git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13727 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -205,7 +205,11 @@ it gives quick access to documentation for all LAMMPS commands.
|
||||
<BR>
|
||||
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
|
||||
<BR>
|
||||
6.25 <A HREF = "Section_howto.html#howto_25">Adiabatic core/shell model</A>
|
||||
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
|
||||
<BR></UL>
|
||||
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
|
||||
<BR></UL>
|
||||
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
|
||||
<BR></UL>
|
||||
<LI><A HREF = "Section_example.html">Example problems</A>
|
||||
|
||||
@ -430,6 +434,8 @@ it gives quick access to documentation for all LAMMPS commands.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -139,7 +139,9 @@ it gives quick access to documentation for all LAMMPS commands.
|
||||
6.22 "Calculating a diffusion coefficient"_howto_22 :b
|
||||
6.23 "Using chunks to calculate system properties"_howto_23 :b
|
||||
6.24 "Setting parameters for pppm/disp"_howto_24 :b
|
||||
6.25 "Adiabatic core/shell model"_howto_25 :ule,b
|
||||
6.25 "Polarizable models"_howto_25 :ule,b
|
||||
6.26 "Adiabatic core/shell model"_howto_26 :ule,b
|
||||
6.27 "Drude induced dipoles"_howto_27 :ule,b
|
||||
"Example problems"_Section_example.html :l
|
||||
"Performance & scalability"_Section_perf.html :l
|
||||
"Additional tools"_Section_tools.html :l
|
||||
@ -233,6 +235,7 @@ it gives quick access to documentation for all LAMMPS commands.
|
||||
:link(howto_24,Section_howto.html#howto_24)
|
||||
:link(howto_25,Section_howto.html#howto_25)
|
||||
:link(howto_26,Section_howto.html#howto_26)
|
||||
:link(howto_27,Section_howto.html#howto_27)
|
||||
|
||||
:link(mod_1,Section_modify.html#mod_1)
|
||||
:link(mod_2,Section_modify.html#mod_2)
|
||||
|
||||
@ -37,7 +37,9 @@
|
||||
6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
|
||||
6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A><BR>
|
||||
6.24 <A HREF = "#howto_24">Setting parameters for the kspace_style pppm/disp command</A><BR>
|
||||
6.25 <A HREF = "#howto_25">Adiabatic core/shell model</A> <BR>
|
||||
6.25 <A HREF = "#howto_25">Polarizable models</A><BR>
|
||||
6.26 <A HREF = "#howto_26">Adiabatic core/shell model</A><BR>
|
||||
6.27 <A HREF = "#howto_27">Drude induced dipoles</A> <BR>
|
||||
|
||||
<P>The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
|
||||
@ -2415,14 +2417,91 @@ to specify this command explicitly.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "howto_25"></A><H4>6.25 Adiabatic core/shell model
|
||||
<A NAME = "howto_25"></A><H4>6.25 Polarizable models
|
||||
</H4>
|
||||
<P>In polarizable force fields the charge distributions in molecules and
|
||||
materials respond to their electrostatic environements. Polarizable
|
||||
systems can be simulated in LAMMPS using three methods:
|
||||
</P>
|
||||
<UL><LI>the fluctuating charge method, implemented in the <A HREF = "fix_qeq.html">QEQ</A>
|
||||
package,
|
||||
|
||||
<LI>the adiabatic core-shell method, implemented in the
|
||||
<A HREF = "#howto_26">CORESHELL</A> package,
|
||||
|
||||
<LI>the thermalized Drude dipole method, implemented in the
|
||||
<A HREF = "#howto_27">USER-DRUDE</A> package.
|
||||
</UL>
|
||||
<P>The fluctuating charge method calculates instantaneous charges on
|
||||
interacting atoms based on the electronegativity equalization
|
||||
principle. It is implemented in the <A HREF = "fix_qeq.html">fix qeq</A> which is
|
||||
available in several variants. It is a relatively efficient technique
|
||||
since no additional particles are introduced. This method allows for
|
||||
charge transfer between molecules or atom groups. However, because the
|
||||
charges are located at the interaction sites, off-plane components of
|
||||
polarization cannot be represented in planar molecules or atom groups.
|
||||
</P>
|
||||
<P>The two other methods share the same basic idea: polarizable atoms are
|
||||
split into one core atom and one satellite particle (called shell or
|
||||
Drude particle) attached to it by a harmonic spring. Both atoms bear
|
||||
a charge and they represent collectively an induced electric dipole.
