From 07c6376bcf80fd0183b9f1eb8b0b700f3b95863f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 11 Mar 2008 17:15:19 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1590 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_langevin.html | 56 ++++++++++------ doc/fix_langevin.txt | 56 ++++++++++------ doc/fix_npt.html | 35 ++++++++-- doc/fix_npt.txt | 35 ++++++++-- doc/fix_nvt.html | 32 ++++++++- doc/fix_nvt.txt | 32 ++++++++- doc/fix_temp_berendsen.html | 125 ++++++++++++++++++++++++++++++++++++ doc/fix_temp_berendsen.txt | 120 ++++++++++++++++++++++++++++++++++ doc/fix_temp_rescale.html | 81 +++++++++++------------ doc/fix_temp_rescale.txt | 78 +++++++++++----------- 10 files changed, 512 insertions(+), 138 deletions(-) create mode 100644 doc/fix_temp_berendsen.html create mode 100644 doc/fix_temp_berendsen.txt diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index e46923c999..794356816c 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -27,14 +27,10 @@
  • zero or more keyword/value pairs may be appended -keyword = axes or scale or region - axes values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat +keyword = scale scale values = type ratio type = atom type (1-N) ratio = factor to scale the damping coefficient by - region value = region-ID - region-ID = ID of region to apply thermostat to

    Examples: @@ -71,9 +67,36 @@ used to randomize the direction and magnitude of this force as described in (Dunweg), where a uniform random number is used (instead of a Gaussian random number) for speed.

    +

    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 +thermostatting. Thus you must use a separate time integration fix, +like fix nve to actually update the velocities and +positions of atoms using the the modified forces. Likewise, this fix +should not normally be used on atoms that also have their temperature +controlled by another fix - e.g. by fix nvt or fix +temp/rescale commands. +

    +
    +

    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 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. +

    The damp 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 @@ -108,17 +131,6 @@ includes the particle mass in Ff, unlike fix viscous. Thus the mass and size of different atom types should be accounted for in the choice of ratio values.

    -

    The keyword region applies the fix only to atoms that are in the -specified geometric region (and in the fix group). Since atoms can -enter/leave a region, this test is performed each timestep. -

    -

    As noted above, fix langevin does not update the coordinates or -velocities of its atoms, only the forces. It is normally used with a -fix nve that does the time integration. Fix langevin -should not normally be used on atoms that also have their temperature -controlled by another fix - e.g. a nvt or -temp/rescale fix. -

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart @@ -128,10 +140,14 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior.

    -

    None of the fix_modify options are relevant to this -fix. No global scalar or vector or per-atom quantities are stored by -this fix for access by various output -commands. +

    The fix_modify temp option is supported by this +fix. You can use it to assign a temperature compute +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. +

    +

    No global scalar or vector or per-atom quantities are stored by this +fix for access by various output commands.

    This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index e18f8be14f..74a60aa637 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -18,14 +18,10 @@ 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 = {axes} or {scale} or {region} - {axes} values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat +keyword = {scale} {scale} values = type ratio type = atom type (1-N) ratio = factor to scale the damping coefficient by - {region} value = region-ID - region-ID = ID of region to apply thermostat to :ule [Examples:] @@ -62,9 +58,36 @@ 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. +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 +thermostatting. Thus you must use a separate time integration fix, +like "fix nve"_fix_nve.html to actually update the velocities and +positions of atoms using the the modified forces. Likewise, this fix +should not normally be used on atoms that also have their temperature +controlled by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix +temp/rescale"_fix_temp_rescale.html commands. + +:line + 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. + The {damp} 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 @@ -99,17 +122,6 @@ includes the particle mass in Ff, unlike fix {viscous}. Thus the mass and size of different atom types should be accounted for in the choice of ratio values. -The keyword {region} applies the fix only to atoms that are in the -specified geometric region (and in the fix group). Since atoms can -enter/leave a region, this test is performed each timestep. - -As noted above, fix {langevin} does not update the coordinates or -velocities of its atoms, only the forces. It is normally used with a -"fix nve"_fix_nve.html that does the time integration. Fix {langevin} -should not normally be used on atoms that also have their temperature -controlled by another fix - e.g. a "nvt"_fix_nvt.html or -"temp/rescale"_fix_temp_rescale.html fix. - [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart @@ -119,10 +131,14 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global scalar or vector or per-atom quantities are stored by -this fix for access by various "output -commands"_Section_howto.html#4_15. +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a temperature "compute"_compute.html +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +No global scalar or vector or per-atom quantities are stored by this +fix for access by various "output commands"_Section_howto.html#4_15. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/fix_npt.html b/doc/fix_npt.html index bbdca5c754..b806b95384 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -77,6 +77,16 @@ only the atoms in the fix group are re-scaled. The latter can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid.

