fix mdi/qm command
fix ID group-ID mdi/qm keyword value(s) keyword value(s) ...
ID, group-ID are documented in fix command
mdi/qm = style name of this fix command
zero or more keyword/value pairs may be appended
keyword = virial or add or every or connect or elements or mc
virial args = yes or no yes = request virial tensor from server code no = do not request virial tensor from server code add args = yes or no yes = add returned value from server code to LAMMPS quantities no = do not add returned values to LAMMPS quantities every args = Nevery Nevery = request values from server code once every Nevery steps connect args = yes or no yes = perform a one-time connection to the MDI engine code no = do not perform the connection operation elements args = N_1 N_2 ... N_ntypes N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types mc args = mcfixID mcfixID = ID of a Monte Carlo fix designed to work with this fix
fix 1 all mdi/qm fix 1 all mdi/qm virial yes fix 1 all mdi/qm add no every 100 elements C C H O
New in version 3Aug2022.
This command enables LAMMPS to act as a client with another server code that will compute the total energy, per-atom forces, and total virial for atom conformations and simulation box size/shapes that LAMMPS sends it.
Typically the server code will be a quantum mechanics (QM) code, hence the name of the fix. However this is not required, the server code could be another classical molecular dynamics code or LAMMPS itself. The server code must support use of the MDI Library as explained below.
Typically, to use this fix, the input script should not define any other classical force field components, e.g. a pair style, bond style, etc.
These are example use cases for this fix, discussed further below:
perform an ab initio MD (AIMD) simulation with quantum forces
perform an energy minimization with quantum forces
perform a nudged elastic band (NEB) calculation with quantum forces
perform a QM calculation for a series of independent systems which LAMMPS reads or generates once
run a classical MD simulation and calculate QM energy/forces once every N steps on the current configuration
More generally any command which calculates per-atom forces can instead use quantum forces by defining this fix. Examples are the Monte Carlo commands fix gcmc and fix atom/swap, as well as the compute born/matrix command. The only requirement is that internally the command invokes the post_force() method of fixes such as this one, which will trigger the quantum calculation.
The code coupling performed by this command is done via the MDI Library. LAMMPS runs as an MDI driver (client), and sends MDI commands to an external MDI engine code (server), e.g. a QM code which has support for MDI. See the Howto mdi page for more information about how LAMMPS can operate as either an MDI driver or engine.
examples/mdi directory contains input scripts using this fix in
the various use cases discussed below. In each case, two instances of
LAMMPS are used, once as an MDI driver, once as an MDI engine (surrogate
for a QM code). The
examples/mdi/README file explains how to launch
two codes so that they communicate via the MDI library using either MPI
or sockets. Any QM code that supports MDI could be used in place of
LAMMPS acting as a QM surrogate. See the Howto mdi
page for a current list (March 2022) of such QM codes. The
examples/QUANTUM directory has examples for coupling LAMMPS to 3 QM
codes either via this fix or the fix mdi/qmmm
Note that an engine code can support MDI in either or both of two modes.
It can be used as a stand-alone code, launched at the same time as
LAMMPS. Or it can be used as a plugin library, which LAMMPS loads. See
the mdi plugin command for how to trigger LAMMPS to load a
plugin library. The
examples/mdi/README file and
examples/QUANTUM/QM-code/README files explain how to launch the two
codes in either mode.
The virial keyword setting of yes or no determines whether LAMMPS will request the QM code to also compute and return the QM contribution to a stress tensor for the system which LAMMPS will convert to a 6-element symmetric virial tensor.
The add keyword setting of yes or no determines whether the energy and forces and virial returned by the QM code will be added to the LAMMPS internal energy and forces and virial or not. If the setting is no then the default fix_modify energy and fix_modify virial settings are also set to no and your input scripts should not set them to yes. See more details on these fix_modify settings below.
Whatever the setting for the add keyword, the QM energy, forces, and virial will be stored by the fix, so they can be accessed by other commands. See details below.
The every keyword determines how often the QM code will be invoked during a dynamics run with the current LAMMPS simulation box and configuration of atoms. The QM code will be called once every Nevery timesteps. By default Nevery = 1.
The connect keyword determines whether this fix performs a one-time
connection to the QM code. The default is yes. The only time a no
is needed is if this command is used multiple times in an input script
and the MDI coupling is between two stand-alone codes (not plugin mode).
E.g. if it used inside a loop which also uses the clear
command to destroy the system (including this fix). See the
examples/mdi/in.series.driver script as an example of this, where
LAMMPS is using the QM code to compute energy and forces for a series of
system configurations. In this use case connect no is used along with
the mdi connect and exit command to one-time
initiate/terminate the connection outside the loop.
The elements keyword allows specification of what element each LAMMPS atom type corresponds to. This is specified by the chemical symbol of the element, e.g. C or Al or Si. A symbol must be specified for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can represent the same element. Ntypes is typically specified via the create_box command or in the data file read by the read_data command.
