Note that the thermostat effect of this fix is applied to only the +translational degrees of freedom for the particles, which is an +important consideration if extended spherical or aspherical particles +which have rotational degrees of freedom are being thermostatted with +this fix. The translational degrees of freedom can also have a bias +velocity removed from them before thermostatting takes place; see the +description below. +
IMPORTANT NOTE: Unlike the fix nvt command which performs Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies forces to effect @@ -111,10 +119,6 @@ generate its own unique seed and its own stream of random numbers. Thus the dynamics of the system will not be identical on two runs on different numbers of processors.
-The keyword axes can be used to specify which dimensions to add Ff -and Fr to. A flag of 0 means skip that dimension; a flag of 1 means -include that dimension. The default is 1 for all 3 dimensions. -
The keyword scale allows the damp factor to be scaled up or down by the specified factor for atoms of that type. This can be useful when different atom types have different sizes or masses. It can be used @@ -158,7 +162,7 @@ fix for access by various output commandsRelated commands:
fix nvt, fix temp/rescale, fix -viscous +viscous, fix nvt
Default:
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index cd0bbafb19..b9318e3558 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -17,6 +17,7 @@ langevin = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run (temperature units) :l damp = damping parameter (time units) :l seed = random # seed to use for white noise (positive integer) :l + zero or more keyword/value pairs may be appended :l keyword = {scale} {scale} values = type ratio @@ -57,6 +58,14 @@ used to randomize the direction and magnitude of this force as described in "(Dunweg)"_#Dunweg, where a uniform random number is used (instead of a Gaussian random number) for speed. +Note that the thermostat effect of this fix is applied to only the +translational degrees of freedom for the particles, which is an +important consideration if extended spherical or aspherical particles +which have rotational degrees of freedom are being thermostatted with +this fix. The translational degrees of freedom can also have a bias +velocity removed from them before thermostatting takes place; see the +description below. + IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.html command which performs Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies forces to effect @@ -101,10 +110,6 @@ generate its own unique seed and its own stream of random numbers. Thus the dynamics of the system will not be identical on two runs on different numbers of processors. -The keyword {axes} can be used to specify which dimensions to add Ff -and Fr to. A flag of 0 means skip that dimension; a flag of 1 means -include that dimension. The default is 1 for all 3 dimensions. - The keyword {scale} allows the damp factor to be scaled up or down by the specified factor for atoms of that type. This can be useful when different atom types have different sizes or masses. It can be used @@ -148,7 +153,7 @@ This fix is not invoked during "energy minimization"_minimize.html. [Related commands:] "fix nvt"_fix_nvt.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -viscous"_fix_viscous.html +viscous"_fix_viscous.html, "fix nvt"_fix_nvt.html [Default:] diff --git a/doc/fix_npt.html b/doc/fix_npt.html index 6c099d2763..d6ba128413 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -58,6 +58,11 @@ thermostat (Hoover1) and Nose/Hoover pressure barostat creates a system trajectory consistent with the isothermal-isobaric ensemble. +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed from them 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 diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 8244edc553..c845e2b5de 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -47,6 +47,11 @@ thermostat "(Hoover1)"_#Hoover1 and Nose/Hoover pressure barostat creates a system trajectory consistent with the isothermal-isobaric ensemble. +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed from them 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 diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index 12634a1a3e..d4700aa840 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -50,13 +50,20 @@ fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0
Description:
-Perform constant NPT integration to update positions, velocities, -and angular velocity each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature +
Perform constant NPT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature thermostat and Nose/Hoover pressure barostat. P is pressure; T is temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble.
+The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -150,6 +157,21 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.
+Like other fixes that perform thermostatting, this fix can be used +with compute commands that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the fix_modify command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual compute +commands to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. +
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat and barostat @@ -189,6 +211,11 @@ this. LAMMPS was built with that package. See the Making LAMMPS section for more info.
+This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the shape +command. +
Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be non-periodic or periodic. @@ -199,8 +226,8 @@ the Nose/Hoover formulation.
