Realistic-temperature fuel pyrolysis with collective variable-driven hyperdynamics (CVHD)¶

Overview¶

This advanced tutorial demonstrates the use of a novel acceleration technique called collective variable-driven hyperdynamics (CVHD). The tutorial is based on the results presented and discussed in the publication

Kristof M. Bal and Erik C. Neyts, Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations, Chem. Sci., 2016, 7, 5280

Background information¶

When dealing with acceleration techniques it can be helpful to revisit some of the fundamental problems and ideas associated with rare events. An outline of this information is given in this subsection. If you want to jump forward to the hands-on part of tutorial, click here.

Many interesting problems are driven by rare events, i.e. events that take place far outside the realm of accessible timescales in molecular dynamics simulations. These events can be chemical reactions (catalysis, industrial, enzymes) or physical processes (diffusion, phase transitions).

To illustrate the scaling problem we are dealing with, assume a hypothetical “wonder CPU” that can compute one MD time step (1fs) per clock cycle (1 ns). Even with this ideal machinery, simulating 1 s of dynamics will require 10 ⁶wall-s (12 days). Brute-force MD is not feasible and one needs to come up with a different strategy.

Two main approaches are commonly used

• Lowering the effective barrier - biased MD
• Cherry-pick interesting trajectories, e.g. parallel replica MD

The biased MD philosophy can be summed up into two steps: First, running the dynamics using a modified potential or equations of motion to accelerate, followed by an un-biasing in which the effect of the bias is removed from the results.

Free-energy methods (Potential of Mean Force) need to record the bias applied for the unbiasing step. For these methods, suitable collective variables (CVs) need to be defined to reduce dimensionality. In practice up to 2 (3) CVs are feasible (Umbrella, Metadynamics, ABF,...) but it’s also possible to sample along a pre-defined reaction path taken from a Nudged Elastic Band calculation or similar.

Either way, setting up a “good” CV is crucial for obtaining meaningful results. “Good” CVs should

• unambiguously define the state of the system (different states must not overlap)
• ensure that orthogonal processes average out
• be smooth and continuous

CVs in this sense are usually not trivial to construct and not suited for studying many independent simultaneous processes. To illustrate the idea, consider Metdadynamics as a prominent example of a free energy sampling method. The bias - usually Gaussian - is periodically deposited at the current CV value ξ _i. It fills the energy values incrementally until there are no barriers left (diffusive regime).

The free energy is then obtained as the negative of the converged V _bias

Alternatives to free energy sampling methods can be based on a biased sampling of trajectories, e.g. Transition Path Sampling or on an on-the-fly “Unbias” during the dynamics. The latter ansatz leads to Hyperdynamics. The free energy information is lost by the on-the-fly unbiasing but the time can be recovered from the simulation. When the simulation is run on a modified potential:

the “hypertime clock” is advanced by

In simple words, the Hypertime will tell you “How long would it take to get here in an unbiased simulation?”. It must be ensured that the transition state regions remain bias-free. Similar to the choice of the CV, choosing a suitable bias V _biasis hard and error-prone.

A possible remedy is the use of self-learning bias which will lead to CV-based Hyperdynamics (CVHD). In this approach V_{bias} is built on the fly using Metadynamics with a suitable CV η. As opposed to metadynamics, the bias is reset once a transition was detected. The CV now only needs to be valid for a single transition.

In ReaxFF the global CV η is composed of primitive local CVs χ _i. It will be dominated by the bond with the highest χ _iat the time.

At this moment in time only a local bond-breaking CV is implemented (see Bal and Neyts, J. Chem. Theory Comput. 2015 ):

The bias is applied to bonds approaching a transition - defined as the distance between r _i^max and r _i^min. If the CV η = 1 for a specified time a transition is assumed.

The System¶

As a simple example, the low temperature pyrolisis of dodecane under realistic conditions (1000 K, 50 kg/m3) is simulated. This is a challenging reaction to simulate, because the pyrolisis products of alkanes depend on the temperature, resulting in the following trends:

• High T (> 2000K) - Ethylene is by far the dominant reaction product as entropically favored decomposition reactions become the dominant process.
• Lower T - Formation of larger 1-alkanes results in larger product molecules C3 and higher become much more dominant.

For this reason the dynamics of the low-T pyrolisis cannot just be simulated by increasing the simulation temperature. Also a brute force approach of the dynamics is not feasible given the rare-event nature of the bond breaking reactions as will become clear in this tutorial.

With respect to the paper, the following changes were made for the sake of computational efficiency

• The timestep was increased to 0.2 fs (→ lower accuracy)
• A smaller system of only 114 atoms is used

As a result there will not be enough data for proper statistics or rate constants. Still one can estimate the timescales of the different processes.

Preparation¶

Begin by packing a periodic box with 3 dodecane molecules:

Switch to the ReaxFF module

Edit → Builder

Enter 25, 25 , 25 on the diagonal to create a 25 Å cubic box

Enter dodecane into the text field and select Dodecane (ADF) | Enter 3 into the textfield Fill box with | Click Generate Molecules and Close

Use the following ReaxFF settings

Select the CHO.ff force field

Enter a timestep of 0.2 fs

Select the NVT Nose-Hoover chains thermostat

Set a temperature of 1000 K | Set the number of steps to 2000000

To lower the framerate:

Go to Details → Molecular Dynamics

Enter 1000 as the KF result file output frequency

Enter 1000 as the Energies, temperatures and more output frequency

Finally, two local collective variables are setup

• C-C with Rmin = 1.55 Å and Rmax = 2.20 Å
• C-H with Rmin = 1.05 Å and Rmax = 1.65 Å

