Implicit in the discussion above was an assumption of conservation of energy, which implies dynamics run in the microcanonical () ensemble. Alternatively, the AIMD code in Q-Chem can sample the canonical () ensemble with the aid of thermostats. These mimic the thermal effects of a surrounding temperature bath, and the time average of a trajectory (or trajectories) then affords thermodynamic averages at a chosen temperature. This option is appropriate in particular when multiple minima are thermally accessible. All sampled information is once again saved in the AIMD/ subdirectory of the $QCSCRATCH directory for the job. Thermodynamic averages and error analysis may be performed externally, using these data. Two commonly used thermostat options, both of which yield proper canonical distributions of the classical molecular motion, are implemented in Q-Chem and are described in more detail below. Constant-pressure barostats (for simulations) are not yet implemented.
As with any canonical sampling, the trajectory evolves at the mercy of barrier heights. Short trajectories will sample only within the local minimum of the initial conditions, which may be desired for sampling the properties of a given isomer, for example. Due to the energy fluctuations induced by the thermostat, the trajectory is neither guaranteed to stay within this potential energy well nor guaranteed to overcome barriers to neighboring minima, except in the infinite-sampling limit for the latter case, which is likely never reached in practice. Importantly, the user should note that the introduction of a thermostat destroys the validity of any real-time trajectory information; thermostatted trajectories should not be used to assess real-time dynamical observables, but only to compute thermodynamic averages.
A stochastic, white-noise Langevin thermostat (AIMD_THERMOSTAT =
LANGEVIN) combines random “kicks” to the nuclear momenta with a
dissipative, friction term. The balance of these two contributions mimics the
exchange of energy with a surrounding heat bath. The resulting trajectory, in
the long-time sampling limit, generates the correct canonical distribution.
The implementation in Q-Chem follows the velocity Verlet formulation of Bussi
Phys. Rev. E
(2007), 75, pp. 056707. which remains a valid propagator for all time steps and thermostat parameters. The thermostat is coupled to each degree of freedom in the simulated system. The MD integration time step (TIME_STEP) should be chosen in the same manner as in an NVE trajectory. The only user-controllable parameter for this thermostat, therefore, is the timescale over which the implied bath influences the trajectory. The AIMD_LANGEVIN_TIMESCALE keyword determines this parameter, in units of femtoseconds. For users who are more accustomed to thinking in terms of friction strength, this parameter is proportional to the inverse friction. A small value of the timescale parameter yields a “tight” thermostat, which strongly maintains the system at the chosen temperature but does not typically allow for rapid configurational flexibility. (Qualitatively, one may think of such simulations as sampling in molasses. This analogy, however, only applies to the thermodynamic sampling properties and does not suggest any electronic role of the solvent!) These small values are generally more appropriate for small systems, where the few degrees of freedom do not rapidly exchange energy and behave may behave in a non-ergodic fashion. Alternatively, large values of the time-scale parameter allow for more flexible configurational sampling, with the tradeoff of more (short-term) deviation from the desired average temperature. These larger values are more appropriate for larger systems since the inherent, microcanonical exchange of energy within the large number of degrees of freedom already tends toward canonical properties. (Think of this regime as sampling in a light, organic solvent.) Importantly, thermodynamic averages in the infinite-sampling limit are completely independent of this time-scale parameter. Instead, the time scale merely controls the efficiency with which the ensemble is explored. If maximum efficiency is desired, the user may externally compute lifetimes from the time correlation function of the desired observable and minimize the lifetime as a function of this timescale parameter. At the end of the trajectory, the average computed temperature is compared to the requested target temperature for validation purposes.
$comment Short example of using the Langevin thermostat for canonical (NVT) sampling $end $molecule 0 1 H O 1 1.0 H 2 1.0 1 104.5 $end $rem JOBTYPE aimd EXCHANGE hf BASIS sto-3g AIMD_TIME_STEP 20 !in au AIMD_STEPS 100 AIMD_THERMOSTAT langevin AIMD_INIT_VELOC thermal AIMD_TEMP 298 !in K - initial conditions AND thermostat AIMD_LANGEVIN_TIMESCALE 100 !in fs $end
An alternative thermostat approach is also available, namely, the Nosé-Hoover
J. Chem. Phys.
(1992), 97, pp. 2635. (also known as a Nosé-Hoover “chain”), which mimics the role of a surrounding thermal bath by performing a microcanonical () trajectory in an extended phase space. By allowing energy to be exchanged with a chain of fictitious particles that are coupled to the target system, sampling is properly obtained for those degrees of freedom that represent the real system. (Only the target system properties are saved in $QCSCRATCH/AIMD for subsequent analysis and visualization, not the fictitious Nosé-Hoover degrees of freedom.) The implementation in Q-Chem follows that of Martyna, 735 J. Chem. Phys.
(1992), 97, pp. 2635. which augments the original extended-Lagrangian approach of Nosé 799 J. Chem. Phys.
(1984), 81, pp. 511. , 800 Prog. Theor. Phys. Supp.
(1991), 103, pp. 1. and Hoover, 465 Phys. Rev. A
(1985), 31, pp. 1695. using a chain of auxiliary degrees of freedom to restore ergodicity in stiff systems and thus afford the correct ensemble. Unlike the Langevin thermostat, the collection of system and auxiliary chain particles can be propagated in a time-reversible fashion with no need for stochastic perturbations.
Rather than directly setting the masses and force constants of the auxiliary chain particles, the Q-Chem implementation focuses instead, on the time scale of the thermostat, as was the case for the Langevin thermostat described above. The time-scale parameter is controlled by the keyword NOSE_HOOVER_TIMESCALE, given in units of femtoseconds. The only other user-controllable parameter for this function is the length of the Nosé-Hoover chain, which is typically chosen to be 3–6 fictitious particles. Importantly, the version in Q-Chem is currently implemented as a single chain that is coupled to the system, as a whole. Comprehensive thermostatting in which every single degree of freedom is coupled to its own thermostat, which is sometimes used for particularly stiff systems, is not implemented and for such cases the Langevin thermostat is recommended instead. For large and/or fluxional systems, the single-chain Nosé-Hoover approach is appropriate.
$molecule 0 1 H O 1 1.0 H 2 1.0 1 104.5 $end $rem JOBTYPE aimd EXCHANGE hf BASIS sto-3g AIMD_TIME_STEP 20 !in au AIMD_STEPS 100 AIMD_THERMOSTAT nose_hoover AIMD_INIT_VELOC thermal AIMD_TEMP 298 !in K - initial conditions AND thermostat NOSE_HOOVER_LENGTH 3 !chain length NOSE_HOOVER_TIMESCALE 100 !in fs $end