10.7 Ab Initio Molecular Dynamics

10.7.3 Thermostats: Sampling the NVT Ensemble

Implicit in the discussion above was an assumption of conservation of energy, which implies dynamics run in the microcanonical (NVE) ensemble. Alternatively, the AIMD code in Q-Chem can sample the canonical (NVT) 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 NPT 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.

10.7.3.1 Langevin Thermostat

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 and Parrinello,129 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.

Example 10.25  Canonical (NVT) sampling using AIMD with the Langevin thermostat

$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

10.7.3.2 Nosé-Hoover Thermostat

An alternative thermostat approach is also available, namely, the Nosé-Hoover thermostat616 (also known as a Nosé-Hoover “chain”), which mimics the role of a surrounding thermal bath by performing a microcanonical (NVE) 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, NVT 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,616 which augments the original extended-Lagrangian approach of Nosé668, 669 and Hoover,388 using a chain of auxiliary degrees of freedom to restore ergodicity in stiff systems and thus afford the correct NVT 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.

Example 10.26  Canonical (NVT) sampling using AIMD with the Nosé-Hoover chain thermostat

$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

AIMD_THERMOSTAT
       Applies thermostatting to AIMD trajectories.
TYPE:
       INTEGER
DEFAULT:
       none
OPTIONS:
       LANGEVIN Stochastic, white-noise Langevin thermostat NOSE_HOOVER Time-reversible, Nosé-Hoovery chain thermostat
RECOMMENDATION:
       Use either thermostat for sampling the canonical (NVT) ensemble.

AIMD_LANGEVIN_TIMESCALE
       Sets the timescale (strength) of the Langevin thermostat
TYPE:
       INTEGER
DEFAULT:
       none
OPTIONS:
       n Thermostat timescale,asn n fs
RECOMMENDATION:
       Smaller values (roughly 100) equate to tighter thermostats but may inhibit rapid sampling. Larger values (1000) allow for more rapid sampling but may take longer to reach thermal equilibrium.

NOSE_HOOVER_LENGTH
       Sets the chain length for the Nosé-Hoover thermostat
TYPE:
       INTEGER
DEFAULT:
       none
OPTIONS:
       n Chain length of n auxiliary variables
RECOMMENDATION:
       Typically 3-6

NOSE_HOOVER_TIMESCALE
       Sets the timescale (strength) of the Nosé-Hoover thermostat
TYPE:
       INTEGER
DEFAULT:
       none
OPTIONS:
       n Thermostat timescale, as n fs
RECOMMENDATION:
       Smaller values (roughly 100) equate to tighter thermostats but may inhibit rapid sampling. Larger values (1000) allow for more rapid sampling but may take longer to reach thermal equilibrium.