html> Quantum-ESPRESSO tutorial: Car-Parrinello Molecular Dynamics

Car-Parrinello Molecular Dynamics (part 2)



    Playing with emass and dt

      We will change the values of "emass" (the electronic fictitious mass) and "dt" and try to see the effects that these changes produce on the quality of the results.


    Born-Oppenheimer Molecular Dynamics

      Download the sample input file "si_bo.in.00" here. Most of the input parameters are already familiar to us. Let's look at the differences with respect to the Car-Parrinello input file 
              prompt> diff si_bo.in.00 si.in.00
        3c3
        <     calculation = 'cp',
        ---
        >     calculation = 'fpmd',
        13c13
        <     prefix = 'si_bo'
        ---
        >     prefix = 'si'
        32c32
        <     electron_dynamics = 'cg',
        ---
        >     electron_dynamics = 'sd',
      The different value of "calculation" is related to the still incomplete merging of two different codes. It will disappear in future distributions of the package. The main difference consists in the different minimization algorithm used to find the electronic ground state. "cg" stands for "conjugate gradients". Notice that the variables "nstep" and "dt" are not used in a cg minimization. We are now ready to execute the electronic minimization: 
              ../bin/cp.x < si_bo.in.00 > si_bo.out.00


    Random displacement of the atoms from their ideal positions

      NB: This section is identical to the corresponding CP section


      After having determined the electronic ground state of the ideal system, we now diplace the atoms randomly from their ideal positions. Let's construct the input file for the next calculation ("01"). Copy the previous file into a new file 
              cp  si_bo.in.00  si_bo.in.01
      and modify the new file "si_bo.in.01" as follows. We need to read the old configuration from the stored unit "50", so we need to change the restart mode from "from_scratch" to 
              restart_mode = "restart"
      and we need to add the line 
              ndr = 50
      If we want to keep the information (positions, wfc's, etc) of the "ideal" crystal, we better write on a different unit, so we need to change the value of "ndw" as 
              ndw = 51
      Notice that unit "50" will not be touched if ndr.ne.ndw.
      The randomization is obtained by adding to the "&ions" namelist the following parameters: 
              tranp = .true.        
        amprp = 0.1d0
      All ionic positions will be displaced with respect to the positions read from unit "ndr", by a random quantity of the order of "amprp" (in atomic units).
      The code will now displace the ions randomly, and perform a "conjugate gradients" electronic minimization on the distorted configuration: 
              ../bin/cp.x < si_bo.in.01 > si_bo.out.01


    Let's dance! (BO)

      We are now ready to perform a BO-MD simulation. Let's construct the new input file ("02"). Copy the previous file into a new file 
              cp  si_bo.in.01  si_bo.in.02
      and modify the new file "si_bo.in.01" as follows.
      For "safety" reasons, it is convenient to update the read-write units as 
              ndr = 51 
        ndw = 52
      It is also essential to remove the randomization parameters (we don't want to randomize the ions again, they are already displaced). The "tranp" and "amprp" parameters must be removed.
      Ions will move according to a second-order (Verlet) dynamics, and we want them to start with zero velocities, so we need to set 
              ion_dynamics = 'verlet'
        ion_velocities = 'zero'
      in the "&ions" namelist. On the contrary, electrons will now have to be minimized at every step using a cg algorithm. The value of "dt" can be increased to 
              dt    = 40.0d0,
      and the value of "nstep" can be correspondingly decreased to 
              nstep  = 250,
      In this way we will produce a trajectory with the same total duration (0.24 ps) as the CP one. The variable "iprint" can be removed, as we want to print out the relevant quantities every step now. For convenience, we may also want to reset the time step counter 
              restart_mode = 'reset_counters',
      We also clean up the directory by removing the si_bo.cel and si_bo.pos files. 
              rm si_bo.pos si_bo.cel
      The code will now perform a Born-Oppenheimer MD simulation: 
              ../bin/cp.x < si_bo.in.02 > si_bo.out.02
      We will use XCrysDen to visualize the trajectories and the utility "gofr.x" to produce pair correlations functions that we will compare with the ones obtained from the CP run.





    S. Scandolo -- Latin American School on Computational Materials Science, Santiago Chile, January 19-30, 2009