CP Dynamics Output

This run should be completed in a few minutes. There are several new files TRAJEC.xyz, TRAJECTORY, ENERGIES), be we'll have a closer look at the output file first.

 CAR-PARRINELLO MOLECULAR DYNAMICS

 PATH TO THE RESTART FILES:                                    ./
 RESTART WITH OLD ORBITALS
 RESTART WITH OLD ION POSITIONS
 RESTART WITH LATEST RESTART FILE
[...]
 MAXIMUM NUMBER OF STEPS:                               200 STEPS
[...]
 TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE

The header is unchanged up to the point where the settings from the &CPMD section are printed. As you can see, the program has recognized the RESTART, MAXSTEP and the ISOLATED MOLECULE keywords.

In CPMD (and other similar codes), atoms are frequently referred to as ions, which may be confusing to some. This is due to the pseudopotential approach, where you integrate the core electrons into the (pseudo)atom which then could be also described as an ion. See for example the following output segment.

 FICTITIOUS ELECTRON MASS:                               400.0000
 TIME STEP FOR ELECTRONS:                                  4.0000
 TIME STEP FOR IONS:                                       4.0000
 TRAJECTORIES ARE SAVED ON FILE
 TRAJEC.xyz IS SAVED ON FILE
 ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
 ION DYNAMICS:      THE TEMPERATURE IS NOT CONTROLLED

This part of the output tells us, that the TIMESTEP keyword was recognized as well as the output option and that there will be no temperature control, i.e. we will do a microcanonical (NVE-ensemble) simulation.

Skipping ahead we see:

 ***      MDPT| SIZE OF THE PROGRAM IS   32356/ 128480 kBYTES ***
 RV30| WARNING! NO WAVEFUNCTION VELOCITIES

 RESTART INFORMATION READ ON FILE                     ./RESTART.1

Here we get notified, that the program has read the requested data from the restart file. The warning about the missing wavefunction velocities is to be expected, since they will only be available when the restart was written by a previous Car-Parrinello MD run.

  NFI    EKINC   TEMPP        EKS   ECLASSIC       EHAM         DIS    TCPU
    1  0.00000    84.5   -1.12849   -1.12835   -1.12835   0.908E-06    0.34
    2  0.00000   131.4   -1.12856   -1.12835   -1.12835   0.466E-05    0.34
    3  0.00000   189.2   -1.12866   -1.12836   -1.12835   0.132E-04    0.34
    4  0.00001   256.5   -1.12877   -1.12836   -1.12835   0.287E-04    0.34
    5  0.00002   332.0   -1.12890   -1.12837   -1.12835   0.541E-04    0.34
    6  0.00004   415.0   -1.12905   -1.12839   -1.12835   0.922E-04    0.34
    7  0.00006   504.9   -1.12921   -1.12841   -1.12835   0.146E-03    0.34
    8  0.00008   601.2   -1.12938   -1.12843   -1.12835   0.220E-03    0.34
    9  0.00010   703.0   -1.12956   -1.12845   -1.12835   0.317E-03    0.34
   10  0.00012   809.3   -1.12975   -1.12847   -1.12835   0.442E-03    0.34
   11  0.00014   918.5   -1.12995   -1.12849   -1.12835   0.598E-03    0.34
   12  0.00016  1028.9   -1.13014   -1.12851   -1.12835   0.790E-03    0.34
 [...]
  190  0.00020  1412.7   -1.13079   -1.12855   -1.12835   0.182E-01    0.34
  191  0.00021  1504.1   -1.13094   -1.12856   -1.12835   0.187E-01    0.34
  192  0.00021  1585.4   -1.13108   -1.12857   -1.12835   0.192E-01    0.34
  193  0.00022  1654.2   -1.13119   -1.12857   -1.12835   0.198E-01    0.34
  194  0.00022  1708.3   -1.13128   -1.12858   -1.12835   0.204E-01    0.34
  195  0.00023  1745.9   -1.13135   -1.12858   -1.12836   0.210E-01    0.34
  196  0.00023  1765.4   -1.13138   -1.12859   -1.12836   0.218E-01    0.34
  197  0.00024  1766.0   -1.13139   -1.12859   -1.12836   0.225E-01    0.34
  198  0.00024  1747.3   -1.13136   -1.12859   -1.12836   0.234E-01    0.34
  199  0.00024  1709.4   -1.13130   -1.12859   -1.12836   0.242E-01    0.34
  200  0.00024  1653.1   -1.13121   -1.12859   -1.12836   0.251E-01    0.34

 RESTART INFORMATION WRITTEN ON FILE                  ./RESTART.1

After some more output, we already discussed for the wavefunction optimization, this is now part of the energy progression for a Car-Parrinello-MD run.

The individual columns have the following meaning:

NFI

step number (number of finite iterations)

EKINC

fictitious kinetic energy of the electronic degrees of freedom

TEMPP

temperature (= kinetic energy / degrees of freedom) for atoms (ions)

EKS

Kohn-Sham energy; equivalent to the potential energy in classical MD

ECLASSIC

the total energy in a classical MD, but not the conserved quantity for CP-dynamics (ECLASSIC = EHAM - EKINC).

EHAM

energy of the total CP-Hamiltonian; the conserved quantity.

DIS

mean squared displacement of the atoms from the initial coordinates.

TCPU

time needed for this step

Since the geometry optimization has shown, that the hydrogen molecule was not in the full minimum we see that after starting the MD, potential energy is converted into initial kinetic energy and the molecule gains kinetic energy while the potential energy (EKS) decreases as the bond is shrinks. You can also see, that a little bit of energy is transferred into the fictitious dynamic of the electronic degrees of freedom. For a meaningful Car-Parrinello MD this value has to be (and stay) very small, although the absolute value of EKINC varies with the number of electrons, the fictitious electron mass and the kinetic energy of the ions (see sections 6.7 and 9.5 for more details).

 ****************************************************************
 *                      AVERAGED QUANTITIES                     *
 ****************************************************************
                              MEAN VALUE       +/-  RMS DEVIATION
                                     <x>     [<x^2>-<x>^2]**(1/2)
 ELECTRON KINETIC ENERGY        0.000128             0.860050E-04
 IONIC TEMPERATURE              913.2199              611.534
 DENSITY FUNCTIONAL ENERGY     -1.129927             0.105535E-02
 CLASSICAL ENERGY              -1.128481             0.873761E-04
 CONSERVED ENERGY              -1.128353             0.140134E-05
 NOSE ENERGY ELECTRONS          0.000000              0.00000
 NOSE ENERGY IONS               0.000000              0.00000
 CONSTRAINTS ENERGY             0.000000              0.00000
 RESTRAINTS ENERGY              0.000000              0.00000
 ION DISPLACEMENT           0.120455E-01             0.726560E-02
 CPU TIME                         0.3391

Finally we get a summary of some averages and root mean squared deviations for some of the monitored quantities. This is quite useful to detect unwanted energy drifts or too large fluctuations in the simulation.