neb etol ftol N1 N2 Nevery filename
neb 0.1 0.0 1000 500 50 coords.final neb 0.0 0.001 1000 500 50 coords.final
Perform a nudged elastic band (NEB) calculation using multiple replicas of a system. Two or more replicas must be used, two of which are the end points of the transition path.
NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an atom to perform a diffusive hop from one energy basin to another in a coordinated fashion with its neighbors. The implementation in LAMMPS follows the discussion in these 3 papers: (Henkelman1), (Henkelman2), and (Nakano).
Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line switch; see Section_start 6 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or two processors. You will simply not get the performance speed-up you would see with one or more physical processors per replica. See this section of the manual for further discussion.
NOTE: The current NEB implementation in LAMMPS restricts you to having exactly one processor per replica.
When a NEB calculation is performed, it is assumed that each replica is running the same model, though LAMMPS does not check for this. I.e. the simulation domain, the number of atoms, the interaction potentials, and the starting configuration when the neb command is issued should be the same for every replica.
In a NEB calculation each atom in a replica is connected to the same atom in adjacent replicas by springs, which induce inter-replica forces. These forces are imposed by the fix neb command, which must be used in conjunction with the neb command. The group used to define the fix neb command specifies which atoms the inter-replica springs are applied to. These are the NEB atoms. Additional atoms can be present in your system, e.g. to provide a background force field or simply to hold fixed during the NEB procedure, but they will not be part of the barrier finding procedure.
The "starting configuration" for NEB should be a state with the NEB atoms (and all other atoms) having coordinates on one side of the energy barrier. These coordinates will be assigned to the first replica #1. The coordinates should be close to a local energy minimum. A perfect energy minimum is not required, since NEB runs via damped dynamics which will tend to drive the configuration of replica #1 to a true energy minimum, but you will typically get better convergence if the initial state is already at a minimum. For example, for a system with a free surface, the surface should be fully relaxed before attempting a NEB calculation.
The final configuration is specified in the input filename, which is formatted as described below. Only coordinates for NEB atoms or a subset of them should be listed in the file; they represent the state of the system on the other side of the barrier, at or near an energy minimum. These coordinates will be assigned to the last replica #M. The final coordinates of atoms not listed in filename are set equal to their initial coordinates. Again, a perfect energy minimum is not required for the final configuration, since the atoms in replica #M will tend to move during the NEB procedure to the nearest energy minimum. Also note that a final coordinate does not need to be specified for a NEB atom if you expect it to only displace slightly during the NEB procedure. For example, only the final coordinate of the single atom diffusing into a vacancy need be specified if the surrounding atoms will only relax slightly in the final configuration.
The initial coordinates of all atoms (not just NEB atoms) in the intermediate replicas #2,#3,...,#M-1 are set to values linearly interpolated between the corresponding atoms in replicas #1 and #M.
A NEB calculation has two stages, each of which is a minimization procedure, performed via damped dynamics. To enable this, you must first define an appropriate min_style, such as quickmin or fire. The cg, sd, and hftn styles cannot be used, since they perform iterative line searches in their inner loop, which cannot be easily synchronized across multiple replicas.
The minimizer tolerances for energy and force are set by etol and ftol, the same as for the minimize command.
A non-zero etol means that the NEB calculation will terminate if the energy criterion is met by every replica. The energies being compared to etol do not include any contribution from the inter-replica forces, since these are non-conservative. A non-zero ftol means that the NEB calculation will terminate if the force criterion is met by every replica. The forces being compared to ftol include the inter-replica forces between an atom and its images in adjacent replicas.
The maximum number of iterations in each stage is set by N1 and N2. These are effectively timestep counts since each iteration of damped dynamics is like a single timestep in a dynamics run. During both stages, the potential energy of each replica and its normalized distance along the reaction path (reaction coordinate RD) will be printed to the screen and log file every Nevery timesteps. The RD is 0 and 1 for the first and last replica. For intermediate replicas, it is the cumulative distance (normalized by the total cumulative distance) between adjacent replicas, where "distance" is defined as the length of the 3N-vector of differences in atomic coordinates, where N is the number of NEB atoms involved in the transition. These outputs allow you to monitor NEB's progress in finding a good energy barrier. N1 and N2 must both be multiples of Nevery.
In the first stage of NEB, the set of replicas should converge toward the minimum energy path (MEP) of conformational states that transition over the barrier. The MEP for a barrier is defined as a sequence of 3N-dimensional states that cross the barrier at its saddle point, each of which has a potential energy gradient parallel to the MEP itself. The replica states will also be roughly equally spaced along the MEP due to the inter-replica spring force added by the fix neb command.
In the second stage of NEB, the replica with the highest energy is selected and the inter-replica forces on it are converted to a force that drives its atom coordinates to the top or saddle point of the barrier, via the barrier-climbing calculation described in (Henkelman2). As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced.
When both stages are complete, if the NEB calculation was successful, one of the replicas should be an atomic configuration at the top or saddle point of the barrier, the potential energies for the set of replicas should represent the energy profile of the barrier along the MEP, and the configurations of the replicas should be a sequence of configurations along the MEP.
