Running LAMMPS with PyRETIS¶
We have prepared some extra documentation for instructions on how to use the LAMMPS Molecular Dynamics Simulator with PyRETIS.
Standard LAMMPS input¶
The LAMMPS – PyRETIS interface is constructing to take advantage of LAMMPS internal ability to perform on-the-fly calculations. PyRETIS expects a LAMMPS input file to be present in the folder from which it is executed. This input file should refer to all the information LAMMPS needs to run a simulation on your system, including but not limited to:
- Initial coordinates, molecular topology (optional: force field coefficients) in a LAMMPS data file. This file can be read into LAMMPS using the read_data command.
- Information about units, bonded and non-bonded force field coefficients, (if applicable) long-range electrostatics methods.
- A LAMMPS fix that will integrate the motion of the atoms in the system.
The LAMMPS input file should contain everything that is needed to run a normal MD simulation except for the run command.
PyRETIS requirements for LAMMPS input¶
In addition to the standard input requirements for a LAMMPS simulation, there are additional requirements for running LAMMPS with PyRETIS.
Mandatory Format: The target temperature for the RETIS simulations must be set to a LAMMPS equal-style variable called SET_TEMP. An example is shown below:
variable SET_TEMP equal 300.0
In the above example, the system temperature is set to 300.0 K (assuming real LAMMPS units).
Mandatory Format: The order parameter(s) that PyRETIS will keep track of should be declared as LAMMPS equal-style variable(s). Multiple order parameters can be defined, but the first order parameter (op_1) will be used by PyRETIS to determine interface crossing.
variable op_1 equal c_1 variable op_2 equal c_2
In the above example, two order parameters will be tracked and output by LAMMPS to a file called order.txt. The first column of order.txt will be the LAMMPS step, the second column will be op_1, the third column will be op_2. Only op_1 will be used by LAMMPS to determine the crossing of the first or last interface and stop the simulation.
The above example refers to LAMMPS compute, referenced by c_1 and c_2, that return scalar values. Using combination of LAMMPS compute and LAMMPS variable commands, a large number of calculations can be performed internally by LAMMPS. LAMMPS can also call Python scripts to facilitate more calculations. For best coding practices, the order parameter calculations can be scripted in a separate file (order.in) and included in the main LAMMPS input script as follows:
There are some restrictions for the LAMMPS-PyRETIS interface.
- Motion should be propagated using NVE dynamics, as NVT/NPT dynamics have not been shown to be accurately time-reversible in practice.
- We recommend that the SHAKE algorithm not be used, because in practice it produces non-time reversible results due to the iterative nature of the algorithm.
- Order Parameters must NOT depend on the direction of velocity components.
The subcycle length, defined in the PyRETIS input file, refers to how often LAMMPS will print to the log file and the order.txt file.