Merge pull request #764 from YuLiu98/md_input_para

Refactor : refactor md input parameters

Author: dyzheng

doc/examples/md.md

@@ -33,24 +33,22 @@ basis_type          lcao
 mixing_beta         0.4
 charge_extrap       second-order
 
-md_mdtype           1    //choose ensemble
+md_type           1    //choose ensemble
 md_dt               1    //time step
 md_tfirst           700  //the first target temperature
-md_rstmd            0    //whether restart md
-md_qmass            1    //mass of themostat
-md_dumpfred       10   //The period to dump MD information for monitoring and restarting MD
+md_restart            0    //whether restart md
+md_dumpfreq       10   //The period to dump MD information
 ```
 
 These MD parameters means that ABACUS will use NVT ensemble with Nosé-hoover themostat; the time step is 1fs, and target temperature is 700K; start renew without restart file, set the mass of themostat as 1g/mol, and calculate the MSD and diffusion coefficent from first step.
 
 Note: *Please turn off symmetry when do MD simulation.*
 
-- md_mdtype : 0, NVE; 1, NVT; 2, velocity scaling
+- md_type : -1, FIRE; 0, NVE; 1, NHC; 2, LGV; 3, ADS; 4, MSST
 - md_dt : time step in md simulation (fs)
-- md_tfirst : target temperature in md simulation(K), you should set parameter md_tlast and md_fixtemperature when you want to change temperature during md simulation.
-- md_rstmd : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRU_MD before you run the restart task.
-- md_qmass : mass of thermostat, set by experience, if you don’t know how to set, set it to 0 will have a number autosetted by ABACUS
-- md_dumpfred : frequency for output consequence of md simulation
+- md_tfirst : target temperature in md simulation(K), you should set parameter md_tlast when you want to change temperature during md simulation.
+- md_restart : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRU_MD before you run the restart task.
+- md_dumpfreq : frequency for output consequence of md simulation
 
 The STRU file is:
 ```
@@ -149,9 +147,9 @@ Gamma
 ```
 
 Run the program, and see results in the output directory. The following files are about MD:
-- md_pos_$num.cif optimized structure in direct coordinate
-- MD_RESTART output the information of md for restart
-- STRU_MD if you want to restart md, you must replace the STRU with this file.
+- STRU_MD_$num: optimized structures in direct coordinate
+- Restart_md.dat: output the information of md for restart
+- If you want to restart md, you must replace the STRU with STRU_MD_$num.
 
 MD information can be found in file running_md.log or in file MD_OUT
 

doc/examples/tddft.md

@@ -25,20 +25,12 @@ out_charge 1
 gamma_only 0
 nstep 2000
 dr2 1.0e-6
-md_mdtype 0
+md_type 0
 md_dt 0.01
 md_tfirst 30
-md_mdoutpath mdtest
-md_rstmd 0
-md_fixtemperature 20000
-md_nresn 3
-md_nyosh 3
-md_qmass 0
+md_restart 0
 md_tlast 30
-md_dumpfred 1
-md_domsd 0
-md_domsdatom 0
-md_outputstressperiod 0
+md_dumpfreq 1
 tddft 1
 set_vel 1
 ocp 1

doc/input-main.md

@@ -43,7 +43,7 @@
 
     - [Molecular dynamics](#molecular-dynamics)
 
-        [md_type](#md-type) | [md_potential](#md-potential) | [md_rstmd](#md-rstmd) | [md_dt](#md_dt) | [md_t](#md-t) | [md_qmass](#md-qmass) | [md_dumpfred](#md-dumpfred) | [md_rstfred](#md-rstfred) | [md_tfreq](#md-tfreq) | [MNHC](#mnhc) | [rcut_lj](#rcut_lj) | [epsilon_lj](#epsilon_lj) | [sigma_lj](#sigma_lj) | [direction](#direction) | [velocity](#velocity) | [viscosity](#viscosity) | [tscale](#tscale) | [damp](#damp)
+        [md_type](#md-type) | [md_ensolver](#md-ensolver) | [md_restart](#md-restart) | [md_dt](#md-dt) | [md_t](#md-t) | [md_dumpfreq](#md-dumpfreq) | [md_restartfreq](#md-restartfreq) | [md_tfreq](#md-tfreq) | [md_mnhc](#md-mnhc) | [lj_rcut](#lj-rcut) | [lj_epsilon](#lj-epsilon) | [lj_sigma](#lj-sigma) | [msst_direction](#msst-direction) | [msst_vel](#msst-vel) | [msst_vis](#msst-vis) | [msst_tscale](#msst-tscale) | [msst_qmass](#msst-qmass) | [md_damp](#md-damp)
 
     - [DFT+U correction](#DFT_U-correction)
 
@@ -1113,61 +1113,56 @@ This part of variables are used to control the molecular dynamics calculations.
     - *Description*: control the ensemble to run md.
         - -1: FIRE method to relax;
         - 0: NVE ensemble;
-        - 1: NVT ensemble with Anderson thermostat;
-        - 2: NVT ensemble with Nose Hoover Chain;
-        - 3: NVT ensemble with Langevin method;
+        - 1: NVT ensemble with Nose Hoover Chain;
+        - 2: NVT ensemble with Langevin method;
+        - 3: NVT ensemble with Anderson thermostat;
         - 4: MSST method; 
-    - *Default*: 2
+    - *Default*: 1
 
     [back to top](#input-file)
 
-- md_potential<a id="md-potential"></a>
+- md_ensolver<a id="md-ensolver"></a>
     - *Type*: String
-    - *Description*: choose the potential type.
+    - *Description*: choose the energy solver for MD.
