forked from lijiext/lammps
spell check, minor typos
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dstelter92
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4641c9e568
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\@writefile{toc}{\contentsline {section}{\numberline {1}LAMMPS source files}{2}}
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\@writefile{toc}{\contentsline {section}{\numberline {2}Class hierarchy of LAMMPS}{3}}
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\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Class hierarchy within LAMMPS source code.}}{4}}
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\newlabel{fig:classes}{{1}{4}}
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\@writefile{toc}{\contentsline {section}{\numberline {3}How a timestep works}{6}}
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\@writefile{toc}{\contentsline {section}{\numberline {4}Extending LAMMPS}{9}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}New fixes}{9}}
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\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Pseudo-code for the Verlet::run() method.}}{14}}
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\newlabel{fig:verlet}{{2}{14}}
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**developer
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[1
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\OT1/cmr/m/n/10 ment spe-cific com-mands in the in-put script that can be in-vo
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\OT1/cmr/m/n/10 PAIR[]CLASS, BOND[]CLASS, RE-GION[]CLASS, FIX[]CLASS, COM-PUTE[
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]CLASS,
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[]\OT1/cmr/m/n/10 The Comm class per-forms in-ter-pro-ces-sor com-mu-ni-ca-tion
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, typ-i-cally of ghost
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[]
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[5]
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[]\OT1/cmr/m/n/10 At var-i-ous points of the timestep, fixes are in-voked, e.g.
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fix$\OMS/cmsy/m/n/10 !$\OT1/cmr/m/n/10 initial[]integrate().
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[]
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@ -0,0 +1,5 @@
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\contentsline {section}{\numberline {1}LAMMPS source files}{2}
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\contentsline {section}{\numberline {2}Class hierarchy of LAMMPS}{3}
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\contentsline {section}{\numberline {3}How a timestep works}{6}
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\contentsline {section}{\numberline {4}Extending LAMMPS}{9}
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\contentsline {subsection}{\numberline {4.1}New fixes}{9}
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@ -29,12 +29,13 @@ fix fxgREM all grem 502 -0.15 -80000 fxnvt
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[Description:]
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This fix implements the molecular dynamics version
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of the generlized replica
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of the generalized replica
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exchange method (gREM) originally developed by "(Kim)"_#Kim,
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which uses non-Boltzmann ensembles to sample over first
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order phase transitions.
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The is done by defining replicas with an effective temperature
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The is done by defining replicas with an enthalpy dependent
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effective temperature
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:c,image(Eqs/fix_grem.jpg)
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@ -42,7 +43,7 @@ with {eta} negative and steep enough to only intersect
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the characteristic microcanonical temperature (Ts) of the
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system once, ensuring a unimodal enthalpy distribution in
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that replica. {Lambda} is the intercept and effects the
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generalized ensemble simliar to how temperature effects
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generalized ensemble similar to how temperature effects
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a Boltzmann ensemble. {H0} is a reference enthalpy, and
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is typically set as the lowest desired sampled enthalpy.
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Further explanation can be found in our recent papers
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@ -50,7 +51,7 @@ Further explanation can be found in our recent papers
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This fix requires a thermostat, with ID passed to fix_grem
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by {thermostat-ID}. Two distinct temperatures exist in this
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generlized ensemble, the effective temperature defined above,
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generalized ensemble, the effective temperature defined above,
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and a kinetic temperature that controls the velocity
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distribution of particles as usual. Either constant volume
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or constant pressure algorithms can be used.
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@ -59,17 +60,17 @@ The fix enforces a generalized ensemble in a single replica
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only. Typically, different replicas only differ by {lambda}
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for simplicity, but this is not necessary. Multi-replica
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runs need to be run outside of LAMMPS. An example of this
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can be found in examples/USER/misc/grem .
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can be found in examples/USER/misc/grem
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In general, defining the generalized ensembles is unique for
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every system. When starting a many-replica simulation without
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any knowledge of the underlying microcanonical temperature,
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there are several tricks we have utilized to optimze the process.
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there are several tricks we have utilized to optimize the process.
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Choosing a less-steep {eta} yields broader distributions,
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requiring fewer replicas to map the microcanonical temperature.
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While this likely struggles from the same sampling problems
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gREM was built to avoid, it provides quick insight to Ts.
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Initially using an evenly-spaced {lambda} distribtuion identifies
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Initially using an evenly-spaced {lambda} distribution identifies
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regions where small changes in enthalpy lead to large temperature
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changes. Replicas are easily added where needed.
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@ -103,5 +104,5 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[(Kim)] Kim, Keyes, Straub, J. Chem. Phys., 132, 224107 (2010).
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:link(Malolepsza)
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[(Brooks)] Malolepsza, Secor, Keyes, J. Phys. Chem. B. 119 (42),
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[(Malolepsza)] Malolepsza, Secor, Keyes, J. Phys. Chem. B. 119 (42),
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13379-13384 (2015).
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