From 059f719d6220fc6e99b15a8a34de637d614918ba Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 27 Jul 2015 18:05:31 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13732 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_intro.html | 8 ++--- doc/Section_intro.txt | 13 ++++---- doc/Section_packages.html | 14 ++++----- doc/Section_packages.txt | 2 +- doc/compute_temp_drude.html | 57 ++++++++++++++++++++++++++---------- doc/compute_temp_drude.txt | 55 ++++++++++++++++++++++++---------- doc/fix_drude_transform.html | 48 ++++++++---------------------- doc/fix_drude_transform.txt | 44 ++++++++-------------------- doc/fix_langevin_drude.html | 50 ++++++++++++++++++------------- doc/fix_langevin_drude.txt | 50 ++++++++++++++++++------------- 10 files changed, 184 insertions(+), 157 deletions(-) diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 3d9524056d..c5bc330f04 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -145,10 +145,12 @@ commands) diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 25fc9ff35f..ae093108be 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -142,10 +142,15 @@ commands) manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire + long-range interactions for charge, point-dipoles, and LJ dispersion: \ + Ewald, Wolf, PPPM (similar to particle-mesh Ewald) + polarization models: "QEq"_fix_qeq.html, \ + "core/shell model"_Section_howto.html#howto_26, \ + "Drude dipole model"_Section_howto.html#howto_27 charge equilibration (QEq via dynamic, point, shielded, Slater methods) - electron force field (eFF, AWPMD) coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO mesoscopic potentials: granular, Peridynamics, SPH + electron force field (eFF, AWPMD) bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ quartic (breakable) angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ @@ -156,12 +161,10 @@ commands) polymer potentials: all-atom, united-atom, bead-spring, breakable water potentials: TIP3P, TIP4P, SPC implicit solvent potentials: hydrodynamic lubrication, Debye - "KIM archive"_http://openkim.org of potentials - long-range interactions for charge, point-dipoles, and LJ dispersion: \ - Ewald, Wolf, PPPM (similar to particle-mesh Ewald) force-field compatibility with common CHARMM, AMBER, DREIDING, \ OPLS, GROMACS, COMPASS options - handful of GPU-enabled pair styles + access to "KIM archive"_http://openkim.org of potentials via \ + "pair kim"_pair_kim.html hybrid potentials: multiple pair, bond, angle, dihedral, improper \ potentials can be used in one simulation overlaid potentials: superposition of multiple pair potentials :ul diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 51bfa4a382..ce890b4ffd 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -368,13 +368,13 @@ in LAMMPS using thermalized Drude oscillators.

See these doc pages and their related commands to get started:

-

Drude tutorial -fix drude -compute temp/drude -fix langevin/drude -fix drude/transform/... -pair thole -

+

There are auxiliary tools for using this package in tools/drude.

The person who created this package is Alain Dequidt at Universite diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 5d0450de25..4331e34aea 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -360,7 +360,7 @@ See these doc pages and their related commands to get started: "compute temp/drude"_compute_temp_drude.html "fix langevin/drude"_fix_langevin_drude.html "fix drude/transform/..."_fix_drude_transform.html -"pair thole"_pair_thole.html +"pair thole"_pair_thole.html :ul There are auxiliary tools for using this package in tools/drude. diff --git a/doc/compute_temp_drude.html b/doc/compute_temp_drude.html index 6e50495d5a..96d3aac384 100644 --- a/doc/compute_temp_drude.html +++ b/doc/compute_temp_drude.html @@ -24,38 +24,63 @@

Description:

-

Define a computation that calculates the temperature based on the -center-of-mass velocities of pairs of Drude cores and Drude particles, -bonded by springs. This compute is designed to be used with the +

Define a computation that calculates the temperatures of core-Drude +pairs. This compute is designed to be used with the thermalized Drude +oscillator model. This compute is designed to be used with the thermalized Drude oscillator model. Polarizable models in LAMMPS are described in this Section.

-

Specifically, this compute enables calculation of the temperature of -the Drude particles in relative coordinates with respect to their -cores. +

Drude oscillators consist of a core particle and a Drude particle +connected by a harmonic bond, and the relative motion of these Drude +oscillators is usually maintained cold by a specific thermostat that +acts on the relative motion of the core-Drude particle +pairs. Therefore, because LAMMPS considers Drude particles as normal +atoms in its default temperature compute (compute +temp command), the reduced temperature of the +core-Drude particle pairs is not calculated correctly. +

+

By contrast, this compute calculates the temperature of the cores +using center-of-mass velocities of the core-Drude pairs, and the +reduced temperature of the Drude particles using the relative +velocities of the Drude particles with respect to their cores. +Non-polarizable atoms are considered as cores. Their velocities +contribute to the temperature of the cores.