If this keyword is specified, then this fix will send the MDI “>ELEMENTS” command to the engine, to ensure the two codes are consistent in their definition of atomic species. If this keyword is not specified, then this fix will send the MDI >TYPES command to the engine. This is fine if both the LAMMPS driver and the MDI engine are initialized so that the atom type values are consistent in both codes.
The mc keyword enables this fix to be used with a Monte Carlo (MC) fix to calculate before/after quantum energies as part of the MC accept/reject criterion. The fix gcmc and fix atom/swap commands can be used in this manner. Specify the ID of the MC fix following the mc keyword. This allows the two fixes to coordinate when MC events are being calculated versus MD timesteps between the MC events.
The following 3 example use cases are illustrated in the
examples/mdi directory. See its README file for more details.
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy minimization with QM forces, or a multi-replica NEB calculation, use add yes and every 1 (the defaults). This is so that every time LAMMPS needs energy and forces, the QM code will be invoked.
Both LAMMPS and the QM code should define the same system (simulation box, atoms and their types) in their respective input scripts. Note that on this scenario, it may not be necessary for LAMMPS to define a pair style or use a neighbor list.
LAMMPS will then perform the timestepping or minimization iterations for the simulation. At the point in each timestep or iteration when LAMMPS needs the force on each atom, it communicates with the engine code. It sends the current simulation box size and shape (if they change dynamically, e.g. during an NPT simulation), and the current atom coordinates. The engine code computes quantum forces on each atom and the total energy of the system and returns them to LAMMPS.
Note that if the AIMD simulation is an NPT or NPH model, or the energy minimization includes fix box relax to equilibrate the box size/shape, then LAMMPS computes a pressure. This means the virial keyword should be set to yes so that the QM contribution to the pressure can be included.
(2) To run dynamics with a LAMMPS interatomic potential, and evaluate the QM energy and forces once every 1000 steps, use add no and every 1000. This could be useful for using an MD run to generate randomized configurations which are then passed to the QM code to produce training data for a machine learning potential. A dump custom command could be invoked every 1000 steps to dump the atom coordinates and QM forces to a file. Likewise the QM energy and virial could be output with the thermo_style custom command.
(3) To do a QM evaluation of energy and forces for a series of N independent systems (simulation box and atoms), use add no and every 1. Write a LAMMPS input script which loops over the N systems. See the Howto multiple doc page for details on looping and removing old systems. The series of systems could be initialized by reading them from data files with read_data commands. Or, for example, by using the lattice , create_atoms, delete_atoms, and/or displace_atoms random commands to generate a series of different systems. At the end of the loop perform run 0 and write_dump commands to invoke the QM code and output the QM energy and forces. As in (2) this be useful to produce QM data for training a machine learning potential.
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 potential energy computed by the QM code to the global potential energy of the system as part of thermodynamic output. The default setting for this fix is fix_modify energy yes, unless the add keyword is set to no, in which case the default setting is no.
The fix_modify virial option is supported by this fix to add the contribution computed by the QM code to the global pressure of the system as part of thermodynamic output. The default setting for this fix is fix_modify virial yes, unless the add keyword is set to no, in which case the default setting is no.
This fix computes a global scalar which can be accessed by various output commands. The scalar is the energy returned by the QM code. The scalar value calculated by this fix is “extensive”.
This fix also computes a global vector with of length 6 which contains the symmetric virial tensor values returned by the QM code. It can likewise be accessed by various output commands.
The ordering of values in the symmetric virial tensor is as follows: vxx, vyy, vzz, vxy, vxz, vyz. The values will be in pressure units.
This fix also computes a peratom array with 3 columns which contains the peratom forces returned by the QM code. It can likewise be accessed by various output commands.
No parameter of this fix can be used with the start/stop keywords of the run command.
Assuming the add keyword is set to yes (the default), the forces computed by the QM code are used during an energy minimization, invoked by the minimize command.
If you want the potential energy associated with the QM forces to be included in the total potential energy of the system (the quantity being minimized), you MUST not disable the fix_modify energy option for this fix, which means the add keyword should also be set to yes (the default).
This fix is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled codes (MD or QM codes), the units command should be used to specify real or metal units. This will ensure the correct unit conversions between LAMMPS and MDI units. The other code will also perform similar unit conversions into its preferred units.
LAMMPS can also be used as an MDI driver in other unit choices it supports, e.g. lj, but then no unit conversion to MDI units is performed.
If this fix is used in conjunction with a QM code that does not support
periodic boundary conditions (more specifically, a QM code that does not
>CELL MDI command), the LAMMPS system must be fully
non-periodic. I.e. no dimension of the system can be periodic.
The default for the optional keywords are virial = no, add = yes, every = 1, connect = yes.