-orbital coupling effect, and `nspin` is also automatically set to 4.
+  - False: Do not consider spin-orbital coupling effect.
 - **Default**: False
 
 ### noncolin
 
 - **Type**: Boolean
 - **Description**: Whether to allow non-collinear polarization, in which case the coupling between spin up and spin down will be taken into account.
-  - **True**: Allow non-collinear polarization, and `nspin` is also automatically set to 4.
-  - **False**: Do not allow non-collinear polarization.
+  - True: Allow non-collinear polarization, and `nspin` is also automatically set to 4.
+  - False: Do not allow non-collinear polarization.
 - **Default**: False
 
 ### soc_lambda
@@ -1454,14 +1459,14 @@ These variables are used to control the geometry relaxation.
 ### force_thr
 
 - **Type**: Real
-- **Description**: Threshold of the force convergence in Ry/Bohr. The threshold is compared with the largest force among all of the atoms. The recommended value for using atomic orbitals is 0.04 eV/Angstrom (0.0016 Ry/Bohr). The parameter is equivalent to [force_thr_ev](#force_thr_ev) except for the unit. You may choose either you like.
+- **Description**: Threshold of the force convergence. The threshold is compared with the largest force among all of the atoms. The recommended value for using atomic orbitals is 0.04 eV/Angstrom (0.0016 Ry/Bohr). The parameter is equivalent to [force_thr_ev](#force_thr_ev) except for the unit, you can choose either you like.
 - **Default**: 0.001
 - **Unit**: Ry/Bohr (25.7112 eV/Angstrom)
 
 ### force_thr_ev
 
 - **Type**: Real
-- **Description**: Threshold of the force convergence in eV/Angstrom. The threshold is compared with the largest force among all of the atoms. The recommended value for using atomic orbitals is 0.04 eV/Angstrom (0.0016 Ry/Bohr). The parameter is equivalent to [force_thr](#force_thr) except for the unit. You may choose either you like.
+- **Description**: Threshold of the force convergence. The threshold is compared with the largest force among all of the atoms. The recommended value for using atomic orbitals is 0.04 eV/Angstrom (0.0016 Ry/Bohr). The parameter is equivalent to [force_thr](#force_thr) except for the unit. You may choose either you like.
 - **Default**: 0.0257112
 - **Unit**: eV/Angstrom (0.03889 Ry/Bohr)
 
@@ -1532,15 +1537,15 @@ These variables are used to control the geometry relaxation.
 - **Type**: String
 - **Availability**: only used when `calculation` set to `cell-relax`
 - **Description**: Axes that are fixed during cell relaxation. Possible choices are:
-  - **None**: default; all of the axes can relax
-  - **volume**: relaxation with fixed volume
-  - **shape**: fix shape but change volume (i.e. only lattice constant changes)
-  - **a**: fix a axis during relaxation
-  - **b**: fix b axis during relaxation
-  - **c**: fix c axis during relaxation
-  - **ab**: fix both a and b axes during relaxation
-  - **ac**: fix both a and c axes during relaxation
-  - **bc**: fix both b and c axes during relaxation
+  - None**: default; all of the axes can relax
+  - volume**: relaxation with fixed volume
+  - shape**: fix shape but change volume (i.e. only lattice constant changes)
+  - a: fix a axis during relaxation
+  - b: fix b axis during relaxation
+  - c: fix c axis during relaxation
+  - ab: fix both a and b axes during relaxation
+  - ac: fix both a and c axes during relaxation
+  - bc: fix both b and c axes during relaxation
 
 > Note : fixed_axes = "shape" and "volume" are only available for [relax_new](#relax_new) = True
 
@@ -1551,8 +1556,8 @@ These variables are used to control the geometry relaxation.
 - **Type**: Boolean
 - **Availability**: Must be used along with [relax_new](#relax_new) set to True, and a specific [latname](#latname) must be provided
 - **Description**:
-  - **True**: the lattice type will be preserved during relaxation
-  - **False**: No restrictions are exerted during relaxation in terms of lattice type
+  - True: the lattice type will be preserved during relaxation
+  - False: No restrictions are exerted during relaxation in terms of lattice type
 
 > Note: it is possible to use `fixed_ibrav` with `fixed_axes`, but please make sure you know what you are doing. For example, if we are doing relaxation of a simple cubic lattice (`latname` = "sc"), and we use `fixed_ibrav` along with `fixed_axes` = "volume", then the cell is never allowed to move and as a result, the relaxation never converges.
 
@@ -1562,8 +1567,8 @@ These variables are used to control the geometry relaxation.
 
 - **Type**: Boolean
 - **Description**:
-  - **True**: The direct coordinates of atoms will be preserved during variable-cell relaxation.
-  - **False**: No restrictions are exerted on positions of all atoms. However, users can still fix certain components of certain atoms by using the `m` keyword in `STRU` file. For the latter option, check the end of this [instruction](stru.md).
+  - True: The direct coordinates of atoms will be preserved during variable-cell relaxation.
+  - False: No restrictions are exerted on positions of all atoms. However, users can still fix certain components of certain atoms by using the `m` keyword in `STRU` file. For the latter option, check the end of this [instruction](stru.md).
 - **Default**: False
 
 ### cell_factor