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\contentsline {section}{\numberline {1}LAMMPS source files}{2}

\contentsline {section}{\numberline {2}Class hierarchy of LAMMPS}{3}

\contentsline {section}{\numberline {3}How a timestep works}{6}

\contentsline {section}{\numberline {4}Extending LAMMPS}{9}

\contentsline {subsection}{\numberline {4.1}New fixes}{9}

[Description:]

This fix implements the molecular dynamics version

of the generlized replica 

of the generalized replica 

exchange method (gREM) originally developed by "(Kim)"_#Kim,

which uses non-Boltzmann ensembles to sample over first

order phase transitions.

The is done by defining replicas with an effective temperature

The is done by defining replicas with an enthalpy dependent

effective temperature

:c,image(Eqs/fix_grem.jpg)

the characteristic microcanonical temperature (Ts) of the

system once, ensuring a unimodal enthalpy distribution in 

that replica. {Lambda} is the intercept and effects the 

generalized ensemble simliar to how temperature effects 

generalized ensemble similar to how temperature effects 

a Boltzmann ensemble. {H0} is a reference enthalpy, and

is typically set as the lowest desired sampled enthalpy.

Further explanation can be found in our recent papers 

This fix requires a thermostat, with ID passed to fix_grem

by {thermostat-ID}. Two distinct temperatures exist in this

generlized ensemble, the effective temperature defined above,

generalized ensemble, the effective temperature defined above,

and a kinetic temperature that controls the velocity 

distribution of particles as usual. Either constant volume

or constant pressure algorithms can be used.

only. Typically, different replicas only differ by {lambda}

for simplicity, but this is not necessary. Multi-replica 

runs need to be run outside of LAMMPS. An example of this 

can be found in examples/USER/misc/grem .

can be found in examples/USER/misc/grem

In general, defining the generalized ensembles is unique for 

every system. When starting a many-replica simulation without 

any knowledge of the underlying microcanonical temperature, 

there are several tricks we have utilized to optimze the process. 

there are several tricks we have utilized to optimize the process. 

Choosing a less-steep {eta} yields broader distributions, 

requiring fewer replicas to map the microcanonical temperature. 

While this likely struggles from the same sampling problems 

gREM was built to avoid, it provides quick insight to Ts. 

Initially using an evenly-spaced {lambda} distribtuion identifies

Initially using an evenly-spaced {lambda} distribution identifies

regions where small changes in enthalpy lead to large temperature

changes. Replicas are easily added where needed. 

[(Kim)] Kim, Keyes, Straub, J. Chem. Phys., 132, 224107 (2010).

:link(Malolepsza)

[(Brooks)] Malolepsza, Secor, Keyes, J. Phys. Chem. B. 119 (42), 

[(Malolepsza)] Malolepsza, Secor, Keyes, J. Phys. Chem. B. 119 (42), 

13379-13384 (2015).