Molecular dynamics

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A typical INPUT file for MD simulation is given below, which contains additional keywords that need to added.

INPUT_PARAMETERS
#Parameters (1.General)
pseudo_dir          ./
ntype               1
nbands              600
pseudo_type         upf
gamma_only          1
calculation         md
symmetry            0
out_level           m

#Parameters (2.SCF)
ecutwfc             60
scf_thr             1e-6
scf_nmax            100

#Parameters (3.Basis)
basis_type          lcao
ks_solver           genelpa

#Parameters (4.Smearing)
smearing_method     gaussian
smearing_sigma      0.02

#Parameters (5.Mixing)
mixing_type         pulay
mixing_beta         0.4
chg_extrap          second-order

#Parameters (6.MD)
md_nstep            10   // md steps
md_type             1    // choose ensemble
md_dt               1    // time step
md_tfirst           700  // the first target temperature
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 chain themostat; the time step is 1fs, and target temperature is 700K; start new MD without restart file.

Note: Please turn off symmetry during MD simulations.

• md_type :
• -1, FIRE : an ionic relaxation method using MD;
• 0, NVE : microcanonical ensemble;
• 1, NHC : canonical ensemble (NVT) with Nosé-hoover chain themostat ;
• 2, LGV : ion dynamics is over-damped Langevin, modeling an interaction with a background implicit solvent.;
• 3, ADS : NVT, control ionic temperature using Andersen thermostat;
• 4, MSST : Multi-Scale Shock Technique (MSST) integration to mimic a compressive shock wave passing over the system.
• md_dt : time step in md simulation (fs)
• mdtfirst : target temperature in md simulation (K), you should set parameter mdtlast when you want to change temperature during md simulation.
• mdrestart : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRUMD before you run the restart task.
• md_dumpfreq : frequency for output consequence of md simulations.

The STRU file is:

ATOMIC_SPECIES
Sn 118.71  ./Sn.pz-bhs.UPF 

LATTICE_CONSTANT
23.45378

NUMERICAL_ORBITAL
./Sn_pz-bhs_8.0au_16Ry_2s2p1d

LATTICE_VECTORS
1.00     0.00     0.00
0.00     1.00     0.00
0.00     0.00     1.00

ATOMIC_POSITIONS
Direct 

Sn
0.0
64
0    0   0   1   1   1
0    0.25    0.25    1   1   1
0.25    0   0.25    1   1   1
0.25    0.25    0   1   1   1
0.375    0.125   0.375   1   1   1
0.125    0.125   0.125   1   1   1
0.125    0.375   0.375   1   1   1
0.375    0.375   0.125   1   1   1
0.5    0   0   1   1   1
0.5    0.25    0.25    1   1   1
0.75    0   0.25    1   1   1
0.75    0.25    0   1   1   1
0.875    0.125   0.375   1   1   1
0.625    0.125   0.125   1   1   1
0.625    0.375   0.375   1   1   1
0.875    0.375   0.125   1   1   1
0    0.5 0   1   1   1
0    0.75    0.25    1   1   1
0.25    0.5 0.25    1   1   1
0.25    0.75    0   1   1   1
0.375    0.625   0.375   1   1   1
0.125    0.625   0.125   1   1   1
0.125    0.875   0.375   1   1   1
0.375    0.875   0.125   1   1   1
0.5    0.5 0   1   1   1
0.5    0.75    0.25    1   1   1
0.75    0.5 0.25    1   1   1
0.75    0.75    0   1   1   1
0.875    0.625   0.375   1   1   1
0.625    0.625   0.125   1   1   1
0.625    0.875   0.375   1   1   1
0.875    0.875   0.125   1   1   1
0    0   0.5 1   1   1
0    0.25    0.75    1   1   1
0.25    0   0.75    1   1   1
0.25    0.25    0.5 1   1   1
0.375    0.125   0.875   1   1   1
0.125    0.125   0.625   1   1   1
0.125    0.375   0.875   1   1   1
0.375    0.375   0.625   1   1   1
0.5    0   0.5 1   1   1
0.5    0.25    0.75    1   1   1
0.75    0   0.75    1   1   1
0.75    0.25    0.5 1   1   1
0.875    0.125   0.875   1   1   1
0.625    0.125   0.625   1   1   1
0.625    0.375   0.875   1   1   1
0.875    0.375   0.625   1   1   1
0    0.5 0.5 1   1   1
0    0.75    0.75    1   1   1
0.25    0.5 0.75    1   1   1
0.25    0.75    0.5 1   1   1
0.375    0.625   0.875   1   1   1
0.125    0.625   0.625   1   1   1
0.125    0.875   0.875   1   1   1
0.375    0.875   0.625   1   1   1
0.5    0.5 0.5 1   1   1
0.5    0.75    0.75    1   1   1
0.75    0.5 0.75    1   1   1
0.75    0.75    0.5 1   1   1
0.875    0.625   0.875   1   1   1
0.625    0.625   0.625   1   1   1
0.625    0.875   0.875   1   1   1
0.875    0.875   0.625   1   1   1

The KPT file is:

K_POINTS
0
Gamma
1 1 1 0 0 0

Run the program, and see results in the output directory. The following files are about MD:

• STRU/STRUMD$num: optimized structures in direct coordinate
• Restart_md.dat: output the information of md for restart
• If you want to restart md, you must replace the STRU with STRU/STRUMD$num.

MD information can be found in file running_md.log.

------------------------------------------------------------------------------------------------
Energy              Potential           Kinetic             Temperature         Pressure (KBAR)     
-7.7824215          -7.782469           +4.7502231e-05      +10                 +124.19599          
------------------------------------------------------------------------------------------------

All energy values are in atomic unit (Ry), and temperature is Kelvin.

Check these information to confirm whether temperature and conservation is steady.

The MD post-processing tools can be found as follows:

• Candela : https://github.com/MCresearch/Candela
• dpdata : https://github.com/deepmodeling/dpdata

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