A few other settings in your input script are required or advised to perform a NEB calculation.
An atom map must be defined which it is not by default for atom_style atomic problems. The atom_modify map command can be used to do this.
The "atom_modify sort 0 0.0" command should be used to turn off atom sorting.
NOTE: This sorting restriction will be removed in a future version of NEB in LAMMPS.
The minimizers in LAMMPS operate on all atoms in your system, even non-NEB atoms, as defined above. To prevent non-NEB atoms from moving during the minimization, you should use the fix setforce command to set the force on each of those atoms to 0.0. This is not required, and may not even be desired in some cases, but if those atoms move too far (e.g. because the initial state of your system was not well-minimized), it can cause problems for the NEB procedure.
The damped dynamics minimizers, such as quickmin and fire), adjust the position and velocity of the atoms via an Euler integration step. Thus you must define an appropriate timestep to use with NEB. Using the same timestep that would be used for a dynamics run of your system is advised.
The specified filename contains atom coordinates for the final configuration. Only atoms with coordinates different than the initial configuration need to be specified, i.e. those geometrically near the barrier.
The file can be ASCII text or a gzipped text file (detected by a .gz suffix). The file should contain one line per atom, formatted with the atom ID, followed by the final x,y,z coordinates:
125 24.97311 1.69005 23.46956 126 1.94691 2.79640 1.92799 127 0.15906 3.46099 0.79121 ...
The lines can be listed in any order.
Four kinds of output can be generated during a NEB calculation: energy barrier statistics, thermodynamic output by each replica, dump files, and restart files.
When running with multiple partitions (each of which is a replica in this case), the print-out to the screen and master log.lammps file contains a line of output, printed once every Nevery timesteps. It contains the timestep, the maximum force per replica, the maximum force per atom (in any replica), potential gradients in the initial, final, and climbing replicas, the forward and backward energy barriers, the total reaction coordinate (RDT), and the normalized reaction coordinate and potential energy of each replica.
The "maximum force per replica" is the two-norm of the 3N-length force vector for the atoms in each replica, maximized across replicas, which is what the ftol setting is checking against. In this case, N is all the atoms in each replica. The "maximum force per atom" is the maximum force component of any atom in any replica. The potential gradients are the two-norm of the 3N-length force vector solely due to the interaction potential i.e. without adding in inter-replica forces. Note that inter-replica forces are zero in the initial and final replicas, and only affect the direction in the climbing replica. For this reason, the "maximum force per replica" is often equal to the potential gradient in the climbing replica. In the first stage of NEB, there is no climbing replica, and so the potential gradient in the highest energy replica is reported, since this replica will become the climbing replica in the second stage of NEB.
The "reaction coordinate" (RD) for each replica is the two-norm of the 3N-length vector of distances between its atoms and the preceding replica's atoms, added to the RD of the preceding replica. The RD of the first replica RD1 = 0.0; the RD of the final replica RDN = RDT, the total reaction coordinate. The normalized RDs are divided by RDT, so that they form a monotonically increasing sequence from zero to one. When computing RD, N only includes the atoms being operated on by the fix neb command.
The forward (reverse) energy barrier is the potential energy of the highest replica minus the energy of the first (last) replica.
When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a NEB calculation, these contain the thermodynamic output for each replica.
If dump commands in the input script define a filename that includes a universe or uloop style variable, then one dump file (per dump command) will be created for each replica. At the end of the NEB calculation, the final snapshot in each file will contain the sequence of snapshots that transition the system over the energy barrier. Earlier snapshots will show the convergence of the replicas to the MEP.
Likewise, restart filenames can be specified with a universe or uloop style variable, to generate restart files for each replica. These may be useful if the NEB calculation fails to converge properly to the MEP, and you wish to restart the calculation from an intermediate point with altered parameters.
There are 2 Python scripts provided in the tools/python directory, neb_combine.py and neb_final.py, which are useful in analyzing output from a NEB calculation. Assume a NEB simulation with M replicas, and the NEB atoms labelled with a specific atom type.
The neb_combine.py script extracts atom coords for the NEB atoms from all M dump files and creates a single dump file where each snapshot contains the NEB atoms from all the replicas and one copy of non-NEB atoms from the first replica (presumed to be identical in other replicas). This can be visualized/animated to see how the NEB atoms relax as the NEB calculation proceeds.
The neb_final.py script extracts the final snapshot from each of the M dump files to create a single dump file with M snapshots. This can be visualized to watch the system make its transition over the energy barrier.
To illustrate, here are images from the final snapshot produced by the neb_combine.py script run on the dump files produced by the two example input scripts in examples/neb. Click on them to see a larger image.
This command can only be used if LAMMPS was built with the REPLICA package. See the Making LAMMPS section for more info on packages.
prd, temper, fix langevin, fix viscous
(Henkelman1) Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
(Henkelman2) Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000).
(Nakano) Nakano, Comp Phys Comm, 178, 280-289 (2008).