    +

    IMPORTANT NOTE: Unlike the fix temp/berendsen +command which performs thermostatting but NO time integration, this +fix performs thermostatting/barostatting AND time integration. Thus +you should not use any other time integration fix, such as fix +nve on atoms to which this fix is applied. Likewise, +this fix should not normally be used on atoms that also have their +temperature controlled by another fix - e.g. by fix +langevin or fix temp/rescale +commands. +

    The pressure can be controlled in one of several styles, as specified @@ -151,6 +161,21 @@ 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 @@ -162,11 +187,11 @@ operation of the fix continues in an uninterrupted fashion.

    The fix_modify temp and press options are supported by this fix. You can use them to assign a compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -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. +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be 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 diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 40f50aa1b9..761c8e0d12 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -66,6 +66,16 @@ only the atoms in the fix group are re-scaled. The latter can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. +IMPORTANT NOTE: Unlike the "fix temp/berendsen"_fix_berendsen.html +command which performs thermostatting but NO time integration, this +fix performs thermostatting/barostatting AND time integration. Thus +you should not use any other time integration fix, such as "fix +nve"_fix_nve.html on atoms to which this fix is applied. Likewise, +this fix should not normally be used on atoms that also have their +temperature controlled by another fix - e.g. by "fix +langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html +commands. + :line The pressure can be controlled in one of several styles, as specified @@ -140,6 +150,21 @@ 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 @@ -151,11 +176,11 @@ operation of the fix continues in an uninterrupted fashion. The "fix_modify"_fix_modify.html {temp} and {press} options are supported by this fix. You can use them to assign a "compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -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. +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be 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 diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index 07026a1033..d489430d06 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -60,6 +60,16 @@ Performing a short run and monitoring the temperature is the best way 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.

    +

    IMPORTANT NOTE: Unlike the fix temp/berendsen +command which performs thermostatting but NO time integration, this +fix performs thermostatting/barostatting AND time integration. Thus +you should not use any other time integration fix, such as fix +nve on atoms to which this fix is applied. Likewise, +this fix should not normally be used on atoms that also have their +temperature controlled by another fix - e.g. by fix +langevin or fix temp/rescale +commands. +

    This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp", as if this command had been issued: @@ -80,6 +90,21 @@ 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 @@ -89,9 +114,10 @@ reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used in its thermostatting -procedure. +fix. You can use it to assign a temperature compute +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same.

    The fix_modify energy option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index 1534ed89cb..9581d00218 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -51,6 +51,16 @@ Performing a short run and monitoring the temperature is the best way 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. +IMPORTANT NOTE: Unlike the "fix temp/berendsen"_fix_berendsen.html +command which performs thermostatting but NO time integration, this +fix performs thermostatting/barostatting AND time integration. Thus +you should not use any other time integration fix, such as "fix +nve"_fix_nve.html on atoms to which this fix is applied. Likewise, +this fix should not normally be used on atoms that also have their +temperature controlled by another fix - e.g. by "fix +langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html +commands. + This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp", as if this command had been issued: @@ -71,6 +81,21 @@ 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 @@ -80,9 +105,10 @@ reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. +fix. You can use it to assign a temperature "compute"_compute.html +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html new file mode 100644 index 0000000000..0d8a2bea2b --- /dev/null +++ b/doc/fix_temp_berendsen.html @@ -0,0 +1,125 @@ + +

    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix temp/berendsen command +

    +

    Syntax: +

    +
    fix ID group-ID temp/berendsen Tstart Tstop Tdamp 
+
    + +

    Examples: +

    +
    fix 1 all nvt 300.0 300.0 100.0
+fix 1 all nvt 300.0 300.0 100.0 drag 0.2 
+
    +

    Description: +

    +

    Reset the temperature of a group of atoms by using a Berendsen +thermostat (Berendsen), which rescale their velocities +every timestep. +

    +

    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 fmsec or psec - see the +units command). +

    +

    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 velocities to +effect thermostatting. Thus you must use a separate time integration +fix, like fix nve to actually update the positions of +atoms using the modified velocities. Likewise, this fix should not +normally be used on atoms that also have their temperature controlled +by another fix - e.g. by fix nvt or fix +langevin commands. +

