diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index f3ffd5bff2..3c5ebcbd03 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -687,6 +687,7 @@ package"_Section_start.html#start_3. "eos/table/rx"_fix_eos_table_rx.html, "flow/gauss"_fix_flow_gauss.html, "gle"_fix_gle.html, +"grem"_fix_grem.html, "imd"_fix_imd.html, "ipi"_fix_ipi.html, "langevin/drude"_fix_langevin_drude.html, diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 1f62b00104..d93cb10f80 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -10,69 +10,62 @@ fix grem command :h3 [Syntax:] -fix ID group-ID grem lambda eta H0 thermostat-ID +fix ID group-ID grem lambda eta H0 thermostat-ID :pre -ID, group-ID are documented in "fix"_fix.html command -grem = style name of this fix command -lambda = intercept parameter of linear effective temperature function -eta = slope parameter of linear effective temperature function -H0 = shift parameter of linear effective temperature function -thermostat-ID = ID of thermostat used in simulation +ID, group-ID are documented in "fix"_fix.html command :ulb,l +grem = style name of this fix command :l +lambda = intercept parameter of linear effective temperature function :l +eta = slope parameter of linear effective temperature function :l +H0 = shift parameter of linear effective temperature function :l +thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation :l,ule [Examples:] fix fxgREM all grem 400 -0.01 -30000 fxnpt -thermo_modify press fxgREM_press +thermo_modify press fxgREM_press :pre -fix fxgREM all grem 502 -0.15 -80000 fxnvt +fix fxgREM all grem 502 -0.15 -80000 fxnvt :pre [Description:] -This fix implements the molecular dynamics version -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 enthalpy dependent +This fix implements the molecular dynamics version 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 enthalpy dependent effective temperature :c,image(Eqs/fix_grem.jpg) -with {eta} negative and steep enough to only intersect -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 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 -"(Malolepsza)"_#Malolepsza. +with {eta} negative and steep enough to only intersect 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 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 "(Malolepsza)"_#Malolepsza. -This fix requires a thermostat, with ID passed to fix_grem -by {thermostat-ID}. Two distinct temperatures exist in this -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. +This fix requires a Nose-Hoover thermostat reference passed to the grem +by {thermostat-ID}. Two distinct temperatures exist in this 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. -The fix enforces a generalized ensemble in a single replica -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 +The fix enforces a generalized ensemble in a single replica 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 -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 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} distribution identifies +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 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} distribution identifies regions where small changes in enthalpy lead to large temperature -changes. Replicas are easily added where needed. +changes. Replicas are easily added where needed. :line @@ -93,8 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"fix_nh"_fix_nh.html -"thermo_modify"_thermo_modify.html +"fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, "thermo_modify"_thermo_modify.html [Default:] none diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 10f4dfa86c..d17b88306d 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -48,6 +48,7 @@ Fixes :h1 fix_gld fix_gle fix_gravity + fix_grem fix_halt fix_heat fix_imd diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 5803560cd5..2afbdda740 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -170,6 +170,7 @@ fix_gcmc.html fix_gld.html fix_gle.html fix_gravity.html +fix_grem.html fix_halt.html fix_heat.html fix_imd.html