Loading doc/src/fix_grem.txt +15 −6 Original line number Original line Diff line number Diff line Loading @@ -57,10 +57,20 @@ distribution of particles as usual. Either constant volume or constant pressure algorithms can be used. or constant pressure algorithms can be used. The fix enforces a generalized ensemble in a single replica The fix enforces a generalized ensemble in a single replica only. Typically, different replicas only differ by {lambda} only. Typically, this ideaology is combined with replica for simplicity, but this is not necessary. Multi-replica exchange with replicas differing by {lambda} only runs need to be run outside of LAMMPS. An example of this for simplicity, but this is not required. A multi-replica can be found in examples/USER/misc/grem simulation can be run within the LAMMPS environment using the "grem"_temper_grem.html command. This utilizes LAMMPS partition mode and requires the number of available processors be on the order of the number of desired replicas. A 100-replica simulation would require at least 100 processors (1 per world at minimum). If a many replicas are needed on a small number of processors, multi-replica runs can be run outside of LAMMPS. An example of this can be found in examples/USER/misc/grem and has no limit on the number of replicas per processor. However, this is very inefficient and error prone and should be avoided if possible. In general, defining the generalized ensembles is unique for In general, defining the generalized ensembles is unique for every system. When starting a many-replica simulation without every system. When starting a many-replica simulation without Loading Loading @@ -93,8 +103,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] [Related commands:] "fix_nh"_fix_nh.html "grem"_temper_grem.html, "fix_nh"_fix_nh.html, "thermo_modify"_thermo_modify.html "thermo_modify"_thermo_modify.html [Default:] none [Default:] none Loading doc/src/temper_grem.txt +12 −12 Original line number Original line Diff line number Diff line Loading @@ -23,18 +23,18 @@ index = which temperature (0 to N-1) I am simulating (optional) :ul [Examples:] [Examples:] grem 100000 100 ${lambda} fxgREM fxnvt 0 58728 grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728 grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 $w :pre grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers} :pre [Description:] [Description:] Run a parallel tempering or replica exchange simulation using multiple Run a parallel tempering or replica exchange simulation in LAMMPS partition generalized replicas (ensembles) of a system defined by mode using multiple generalized replicas (ensembles) of a system defined by "fix_grem"_fix_grem.html. Two or more replicas must be used. "fix_grem"_fix_grem.html. Two or more replicas must be used. This command is a modification of the "temper"_temper.html command and has the This command is a modification of the "temper"_temper.html command and has same dependencies, restraints, and input variables which are discussed there the same dependencies, restraints, and input variables which are discussed in detail. there in greater detail. Instead of temperature, this command performs replica exchanges in lambda Instead of temperature, this command performs replica exchanges in lambda as per the generalized ensemble enforced by "fix_grem"_fix_grem.html. as per the generalized ensemble enforced by "fix_grem"_fix_grem.html. Loading @@ -48,9 +48,9 @@ fix fxnvt all nvt temp 300.0 300.0 100.0 fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre would define 4 lambdas with constant kinetic temperature, and assign one would define 4 lambdas with constant kinetic temperature but unique of them to "fix_grem"_fix_grem.html used by each replica, and to the grem generalized temperature, and assign one of them to command. "fix_grem"_fix_grem.html used by each replica, and to the grem command. As the gREM simulation runs for {N} timesteps, a swap As the gREM simulation runs for {N} timesteps, a swap between adjacent ensembles will be attempted every {M} timesteps. If between adjacent ensembles will be attempted every {M} timesteps. If Loading @@ -75,10 +75,10 @@ log file listed the following for a simulation with 5 replicas: then a setting of then a setting of variable w world 2 4 0 1 3 :pre variable walkers world 2 4 0 1 3 :pre would be used to restart the run with a grem command like the would be used to restart the run with a grem command like the example above with $w as the last argument. This functionality example above with ${walkers} as the last argument. This functionality is identical to "temper"_temper.html. is identical to "temper"_temper.html. :line :line Loading Loading
