From fb4cc15d79d09bbe6ac5b808d30d8f62c059874e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 15 Nov 2007 15:29:14 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1170 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_langevin.html | 8 +++++++- doc/fix_langevin.txt | 7 ++++++- doc/fix_nph.html | 20 ++++++++++++++++---- doc/fix_nph.txt | 18 ++++++++++++++---- doc/fix_npt.html | 23 ++++++++++++++++++++--- doc/fix_npt.txt | 20 +++++++++++++++++--- doc/fix_nvt.html | 10 ++++++++-- doc/fix_nvt.txt | 9 +++++++-- 8 files changed, 95 insertions(+), 20 deletions(-) diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index c6e54a7734..4498d1b134 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -68,7 +68,9 @@ into the particle. As derived from the fluctuation/dissipation theorum, its magnitude is proportional to sqrt(T m / dt damp), where T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are -used to randomize the direction and magnitude of this force. +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.

The desired temperature at each timestep is a ramped value during the run from Tstart to Tstop. @@ -146,4 +148,8 @@ viscous

Default: none

+ + +

(Dunweg) Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). +

diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index d7f1bbde20..fa652f0058 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -58,7 +58,9 @@ into the particle. As derived from the fluctuation/dissipation theorum, its magnitude is proportional to sqrt(T m / dt damp), where T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are -used to randomize the direction and magnitude of this force. +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. The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. @@ -135,3 +137,6 @@ This fix is not invoked during "energy minimization"_minimize.html. viscous"_fix_viscous.html [Default:] none + +:link(Dunweg) +[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). diff --git a/doc/fix_nph.html b/doc/fix_nph.html index 4ec5813d58..105e87f365 100644 --- a/doc/fix_nph.html +++ b/doc/fix_nph.html @@ -52,10 +52,11 @@ fix 2 all nph aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0

Perform constant NPH integration to update positions and velocities each timestep for atoms in the group using a Nose/Hoover pressure -barostat. P is pressure. This creates a system trajectory consistent -with the isobaric ensemble. Unlike fix npt, -temperature will not be controlled if no other fix is used. -Temperature can be controlled independently by using "fix +barostat (Hoover), implemented as described in +(Melchionna). P is pressure. This creates a system +trajectory consistent with the isobaric ensemble. Unlike fix +npt, temperature will not be controlled if no other fix +is used. Temperature can be controlled independently by using "fix langevin or fix temp/rescale.

@@ -197,4 +198,15 @@ pressure via Nose/Hoover.

The keyword defaults are drag = 0.0 and dilate = all.

+
+ + + +

(Hoover) Hoover, Phys Rev A, 34, 2499 (1986). +

+ + +

(Melchionna) Melchionna, Ciccotti, Holian, Molecular Physics, 78, +533-44 (1993). +

diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt index a66ae68ea0..2f8893f847 100644 --- a/doc/fix_nph.txt +++ b/doc/fix_nph.txt @@ -43,10 +43,11 @@ fix 2 all nph aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 :pre Perform constant NPH integration to update positions and velocities each timestep for atoms in the group using a Nose/Hoover pressure -barostat. P is pressure. This creates a system trajectory consistent -with the isobaric ensemble. Unlike "fix npt"_fix_npt.html, -temperature will not be controlled if no other fix is used. -Temperature can be controlled independently by using ""fix +barostat "(Hoover)"_#Hoover, implemented as described in +"(Melchionna)"_#Melchionna. P is pressure. This creates a system +trajectory consistent with the isobaric ensemble. Unlike "fix +npt"_fix_npt.html, temperature will not be controlled if no other fix +is used. Temperature can be controlled independently by using ""fix langevin"_fix_langevin.html or "fix temp/rescale"_fix_temp_rescale.html. @@ -186,3 +187,12 @@ pressure via Nose/Hoover. [Default:] The keyword defaults are drag = 0.0 and dilate = all. + +:line + +:link(Hoover) +[(Hoover)] Hoover, Phys Rev A, 34, 2499 (1986). + +:link(Melchionna) +[(Melchionna)] Melchionna, Ciccotti, Holian, Molecular Physics, 78, +533-44 (1993). diff --git a/doc/fix_npt.html b/doc/fix_npt.html index 2f81a84fac..a6849785d4 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -52,9 +52,11 @@ fix 2 water npt 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate

Perform constant NPT integration to update positions and velocities each timestep for atoms 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. +thermostat (Hoover1) and Nose/Hoover pressure barostat +(Hoover2), implemented as described in +(Melchionna). P is pressure; T is temperature. This +creates a system trajectory consistent with the isothermal-isobaric +ensemble.

The desired temperature at each timestep is a ramped value during the run from Tstart to Tstop. The Tdamp parameter is specified in @@ -201,4 +203,19 @@ the Nose/Hoover formulation.

The keyword defaults are drag = 0.0 and dilate = all.

+
+ + + +

(Hoover1) Hoover, Phys Rev A, 31, 1695 (1985). +

+ + +

(Hoover2) Hoover, Phys Rev A, 34, 2499 (1986). +

+ + +

(Melchionna) Melchionna, Ciccotti, Holian, Molecular Physics, 78, +533-44 (1993). +

diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 92fbe3e84e..28a6aae4ec 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -41,9 +41,11 @@ fix 2 water npt 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate Perform constant NPT integration to update positions and velocities each timestep for atoms 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. +thermostat "(Hoover1)"_#Hoover1 and Nose/Hoover pressure barostat +"(Hoover2)"_#Hoover2, implemented as described in +"(Melchionna)"_#Melchionna. P is pressure; T is temperature. This +creates a system trajectory consistent with the isothermal-isobaric +ensemble. The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in @@ -189,3 +191,15 @@ the Nose/Hoover formulation. [Default:] The keyword defaults are drag = 0.0 and dilate = all. + +:line + +:link(Hoover1) +[(Hoover1)] Hoover, Phys Rev A, 31, 1695 (1985). + +:link(Hoover2) +[(Hoover2)] Hoover, Phys Rev A, 34, 2499 (1986). + +:link(Melchionna) +[(Melchionna)] Melchionna, Ciccotti, Holian, Molecular Physics, 78, +533-44 (1993). diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index e7a8b3e225..009b9124db 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -40,8 +40,8 @@ fix 1 all nvt 300.0 300.0 100.0 drag 0.2

Perform constant NVT integration to update positions and velocities each timestep for atoms 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. +thermostat (Hoover). V is volume; T is temperature. This +creates a system trajectory consistent with the canonical ensemble.

The desired temperature at each timestep is a ramped value during the run from Tstart to Tstop. The Tdamp parameter is specified in @@ -125,4 +125,10 @@ temp/rescale, fix langevin,

The keyword defaults are drag = 0.0.

+
+ + + +

(Hoover) Hoover, Phys Rev A, 31, 1695 (1985). +

diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index d701aa56e7..0987a19e7c 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -31,8 +31,8 @@ fix 1 all nvt 300.0 300.0 100.0 drag 0.2 :pre Perform constant NVT integration to update positions and velocities each timestep for atoms 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. +thermostat "(Hoover)"_#Hoover. V is volume; T is temperature. This +creates a system trajectory consistent with the canonical ensemble. The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in @@ -115,3 +115,8 @@ temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, [Default:] The keyword defaults are drag = 0.0. + +:line + +:link(Hoover) +[(Hoover)] Hoover, Phys Rev A, 31, 1695 (1985).