Related commands:
-fix npt, fix nve_asphere, -fix_modify +
fix npt, fix nve_asphere, fix +npt_asphere, fix_modify
Default:
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 3876b35273..0e4feaa938 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -39,13 +39,20 @@ fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 [Description:] -Perform constant NPT integration to update positions, velocities, -and angular velocity each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature +Perform constant NPT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature thermostat and Nose/Hoover pressure barostat. P is pressure; T is temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble. +The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -139,6 +146,21 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or {thermo_press} will have no effect on this fix. +Like other fixes that perform thermostatting, this fix can be used +with "compute commands"_compute.html that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the "fix_modify"_fix_modify.html command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat and barostat @@ -178,6 +200,11 @@ This fix is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. +This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the "shape"_shape.html +command. + Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be non-periodic or periodic. @@ -188,8 +215,8 @@ the Nose/Hoover formulation. [Related commands:] -"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, -"fix_modify"_fix_modify.html +"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix +npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html [Default:] diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html index 12634a1a3e..18867d5df9 100644 --- a/doc/fix_npt_sphere.html +++ b/doc/fix_npt_sphere.html @@ -9,15 +9,15 @@Syntax:
-fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ... +fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ...
Examples:
-fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0 -fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 -fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2 -fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial +fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0 +fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 +fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2 +fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partialDescription:
-Perform constant NPT integration to update positions, velocities, -and angular velocity each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature -thermostat and Nose/Hoover pressure barostat. P is pressure; T is -temperature. This creates a system trajectory consistent with the -isothermal-isobaric ensemble. +
Perform constant NPT integration to update position, velocity, and +angular velocity each timestep for extended spherical particles in the +group using a Nose/Hoover temperature thermostat and Nose/Hoover +pressure barostat. P is pressure; T is temperature. This creates a +system trajectory consistent with the isothermal-isobaric ensemble. +
+This fix differs from the fix npt command, which +assumes point particles and only updates their position and velocity. +
+The thermostat is applied to both the translational and rotational +degrees of freedom for the spherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -131,10 +140,10 @@ timespan of (roughly) 1000 time units (tau or fmsec or psec - see the this, the fix creates its own computes of style "temp/asphere" and "pressure", as if these commands had been issued:
-compute fix-ID_temp group-ID temp/asphere +compute fix-ID_temp group-ID temp/sphere compute fix-ID_press group-ID pressure fix-ID_temp-See the compute temp/asphere and compute +
+See the compute temp/sphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is the same @@ -150,6 +159,21 @@ custom
command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.Like other fixes that perform thermostatting, this fix can be used +with compute commands that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the fix_modify command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual compute +commands to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. +
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat and barostat @@ -185,9 +209,10 @@ this.
Restrictions:
-This fix is part of the "asphere" package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. +
This fix requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined by the shape +command.
Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be @@ -199,8 +224,9 @@ the Nose/Hoover formulation.
Related commands:
-fix npt, fix nve_asphere, -fix_modify +
fix npt, fix nve_sphere, fix +nvt_sphere, fix +npt_asphere, fix_modify
Default:
diff --git a/doc/fix_npt_sphere.txt b/doc/fix_npt_sphere.txt index 3876b35273..b65b9259ac 100755 --- a/doc/fix_npt_sphere.txt +++ b/doc/fix_npt_sphere.txt @@ -6,14 +6,14 @@ :line -fix npt/asphere command :h3 +fix npt/sphere command :h3 [Syntax:] -fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ... :pre +fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l -npt/asphere = style name of this fix command :l +npt/sphere = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tdamp = temperature damping parameter (time units) :l p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l @@ -32,19 +32,28 @@ keyword = {drag} or {dilate} :l [Examples:] -fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0 -fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 -fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2 -fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre +fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0 +fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 +fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2 +fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre [Description:] -Perform constant NPT integration to update positions, velocities, -and angular velocity each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature -thermostat and Nose/Hoover pressure barostat. P is pressure; T is -temperature. This creates a system trajectory consistent with the -isothermal-isobaric ensemble. +Perform constant NPT integration to update position, velocity, and +angular velocity each timestep for extended spherical particles in the +group using a Nose/Hoover temperature thermostat and Nose/Hoover +pressure barostat. P is pressure; T is temperature. This creates a +system trajectory consistent with the isothermal-isobaric ensemble. + +This fix differs from the "fix npt"_fix_npt.html command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the spherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -120,10 +129,10 @@ This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/asphere" and "pressure", as if these commands had been issued: -compute fix-ID_temp group-ID temp/asphere +compute fix-ID_temp group-ID temp/sphere compute fix-ID_press group-ID pressure fix-ID_temp :pre -See the "compute temp/asphere"_compute_temp_asphere.html and "compute +See the "compute temp/sphere"_compute_temp_sphere.html and "compute pressure"_compute_pressure.html commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is the same @@ -139,6 +148,21 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or {thermo_press} will have no effect on this fix. +Like other fixes that perform thermostatting, this fix can be used +with "compute commands"_compute.html that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the "fix_modify"_fix_modify.html command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat and barostat @@ -174,9 +198,10 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -This fix is part of the "asphere" package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. +This fix requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined by the "shape"_shape.html +command. Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be @@ -188,8 +213,9 @@ the Nose/Hoover formulation. [Related commands:] -"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, -"fix_modify"_fix_modify.html +"fix npt"_fix_npt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix +nvt_sphere"_fix_nvt_sphere.html, "fix +npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html [Default:] diff --git a/doc/fix_nve.html b/doc/fix_nve.html index 49336f0231..31847666e0 100644 --- a/doc/fix_nve.html +++ b/doc/fix_nve.html @@ -24,9 +24,10 @@Description:
-Perform constant NVE updates of position and velocity for atoms in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. +
Perform constant NVE integration to update position and velocity for +atoms in the group each timestep. V is volume; E is energy. This +creates a system trajectory consistent with the microcanonical +ensemble.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt index fca542b675..70d60a15b5 100644 --- a/doc/fix_nve.txt +++ b/doc/fix_nve.txt @@ -21,9 +21,10 @@ fix 1 all nve :pre [Description:] -Perform constant NVE updates of position and velocity for atoms in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. +Perform constant NVE integration to update position and velocity for +atoms in the group each timestep. V is volume; E is energy. This +creates a system trajectory consistent with the microcanonical +ensemble. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html index e62a9e593d..39ccb03fe1 100644 --- a/doc/fix_nve_asphere.html +++ b/doc/fix_nve_asphere.html @@ -24,10 +24,10 @@
Description:
-Perform constant NVE updates of position, velocity, orientation, and -angular velocity for aspherical particles in the group each timestep. -V is volume; E is energy. This creates a system trajectory consistent -with the microcanonical ensemble. +
Perform constant NVE integration to update position, velocity, +orientation, and angular velocity for aspherical particles in the +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble.
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity. diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt index c8139de627..e8db237993 100755 --- a/doc/fix_nve_asphere.txt +++ b/doc/fix_nve_asphere.txt @@ -21,10 +21,10 @@ fix 1 all nve/asphere :pre [Description:] -Perform constant NVE updates of position, velocity, orientation, and -angular velocity for aspherical particles in the group each timestep. -V is volume; E is energy. This creates a system trajectory consistent -with the microcanonical ensemble. +Perform constant NVE integration to update position, velocity, +orientation, and angular velocity for aspherical particles in the +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html index 2d567af77c..fea7fd08a9 100644 --- a/doc/fix_nve_sphere.html +++ b/doc/fix_nve_sphere.html @@ -35,10 +35,10 @@ fix 1 all nve/sphere update dipole
Description:
-Perform constant NVE updates of position, velocity, and angular -velocity for spherical particles in the group each timestep. V is -volume; E is energy. This creates a system trajectory consistent with -the microcanonical ensemble. +
Perform constant NVE integration to update position, velocity, and +angular velocity for extended spherical particles in the group each +timestep. V is volume; E is energy. This creates a system trajectory +consistent with the microcanonical ensemble.
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity. diff --git a/doc/fix_nve_sphere.txt b/doc/fix_nve_sphere.txt index 36bb5db274..09c4f96f29 100755 --- a/doc/fix_nve_sphere.txt +++ b/doc/fix_nve_sphere.txt @@ -27,10 +27,10 @@ fix 1 all nve/sphere update dipole :pre [Description:] -Perform constant NVE updates of position, velocity, and angular -velocity for spherical particles in the group each timestep. V is -volume; E is energy. This creates a system trajectory consistent with -the microcanonical ensemble. +Perform constant NVE integration to update position, velocity, and +angular velocity for extended spherical particles in the group each +timestep. V is volume; E is energy. This creates a system trajectory +consistent with the microcanonical ensemble. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index d489430d06..55a08a000a 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -43,6 +43,11 @@ each timestep for atoms in the group using a Nose/Hoover temperature thermostat (Hoover). V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble.
+The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed from them 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 diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index 9581d00218..8afd202297 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -34,6 +34,11 @@ each timestep for atoms in the group using a Nose/Hoover temperature thermostat "(Hoover)"_#Hoover. V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble. +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed from them 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 diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index 469ff8e371..32f44e4b98 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -38,11 +38,18 @@ fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2
Description:
-Perform constant NVT integration to update positions, velocities, -and angular velocities each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature thermostat. -V is volume; T is temperature. This creates a system trajectory -consistent with the canonical ensemble. +
Perform constant NVT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. +
+The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -82,6 +89,21 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.
