Molecular dynamics using VASP

[valln59]

Dear Admin and Users,
now I am trying AIMD in vasp. I tried to gain some experience using Si example input from vasp site. but left out with many
questions and searched for discussion, but no use at all.

In my view, there is no proper documentation to explain the steps for Proper AIMD.

What we do in normal DFT simulation:
1. relax structure by selecting required IBRION(1/2) and ISIF(2/3).
2. then using the relaxed CONTCAR file we repeat single point energy calculation [ IBRION(-1) ] to get ground state energy.
3. then proceed further for calculations like DOS, BAND ...

but what about MD simulation?
I used Si-standard AIMD input files to relax Si at 2000 K (using NVT ensemble, Nose-Hoover thermostat). as per the vasp site,
I can repeat the calculation up to any time scale. but after that, it is explained that we use Microcanonical ensemble using
MDALGO = 1
ANDERSEN_PROB = 0.0
and repeat the calculation up to 100 steps. So

1. does it mean that we do single-point energy calculation for MD (as in step2 for normal DFT cal.)??
2. in this step I get the mean temperature as 2235 K. But the target temperature is 2000 K. Does it mean that the NVT simulation
time scale is not enough to get thermal equilibrium ??

Note: I used exactly the same input as provided in vasp example site

thanks for your time to answer this question

thank you

[ferenc_karsai]

Molecular-dynamics calculations are little bit different than static ab-initio calculations, because the type of ensemble that one needs to choose depends on your target quantity that you want to calculate. Also a lot of statistics has to be involved.
The purpose of the first example on the wiki is to learn the most important step for all MD calculations: how to monitor the equilibration of the NVT ensemble (by e.g. monitoring the pair-correlation function with respect to length of the MD). In other words obtaining the right structure for your desired conditions. From this structure one can calculate the statistics for the target observables, but this step would be beyond the scope of the tutorial. The calculational parameters were chosen to give demonstrative results far away from being converged, since MD calculations are quite time consuming already with this minimal setup.

The purpose of the "Microcanonical ensemble" chapter is to show that the energy fluctuations in the NVE are much smaller than in NVT. Also it should demonstrate that since NVE doesn't have a thermostat and hence the temperature is not a conserved quantity.


To answer your questions:

"1. does it mean that we do single-point energy calculation for MD (as in step2 for normal DFT cal.)??"
No in this example we just continue the MD in the NVE ensemble. In the NVE ensemble no thermostat and the total energy is the conserved variable. The total energy fluctations are usually an order of magnitude or more smaller than in the NVT ensembe.


2. in this step I get the mean temperature as 2235 K. But the target temperature is 2000 K. Does it mean that the NVT simulation
time scale is not enough to get thermal equilibrium ??
The calculation was definitely not run long enough, so by retrying the calculation with a smaller time step and a much longer equilibration in the NVT ensemble should be closer to the desired temperature. But one should keep in mind that the NVE doesn't necessary keep the right temperature since the temperature is not a conserved value in this ensemble.

[bhubnesh]

Hi All,
I am new to molecular dynamics simulation. I am doing NVT calculation with TEBEG= 2000 K and TEND = 2000 K. I found that the mean temperature in OUTCAR does not reach the value of 2000 k. Also, I need to do the calculation at different temperatures to calculate the mean square displacement of the ions at those temperatures. How can I attain the temperature given by TEBEG ?

system = 6.25%Ru_LFP
ENCUT = 520 eV
LMAXMIX = 4 # L channel mixing for the mixing charge and wavefunction
PREC = Accurate

#Others variable
ADDGRID = .TRUE.
EDIFF = 1E-6
SYMPREC = 1E-4
#LORBIT = 11
LREAL = .FALSE
ISYM = -1

# Few more
ISMEAR = 0 # Gaussian Smearing of the Fermi function
SIGMA = 0.05 # Width of the the gaussian smearing ( -2 read the occupancies formt the incar or potcar file and keep it constant)

LDAU = .TRUE
LDAUTYPE = 2
LDAUL = 2 -1 -1 -1
LDAUU = 5 0.0 0.0 0.0
LDAUJ = 0.0 0.0 0.0 0.0
LDAUPRINT = 2

# Parallization
ALGO = Normal
WEIMIN = 0 # Maximum Wight for the band to be considered empty.
#ISPIN = 2
#MAGMOM = 16*3.0 16*0.0 64*0.0 16*0.0

