The removal of the center-of-mass velocity by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include fix nvt, fix +temp/rescale, fix +temp/berendsen, and fix +langevin. +
This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of diff --git a/doc/compute_temp_com.txt b/doc/compute_temp_com.txt index 56c6a0584a..30d519d792 100644 --- a/doc/compute_temp_com.txt +++ b/doc/compute_temp_com.txt @@ -44,6 +44,17 @@ The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the "compute_modify"_compute_modify.html command if this is not the case. +The removal of the center-of-mass velocity by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include "fix nvt"_fix_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. + This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the temperature of groups of diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index ea3cb06f17..23f93752e2 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -69,6 +69,17 @@ v^2 is replaced by vx * vy for the xy component, etc. constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case.
+The removal of the box deformation velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include fix nvt, fix +temp/rescale, fix +temp/berendsen, and fix +langevin. +
This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index 0d427964d3..b3fe7e5c8d 100644 --- a/doc/compute_temp_deform.txt +++ b/doc/compute_temp_deform.txt @@ -66,6 +66,17 @@ The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the "compute_modify"_compute_modify.html command if this is not the case. +The removal of the box deformation velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include "fix nvt"_fix_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. + This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the temperature of groups of diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html index c646e9a122..158795fc1a 100644 --- a/doc/compute_temp_partial.html +++ b/doc/compute_temp_partial.html @@ -48,6 +48,17 @@ v^2 is replaced by vx * vy for the xy component, etc. constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case.
+The removal of velocity components by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include fix nvt, fix +temp/rescale, fix +temp/berendsen, and fix +langevin. +
This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt index a6918e250d..e1ef41d283 100644 --- a/doc/compute_temp_partial.txt +++ b/doc/compute_temp_partial.txt @@ -45,6 +45,17 @@ The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the "compute_modify"_compute_modify.html command if this is not the case. +The removal of velocity components by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include "fix nvt"_fix_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. + This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the temperature of groups of diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html index 0e821c0808..0e2a170e56 100644 --- a/doc/compute_temp_ramp.html +++ b/doc/compute_temp_ramp.html @@ -60,6 +60,17 @@ v^2 is replaced by vx * vy for the xy component, etc. constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case.
+The removal of the ramped velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include fix nvt, fix +temp/rescale, fix +temp/berendsen, and fix +langevin. +
This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt index d4d371c418..3fd44ff25d 100644 --- a/doc/compute_temp_ramp.txt +++ b/doc/compute_temp_ramp.txt @@ -56,6 +56,17 @@ The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the "compute_modify"_compute_modify.html command if this is not the case. +The removal of the ramped velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include "fix nvt"_fix_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. + This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the temperature of groups of diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html index 14633cbbee..ba5f909c47 100644 --- a/doc/compute_temp_region.html +++ b/doc/compute_temp_region.html @@ -57,6 +57,19 @@ enter/leave the region. Thus there is no need to use the dynamic option of the compute_modify command for this compute style.
