IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for +arbitrary values of Tdamp. If Tdamp is too small, the temperature +can fluctuate wildly; if it is too large, the temperature will take a +very long time to equilibrate. A good choice for many models is a +Tdamp of around 100 timesteps. Note that this is NOT the same as +100 time units for most units settings. +
The barostat for fix styles npt and nph is specified using one or @@ -137,10 +144,17 @@ simulation box must be triclinic, even if its initial tilt factors are
For all barostat keywords, the Pdamp parameter operates like the Tdamp parameter, determining the time scale on which pressure is -relaxed. For example, a value of 1000.0 means to relax the pressure -in a timespan of (roughly) 1000 time units (tau or fmsec or psec - see +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see the units command).
+IMPORTANT NOTE: A Nose-Hoover barostat will not work well for +arbitrary values of Pdamp. If Pdamp is too small, the pressure +and volume can fluctuate wildly; if it is too large, the pressure will +take a very long time to equilibrate. A good choice for many models +is a Pdamp of around 1000 timesteps. Note that this is NOT the same +as 1000 time units for most units settings. +
Regardless of what atoms are in the fix group, a global pressure or stress tensor is computed for all atoms. Similarly, when the size of the simulation box is changed, all atoms are re-scaled to new diff --git a/doc/fix_nh.txt b/doc/fix_nh.txt index 541472d5e7..78a510402a 100644 --- a/doc/fix_nh.txt +++ b/doc/fix_nh.txt @@ -85,12 +85,19 @@ a bias velocity removed before thermostatting takes place; see the description below. The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or +temperature is relaxed. For example, a value of 10.0 means to relax +the temperature in a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see the "units"_units.html command). The atoms in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the integration. +IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for +arbitrary values of {Tdamp}. If {Tdamp} is too small, the temperature +can fluctuate wildly; if it is too large, the temperature will take a +very long time to equilibrate. A good choice for many models is a +{Tdamp} of around 100 timesteps. Note that this is NOT the same as +100 time units for most "units"_units.html settings. + :line The barostat for fix styles {npt} and {nph} is specified using one or @@ -129,10 +136,17 @@ simulation box must be triclinic, even if its initial tilt factors are For all barostat keywords, the {Pdamp} parameter operates like the {Tdamp} parameter, determining the time scale on which pressure is -relaxed. For example, a value of 1000.0 means to relax the pressure -in a timespan of (roughly) 1000 time units (tau or fmsec or psec - see +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see the "units"_units.html command). +IMPORTANT NOTE: A Nose-Hoover barostat will not work well for +arbitrary values of {Pdamp}. If {Pdamp} is too small, the pressure +and volume can fluctuate wildly; if it is too large, the pressure will +take a very long time to equilibrate. A good choice for many models +is a {Pdamp} of around 1000 timesteps. Note that this is NOT the same +as 1000 time units for most "units"_units.html settings. + Regardless of what atoms are in the fix group, a global pressure or stress tensor is computed for all atoms. Similarly, when the size of the simulation box is changed, all atoms are re-scaled to new