These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 074a7c7165..6c9491a007 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -474,6 +474,7 @@ description: "temp/com"_compute_temp_com.html, "temp/deform"_compute_temp_deform.html, "temp/partial"_compute_temp_partial.html, +"temp/profile"_compute_temp_profile.html, "temp/ramp"_compute_temp_ramp.html, "temp/region"_compute_temp_region.html, "temp/sphere"_compute_temp_sphere.html :tb(c=6,ea=c) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 505910f4c7..aa960dcb4f 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1178,6 +1178,7 @@ pressure command calculates pressure.
Thermostatting in LAMMPS is performed by fixes. Four thermostatting fixes are currently available: Nose-Hoover (nvt), @@ -1203,7 +1205,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
Fix nvt only thermostats the translational velocity of
-particles. Fix nvt/sllod does as well, except
+particles. Fix nvt/sllod also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the NEMD
simulations section of this page for further details. Fix
@@ -1225,8 +1227,9 @@ the x and z components of velocity by using it in conjunction with
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
-velocities; they do NOT perform time integration. Thus they should be
-used in conjunction with a constant NVE integration fix such as these:
+velocities; they do NOT perform time integration updates. Thus they
+should be used in conjunction with a constant NVE integration fix such
+as these:
All of the barostatting fixes use the compute pressure compute to calculate a current -pressure. The barostatting fixes can also use temperature computes -that remove bias for the purpose of computing the current temperature -which contributes to the current pressure. See the doc pages for the -individual fixes and for the fix_modify command for -instructions on how to assign a temperature or pressure compute to a -barostatting fix. +pressure. By default, this compute is created with a simple compute +temp (see the last argument of the compute +pressure command), which is used to calculated +the kinetic componenet of the pressure. The barostatting fixes can +also use temperature computes that remove bias for the purpose of +computing the kinetic componenet which contributes to the current +pressure. See the doc pages for the individual fixes and for the +fix_modify command for instructions on how to assign +a temperature or pressure compute to a barostatting fix.
IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (fix npt and fix nph) perform time diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index fddfda22ad..8dfa2dfd67 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1169,6 +1169,7 @@ pressure"_compute_pressure.html command calculates pressure. "compute temp/com"_compute_temp_com.html "compute temp/deform"_compute_temp_deform.html "compute temp/partial"_compute_temp_partial.html +"compute temp/profile"_compute_temp_profile.html "compute temp/ramp"_compute_temp_ramp.html "compute temp/region"_compute_temp_region.html :ul @@ -1177,9 +1178,10 @@ velocities) that are removed when computing the thermal temperature. "Fix temp/sphere"_fix_temp_sphere.html and "fix temp/asphere"_fix_temp_asphere.html compute kinetic energy for extended particles that includes rotational degrees of freedom. They -both allow, as an extra argument, another temperature compute that -subtracts a velocity bias, so the translational velocity of extended -spherical or aspherical particles can be adjusted in prescribed ways. +both allow, as an extra argument, which is another temperature compute +that subtracts a velocity bias. This allows the translational +velocity of extended spherical or aspherical particles to be adjusted +in prescribed ways. Thermostatting in LAMMPS is performed by "fixes"_fix.html. Four thermostatting fixes are currently available: Nose-Hoover (nvt), @@ -1194,7 +1196,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale): "fix temp/rescale"_fix_temp_rescale.html :ul "Fix nvt"_fix_nvt.html only thermostats the translational velocity of -particles. "Fix nvt/sllod"_fix_nvt_sllod.html does as well, except +particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except that it subtracts out a velocity bias due to a deforming box and integrates the SLLOD equations of motion. See the "NEMD simulations"_#4_13 section of this page for further details. "Fix @@ -1216,8 +1218,9 @@ the x and z components of velocity by using it in conjunction with IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning they update the velocities and positions of particles due to forces and velocities respectively. The other thermostat fixes only adjust -velocities; they do NOT perform time integration. Thus they should be -used in