fix hyper/local command
Syntax
fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget
ID, group-ID are documented in fix command
hyper/local = style name of this fix command
cutbond = max distance at which a pair of atoms is considered bonded (distance units)
qfactor = max strain at which bias potential goes to 0.0 (unitless)
Vmax = estimated height of bias potential (energy units)
Tequil = equilibration temperature (temperature units)
Dcut = minimum distance between boosted bonds (distance units)
alpha = boostostat relaxation time (time units)
Btarget = desired time boost factor (unitless)
zero or more keyword/value pairs may be appended
keyword = check/ghost or check/bias
check/ghost values = none check/bias values = Nevery error/warn/ignore
Examples
fix 1 all hyper/local 1.0 0.3 0.8 300.0
Description
This fix is meant to be used with the hyper command to perform a bond-boost local hyperdynamics (LHD) simulation. The role of this fix is to a select multiple pairs of atoms in the system at each timestep to add a local bias potential to, which will alter the dynamics of the system in a manner that effectively accelerates time. This is in contrast to the fix hyper/global command, which can be user to perform a global hyperdynamics (GHD) simulation, by adding a global bias potential to a single pair of atoms at each timestep. GHD can time accelerate a small simulation with up to a few 100 atoms. For larger systems, LHD is needed to achieve good time acceleration.
For a system that undergoes rare transition events, where one or more atoms move over an energy barrier to a new potential energy basin, the effect of the bias potential is to induce more rapid transitions. This can lead to a dramatic speed-up in the rate at which events occurs, without altering their relative frequencies, thus leading to an overall increase in the elapsed real time of the simulation as compared to running for the same number of timesteps with normal MD. See the hyper doc page for a more general discussion of hyperdynamics and citations that explain both GHD and LHD.
The equations and logic used by this fix and described here to perform LHD follow the description given in (Voter2013). The bond-boost form of a bias potential for HD is due to Miron and Fichthorn as described in (Miron).
To understand this description, you should first read the description of the GHD algorithm on the fix hyper/global doc page. This description of LHD builds on the GHD description.
The definition of bonds and Eij are the same for GHD and LHD. The formulas for Vij(max) and Fij(max) are also the same except for a pre-factor Cij, explained below.
The bias energy Vij applied to a bond IJ with maximum strain is
Vij(max) = Cij * Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor
= 0 otherwise
The derivative of Vij(max) with respect to the position of each atom in the IJ bond gives a bias force Fij(max) acting on the bond as
Fij(max) = - dVij(max)/dEij = 2 Cij Vmax Eij / qfactor^2 for abs(Eij) < qfactor
= 0 otherwise
which can be decomposed into an equal and opposite force acting on only the two I,J atoms in the IJ bond.
The key difference is that in GHD a bias energy and force is added (on a particular timestep) to only one bond (pair of atoms) in the system, which is the bond with maximum strain Emax.
In LHD, a bias energy and force can be added to multiple bonds separated by the specified Dcut distance or more. A bond IJ is biased if it is the maximum strain bond within its local “neighborhood”, which is defined as the bond IJ plus any neighbor bonds within a distance Dcut from IJ. The “distance” between bond IJ and bond KL is the minimum distance between any of the IK, IL, JK, JL pairs of atoms.
For a large system, multiple bonds will typically meet this requirement, and thus a bias potential Vij(max) will be applied to many bonds on the same timestep.
In LHD, all bonds store a Cij prefactor which appears in the Vij(max) and Fij(max) equations above. Note that the Cij factor scales the strength of the bias energy and forces whenever bond IJ is the maximum strain bond in its neighborhood.
Cij is initialized to 1.0 when a bond between the I,J atoms is first defined. The specified Btarget factor is then used to adjust the Cij prefactors for each bond every timestep in the following manner.
An instantaneous boost factor Bij is computed each timestep for each bond, as
Bij = exp(beta * Vkl(max))
where Vkl(max) is the bias energy of the maxstrain bond KL within bond IJ’s neighborhood, beta = 1/kTequil, and Tequil is the temperature of the system and an argument to this fix.