doc/src/fix_grem.txt +15 −6 Original line number Original line Diff line number Diff line Loading @@ -57,10 +57,20 @@ distribution of particles as usual. Either constant volume or constant pressure algorithms can be used. or constant pressure algorithms can be used. The fix enforces a generalized ensemble in a single replica The fix enforces a generalized ensemble in a single replica only. Typically, different replicas only differ by {lambda} only. Typically, this ideaology is combined with replica for simplicity, but this is not necessary. Multi-replica exchange with replicas differing by {lambda} only runs need to be run outside of LAMMPS. An example of this for simplicity, but this is not required. A multi-replica can be found in examples/USER/misc/grem simulation can be run within the LAMMPS environment using the "grem"_temper_grem.html command. This utilizes LAMMPS partition mode and requires the number of available processors be on the order of the number of desired replicas. A 100-replica simulation would require at least 100 processors (1 per world at minimum). If a many replicas are needed on a small number of processors, multi-replica runs can be run outside of LAMMPS. An example of this can be found in examples/USER/misc/grem and has no limit on the number of replicas per processor. However, this is very inefficient and error prone and should be avoided if possible. In general, defining the generalized ensembles is unique for In general, defining the generalized ensembles is unique for every system. When starting a many-replica simulation without every system. When starting a many-replica simulation without Loading Loading @@ -93,8 +103,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] [Related commands:] "fix_nh"_fix_nh.html "grem"_temper_grem.html, "fix_nh"_fix_nh.html, "thermo_modify"_thermo_modify.html "thermo_modify"_thermo_modify.html [Default:] none [Default:] none Loading
doc/src/temper_grem.txt +12 −12 Original line number Original line Diff line number Diff line Loading @@ -23,18 +23,18 @@ index = which temperature (0 to N-1) I am simulating (optional) :ul [Examples:] [Examples:] grem 100000 100 ${lambda} fxgREM fxnvt 0 58728 grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728 grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 $w :pre grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers} :pre [Description:] [Description:] Run a parallel tempering or replica exchange simulation using multiple Run a parallel tempering or replica exchange simulation in LAMMPS partition generalized replicas (ensembles) of a system defined by mode using multiple generalized replicas (ensembles) of a system defined by "fix_grem"_fix_grem.html. Two or more replicas must be used. "fix_grem"_fix_grem.html. Two or more replicas must be used. This command is a modification of the "temper"_temper.html command and has the This command is a modification of the "temper"_temper.html command and has same dependencies, restraints, and input variables which are discussed there the same dependencies, restraints, and input variables which are discussed in detail. there in greater detail. Instead of temperature, this command performs replica exchanges in lambda Instead of temperature, this command performs replica exchanges in lambda as per the generalized ensemble enforced by "fix_grem"_fix_grem.html. as per the generalized ensemble enforced by "fix_grem"_fix_grem.html. Loading @@ -48,9 +48,9 @@ fix fxnvt all nvt temp 300.0 300.0 100.0 fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre would define 4 lambdas with constant kinetic temperature, and assign one would define 4 lambdas with constant kinetic temperature but unique of them to "fix_grem"_fix_grem.html used by each replica, and to the grem generalized temperature, and assign one of them to command. "fix_grem"_fix_grem.html used by each replica, and to the grem command. As the gREM simulation runs for {N} timesteps, a swap As the gREM simulation runs for {N} timesteps, a swap between adjacent ensembles will be attempted every {M} timesteps. If between adjacent ensembles will be attempted every {M} timesteps. If Loading @@ -75,10 +75,10 @@ log file listed the following for a simulation with 5 replicas: then a setting of then a setting of variable w world 2 4 0 1 3 :pre variable walkers world 2 4 0 1 3 :pre would be used to restart the run with a grem command like the would be used to restart the run with a grem command like the example above with $w as the last argument. This functionality example above with ${walkers} as the last argument. This functionality is identical to "temper"_temper.html. is identical to "temper"_temper.html. :line :line Loading