#LDIPOL = TRUE
#IDIPOL = 3
NPAR = 4
AMIN = 0.01
NBLOCK = 10

#MD
IBRION = 0
POTIM = 1.0
NSW = 10000
MDALGO = 2
#ANDERSEN_PROB=0.0
TEBEG = 2000
TEEND = 2000

Machine learning parameter
ML_LMLFF = .TRUE.
ML_ISTART = 0

#Dont write WaVECAR CHGCAR
LWAVE = .FALSE
LCHARG = .FALSE


Output in OSZICAR:
9954 T= 702. E= -.70561552E+03 F= -.71578523E+03 E0= -.71578523E+03 EK= 0.10170E+02 SP= 0.00E+00 SK= 0.00E+00
9955 T= 711. E= -.70561625E+03 F= -.71590543E+03 E0= -.71590543E+03 EK= 0.10289E+02 SP= 0.00E+00 SK= 0.00E+00
9956 T= 717. E= -.70561670E+03 F= -.71599313E+03 E0= -.71599313E+03 EK= 0.10376E+02 SP= 0.00E+00 SK= 0.00E+00
9957 T= 720. E= -.70561677E+03 F= -.71604075E+03 E0= -.71604075E+03 EK= 0.10424E+02 SP= 0.00E+00 SK= 0.00E+00
9958 T= 720. E= -.70561644E+03 F= -.71604656E+03 E0= -.71604656E+03 EK= 0.10430E+02 SP= 0.00E+00 SK= 0.00E+00
9959 T= 718. E= -.70561580E+03 F= -.71601486E+03 E0= -.71601486E+03 EK= 0.10399E+02 SP= 0.00E+00 SK= 0.00E+00
9960 T= 714. E= -.70561498E+03 F= -.71595489E+03 E0= -.71595489E+03 EK= 0.10340E+02 SP= 0.00E+00 SK= 0.00E+00
9961 T= 709. E= -.70561413E+03 F= -.71587880E+03 E0= -.71587880E+03 EK= 0.10265E+02 SP= 0.00E+00 SK= 0.00E+00
9962 T= 704. E= -.70561339E+03 F= -.71579923E+03 E0= -.71579923E+03 EK= 0.10186E+02 SP= 0.00E+00 SK= 0.00E+00
9963 T= 699. E= -.70561285E+03 F= -.71572719E+03 E0= -.71572719E+03 EK= 0.10114E+02 SP= 0.00E+00 SK= 0.00E+00
9964 T= 695. E= -.70561250E+03 F= -.71567084E+03 E0= -.71567084E+03 EK= 0.10058E+02 SP= 0.00E+00 SK= 0.00E+00
9965 T= 692. E= -.70561232E+03 F= -.71563526E+03 E0= -.71563526E+03 EK= 0.10023E+02 SP= 0.00E+00 SK= 0.00E+00
9966 T= 691. E= -.70561226E+03 F= -.71562291E+03 E0= -.71562291E+03 EK= 0.10011E+02 SP= 0.00E+00 SK= 0.00E+00
9967 T= 692. E= -.70561229E+03 F= -.71563431E+03 E0= -.71563431E+03 EK= 0.10022E+02 SP= 0.00E+00 SK= 0.00E+00
9968 T= 695. E= -.70561240E+03 F= -.71566854E+03 E0= -.71566854E+03 EK= 0.10056E+02 SP= 0.00E+00 SK= 0.00E+00
9969 T= 698. E= -.70561259E+03 F= -.71572338E+03 E0= -.71572338E+03 EK= 0.10111E+02 SP= 0.00E+00 SK= 0.00E+00
9970 T= 703. E= -.70561290E+03 F= -.71579516E+03 E0= -.71579516E+03 EK= 0.10182E+02 SP= 0.00E+00 SK= 0.00E+00
9971 T= 709. E= -.70561333E+03 F= -.71587847E+03 E0= -.71587847E+03 EK= 0.10265E+02 SP= 0.00E+00 SK= 0.00E+00
9972 T= 715. E= -.70561383E+03 F= -.71596627E+03 E0= -.71596627E+03 EK= 0.10352E+02 SP= 0.00E+00 SK= 0.00E+00
9973 T= 721. E= -.70561437E+03 F= -.71605036E+03 E0= -.71605036E+03 EK= 0.10436E+02 SP= 0.00E+00 SK= 0.00E+00
9974 T= 726. E= -.70561487E+03 F= -.71612230E+03 E0= -.71612230E+03 EK= 0.10507E+02 SP= 0.00E+00 SK= 0.00E+00
9975 T= 729. E= -.70561525E+03 F= -.71617450E+03 E0= -.71617450E+03 EK= 0.10559E+02 SP= 0.00E+00 SK= 0.00E+00
9976 T= 731. E= -.70561547E+03 F= -.71620130E+03 E0= -.71620130E+03 EK= 0.10586E+02 SP= 0.00E+00 SK= 0.00E+00
9977 T= 731. E= -.70561548E+03 F= -.71619991E+03 E0= -.71619991E+03 EK= 0.10584E+02 SP= 0.00E+00 SK= 0.00E+00