         - FP: First-Principles MD;
         - LJ: Leonard Jones potential;
         - DP: DeeP potential;
     - *Default*: FP
 
     [back to top](#input-file)
 
-- md_rstmd<a id="md-rstmd"></a>
+- md_restart<a id="md-restart"></a>
     - *Type*: Boolean
     - *Description*: to control whether restart md.
         - 0: When set to 0, ABACUS will calculate md normolly.
         - 1: When set to 1, ABACUS will calculate md from last step in your test before.
     - *Default*: 0
 
     [back to top](#input-file)
-- md_dt<a id="md_dt"></a>
+- md_dt<a id="md-dt"></a>
     - *Type*: Double
     - *Description*: This is the time step(fs) used in md simulation .
     - *Default*: 1
 
     [back to top](#input-file)
 - md_tfirst & md_tlast<a id="md-t"></a>
     - *Type*: Double
-    - *Description*: This is the temperature used in md simulation, md_tlast’s default value is md_tfirst. If md_tlast is setted and be different from the md_tfirst, ABACUS will automatically generate a linear temperature gradient file named ”ChangeTemp.dat”, you can also set this file according to your needs instead.
+    - *Description*: This is the temperature (K) used in md simulation, md_tlast’s default value is md_tfirst. If md_tlast is set to be different from md_tfirst, ABACUS will automatically change the temperature from md_tfirst to md_tlast.
     - *Default*: No default
 
     [back to top](#input-file)
-- md_qmass<a id="md-qmass"></a>
-    - *Type*: Double
-    - *Description*: Inertia of extended system variable. Used only when md_type is 4, you should set a number which is larger than 0. Note that Qmass of NHC is set by md_tfreq.
-    - *Default*: No default
 
-    [back to top](#input-file)
-- md_dumpfred<a id="md-dumpfred"></a>
+- md_dumpfreq<a id="md-dumpfreq"></a>
     - *Type*: Integer
     - *Description*:This is the frequence to dump md information.
     - *Default*: 1
 
     [back to top](#input-file)
 
-- md_rstfred<a id="md-rstfred"></a>
+- md_restartfreq<a id="md-restartfreq"></a>
     - *Type*: Integer
     - *Description*:This is the frequence to output restart information.
-    - *Default*: 1
+    - *Default*: 5
 
     [back to top](#input-file)
 
@@ -1180,63 +1175,70 @@ This part of variables are used to control the molecular dynamics calculations.
 
     [back to top](#input-file)
 
-- MNHC<a id="mnhc"></a>
+- md_mnhc<a id="md-mnhc"></a>
     - *Type*: Integer
     - *Description*: Number of Nose-Hoover chains.
     - *Default*: 4
 
     [back to top](#input-file)
 
-- rcut_lj<a id="rcut_lj"></a>
+- lj_rcut<a id="lj-rcut"></a>
     - *Type*: Real
     - *Description*: Cut-off radius for Leonard Jones potential (angstrom).
     - *Default*: 8.5 (for He)
 
     [back to top](#input-file)
 
-- epsilon_lj<a id="epsilon_lj"></a>
+- lj_epsilon<a id="lj-epsilon"></a>
     - *Type*: Real
     - *Description*: The value of epsilon for Leonard Jones potential (eV).
     - *Default*: 0.01032 (for He)
 
     [back to top](#input-file)
 
-- sigma_lj<a id="sigma_lj"></a>
+- lj_sigma<a id="lj-sigma"></a>
     - *Type*: Real
     - *Description*: The value of sigma for Leonard Jones potential (angstrom).
     - *Default*: 3.405 (for He)
 
     [back to top](#input-file)
 
-- direction<a id="direction"></a>
+- msst_direction<a id="msst-direction"></a>
     - *Type*: Integer
     - *Description*: the direction of shock wave for MSST.
     - *Default*: 2 (z direction)
 
     [back to top](#input-file)
 
-- velocity<a id="velocity"></a>
+- msst_vel<a id="msst-vel"></a>
     - *Type*: Real
     - *Description*: the velocity of shock wave (\AA/fs) for MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- viscosity<a id="viscosity"></a>
+- msst_vis<a id="msst-vis"></a>
     - *Type*: Real
     - *Description*: artificial viscosity (mass/length/time) for MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- tscale<a id="tscale"></a>
+- msst_tscale<a id="msst-tscale"></a>
     - *Type*: Real
     - *Description*: reduction in initial temperature (0~1) used to compress volume in MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- damp<a id="damp"></a>
+- msst_qmass<a id="msst-qmass"></a>
+    - *Type*: Double
+    - *Description*: Inertia of extended system variable. Used only when md_type is 4, you should set a number which is larger than 0. Note that Qmass of NHC is set by md_tfreq.
+    - *Default*: No default
+
+    [back to top](#input-file)
+
+- md_damp<a id="md-damp"></a>
     - *Type*: Real
     - *Description*: damping parameter (fs) used to add force in Langevin method.
     - *Default*: 1

examples/03a_Sn64_lcao_md/INPUT

@@ -26,7 +26,7 @@ basis_type          lcao
 mixing_beta         0.4
 charge_extrap       second-order
 
-md_mdtype          1
+md_type          1
 md_dt              1
 md_tfirst          1373
-md_rstmd           0
+md_restart           0