    +
    + +

    This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp", as if this command had been +issued: +

    +
    compute fix-ID_temp group-ID temp 
+
    +

    See the compute temp 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. +

    +

    Note that this is NOT the compute used by thermodynamic output (see +the thermo_style command) with ID = thermo_temp. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +compute_modify command or print this temperature +during thermodynamic output via the thermo_style +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: +

    +

    No information about this fix is written to binary restart +files. +

    +

    The fix_modify temp option is supported by this +fix. You can use it to assign a temperature compute +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. +

    +

    No global scalar or vector or per-atom quantities are stored by this +fix for access by various output commands. +

    +

    This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +

    +

    This fix is not invoked during energy minimization. +

    +

    Restrictions: none +

    +

    Related commands: +

    +

    fix nve, fix nvt, fix +temp/rescale, fix langevin, +fix_modify, compute temp +

    +

    Default: none +

    +
    + + + +

    (Berendsen) Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem +Phys, 81, 3684 (1984). +

    + diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt new file mode 100644 index 0000000000..ed8611edef --- /dev/null +++ b/doc/fix_temp_berendsen.txt @@ -0,0 +1,120 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix temp/berendsen command :h3 + +[Syntax:] + +fix ID group-ID temp/berendsen Tstart Tstop Tdamp :pre + +ID, group-ID are documented in "fix"_fix.html command +temp/berendsen = style name of this fix command +Tstart,Tstop = desired temperature at start/end of run +Tdamp = temperature damping parameter (time units) :ul + +[Examples:] + +fix 1 all nvt 300.0 300.0 100.0 +fix 1 all nvt 300.0 300.0 100.0 drag 0.2 :pre + +[Description:] + +Reset the temperature of a group of atoms by using a Berendsen +thermostat "(Berendsen)"_#Berendsen, which rescale their velocities +every timestep. + +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 fmsec or psec - see the +"units"_units.html command). + +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 velocities to +effect thermostatting. Thus you must use a separate time integration +fix, like "fix nve"_fix_nve.html to actually update the positions of +atoms using the modified velocities. Likewise, this fix should not +normally be used on atoms that also have their temperature controlled +by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix +langevin"_fix_langevin.html commands. + +:line + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp", as if this command had been +issued: + +compute fix-ID_temp group-ID temp :pre + +See the "compute temp"_compute_temp.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. + +Note that this is NOT the compute used by thermodynamic output (see +the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +"compute_modify"_compute_modify.html command or print this temperature +during thermodynamic output via the "thermo_style +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:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a temperature "compute"_compute.html +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +No global scalar or vector or per-atom quantities are stored by this +fix for access by various "output commands"_Section_howto.html#4_15. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] none + +[Related commands:] + +"fix nve"_fix_nve.html, "fix nvt"_fix_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, +"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html + +[Default:] none + +:line + +:link(Berendsen) + +[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem +Phys, 81, 3684 (1984). diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index e93c7a95aa..960b26f370 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -20,20 +20,13 @@
  • N = perform rescaling every N steps
  • Tstart,Tstop = desired temperature at start/end of run (temperature units)
  • window = only rescale if temperature is outside this window (temperature units) -
  • fraction = rescale to target temperature by this fraction -
  • zero or more keyword/value pairs may be appended -
  • keyword = region or partial +
  • fraction = rescale to target temperature by this fraction -
      region values = region-ID
-    region-ID = ID of region to apply rescaling to
-  partial values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 if the velocity component should not or should be rescaled 
-

    Examples: 

    fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 region edge
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 partial 0 1 1 
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0

    Description:

    @@ -51,37 +44,27 @@ difference between the actual and desired temperature. E.g. if fraction = 1.0, the temperature is reset to exactly the desired value.

    -

    The keyword region applies the fix only to atoms that are in the -specified geometric region (and in the fix group). Since atoms can -enter/leave a region, this test is performed each timestep. -

    -

    The keyword partial rescales only the specified velocity components. -A compute of style temp/partial is used to compute the current -temperature of just those components (see below). -

    -

    The region and partial keywords cannot currently be used together. -

    -

    A temp/rescale fix does not update the coordinates of its atoms. It -is normally used with a fix of style nve that does that. A -temp/rescale fix should not normally be used on atoms that also have -their temperature controlled by another fix - e.g. a -nvt or langevin fix. +

    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 velocities to +effect thermostatting. Thus you must use a separate time integration +fix, like fix nve to actually update the positions of +atoms using the modified velocities. Likewise, this fix should not +normally be used on atoms that also have their temperature controlled +by another fix - e.g. by fix nvt or fix +langevin commands.