9978 T= 729. E= -.70561527E+03 F= -.71617094E+03 E0= -.71617094E+03 EK= 0.10556E+02 SP= 0.00E+00 SK= 0.00E+00
9979 T= 726. E= -.70561486E+03 F= -.71611854E+03 E0= -.71611854E+03 EK= 0.10504E+02 SP= 0.00E+00 SK= 0.00E+00
9980 T= 721. E= -.70561430E+03 F= -.71605008E+03 E0= -.71605008E+03 EK= 0.10436E+02 SP= 0.00E+00 SK= 0.00E+00
9981 T= 716. E= -.70561364E+03 F= -.71597547E+03 E0= -.71597547E+03 EK= 0.10362E+02 SP= 0.00E+00 SK= 0.00E+00
9982 T= 711. E= -.70561300E+03 F= -.71590586E+03 E0= -.71590586E+03 EK= 0.10293E+02 SP= 0.00E+00 SK= 0.00E+00
9983 T= 707. E= -.70561251E+03 F= -.71585201E+03 E0= -.71585201E+03 EK= 0.10240E+02 SP= 0.00E+00 SK= 0.00E+00
9984 T= 705. E= -.70561230E+03 F= -.71582224E+03 E0= -.71582224E+03 EK= 0.10210E+02 SP= 0.00E+00 SK= 0.00E+00
9985 T= 705. E= -.70561247E+03 F= -.71582036E+03 E0= -.71582036E+03 EK= 0.10208E+02 SP= 0.00E+00 SK= 0.00E+00
9986 T= 707. E= -.70561306E+03 F= -.71584413E+03 E0= -.71584413E+03 EK= 0.10231E+02 SP= 0.00E+00 SK= 0.00E+00
9987 T= 709. E= -.70561400E+03 F= -.71588476E+03 E0= -.71588476E+03 EK= 0.10271E+02 SP= 0.00E+00 SK= 0.00E+00
9988 T= 712. E= -.70561509E+03 F= -.71592811E+03 E0= -.71592811E+03 EK= 0.10313E+02 SP= 0.00E+00 SK= 0.00E+00
9989 T= 714. E= -.70561606E+03 F= -.71595770E+03 E0= -.71595770E+03 EK= 0.10342E+02 SP= 0.00E+00 SK= 0.00E+00
9990 T= 714. E= -.70561663E+03 F= -.71595890E+03 E0= -.71595890E+03 EK= 0.10342E+02 SP= 0.00E+00 SK= 0.00E+00
9991 T= 712. E= -.70561660E+03 F= -.71592320E+03 E0= -.71592320E+03 EK= 0.10307E+02 SP= 0.00E+00 SK= 0.00E+00
9992 T= 707. E= -.70561596E+03 F= -.71585095E+03 E0= -.71585095E+03 EK= 0.10235E+02 SP= 0.00E+00 SK= 0.00E+00
9993 T= 700. E= -.70561489E+03 F= -.71575153E+03 E0= -.71575153E+03 EK= 0.10137E+02 SP= 0.00E+00 SK= 0.00E+00
9994 T= 693. E= -.70561371E+03 F= -.71564076E+03 E0= -.71564076E+03 EK= 0.10027E+02 SP= 0.00E+00 SK= 0.00E+00
9995 T= 685. E= -.70561274E+03 F= -.71553618E+03 E0= -.71553618E+03 EK= 0.99234E+01 SP= 0.00E+00 SK= 0.00E+00
9996 T= 680. E= -.70561224E+03 F= -.71545205E+03 E0= -.71545205E+03 EK= 0.98398E+01 SP= 0.00E+00 SK= 0.00E+00
9997 T= 676. E= -.70561228E+03 F= -.71539548E+03 E0= -.71539548E+03 EK= 0.97832E+01 SP= 0.00E+00 SK= 0.00E+00
9998 T= 674. E= -.70561279E+03 F= -.71536525E+03 E0= -.71536525E+03 EK= 0.97525E+01 SP= 0.00E+00 SK= 0.00E+00
9999 T= 673. E= -.70561355E+03 F= -.71535296E+03 E0= -.71535296E+03 EK= 0.97394E+01 SP= 0.00E+00 SK= 0.00E+00
10000 T= 672. E= -.70561430E+03 F= -.71534640E+03 E0= -.71534640E+03 EK= 0.97321E+01 SP= 0.00E+00 SK= 0.00E+00

[ferenc_karsai]

Please upload the neccessary files according to the forum guidelines (POSCAR, POTCAR, INCAR, KPOINTS, OUTCAR, ML_LOGFILE).

[bhubnesh]

Thanks for the response I got the solution to the problem. I add the SMASS=0 in INCAR and then the calculation reached the TEBEG temperature.

[ferenc_karsai]

Thank you for posting your solution, I'm glad you fixed your problem.

Smass=-3 is the default, which corresponds to microcanonical (NVE) ensemble.