conjunction with a constant NVE integration fix such as these: +velocities; they do NOT perform time integration updates. Thus they +should be used in conjunction with a constant NVE integration fix such +as these: "fix nve"_fix_nve.html "fix nve/sphere"_fix_nve_sphere.html @@ -1249,12 +1252,15 @@ and aspherical particles. All of the barostatting fixes use the "compute pressure"_compute_pressure.html compute to calculate a current -pressure. The barostatting fixes can also use temperature computes -that remove bias for the purpose of computing the current temperature -which contributes to the current pressure. See the doc pages for the -individual fixes and for the "fix_modify"_fix_modify.html command for -instructions on how to assign a temperature or pressure compute to a -barostatting fix. +pressure. By default, this compute is created with a simple "compute +temp"_compute_temp.html (see the last argument of the "compute +pressure"_compute_pressure.html command), which is used to calculated +the kinetic componenet of the pressure. The barostatting fixes can +also use temperature computes that remove bias for the purpose of +computing the kinetic componenet which contributes to the current +pressure. See the doc pages for the individual fixes and for the +"fix_modify"_fix_modify.html command for instructions on how to assign +a temperature or pressure compute to a barostatting fix. IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix npt"_fix_npt.html and "fix nph"_fix_nph.html) perform time diff --git a/doc/compute.html b/doc/compute.html index fd553e4e99..ab5641d615 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -130,6 +130,7 @@ available in LAMMPS:
IMPORTANT NOTE: For 2d models, particles are treated as ellipsoids, not ellipses, meaning their moments of inertia will be diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt index 9e3dbdc209..590b10d21f 100755 --- a/doc/compute_temp_asphere.txt +++ b/doc/compute_temp_asphere.txt @@ -47,9 +47,11 @@ rotational motion to the extra degrees of freedom. E.g. the "GayBerne pair potential"_pair_gayberne.html does not impart torque to spherical particles, so they do not rotate. -The rotational kinetic energy is computed as 1/2 I w^2, where I is the -inertia tensor for the aspherical particle and w is its angular -velocity, which is computed from its angular momentum. +The translational kinetic energy is computed the same as is described +by the "compute temp"_compute_temp.html command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor +for the aspherical particle and w is its angular velocity, which is +computed from its angular momentum. IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated as ellipsoids, not ellipses, meaning their moments of inertia will be diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html index 44b66a8a56..4dc7bf0bc1 100644 --- a/doc/compute_temp_com.html +++ b/doc/compute_temp_com.html @@ -33,7 +33,8 @@ command that computes a temperature, e.g. thermo_modify, fix temp/rescale, fix npt, etc.
-The temperature is calculated by the formula KE = dim/2 N k T, where +
After the center-of-mass velocity has been subtracted from each atom, +the temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. diff --git a/doc/compute_temp_com.txt b/doc/compute_temp_com.txt index 460602d15f..ae21ccfb26 100644 --- a/doc/compute_temp_com.txt +++ b/doc/compute_temp_com.txt @@ -30,7 +30,8 @@ command that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc. -The temperature is calculated by the formula KE = dim/2 N k T, where +After the center-of-mass velocity has been subtracted from each atom, +the temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index 7875d01fb5..f0572b83b9 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -36,10 +36,10 @@ that computes a temperature, e.g. thermo_modifyfix temp/rescale, fix npt, etc.
The deformation fix changes the box size and/or shape over time, so -each point in the simulation box can be thought of as having a +each atom in the simulation box can be thought of as having a "streaming" velocity. For example, if the box is being sheared in x, -relative to y, then points at the bottom of the box (low y) have a -small x velocity, while points at the top of the box (hi y) have a +relative to y, then atoms at the bottom of the box (low y) have a +small x velocity, while atoms at the top of the box (hi y) have a large x velocity. This position-dependent streaming velocity is subtracted from each atom's actual velocity to yield a thermal velocity which is used to compute the temperature. @@ -56,11 +56,12 @@ not changed, and thus they do NOT have the streaming velocity assumed by this compute. LAMMPS will warn you if fix deform is defined and its remap setting is not consistent with this compute.
