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Manual Pseudopotentials and orbitals Examples

 

4.8 Molecular dynamics

 

To run molecular dynamics (MD) simulations with ABACUS. The KPT file and the STRU file should be set in the same way as in Sec. 4.7. A typical INPUT file for MD simulation is given below, which contains additional keywords that need to added.

 

INPUT_PARAMETERS
#Parameters (General)
suffix Sn_md_test
ntype 1
nbands 200
calculation md


#Parameters (Accuracy)
ecutwfc 50
symmetry 0
niter 200
dr2 1.0e-6


#Parameters (Smearing)
smearing gaussian
sigma 0.02


#Parameters (LCAO)
basis_type lcao
mixing_beta 0.1


#Parameters (Technique)
gamma_only 1
charge_extrap second-order

 

#Parameters (Ions)
force 1
force_thr_ev 0.01
move_method cg


#Parameters (md)
md_mdtype 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_dumpmdfred 10 //The period to dump MD information for monitoring and restarting MD

 

These MD parameters means that ABACUS will use NVT ensemble with Nos´e-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_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_dumpmdfred : frequency for output consequence of md simulation

 

see MD information in file running_md.log or in file MD_OUT

 

NVT Temperature : 469.72 (K) //temperature at this second
NVT Kinetic energy : 0.285593 (Hartree) //kinetic energy of system
NVT Potential energy : -35.1068 (Hartree) //potential energy of system
NVT Conservation : -34.8212 (Hartree) //total energy of system
Thermostat Position : -8.49027e-05 //themostat’s information
Thermostat vel : -1.04976e-05
scaling factor of vel : 1.00006

 

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

 

 

 

 


 

 

 

 

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