+Like other fixes that perform thermostatting, this fix can be used +with compute commands that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the fix_modify command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual compute +commands to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. +
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary @@ -116,6 +138,11 @@ commands. LAMMPS was built with that package. See the Making LAMMPS section for more info.
+This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the shape +command. +
The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index 599b8772e4..a918929453 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -29,11 +29,18 @@ fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2 :pre [Description:] -Perform constant NVT integration to update positions, velocities, -and angular velocities each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature thermostat. -V is volume; T is temperature. This creates a system trajectory -consistent with the canonical ensemble. +Perform constant NVT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -73,6 +80,21 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. +Like other fixes that perform thermostatting, this fix can be used +with "compute commands"_compute.html that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the "fix_modify"_fix_modify.html command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat to "binary @@ -107,6 +129,11 @@ This fix is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. +This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the "shape"_shape.html +command. + The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index 95808278ab..7e366ac8f9 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -108,6 +108,21 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.
+Like other fixes that perform thermostatting, this fix can be used +with compute commands that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the fix_modify command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual compute +commands to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. +
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary
diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt
index 740cf141de..742fe25b99 100644
--- a/doc/fix_nvt_sllod.txt
+++ b/doc/fix_nvt_sllod.txt
@@ -99,6 +99,21 @@ custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual "compute
+commands"_compute.html to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
diff --git a/doc/fix_nvt_sphere.html b/doc/fix_nvt_sphere.html
index 469ff8e371..7c0dc36d24 100644
--- a/doc/fix_nvt_sphere.html
+++ b/doc/fix_nvt_sphere.html
@@ -9,15 +9,15 @@
Syntax:
Examples:
Description:
Perform constant NVT integration to update positions, velocities,
-and angular velocities each timestep for aspherical or ellipsoidal
-particles in the group using a Nose/Hoover temperature thermostat.
-V is volume; T is temperature. This creates a system trajectory
-consistent with the canonical ensemble.
+ Perform constant NVT integration to update position, velocity, and
+angular velocity each timestep for extended spherical particles in the
+group using a Nose/Hoover temperature thermostat. V is volume; T is
+temperature. This creates a system trajectory consistent with the
+canonical ensemble.
+ This fix differs from the fix nvt command, which
+assumes point particles and only updates their position and velocity.
+ The thermostat is applied to both the translational and rotational
+degrees of freedom for the spherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below). The translational degrees of freedom
+can also have a bias velocity removed from them 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
@@ -62,12 +72,12 @@ to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
This fix computes a temperature each timestep. To do this, the fix
-creates its own compute of style "temp/asphere", as if this command
+creates its own compute of style "temp/sphere", as if this command
had been issued:
See the compute temp/asphere command for
+ See the compute temp/sphere command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
@@ -82,6 +92,21 @@ custom
-fix nvt/asphere command
+
fix nvt/sphere command
fix ID group-ID nvt/asphere Tstart Tstop Tdamp keyword value ...
+
fix ID group-ID nvt/sphere Tstart Tstop Tdamp keyword value ...
fix 1 all nvt/asphere 300.0 300.0 100.0
-fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2
+
command using the appropriate compute-ID.
It also means that changing attributes of thermo_temp will have no
effect on this fix.
fix 1 all nvt/sphere 300.0 300.0 100.0
+fix 1 all nvt/sphere 300.0 300.0 100.0 drag 0.2
compute fix-ID_temp group-ID temp/asphere
+
compute fix-ID_temp group-ID temp/sphere
-
Like other fixes that perform thermostatting, this fix can be used +with compute commands that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the fix_modify command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual compute +commands to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. +
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary @@ -112,9 +137,10 @@ commands.
Restrictions:
-This fix is part of the "asphere" package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. +
This fix requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined by the shape +command.
The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in @@ -122,8 +148,9 @@ the Nose/Hoover formulation.