-The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. Note that -v in the kinetic energy formula is the atom's thermal velocity. +
After the streaming velocity has been subtracted from each atom, the +temperature is calculated by the formula KE = dim/2 N k T, where KE = +total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 +or 3 = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. Note that v in +the kinetic energy formula is the atom's thermal velocity.
A 6-component kinetic energy tensor is also calculated by this compute for use in the computation of a pressure tensor. The formula for the @@ -104,8 +105,9 @@ the simulation.
Related commands:
-compute temp/ramp, fix -deform, fix nvt/sllod +
compute temp/ramp, compute +temp/profile, fix deform, +fix nvt/sllod
Default: none
diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index c78b48cfc1..7c8bcfaaf8 100644 --- a/doc/compute_temp_deform.txt +++ b/doc/compute_temp_deform.txt @@ -33,10 +33,10 @@ that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc. The deformation fix changes the box size and/or shape over time, so -each point in the simulation box can be thought of as having a +each atom in the simulation box can be thought of as having a "streaming" velocity. For example, if the box is being sheared in x, -relative to y, then points at the bottom of the box (low y) have a -small x velocity, while points at the top of the box (hi y) have a +relative to y, then atoms at the bottom of the box (low y) have a +small x velocity, while atoms at the top of the box (hi y) have a large x velocity. This position-dependent streaming velocity is subtracted from each atom's actual velocity to yield a thermal velocity which is used to compute the temperature. @@ -53,11 +53,12 @@ not changed, and thus they do NOT have the streaming velocity assumed by this compute. LAMMPS will warn you if fix deform is defined and its remap setting is not consistent with this compute. -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. Note that -v in the kinetic energy formula is the atom's thermal velocity. +After the streaming velocity has been subtracted from each atom, the +temperature is calculated by the formula KE = dim/2 N k T, where KE = +total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 +or 3 = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. Note that v in +the kinetic energy formula is the atom's thermal velocity. A 6-component kinetic energy tensor is also calculated by this compute for use in the computation of a pressure tensor. The formula for the @@ -101,7 +102,8 @@ the simulation. [Related commands:] -"compute temp/ramp"_compute_temp_ramp.html, "fix -deform"_fix_deform.html, "fix nvt/sllod"_fix_nvt_sllod.html +"compute temp/ramp"_compute_temp_ramp.html, "compute +temp/profile"_compute_temp_profile.html, "fix deform"_fix_deform.html, +"fix nvt/sllod"_fix_nvt_sllod.html [Default:] none diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html index d3f8863446..642d4db8c1 100644 --- a/doc/compute_temp_ramp.html +++ b/doc/compute_temp_ramp.html @@ -28,20 +28,27 @@Examples:
-temperature 2nd middle ramp vx 0 8 y 2 12 units lattice +compute 2nd middle temp/ramp vx 0 8 y 2 12 units latticeDescription:
Define a computation that calculates the temperature of a group of -atoms, after subtracting out an imposed velocity on the system before +atoms, after subtracting out an ramped velocity profile before computing the kinetic energy. A compute of this style can be used by any command that computes a temperature, e.g. thermo_modify, fix temp/rescale, fix npt, etc.
-The meaning of the arguments for this command is the same as for the -velocity ramp command which was presumably used to -impose the velocity. +
The meaning of the arguments for this command which define the +velocity ramp are the same as for the velocity ramp +command which was presumably used to impose the velocity. +
+After the ramp velocity has been subtracted from the specified +dimension for each atom, the temperature is calculated by the formula +KE = dim/2 N k T, where KE = total kinetic energy of the group of +atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the +simulation, N = number of atoms in the group, k = Boltzmann constant, +and T = temperature.
The units keyword determines the meaning of the distance units used for coordinates (c1,c2) and velocities (vlo,vhi). A box value @@ -93,8 +100,8 @@ the simulation.