Output info:

This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or +vector of length 6, which can be accessed by indices 1-6, whose components +are +

+
  1. temperature of the centers of mass (temperature units) +
  2. temperature of the dipoles (temperature units) +
  3. number of degrees of freedom of the centers of mass +
  4. number of degrees of freedom of the dipoles +
  5. kinetic energy of the centers of mass (energy units) +
  6. kinetic energy of the dipoles (energy units) +
+

These values can be used by any command that uses global scalar or vector values from a compute as input. See this section for an overview of LAMMPS output options.

-

The scalar value calculated by this compute is "intensive". The -vector are "extensive". -

-

The scalar value will be in temperature units. The -vector values will be in energy units. +

Both the scalar value and the first two values of the vector +calculated by this compute are "intensive". The other 4 vector values +are "extensive".

Restrictions:

-

The number of core-Drude pairs contributing to the temperature is -assumed to be constant for the duration of the run. +

The number of degrees of freedom contributing to the temperature is +assumed to be constant for the duration of the run unless the +fix_modify command sets the option dynamic yes.

-

Related commands: none +

Related commands: +

+

fix drude, fix +langevin_drude, fix +drude/transform, pair_style +thole, compute temp

Default: none

diff --git a/doc/compute_temp_drude.txt b/doc/compute_temp_drude.txt index 0b36fc5431..8b0755999c 100644 --- a/doc/compute_temp_drude.txt +++ b/doc/compute_temp_drude.txt @@ -21,37 +21,62 @@ compute TDRUDE all temp/drude :pre [Description:] -Define a computation that calculates the temperature based on the -center-of-mass velocities of pairs of Drude cores and Drude particles, -bonded by springs. This compute is designed to be used with the +Define a computation that calculates the temperatures of core-Drude +pairs. This compute is designed to be used with the thermalized Drude +oscillator model. This compute is designed to be used with the "thermalized Drude oscillator model"_tutorial_drude.html. Polarizable models in LAMMPS are described in "this Section"_Section_howto.html#howto_25. -Specifically, this compute enables calculation of the temperature of -the Drude particles in relative coordinates with respect to their -cores. +Drude oscillators consist of a core particle and a Drude particle +connected by a harmonic bond, and the relative motion of these Drude +oscillators is usually maintained cold by a specific thermostat that +acts on the relative motion of the core-Drude particle +pairs. Therefore, because LAMMPS considers Drude particles as normal +atoms in its default temperature compute ("compute +temp"_compute_temp.html command), the reduced temperature of the +core-Drude particle pairs is not calculated correctly. + +By contrast, this compute calculates the temperature of the cores +using center-of-mass velocities of the core-Drude pairs, and the +reduced temperature of the Drude particles using the relative +velocities of the Drude particles with respect to their cores. +Non-polarizable atoms are considered as cores. Their velocities +contribute to the temperature of the cores. [Output info:] This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. +vector of length 6, which can be accessed by indices 1-6, whose components +are + +temperature of the centers of mass (temperature units) +temperature of the dipoles (temperature units) +number of degrees of freedom of the centers of mass +number of degrees of freedom of the dipoles +kinetic energy of the centers of mass (energy units) +kinetic energy of the dipoles (energy units) :ol + These values can be used by any command that uses global scalar or vector values from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive". The -vector are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. +Both the scalar value and the first two values of the vector +calculated by this compute are "intensive". The other 4 vector values +are "extensive". [Restrictions:] -The number of core-Drude pairs contributing to the temperature is -assumed to be constant for the duration of the run. +The number of degrees of freedom contributing to the temperature is +assumed to be constant for the duration of the run unless the +{fix_modify} command sets the option {dynamic yes}. -[Related commands:] none +[Related commands:] + +"fix drude"_fix_drude.html, "fix +langevin_drude"_fix_langevin_drude.html, "fix +drude/transform"_fix_drude_transform.html, "pair_style +thole"_pair_thole.html, "compute temp"_compute_temp.html [Default:] none diff --git a/doc/fix_drude_transform.html b/doc/fix_drude_transform.html index ee62f4726b..f19e5df09c 100644 --- a/doc/fix_drude_transform.html +++ b/doc/fix_drude_transform.html @@ -24,22 +24,13 @@ 

fix ID group-ID style keyword value ...
-