Related commands:
-fix nvt, fix nve_asphere, fix -npt_asphere, fix_modify +
fix nvt, fix nve_sphere, fix +nvt_asphere, fix +npt_sphere, fix_modify
Default:
diff --git a/doc/fix_nvt_sphere.txt b/doc/fix_nvt_sphere.txt index 599b8772e4..7384f30594 100755 --- a/doc/fix_nvt_sphere.txt +++ b/doc/fix_nvt_sphere.txt @@ -6,14 +6,14 @@ :line -fix nvt/asphere command :h3 +fix nvt/sphere command :h3 [Syntax:] -fix ID group-ID nvt/asphere Tstart Tstop Tdamp keyword value ... :pre +fix ID group-ID nvt/sphere Tstart Tstop Tdamp keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l -nvt/asphere = style name of this fix command :l +nvt/sphere = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tdamp = temperature damping parameter (time units) :l @@ -24,16 +24,26 @@ keyword = {drag} :l [Examples:] -fix 1 all nvt/asphere 300.0 300.0 100.0 -fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2 :pre +fix 1 all nvt/sphere 300.0 300.0 100.0 +fix 1 all nvt/sphere 300.0 300.0 100.0 drag 0.2 :pre [Description:] -Perform constant NVT integration to update positions, velocities, -and angular velocities each timestep for aspherical or ellipsoidal -particles in the group using a Nose/Hoover temperature thermostat. -V is volume; T is temperature. This creates a system trajectory -consistent with the canonical ensemble. +Perform constant NVT integration to update position, velocity, and +angular velocity each timestep for extended spherical particles in the +group using a Nose/Hoover temperature thermostat. V is volume; T is +temperature. This creates a system trajectory consistent with the +canonical ensemble. + +This fix differs from the "fix nvt"_fix_nvt.html command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the spherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them 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 @@ -53,12 +63,12 @@ to determine if the drag term is working. Typically a value between 0.2 to 2.0 is sufficient to damp oscillations after a few periods. This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/asphere", as if this command +creates its own compute of style "temp/sphere", as if this command had been issued: -compute fix-ID_temp group-ID temp/asphere :pre +compute fix-ID_temp group-ID temp/sphere :pre -See the "compute temp/asphere"_compute_temp_asphere.html command for +See the "compute temp/sphere"_compute_temp_sphere.html command for details. Note that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. @@ -73,6 +83,21 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. +Like other fixes that perform thermostatting, this fix can be used +with "compute commands"_compute.html that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the "fix_modify"_fix_modify.html command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat to "binary @@ -103,9 +128,10 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -This fix is part of the "asphere" package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. +This fix requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined by the "shape"_shape.html +command. The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in @@ -113,8 +139,9 @@ the Nose/Hoover formulation. [Related commands:] -"fix nvt"_fix_nvt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix -npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html +"fix nvt"_fix_nvt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix +nvt_asphere"_fix_nvt_asphere.html, "fix +npt_sphere"_fix_npt_sphere.html, "fix_modify"_fix_modify.html [Default:] diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html index 27473f21f6..ad595c430e 100644 --- a/doc/fix_temp_berendsen.html +++ b/doc/fix_temp_berendsen.html @@ -30,6 +30,13 @@ thermostat (Berendsen), which rescales their velocities every timestep. +The thermostat is applied to only the translational degrees of freedom +for the particles, which is an important consideration if extended +spherical or aspherical particles which have rotational degrees of +freedom are being thermostatted with this fix. The translational +degrees of freedom can also have a bias velocity removed from them +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 diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt index 2f79212f19..b2aad9f1f7 100644 --- a/doc/fix_temp_berendsen.txt +++ b/doc/fix_temp_berendsen.txt @@ -27,6 +27,13 @@ Reset the temperature of a group of atoms by using a Berendsen thermostat "(Berendsen)"_#Berendsen, which rescales their velocities every timestep. +The thermostat is applied to only the translational degrees of freedom +for the particles, which is an important consideration if extended +spherical or aspherical particles which have rotational degrees of +freedom are being thermostatted with this fix. The translational +degrees of freedom can also have a bias velocity removed from them +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 diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index d328d0d1fa..85aa969914 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -33,6 +33,13 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
Reset the temperature of a group of atoms by explicitly rescaling their velocities.
+The rescaling is applied to only the translational degrees of freedom +for the particles, which is an important consideration if extended +spherical or aspherical particles which have rotational degrees of +freedom are being thermostatted with this fix. The translational +degrees of freedom can also have a bias velocity removed from them +before thermostatting takes place; see the description below. +
Rescaling is performed every N timesteps. The target temperature is a ramped value between the Tstart and Tstop temperatures at the beginning and end of the run. diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt index 58a4a310ee..f7e2560374 100644 --- a/doc/fix_temp_rescale.txt +++ b/doc/fix_temp_rescale.txt @@ -30,6 +30,13 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre Reset the temperature of a group of atoms by explicitly rescaling their velocities. +The rescaling is applied to only the translational degrees of freedom +for the particles, which is an important consideration if extended +spherical or aspherical particles which have rotational degrees of +freedom are being thermostatted with this fix. The translational +degrees of freedom can also have a bias velocity removed from them +before thermostatting takes place; see the description below. + Rescaling is performed every N timesteps. The target temperature is a ramped value between the {Tstart} and {Tstop} temperatures at the beginning and end of the run.