Go to Model → Collective Variable-Driven Hyperdynamics

Enter 1000 as the Start iteration

Enter 1000 as the Deposition frequency

Keep the bias for 5000 steps

Use the “+” button next to “Bond-breaking CV” to bring up two CV fields

Enter the CV settings from the paper

Save and Run

CVHD events in the Logfile¶

While the calculation is running, you can inspect the logfile:

Select Logfile from the SCM menu

The HyperTime is the “true” timescale after unbiasing, i.e. how long a process would take without CVHD. Note how the first 1000 steps are unbiased, the hypertime equals the simulation time. When the bias starts building up, the simulation gradually accelerates

• after 1 ps (5000 simulation steps), a speedup of 30% is already reached
• after 20 ps (100 000 simulation steps), 2.2 ns have been sampled
• after 40 ps (200 000 simulation steps), 205 ns have been sampled

At a later stage of the simulation the system will approach a transition which manifests as a slowdown in the hypertime evolution as there will not be much bias in the transition state region. In the current example, a molecule dissociates around simulation step 843 000.

At this moment the algorithm will wait for 5000 steps (as requested in the settings) to see if the system recrosses back into the original state. No recrossing occurs, so a CVHD declares that an event (reaction) just took place and removes all bias. From on step 844 000 a new bias starts building up.

Monitoring the bias deposition¶

It is possible to monitor the deposition of the bias using a small command line utility called cvhd-hills. To plot where the biasing hills are deposited

Open a command line window and cd into the results or tmp directory

type cvhd-hills and hit ENTER

This will generate an output file called cvhd-hills.csv that will be openend in ADFgraphs automatically. Change the default plotting mode of ADFgraphs to Data Points:

Plot → Options → Curves

uncheck Curve and check Data Points

Now you should see a plot similar to the below.

In this graph the MD step is on the x-axis and the CVHD global collective variable η on the y-axis. Each point represents a single Gaussian bias hill.

Let’s take a closer look at the first CVHD event.

Initially, the system stays around η = 0 (all bonds relaxed). With the build up of the bias, η is gradually pushed to higher and higher values (bonds are stretched more and more). On some occasions from on iteration 400000, η reaches 1.0 but returns back to lower values. This means that during the specified wait time no transition occured. Finally, around step 800 000 η stays at 1.0 long enough to indicate that a bond has dissociated.

Improving the CV using the Bias Deposition Plot¶

The above bias deposition plot can be used to improve the collective variable using the following diagnostics:

Initial η not close to zero

Rmin is set too low. CVHD “thinks” the equlibrium structure is already partly dissociated

η doesn’t explore higher values (stays at zero)

Rmin is set too high

Too many recrossings: η keeps hitting 1.0 but no true reaction occurs

Rmax is set too low, not close enough to a transition.

System jumps from low η directly to 1.0, triggering a reaction

Rmax is set too high, past the transition state.

It’s often useful to tune each local CV (bond type) separately before combining them in a single simulation. The global CV contains a weighted sum lof local CVs resulting in an optimal Rmin that is system-size-dependent. Typically, large systems need a somewhat higher Rmin.

Analyzing Event Timescales¶

The hypertime associated with each CVHD event can be plotted with the help of the script cvhd-hypertime. The logfile is passed as an argument to the script:

run cvhd-hypertime jobname.logfile

Change the y-axis in ADFgraphs to a logarithmic scale for best results:

Plot → Options → Left Y axis

Make sure the Minimum value is set to a positive number, e.g. 1e-12.

Check Logscale

Now you should see a plot similar to the below.

The x-axis shows the MD step and the y-axis the hypertime in seconds since the previous event. Each curve shows the gradual acceleration of time as the bias evolves until an event (bond dissociation) is detected. The curves show classes of processes corresponding to different timescales are visible

• The Initiation step (dodecane chain splitting) at a (sub-)millisecond timescale.
• Propagation steps occur at a ns-μs timescales

The curves should be (mostly) smooth. Jagged or staircase-like curves indicate issues with the CVHD setup (Rmin/Rmax, deposition rate, etc...).

Analyzing the System Composition¶

To inspect the reactions more closely

Open ADFmovie

Properties → Molecule Fractions

Check Graph to plot the number of particular molecules/fragments

An example showing the consumption of dodecane (red) and the production of ethylene (blue) from a longer (8000000 steps) CVHD trajectory looks as follows

Discussion¶

This tutorial is using a small example system as well as a minimal amount of steps for the sake of computational efficiency. As a direct consequence

• we can’t expect any reasonable statistics or rate constants
• most elementary reactions are observed only once, some are completely missed
• only a rough order-of-magnitude estimate on timescales can be made
• multiple trajectories yield largely different results

To overcome these limitations, a bigger system and longer simulation times are required.

The chosen timestep of 0.2 fs is possibly to inaccurate during the transitions and the results should be verified using a shorter timestep (0.1 fs). Finally, the Rmin/Rmax parameters for the C-H bonds could probably benefit from further tuning with the help of the bias deposition plots.

Summary¶

The collective variable driven hyperdanymics ansatz implemented in AMS2018:

...is suitable for accelerating bond dissociation

Any process that starts with bond dissociation can be accelerated.

...has a relatively low setup effort

Only Rmin/Rmax distances are needed for each bond which can be estimated and tuned in a few short testing runs. The hill height and deposition rate may need to be adjusted depending on the expected barrier height.

...works best for moderately-sized systems

CVs comprising many thousands of bonds trigger events too often which limits bias buildup and accelerations. Only the number of biased bonds matter as opposed to the overall system size, and those can be limited using suitable regions. See the CVHD manual for more information.