Note
To run an LHD simulation, the input script must also use the fix langevin command to thermostat the atoms at the same Tequil as specified by this fix, so that the system is running constant-temperature (NVT) dynamics. LAMMPS does not check that this is done.
Note that if IJ = KL, then bond IJ is a biased bond on that timestep, otherwise it is not. But regardless, the boost factor Bij can be thought of an estimate of time boost currently being applied within a local region centered on bond IJ. For LHD, we want this to be the specified Btarget value everywhere in the simulation domain.
To accomplish this, if Bij < Btarget, the Cij prefactor for bond IJ is incremented on the current timestep by an amount proportional to the inverse of the specified alpha and the difference (Bij - Btarget). Conversely if Bij > Btarget, Cij is decremented by the same amount. This procedure is termed “boostostatting” in (Voter2013). It drives all of the individual Cij to values such that when Vijmax is applied as a bias to bond IJ, the resulting boost factor Bij will be close to Btarget on average. Thus the LHD time acceleration factor for the overall system is effectively Btarget.
Note that in LHD, the boost factor Btarget is specified by the user. This is in contrast to global hyperdynamics (GHD) where the boost factor varies each timestep and is computed as a function of Vmax, Emax, and Tequil; see the fix hyper/global doc page for details.
Here is additional information on the input parameters for LHD.
Note that the cutbond, qfactor, and Tequil arguments have the same meaning as for GHD. The Vmax argument is slightly different. The Dcut, alpha, and Btarget parameters are unique to LHD.
The cutbond argument is the cutoff distance for defining bonds between pairs of nearby atoms. A pair of I,J atoms in their equilibrium, minimum-energy configuration, which are separated by a distance Rij < cutbond, are flagged as a bonded pair. Setting cubond to be ~25% larger than the nearest-neighbor distance in a crystalline lattice is a typical choice for solids, so that bonds exist only between nearest neighbor pairs.
The qfactor argument is the limiting strain at which the bias potential goes to 0.0. It is dimensionless, so a value of 0.3 means a bond distance can be up to 30% larger or 30% smaller than the equilibrium (quenched) R0ij distance and the two atoms in the bond could still experience a non-zero bias force.
If qfactor is set too large, then transitions from one energy basin to another are affected because the bias potential is non-zero at the transition state (e.g. saddle point). If qfactor is set too small than little boost can be achieved because the Eij strain of some bond in the system will (nearly) always exceed qfactor. A value of 0.3 for qfactor is typically a reasonable value.
The Vmax argument is a fixed prefactor on the bias potential. There is a also a dynamic prefactor Cij, driven by the choice of Btarget as discussed above. The product of these should be a value less than the smallest barrier height for an event to occur. Otherwise the applied bias potential may be large enough (when added to the interatomic potential) to produce a local energy basin with a maxima in the center. This can produce artificial energy minima in the same basin that trap an atom. Or if Cij*Vmax is even larger, it may induce an atom(s) to rapidly transition to another energy basin. Both cases are “bad dynamics” which violate the assumptions of LHD that guarantee an accelerated time-accurate trajectory of the system.
Note
It may seem that Vmax can be set to any value, and Cij will compensate to reduce the overall prefactor if necessary. However the Cij are initialized to 1.0 and the boostostatting procedure typically operates slowly enough that there can be a time period of bad dynamics if Vmax is set too large. A better strategy is to set Vmax to the smallest barrier height for an event (the same as for GHD), so that the Cij remain near unity.
The Tequil argument is the temperature at which the system is simulated; see the comment above about the fix langevin thermostatting. It is also part of the beta term in the exponential factor that determines how much boost is achieved as a function of the bias potential. See the discussion of the Btarget argument below.
As discussed above, the Dcut argument is the distance required between two locally maxstrain bonds for them to both be selected as biased bonds on the same timestep. Computationally, the larger Dcut is, the more work (computation and communication) must be done each timestep within the LHD algorithm. And the fewer bonds can be simultaneously biased, which may mean the specified Btarget time acceleration cannot be achieved.
Physically Dcut should be a long enough distance that biasing two pairs of atoms that close together will not influence the dynamics of each pair. E.g. something like 2x the cutoff of the interatomic potential. In practice a Dcut value of ~10 Angstroms seems to work well for many solid-state systems.