|
||||
These techniques are computationally more expensive than the QEq
|
||||
method because of additional particles and bonds. These two
|
||||
charge-on-spring methods differ in certain features, with the
|
||||
core-shell model being normally used for ionic/crystalline materials,
|
||||
whereas the so-called Drude model is normally used for molecular
|
||||
systems and fluid states.
|
||||
</P>
|
||||
<P>The core-shell model is applicable to crystalline materials where the
|
||||
high symmetry around each site leads to stable trajectories of the
|
||||
core-shell pairs. However, bonded atoms in molecules can be so close
|
||||
that a core would interact too strongly or even capture the Drude
|
||||
particle of a neighbor. The Drude dipole model is relatively more
|
||||
complex in order to remediate this and other issues. Specifically, the
|
||||
Drude model includes specific thermostating of the core-Drude pairs
|
||||
and short-range damping of the induced dipoles.
|
||||
</P>
|
||||
<P>The three polarization methods can be implemented through a
|
||||
self-consistent calculation of charges or induced dipoles at each
|
||||
timestep. In the fluctuating charge scheme this is done by the matrix
|
||||
inversion method in <A HREF = "fix_qeq.html">fix qeq/point</A>, but for core-shell
|
||||
or Drude-dipoles the relaxed-dipoles technique would require an slow
|
||||
iterative procedure. These self-consistent solutions yield accurate
|
||||
trajectories since the additional degrees of freedom representing
|
||||
polarization are massless. An alternative is to attribute a mass to
|
||||
the additional degrees of freedom and perform time integration using
|
||||
an extended Lagrangian technique. For the fluctuating charge scheme
|
||||
this is done by <A HREF = "fix_qeq.html">fix qeq/dynamic</A>, and for the
|
||||
charge-on-spring models by the methods outlined in the next two
|
||||
sections. The assignment of masses to the additional degrees of
|
||||
freedom can lead to unphysical trajectories if care is not exerted in
|
||||
choosing the parameters of the poarizable models and the simulation
|
||||
conditions.
|
||||
</P>
|
||||
<P>In the core-shell model the vibration of the shells is kept faster
|
||||
than the ionic vibrations to mimic the fast response of the
|
||||
polarizable electrons. But in molecular systems thermalizing the
|
||||
core-Drude pairs at temperatures comparable to the rest of the
|
||||
simulation leads to several problems (kinetic energy transfer, too
|
||||
short a timestep, etc.) In order to avoid these problems the relative
|
||||
motion of the Drude particles with respect to their cores is kept
|
||||
"cold" so the vibration of the core-Drude pairs is very slow,
|
||||
approaching the self-consistent regime. In both models the
|
||||
temperature is regulated using the velocities of the center of mass of
|
||||
core+shell (or Drude) pairs, but in the Drude model the actual
|
||||
relative core-Drude particle motion is thermostated separately as
|
||||
well.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "howto_26"></A><H4>6.26 Adiabatic core/shell model
|
||||
</H4>
|
||||
<P>The adiabatic core-shell model by <A HREF = "#MitchellFinchham">Mitchell and
|
||||
Finchham</A> is a simple method for adding
|
||||
polarizability to a system. In order to mimic the electron shell of
|
||||
an ion, a ghost atom is attached to it. This way the ions are split
|
||||
into a core and a shell where the latter is meant to react to the
|
||||
electrostatic environment inducing polarizability.
|
||||
an ion, a satellite particle is attached to it. This way the ions are
|
||||
split into a core and a shell where the latter is meant to react to
|
||||
the electrostatic environment inducing polarizability.
|
||||
</P>
|
||||
<P>Technically, shells are attached to the cores by a spring force f =
|
||||
k*r where k is a parametrized spring constant and r is the distance
|
||||
@ -2600,6 +2679,70 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<A NAME = "howto_27"></A><H4>6.27 Drude induced dipoles
|
||||
</H4>
|
||||
<P>The thermalized Drude model, similarly to the <A HREF = "#howto_26">core-shell</A>
|
||||
model, representes induced dipoles by a pair of charges (the core atom
|
||||
and the Drude particle) connected by a harmonic spring. The Drude
|
||||
model has a number of features aimed at its use in molecular systems
|
||||
(<A HREF = "#Lamoureux">Lamoureux and Roux</A>):
|
||||
</P>
|
||||
<UL><LI>Thermostating of the additional degrees of freedom associated with the
|
||||
induced dipoles at very low temperature, in terms of the reduced
|
||||
coordinates of the Drude particles with respect to their cores. This
|
||||
makes the trajectory close to that of relaxed induced dipoles.
