9.8 Ab Initio Molecular Dynamics

9.8.2 Additional Job Control and Examples

AIMD_INIT_VELOC
       Specifies the method for selecting initial nuclear velocities.
TYPE:
       STRING
DEFAULT:
       None
OPTIONS:
       THERMAL Random sampling of nuclear velocities from a Maxwell-Boltzmann distribution. The user must specify the temperature in Kelvin via the $rem variable AIMD_TEMP. ZPE Choose velocities in order to put zero-point vibrational energy into each normal mode, with random signs. This option requires that a frequency job to be run beforehand. QUASICLASSICAL Puts vibrational energy into each normal mode. In contrast to the ZPE option, here the vibrational energies are sampled from a Boltzmann distribution at the desired simulation temperature. This also triggers several other options, as described below.
RECOMMENDATION:
       This variable need only be specified in the event that velocities are not specified explicitly in a $velocity section.

AIMD_MOMENTS
       Requests that multipole moments be output at each time step.
TYPE:
       INTEGER
DEFAULT:
       0 Do not output multipole moments.
OPTIONS:
       n Output the first n multipole moments.
RECOMMENDATION:
       None

AIMD_TEMP
       Specifies a temperature (in Kelvin) for Maxwell-Boltzmann velocity sampling.
TYPE:
       INTEGER
DEFAULT:
       None
OPTIONS:
       User-specified number of Kelvin.
RECOMMENDATION:
       This variable is only useful in conjunction with AIMD_INIT_VELOC = THERMAL. Note that the simulations are run at constant energy, rather than constant temperature, so the mean nuclear kinetic energy will fluctuate in the course of the simulation.

DEUTERATE
       Requests that all hydrogen atoms be replaces with deuterium.
TYPE:
       LOGICAL
DEFAULT:
       FALSE Do not replace hydrogens.
OPTIONS:
       TRUE Replace hydrogens with deuterium.
RECOMMENDATION:
       Replacing hydrogen atoms reduces the fastest vibrational frequencies by a factor of 1.4, which allow for a larger fictitious mass and time step in ELMD calculations. There is no reason to replace hydrogens in BOMD calculations.

Example 9.23  Simulating thermal fluctuations of the water dimer at 298 K.

$molecule
   0  1
   O   1.386977   0.011218   0.109098
   H   1.748442   0.720970  -0.431026
   H   1.741280  -0.793653  -0.281811
   O  -1.511955  -0.009629  -0.120521
   H  -0.558095   0.008225   0.047352
   H  -1.910308   0.077777   0.749067
$end

$rem
   JOBTYPE              aimd
   AIMD_METHOD          bomd
   METHOD               b3lyp
   BASIS                6-31g*
   TIME_STEP            20        (20 a.u. = 0.48 fs)
   AIMD_STEPS           1000
   AIMD_INIT_VELOC      thermal
   AIMD_TEMP            298
   FOCK_EXTRAP_ORDER    6         request Fock matrix extrapolation
   FOCK_EXTRAP_POINTS   12
$end

Example 9.24  Propagating F-(H2O)4 on its first excited-state potential energy surface, calculated at the CIS level.

$comment
  Note, only a few time steps are taken, a more appropriate
  number would be:
   AIMD_STEPS       827   500 fs
$end

$molecule
   -1   1
   O  -1.969902  -1.946636   0.714962
   H  -2.155172  -1.153127   1.216596
   H  -1.018352  -1.980061   0.682456
   O  -1.974264   0.720358   1.942703
   H  -2.153919   1.222737   1.148346
   H  -1.023012   0.684200   1.980531
   O  -1.962151   1.947857  -0.723321
   H  -2.143937   1.154349  -1.226245
   H  -1.010860   1.980414  -0.682958
   O  -1.957618  -0.718815  -1.950659
   H  -2.145835  -1.221322  -1.158379
   H  -1.005985  -0.682951  -1.978284
   F   1.431477   0.000499   0.010220
$end

$rem
   JOBTYPE           aimd
   AIMD_METHOD       bomd
   METHOD            hf
   BASIS             6-31+G*
   ECP               SRLC
   PURECART          1111
   CIS_N_ROOTS       3
   CIS_TRIPLETS      false
   CIS_STATE_DERIV   1         propagate on first excited state
   AIMD_INIT_VELOC   thermal
   AIMD_TEMP         150
   TIME_STEP         25
   AIMD_STEPS        10
$end

Example 9.25  Simulating vibrations of the NaCl molecule using ELMD.

$molecule
   0  1
   Na   0.000000   0.000000  -1.742298
   Cl   0.000000   0.000000   0.761479
$end

$rem
   JOBTYPE    freq
   METHOD     b3lyp
   ECP        fit-sbkjc
$end

@@@

$molecule
   read
$end

$rem
   JOBTYPE           aimd
   METHOD            b3lyp
   ECP               fit-sbkjc
   TIME_STEP         14
   AIMD_STEPS        500
   AIMD_METHOD       curvy
   AIMD_FICT_MASS    360
   AIMD_INIT_VELOC   zpe
$end

Q-Chem has the ability to do AIMD with frozen bonds by using RATTLE algorithm.Andersen:1983 It can be requested by setting the rem variable AIMD_INTEGRATION to RATTLE. Constraints are imposed via the $rattle input section, whose format is shown below.

$rattle
bond  atom1  atom2  value
....  .....  .....  .....
$end

Note:  The bond length values should be in Ångstrom units.

The convergence threshold and the number of maximum iterations for RATTLE steps are controlled by the following $rem variables: RATTLE_THRESH (with a default value of 6) and RATTLE_MAXIT (with a default value of 100).

Example 9.26  Simulating water molecule using RATTLE algorithm.

$molecule
0 1
O
H 1 0.95
H 1 0.96 2 104.5
$end

$rem
jobtype           aimd
exchange          b3lyp
basis             6-31G*
time_step         15
aimd_steps        10
aimd_init_veloc   thermal Boltzmann distribution
aimd_temp         300     (in Kelvin)
aimd_print        1
AIMD_INTEGRATION  RATTLE
debug_random_seed true
$end

$rattle
bond 1 2 0.950
bond 1 3 0.950
bond 2 3 1.565
$end