+The removal of atoms outside the region by this fix is essentially +computing the temperature after a "bias" has been removed, which in +this case is the velocity of any atoms outside the region. If this +compute is used with a fix command that performs thermostatting then +this bias will be subtracted from each atom, thermostatting of the +remaining thermal velocity will be performed, and the bias will be +added back in. Thermostatting fixes that work in this way include +fix nvt, fix temp/rescale, fix +temp/berendsen, and fix +langevin. This means any of those thermostatting +fixes can operate on a geometric region of atoms, as defined by this +compute. +
Unlike other compute styles that calculate temperature, this compute does NOT currently subtract out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt index b61c70f6cf..290689ef02 100644 --- a/doc/compute_temp_region.txt +++ b/doc/compute_temp_region.txt @@ -54,6 +54,19 @@ enter/leave the region. Thus there is no need to use the {dynamic} option of the "compute_modify"_compute_modify.html command for this compute style. +The removal of atoms outside the region by this fix is essentially +computing the temperature after a "bias" has been removed, which in +this case is the velocity of any atoms outside the region. If this +compute is used with a fix command that performs thermostatting then +this bias will be subtracted from each atom, thermostatting of the +remaining thermal velocity will be performed, and the bias will be +added back in. Thermostatting fixes that work in this way include +"fix nvt"_fix_nvt.html, "fix temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. This means any of those thermostatting +fixes can operate on a geometric region of atoms, as defined by this +compute. + Unlike other compute styles that calculate temperature, this compute does NOT currently subtract out degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and diff --git a/doc/fix.html b/doc/fix.html index cb5db74d7d..5a36ea22b3 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -150,6 +150,7 @@ list of fix styles available in LAMMPS:
IMPORTANT NOTE: If both the temp and press keywords are used in a +single thermo_modify command (or in two separate commands), then the +order in which the keywords are specified is important. Note that a +pressure compute defines its own temperature +compute as an argument when it is specified. The temp keyword will +override this (for the pressure compute being used by fix npt), but +only if the temp keyword comes after the press keyword. If the +temp keyword comes before the press keyword, then the new pressure +compute specified by the press keyword will be unaffected by the +temp setting. +
The fix_modify energy option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index e7aa0ec604..40f50aa1b9 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -157,6 +157,17 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. +IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a +single thermo_modify command (or in two separate commands), then the +order in which the keywords are specified is important. Note that a +"pressure compute"_compute_pressure.html defines its own temperature +compute as an argument when it is specified. The {temp} keyword will +override this (for the pressure compute being used by fix npt), but +only if the {temp} keyword comes after the {press} keyword. If the +{temp} keyword comes before the {press} keyword, then the new pressure +compute specified by the {press} keyword will be unaffected by the +{temp} setting. + The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html index b9178a4e81..49281c44fa 100644 --- a/doc/thermo_modify.html +++ b/doc/thermo_modify.html @@ -103,15 +103,15 @@ compute for pressure with ID = thermo_press. This option allows the user to override the default.
IMPORTANT NOTE: If both the temp and press keywords are used in a -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a pressure -compute defines its own temperature compute as -an argument when it is specified. The temp keyword will override -this (for the pressure compute being used by thermodynamics), but only -if the temp keyword comes after the press keyword. If the temp -keyword comes before the press keyword, then the new pressure -compute specified by the press keyword will be unaffected by the -temp setting. +single thermo_modify command (or in two separate commands), then the +order in which the keywords are specified is important. Note that a +pressure compute defines its own temperature +compute as an argument when it is specified. The temp keyword will +override this (for the pressure compute being used by thermodynamics), +but only if the temp keyword comes after the press keyword. If +the temp keyword comes before the press keyword, then the new +pressure compute specified by the press keyword will be unaffected +by the temp setting.
The drot keyword is used to determine how rotational energy is calculated for dipolar atoms, which is used by the thermo_style diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt index 258343ac55..24d40fea66 100644 --- a/doc/thermo_modify.txt +++ b/doc/thermo_modify.txt @@ -97,15 +97,15 @@ compute for pressure with ID = {thermo_press}. This option allows the user to override the default. IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a "pressure -compute"_compute_pressure.html defines its own temperature compute as -an argument when it is specified. The {temp} keyword will override -this (for the pressure compute being used by thermodynamics), but only -if the {temp} keyword comes after the {press} keyword. If the {temp} -keyword comes before the {press} keyword, then the new pressure -compute specified by the {press} keyword will be unaffected by the -{temp} setting. +single thermo_modify command (or in two separate commands), then the +order in which the keywords are specified is important. Note that a +"pressure compute"_compute_pressure.html defines its own temperature +compute as an argument when it is specified. The {temp} keyword will +override this (for the pressure compute being used by thermodynamics), +but only if the {temp} keyword comes after the {press} keyword. If +the {temp} keyword comes before the {press} keyword, then the new +pressure compute specified by the {press} keyword will be unaffected +by the {temp} setting. The {drot} keyword is used to determine how rotational energy is calculated for dipolar atoms, which is used by the thermo_style