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9.9.3 Additional Job Control and Examples

(December 20, 2021)

AIMD_INIT_VELOC

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 $rem variable AIMD_TEMP. ZPE Choose velocities in order to put zero-point vibrational energy into each normal mode, with random signs. This option requires that a frequency job to be run beforehand. QUASICLASSICAL Puts vibrational energy into each normal mode. In contrast to the ZPE option, here the vibrational energies are sampled from a Boltzmann distribution at the desired simulation temperature. This also triggers several other options, as described below. OLD Use the same initial velocities as the immediately preceding AIMD job. RESTART Use the final velocities from a previous AIMD job, reading them from disk. RECOMMENDATION: This variable need only be specified in the event that velocities are not specified explicitly in a$velocity section.

AIMD_INIT_VELOC_NANO_RANDOM

AIMD_INIT_VELOC_NANO_RANDOM
Uses a more precise random seed for generating random initial velocities.
TYPE:
LOGICAL
DEFAULT:
TRUE Use a more precise random seed.
OPTIONS:
FALSE Use a less precise random seed.
RECOMMENDATION:
Leave this set to TRUE unless necessary. This option determines the source of the random seed used for sampling random initial velocities when AIMD_INIT_VELOC requires such. Setting the option to FALSE will have the seed based on the system time in seconds, meaning that two otherwise identical simulations starting in the same second will produce identical initial velocities. With the option set to TRUE, such collisions are virtually impossible. The option is kept for legacy purposes. There should rarely ever be a need to set it to FALSE.

AIMD_MOMENTS

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

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

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 9.27  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


View output

Example 9.28  Propagating $\rm F^{-}(H_{2}O)_{4}$ 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


View output

Example 9.29  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

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

@@@

$molecule read$end

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


View output

Q-Chem has the ability to do AIMD with frozen bonds by using RATTLE algorithm. 39 Andersen H. C.
J. Comput. Phys.
(1983), 52, pp. 24.
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 9.30  Simulating water molecule using RATTLE algorithm.

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

$rem JOBTYPE aimd METHOD b3lyp BASIS 6-31G* TIME_STEP 15 AIMD_STEPS 10 AIMD_INIT_VELOC thermal Boltzmann distribution AIMD_TEMP 300 (in Kelvin) AIMD_PRINT 1 AIMD_INTEGRATION RATTLE DEBUG_RANDOM_SEED true$end

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


View output