Note
You should insure that ghost atom communication is performed for a distance of at least Dcut + cutevent = the distance one or more atoms move (between quenched states) to be considered an “event”. It is an argument to the “compute event/displace” command used to detect events. By default the ghost communication distance is set by the pair_style cutoff, which will typically be < Dcut. The comm_modify cutoff command should be used to override the ghost cutoff explicitly, e.g.
comm_modify cutoff 12.0
Note that this fix does not know the cutevent parameter, but uses half the cutbond parameter as an estimate to warn if the ghost cutoff is not long enough.
As described above the alpha argument is a pre-factor in the boostostat update equation for each bond’s Cij prefactor. Alpha is specified in time units, similar to other thermostat or barostat damping parameters. It is roughly the physical time it will take the boostostat to adjust a Cij value from a too high (or too low) value to a correct one. An alpha setting of a few ps is typically good for solid-state systems. Note that the alpha argument here is the inverse of the alpha parameter discussed in (Voter2013).
The Btarget argument is the desired time boost factor (a value > 1) that all the atoms in the system will experience. The elapsed time t_hyper for an LHD simulation running for N timesteps is simply
t_hyper = Btarget * N*dt
where dt is the timestep size defined by the timestep command. The effective time acceleration due to LHD is thus t_hyper / N*dt = Btarget, where N*dt is elapsed time for a normal MD run of N timesteps.
You cannot choose an arbitrarily large setting for Btarget. The maximum value you should choose is
Btarget = exp(beta * Vsmall)
where Vsmall is the smallest event barrier height in your system, beta = 1/kTequil, and Tequil is the specified temperature of the system (both by this fix and the Langevin thermostat).
Note that if Btarget is set smaller than this, the LHD simulation will run correctly. There will just be fewer events because the hyper time (t_hyper equation above) will be shorter.
Note
If you have no physical intuition as to the smallest barrier height in your system, a reasonable strategy to determine the largest Btarget you can use for an LHD model, is to run a sequence of simulations with smaller and smaller Btarget values, until the event rate does not change (as a function of hyper time).
Here is additional information on the optional keywords for this fix.
The check/ghost keyword turns on extra computation each timestep to compute statistics about ghost atoms used to determine which bonds to bias. The output of these stats are the vector values 14 and 15, described below. If this keyword is not enabled, the output of the stats will be zero.
The check/bias keyword turns on extra computation and communication to check if any biased bonds are closer than Dcut to each other, which should not be the case if LHD is operating correctly. Thus it is a debugging check. The Nevery setting determines how often the check is made. The error, warn, or ignore setting determines what is done if the count of too-close bonds is not zero. Either the code will exit, or issue a warning, or silently tally the count. The count can be output as vector value 17, as described below. If this keyword is not enabled, the output of that statistic will be 0.
Note that both of these computations are costly, hence they are only enabled by these keywords.
Restart, fix_modify, output, run start/stop, minimize info:
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this fix to add the energy of the bias potential to the system’s potential energy as part of thermodynamic output.
This fix computes a global scalar and global vector of length 21, which can be accessed by various output commands. The scalar is the magnitude of the bias potential (energy units) applied on the current timestep, summed over all biased bonds. The vector stores the following quantities:
1 = # of biased bonds on this step
2 = max strain Eij of any bond on this step (absolute value, unitless)
3 = average bias coeff for all bonds on this step (unitless)
4 = average # of bonds/atom on this step
5 = average neighbor bonds/bond on this step within Dcut
6 = max bond length during this run (distance units)
7 = average # of biased bonds/step during this run
8 = fraction of biased bonds with no bias during this run
9 = fraction of biased bonds with negative strain during this run
10 = average bias coeff for all bonds during this run (unitless)
11 = min bias coeff for any bond during this run (unitless)
12 = max bias coeff for any bond during this run (unitless)
13 = max drift distance of any bond atom during this run (distance units)
14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
16 = count of ghost atoms that could not be found on reneighbor steps during this run
17 = count of bias overlaps (< Dcut) found during this run
18 = cumulative hyper time since fix created (time units)
19 = cumulative count of event timesteps since fix created
20 = cumulative count of atoms in events since fix created
21 = cumulative # of new bonds formed since fix created
The first quantities (1-5) are for the current timestep. Quantities 6-17 are for the current hyper run. They are reset each time a new hyper run is performed. Quantities 18-21 are cumulative across multiple runs (since the point in the input script the fix was defined).