|
||||
|
||||
<LI>Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
|
||||
pair represents a single (polarizable) atom, so the special screening
|
||||
factors in a covalent structure should be the same for the core and
|
||||
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
|
||||
special neighbor relations from their respective cores.
|
||||
|
||||
<LI>Stabilization of the interactions between induced dipoles. Drude
|
||||
dipoles on covalently bonded atoms interact too strongly due to the
|
||||
short distances, so an atom may capture the Drude particle of a
|
||||
neighbor, or the induced dipoles within the same molecule may align
|
||||
too much. To avoid this, damping at short range can be done by Thole
|
||||
functions (for which there are physical grounds). This Thole damping
|
||||
is applied to the point charges composing the induced dipole (the
|
||||
charge of the Drude particle and the opposite charge on the core, not
|
||||
to the total charge of the core atom).
|
||||
</UL>
|
||||
<P>A detailed tutorial covering the usage of Drude induced dipoles in
|
||||
LAMMPS is <A HREF = "tutorial_drude.html">available here</A>.
|
||||
</P>
|
||||
<P>As with the core-shell model, the cores and Drude particles should
|
||||
appear in the data file as standard atoms. The same holds for the
|
||||
springs between them, which are described by standard harmonic bonds.
|
||||
The nature of the atoms (core, Drude particle or non-polarizable) is
|
||||
specified via the <A HREF = "fix_drude.html">fix drude</A> command. The special
|
||||
list of neighbors is automatically refactored to account for the
|
||||
equivalence of core and Drude particles as regards special 1-2 to 1-4
|
||||
screening. It may be necessary to use the <I>extra</I> keyword of the
|
||||
<A HREF = "special_bonds.html">special_bonds</A> command. If using <A HREF = "fix_shake.html">fix
|
||||
shake</A>, make sure no Drude particle is in this fix
|
||||
group.
|
||||
</P>
|
||||
<P>There are two ways to thermostat the Drude particles at a low
|
||||
temperature: use either <A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
|
||||
for a Langevin thermostat, or <A HREF = "fix_drude_transform.html">fix
|
||||
drude/transform</A> for a Nose-Hoover
|
||||
thermostat. The former requires use of the command <A HREF = "comm_modify.html">comm_modify vel
|
||||
yes</A>. The latter requires two separate integration
|
||||
fixes like <I>nvt</I> or <I>npt</I>. The correct temperatures of the reduced
|
||||
degrees of freedom can be calculated using the <A HREF = "compute_temp_drude.html">compute
|
||||
temp/drude</A>. This requires also to use the
|
||||
command <I>comm_modify vel yes</I>.
|
||||
</P>
|
||||
<P>Short-range damping of the induced dipole interactions can be achieved
|
||||
using Thole functions through the the <A HREF = "pair_thole.html">pair style
|
||||
thole</A> in <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
|
||||
with a Coulomb pair style. It may be useful to use <I>coul/long/cs</I> or
|
||||
similar from the CORESHELL package if the core and Drude particle come
|
||||
too close, which can cause numerical issues.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "Berendsen"></A>
|
||||
@ -2650,4 +2793,8 @@ Phys, 79, 926 (1983).
|
||||
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
</P>
|
||||
<A NAME = "Lamoureux"></A>
|
||||
|
||||
<P><B>(Lamoureux and Roux)</B> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
@ -34,7 +34,9 @@ This section describes how to perform common tasks using LAMMPS.
|
||||
6.22 "Calculating a diffusion coefficient"_#howto_22
|
||||
6.23 "Using chunks to calculate system properties"_#howto_23
|
||||
6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
|
||||
6.25 "Adiabatic core/shell model"_#howto_25 :all(b)
|
||||
6.25 "Polarizable models"_#howto_25
|
||||
6.26 "Adiabatic core/shell model"_#howto_26
|
||||
6.27 "Drude induced dipoles"_#howto_27 :all(b)
|
||||
|
||||
The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in "Section_example"_Section_example.html also show how to
|
||||
@ -2400,14 +2402,89 @@ to specify this command explicitly.
