Refactor: update md_type, md_thermostat, md_pmode (#2206)

* Refactor: update md_type, md_thermostat, md_pmode

* Test: update md unit tests

* Test: update new md tests

Author: YuLiu98

docs/advanced/input_files/input-main.md

@@ -1834,29 +1834,30 @@ These variables are used to control the molecular dynamics calculations.
 
 ### md_type
 
-- **Type**: Integer
-- **Description**: control the algorithm to integrate the equation of motion for md. When `md_type` is set to 0, `md_thermostat` is used to specify the thermostat based on the velocity Verlet algorithm.
+- **Type**: String
+- **Description**: control the algorithm to integrate the equation of motion for md.
 
-  - -1: FIRE method to relax;
-  - 0: velocity Verlet algorithm (default: NVE ensemble);
-  - 1: Nose-Hoover style non-Hamiltonian equations of motion;
-  - 2: NVT ensemble with Langevin method;
-  - 4: MSST method;
+  - fire: FIRE method.
+  - nve: NVE ensemble with velocity Verlet algorithm.
+  - nvt: NVT ensemble, see [md_thermostat](#md_thermostat) in detail.
+  - npt: Nose-Hoover style NPT ensemble, see [md_pmode](#md_pmode) in detail.
+  - langevin: NVT ensemble with Langevin thermostat.
+  - msst: MSST method.
 
-  > Note: when md_type is set to 1, md_tfreq is required to stabilize temperature. It is an empirical parameter whose value is system-dependent, ranging from 1/(40\*md_dt) to 1/(100\*md_dt). An improper choice of its value might lead to failure of job.
-- **Default**: 1
+- **Default**: nvt
 
 ### md_thermostat
 
 - **Type**: String
-- **Description**: specify the thermostat based on the velocity Verlet algorithm (useful when `md_type` is set to 0).
+- **Description**: specify the temperature control method used in NVT ensemble.
 
-  - nve: NVE ensemble.
-  - anderson: NVT ensemble with Anderson thermostat, see the parameter `md_nraise`.
-  - berendsen: NVT ensemble with Berendsen thermostat, see the parameter `md_nraise`.
-  - rescaling: NVT ensemble with velocity Rescaling method 1, see the parameter `md_tolerance`.
-  - rescale_v: NVT ensemble with velocity Rescaling method 2, see the parameter `md_nraise`.
-- **Default**: NVE
+  - nhc: Nose-Hoover chain, see [md_tfreq](#md_tfreq) and [md_tchain](#md_tchain) in detail.
+  - anderson: Anderson thermostat, see [md_nraise](#md_nraise) in detail.
+  - berendsen: Berendsen thermostat, see the parameter [md_nraise](#md_nraise) in detail.
+  - rescaling: velocity Rescaling method 1, see the parameter [md_tolerance](#md_tolerance) in detail.
+  - rescale_v: velocity Rescaling method 2, see the parameter [md_nraise](#md_nraise) in detail.
+
+- **Default**: nhc
 
 ### md_nstep
 
@@ -1918,14 +1919,15 @@ These variables are used to control the molecular dynamics calculations.
 
 - **Type**: Real
 - **Description**: 
-  Construct a reference cell bigger than the initial cell. Only used in variable-cell MD, if [md_prec_level](#md_prec_level) is set to 1. The reference cell has to be large enough so that the lattice vectors of the fluctuating cell do not exceed the reference lattice vectors during MD. Typically, 1.02 ~ 1.10 is sufficient. However, the cell fluctuations depend on the specific system and thermodynamic conditions. So users must test for a proper choice. This parameters should be used in conjunction with q2sigma, qcutz, and ecfixed. 
+  Construct a reference cell bigger than the initial cell. Only used in isotropic NPT ensemble currently, if [md_prec_level](#md_prec_level) is set to 1. The reference cell has to be large enough so that the lattice vectors of the fluctuating cell do not exceed the reference lattice vectors during MD. Typically, 1.02 ~ 1.10 is sufficient. However, the cell fluctuations depend on the specific system and thermodynamic conditions. So users must test for a proper choice. This parameters should be used in conjunction with q2sigma, qcutz, and ecfixed. 
 - **Default**: 1.0
 
 ### md_tfreq
 
 - **Type**: Real
 - **Description**: control the frequency of the temperature oscillations during the simulation. If it is too large, the temperature will fluctuate violently; if it is too small, the temperature will take a very long time to equilibrate with the atomic system.
 - **Default**: 1/40/md_dt
+  > Note: It is an empirical parameter whose value is system-dependent, ranging from 1/(40\*md_dt) to 1/(100\*md_dt). An improper choice of its value might lead to failure of job.
 
 ### md_tchain
 
@@ -1936,12 +1938,12 @@ These variables are used to control the molecular dynamics calculations.
 ### md_pmode
 
 - **Type**: String
-- **Description**: specify the NVT or NPT ensemble based on the Nose-Hoover style non-Hamiltonian equations of motion.
-  - none: NVT ensemble.
-  - iso: NPT ensemble with isotropic cetl fluctuations.
-  - aniso: NPT ensemble with anisotropic cetl fluctuations.
-  - tri: NPT ensemble with non-orthogonal (triclinic) simulation box.
-- **Default**: none
+- **Description**: specify the cell fluctuation mode in NPT ensemble based on the Nose-Hoover style non-Hamiltonian equations of motion. 
+  - iso: isotropic cell fluctuations.
+  - aniso: anisotropic cell fluctuations.
+  - tri: non-orthogonal (triclinic) simulation box.
+- **Default**: iso
+- **Relavent**: [md_tfreq](#md_tfreq), [md_tchain](#md_tchain), [md_pcouple](#md_pcouple), [md_pfreq](#md_pfreq), and [md_pchain](#md_pchain).
 