For value 8, the numerator is a count of all biased bonds on each timestep whose bias energy = 0.0 due to Eij >= qfactor. The denominator is the count of all biased bonds on all timesteps.
For value 9, the numerator is a count of all biased bonds on each timestep with negative strain. The denominator is the count of all biased bonds on all timesteps.
Values 13-17 are mostly useful for debugging and diagnostic purposes.
For value 13, drift is the distance an atom moves between two quenched states when the second quench determines an event has occurred. Atoms involved in an event will typically move the greatest distance since others typically remain near their original quenched position.
For values 14-16, neighbor atoms in the full neighbor list with cutoff Dcut may be ghost atoms outside a processor’s sub-box. Before the next event occurs they may move further than Dcut away from the sub-box boundary. Value 14 is the furthest (from the sub-box) any ghost atom in the neighbor list with maxstrain < qfactor was accessed during the run. Value 15 is the same except that the ghost atom’s maxstrain may be >= qfactor, which may mean it is about to participate in an event. Value 16 is a count of how many ghost atoms could not be found on reneighbor steps, presumably because they moved too far away due to their participation in an event (which will likely be detected at the next quench).
Typical values for 14 and 15 should be slightly larger than Dcut, which accounts for ghost atoms initially at a Dcut distance moving thermally before the next event takes place.
Note that for values 14 and 15 to be computed, the optional keyword check/ghost must be specified. Otherwise these values will be zero. This is because computing them incurs overhead, so the values are only computed if requested.
Value 16 should be zero or small. As explained above a small count likely means some ghost atoms were participating in their own events and moved a longer distance. If the value is large, it likely means the communication cutoff for ghosts is too close to Dcut leading to many not-found ghost atoms before the next event. This may lead to a reduced number of bonds being selected for biasing, since the code assumes those atoms are part of highly strained bonds. As explained above, the comm_modify cutoff command can be used to set a longer cutoff.
For value 17, no two bonds should be biased if they are within a Dcut distance of each other. This value should be zero, indicating that no pair of biased bonds are closer than Dcut from each other.
Note that for values 17 to be computed, the optional keyword check/bias must be specified and it determines how often this check is performed. This is because performing the check incurs overhead, so if only computed as often as requested.
The result at the end of the run is the cumulative total from every timestep the check was made. Note that the value is a count of atoms in bonds which found other atoms in bonds too close, so it is almost always an over-count of the number of too-close bonds.
Value 18 is simply the specified boost factor times the number of timesteps times the timestep size.
For value 19, events are checked for by the hyper command once every Nevent timesteps. This value is the count of those timesteps on which one (or more) events was detected. It is NOT the number of distinct events, since more than one event may occur in the same Nevent time window.
For value 20, each time the hyper command checks for an event, it invokes a compute to flag zero or more atoms as participating in one or more events. E.g. atoms that have displaced more than some distance from the previous quench state. Value 20 is the cumulative count of the number of atoms participating in any of the events that were found.
Value 21 tallies the number of new bonds created by the bond reset operation. Bonds between a specific I,J pair of atoms may persist for the entire hyperdynamics simulation if neither I or J are involved in an event.
The scalar and vector values calculated by this fix are all “intensive”.
This fix also computes a local vector of length the number of bonds currently in the system. The value for each bond is its Cij prefactor (bias coefficient). These values can be can be accessed by various output commands. A particularly useful one is the fix ave/histo command which can be used to histogram the Cij values to see if they are distributed reasonably close to 1.0, which indicates a good choice of Vmax.
The local values calculated by this fix are unitless.
No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.
Restrictions
This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.
Default
The check/ghost and check/bias keywords are not enabled by default.
(Voter2013) S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013).
(Miron) R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).