    +
    +

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp" or "temp/region" or -"temp/partial", as if one of these commands had been issued: +creates its own compute of style "temp", as if one of this command had +been issued:

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_temp group-ID temp/region region-ID 
-compute fix-ID_temp group-ID temp/partial xflag yflag zflag 
+
    compute fix-ID_temp group-ID temp 
 
    
-
    Which is used depends on whether the region or partial keywords
-were specified with the fix.  See the compute
-temp, compute
-temp/region, and compute
-temp/partial commands 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.
+
    See the compute temp 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.
 
    
 
    Note that this is NOT the compute used by thermodynamic output (see
 the thermo_style command) with ID = thermo_temp.
@@ -93,17 +76,31 @@ 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:
 
    
 
    No information about this fix is written to binary restart
 files.
 
    
 
    The fix_modify temp option is supported by this
-fix.  You can use it to assign a compute you have
-defined to this fix which will be used in its thermostatting
-procedure.  For consistency, if using the keyword region, the
-compute you assign should also be of style
-temp/region.
+fix.  You can use it to assign a temperature compute
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
 
    
 
    The fix_modify energy option is supported by this
 fix to add the energy change implied by a velocity rescaling to the
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index 5d20c1d67b..d1cc203976 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -17,19 +17,13 @@ temp/rescale = style name of this fix command
 N = perform rescaling every N steps 
 Tstart,Tstop = desired temperature at start/end of run (temperature units)
 window = only rescale if temperature is outside this window (temperature units)
-fraction = rescale to target temperature by this fraction
-zero or more keyword/value pairs may be appended
-keyword = {region} or {partial} :ul
-  {region} values = region-ID
-    region-ID = ID of region to apply rescaling to
-  {partial} values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 if the velocity component should not or should be rescaled :pre
+fraction = rescale to target temperature by this fraction :ul
 
 [Examples:]
 
 fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 region edge
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 partial 0 1 1 :pre
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
 
 [Description:]
 
@@ -47,37 +41,27 @@ difference between the actual and desired temperature.  E.g. if
 {fraction} = 1.0, the temperature is reset to exactly the desired
 value.
 
-The keyword {region} applies the fix only to atoms that are in the
-specified geometric region (and in the fix group).  Since atoms can
-enter/leave a region, this test is performed each timestep.
+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 velocities to
+effect thermostatting.  Thus you must use a separate time integration
+fix, like "fix nve"_fix_nve.html to actually update the positions of
+atoms using the modified velocities.  Likewise, this fix should not
+normally be used on atoms that also have their temperature controlled
+by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
+langevin"_fix_langevin.html commands.
 
-The keyword {partial} rescales only the specified velocity components.
-A compute of style temp/partial is used to compute the current
-temperature of just those components (see below).
-
-The {region} and {partial} keywords cannot currently be used together.
-
-A temp/rescale fix does not update the coordinates of its atoms.  It
-is normally used with a fix of style {nve} that does that.  A
-temp/rescale fix should not normally be used on atoms that also have
-their temperature controlled by another fix - e.g. a
-"nvt"_fix_nvt.html or "langevin"_fix_langevin.html fix.
+:line
 
 This fix computes a temperature each timestep.  To do this, the fix
-creates its own compute of style "temp" or "temp/region" or
-"temp/partial", as if one of these commands had been issued:
+creates its own compute of style "temp", as if one of this command had
+been issued:
 
-compute fix-ID_temp group-ID temp
-compute fix-ID_temp group-ID temp/region region-ID 
-compute fix-ID_temp group-ID temp/partial xflag yflag zflag :pre
+compute fix-ID_temp group-ID temp :pre
 
-Which is used depends on whether the {region} or {partial} keywords
-were specified with the fix.  See the "compute
-temp"_compute_temp.html, "compute
-temp/region"_compute_temp_region.html, and "compute
-temp/partial"_compute_temp_partial.html commands 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.
+See the "compute temp"_compute_temp.html 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.
 
 Note that this is NOT the compute used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
@@ -89,17 +73,31 @@ 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:]
 
 No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {temp} option is supported by this
-fix.  You can use it to assign a "compute"_compute.html you have
-defined to this fix which will be used in its thermostatting
-procedure.  For consistency, if using the keyword {region}, the
-compute you assign should also be of style
-"temp/region"_compute_temp_region.html.
+fix.  You can use it to assign a temperature "compute"_compute.html
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy change implied by a velocity rescaling to the