 ### md_pcouple
 
@@ -2041,7 +2043,7 @@ These variables are used to control the molecular dynamics calculations.
 ### msst_qmass
 
 - **Type**: Real
-- **Description**: Inertia of extended system variable. Used only when md_type is 4, you should set a number that is larger than 0. Note that Qmass of NHC is set by md_tfreq.
+- **Description**: Inertia of extended system variable. Used only when md_type is msst, you should set a number that is larger than 0. Note that Qmass of NHC is set by md_tfreq.
 - **Default**: No default
 
 ### md_damp

docs/advanced/md.md

@@ -4,26 +4,26 @@ Molecular dynamics (MD) is a computer simulation method for analyzing the physic
 
 By setting `calculation` to be `md`, ABACUS currently provides several different MD evolution methods, which is specified by keyword `md_type` in the `INPUT` file:
 
-  - -1: FIRE method
-  - 0: velocity Verlet algorithm (default: NVE ensemble)
-  - 1: Nose-Hoover style non-Hamiltonian equations of motion
-  - 2: NVT ensemble with Langevin thermostat
-  - 4: MSST method
-
-When `md_type` is set to 0, `md_thermostat` is used to specify the thermostat based on the velocity Verlet algorithm.
-
-  - nve: NVE ensemble
-  - anderson: NVT ensemble with Anderson thermostat
-  - berendsen: NVT ensemble with Berendsen thermostat
-  - rescaling: NVT ensemble with velocity Rescaling method 1
-  - rescale_v: NVT ensemble with velocity Rescaling method 2
-
-When `md_type` is set to 1, `md_pmode` is used to specify the NVT or NPT ensemble based on the Nose-Hoover style non-Hamiltonian equations of motion.
-
-  - none: NVT ensemble
-  - iso: NPT ensemble with isotropic cetl fluctuations
-  - aniso: NPT ensemble with anisotropic cetl fluctuations
-  - tri: NPT ensemble with non-orthogonal (triclinic) simulation box
+  - fire: FIRE method
+  - nve: NVE ensemble with velocity Verlet algorithm
+  - nvt: NVT ensemble
+  - npt: Nose-Hoover style NPT ensemble
+  - langevin: NVT ensemble with Langevin thermostat
+  - msst: MSST method
+
+When `md_type` is set to nvt, `md_thermostat` is used to specify the temperature control method used in NVT ensemble.
+
+  - nhc: Nose-Hoover chain
+  - anderson: Anderson thermostat
+  - berendsen: Berendsen thermostat
+  - rescaling: velocity Rescaling method 1
+  - rescale_v: velocity Rescaling method 2
+
+When `md_type` is set to npt, `md_pmode` is used to specify the cell fluctuation mode in NPT ensemble based on the Nose-Hoover style non-Hamiltonian equations of motion.
+
+  - iso: isotropic cell fluctuations
+  - aniso: anisotropic cell fluctuations
+  - tri: non-orthogonal (triclinic) simulation box
 
 Furthermore, ABACUS also provides a [list of keywords](./input_files/input-main.md#molecular-dynamics) to control relevant parmeters used in MD simulations.
 

examples/hefei-namd/INPUT

@@ -22,7 +22,7 @@ INPUT_PARAMETERS
  mixing_type     pulay
  mixing_beta     0.7
 
- md_type          0
+ md_type          nve
  md_restart         0
  md_tfirst        10
  init_vel         1

examples/md/lcao_gammaonly_Sn64/INPUT_0

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                0
+md_type                nve
 md_nstep               10
 md_dt                  1
 md_tfirst              300

examples/md/lcao_gammaonly_Sn64/INPUT_1

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                1
+md_type                nvt
 md_nstep               10
 md_dt                  1
 md_tfirst              300

examples/md/lcao_gammaonly_Sn64/INPUT_2

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                2
+md_type                langevin
 md_nstep               10
 md_dt                  1
 md_tfirst              300

examples/md/lcao_gammaonly_Sn64/INPUT_3

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                0
+md_type                nvt
 md_thermostat          anderson
 md_nraise              40
 md_nstep               10

examples/md/lcao_gammaonly_Sn64/INPUT_4

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                4
+md_type                msst
 md_nstep               10
 md_dt                  1
 md_tfirst              300

examples/md/lcao_gammaonly_Sn64/INPUT_5

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                0
+md_type                nvt
 md_thermostat          berendsen
 md_nraise              40
 md_nstep               10

examples/md/lcao_gammaonly_Sn64/INPUT_6

@@ -28,7 +28,7 @@ mixing_beta            0.3
 chg_extrap             second-order
 
 #Parameters (6.MD)
-md_type                0
+md_type                nvt
 md_thermostat          rescaling
 md_tolerance           10
 md_nstep               10