Related commands:
-compute temp, compute -temp/region, compute +
-compute temp, compute +temp/profie, compute temp/deform, compute pressure
diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt index 2e8b288ac0..260d0fe70b 100644 --- a/doc/compute_temp_ramp.txt +++ b/doc/compute_temp_ramp.txt @@ -24,20 +24,27 @@ keyword = {units} :ul [Examples:] -temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre +compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice :pre [Description:] Define a computation that calculates the temperature of a group of -atoms, after subtracting out an imposed velocity on the system before +atoms, after subtracting out an ramped velocity profile before computing the kinetic energy. A compute of this style can be used by any command that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc. -The meaning of the arguments for this command is the same as for the -"velocity ramp"_velocity.html command which was presumably used to -impose the velocity. +The meaning of the arguments for this command which define the +velocity ramp are the same as for the "velocity ramp"_velocity.html +command which was presumably used to impose the velocity. + +After the ramp velocity has been subtracted from the specified +dimension for each atom, the temperature is calculated by the formula +KE = dim/2 N k T, where KE = total kinetic energy of the group of +atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the +simulation, N = number of atoms in the group, k = Boltzmann constant, +and T = temperature. The {units} keyword determines the meaning of the distance units used for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value @@ -90,11 +97,10 @@ the simulation. [Related commands:] "compute temp"_compute_temp.html, "compute -temp/region"_compute_temp_region.html, "compute +temp/profie"_compute_temp_profile.html, "compute temp/deform"_compute_temp_deform.html, "compute pressure"_compute_pressure.html [Default:] The option default is units = lattice. - diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html index 3ad02ed746..af85c19995 100644 --- a/doc/compute_temp_sphere.html +++ b/doc/compute_temp_sphere.html @@ -36,9 +36,10 @@ particles with only translational kinetic energy. translational, 3 rotational). For 2d spherical particles, each has 3 degrees of freedom (2 translational, 1 rotational).The rotational kinetic energy is computed as 1/2 I w^2, where I is the -moment of inertia for a sphere and w is the particle's angular -velocity. +
The translational kinetic energy is computed the same as is described +by the compute temp command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the moment of +inertia for a sphere and w is the particle's angular velocity.
IMPORTANT NOTE: For 2d models, particles are treated as spheres, not disks, meaning their moment of inertia will be the diff --git a/doc/compute_temp_sphere.txt b/doc/compute_temp_sphere.txt index 4c7878d9b4..308e028e5e 100755 --- a/doc/compute_temp_sphere.txt +++ b/doc/compute_temp_sphere.txt @@ -33,9 +33,10 @@ For 3d spherical particles, each has 6 degrees of freedom (3 translational, 3 rotational). For 2d spherical particles, each has 3 degrees of freedom (2 translational, 1 rotational). -The rotational kinetic energy is computed as 1/2 I w^2, where I is the -moment of inertia for a sphere and w is the particle's angular -velocity. +The translational kinetic energy is computed the same as is described +by the "compute temp"_compute_temp.html command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the moment of +inertia for a sphere and w is the particle's angular velocity. IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated as spheres, not disks, meaning their moment of inertia will be the diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 9e3e9e1fe1..b52b1ca3a0 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -97,19 +97,17 @@ thermostatting. run from Tstart to Tstop.
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. +with compute commands that remove a "bias" from the +atom velocities. E.g. removing the center-of-mass velocity from a +group of atoms or removing the x-component of velocity from the +calculation. 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: bias is removed from each atom, thermostatting is performed on +the remaining thermal degrees of freedom, and the bias is added back +in.
The damp parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index c6ddea6540..b4a888592d 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -88,19 +88,17 @@ The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. 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. +with "compute commands"_compute.html that remove a "bias" from the +atom velocities. E.g. removing the center-of-mass velocity from a +group of atoms or removing the x-component of velocity from the +calculation. 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: bias is removed from each atom, thermostatting is performed on +the remaining thermal degrees of freedom, and the bias is added back +in. The {damp} parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0