|
||||
|
||||
:line
|
||||
|
||||
6.25 Adiabatic core/shell model :link(howto_25),h4
|
||||
6.25 Polarizable models :link(howto_25),h4
|
||||
|
||||
In polarizable force fields the charge distributions in molecules and
|
||||
materials respond to their electrostatic environements. Polarizable
|
||||
systems can be simulated in LAMMPS using three methods:
|
||||
|
||||
the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
|
||||
package, :ulb,l
|
||||
the adiabatic core-shell method, implemented in the
|
||||
"CORESHELL"_#howto_26 package, :l
|
||||
the thermalized Drude dipole method, implemented in the
|
||||
"USER-DRUDE"_#howto_27 package. :l,ule
|
||||
|
||||
The fluctuating charge method calculates instantaneous charges on
|
||||
interacting atoms based on the electronegativity equalization
|
||||
principle. It is implemented in the "fix qeq"_fix_qeq.html which is
|
||||
available in several variants. It is a relatively efficient technique
|
||||
since no additional particles are introduced. This method allows for
|
||||
charge transfer between molecules or atom groups. However, because the
|
||||
charges are located at the interaction sites, off-plane components of
|
||||
polarization cannot be represented in planar molecules or atom groups.
|
||||
|
||||
The two other methods share the same basic idea: polarizable atoms are
|
||||
split into one core atom and one satellite particle (called shell or
|
||||
Drude particle) attached to it by a harmonic spring. Both atoms bear
|
||||
a charge and they represent collectively an induced electric dipole.
|
||||
These techniques are computationally more expensive than the QEq
|
||||
method because of additional particles and bonds. These two
|
||||
charge-on-spring methods differ in certain features, with the
|
||||
core-shell model being normally used for ionic/crystalline materials,
|
||||
whereas the so-called Drude model is normally used for molecular
|
||||
systems and fluid states.
|
||||
|
||||
The core-shell model is applicable to crystalline materials where the
|
||||
high symmetry around each site leads to stable trajectories of the
|
||||
core-shell pairs. However, bonded atoms in molecules can be so close
|
||||
that a core would interact too strongly or even capture the Drude
|
||||
particle of a neighbor. The Drude dipole model is relatively more
|
||||
complex in order to remediate this and other issues. Specifically, the
|
||||
Drude model includes specific thermostating of the core-Drude pairs
|
||||
and short-range damping of the induced dipoles.
|
||||
|
||||
The three polarization methods can be implemented through a
|
||||
self-consistent calculation of charges or induced dipoles at each
|
||||
timestep. In the fluctuating charge scheme this is done by the matrix
|
||||
inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
|
||||
or Drude-dipoles the relaxed-dipoles technique would require an slow
|
||||
iterative procedure. These self-consistent solutions yield accurate
|
||||
trajectories since the additional degrees of freedom representing
|
||||
polarization are massless. An alternative is to attribute a mass to
|
||||
the additional degrees of freedom and perform time integration using
|
||||
an extended Lagrangian technique. For the fluctuating charge scheme
|
||||
this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
|
||||
charge-on-spring models by the methods outlined in the next two
|
||||
sections. The assignment of masses to the additional degrees of
|
||||
freedom can lead to unphysical trajectories if care is not exerted in
|
||||
choosing the parameters of the poarizable models and the simulation
|
||||
conditions.
|
||||
|
||||
In the core-shell model the vibration of the shells is kept faster
|
||||
than the ionic vibrations to mimic the fast response of the
|
||||
polarizable electrons. But in molecular systems thermalizing the
|
||||
core-Drude pairs at temperatures comparable to the rest of the
|
||||
simulation leads to several problems (kinetic energy transfer, too
|
||||
short a timestep, etc.) In order to avoid these problems the relative
|
||||
motion of the Drude particles with respect to their cores is kept
|
||||
"cold" so the vibration of the core-Drude pairs is very slow,
|
||||
approaching the self-consistent regime. In both models the
|
||||
temperature is regulated using the velocities of the center of mass of
|
||||
core+shell (or Drude) pairs, but in the Drude model the actual
|
||||
relative core-Drude particle motion is thermostated separately as
|
||||
well.
|
||||
|
||||
:line
|
||||
|
||||
6.26 Adiabatic core/shell model :link(howto_26),h4
|
||||
|
||||
The adiabatic core-shell model by "Mitchell and
|
||||
Finchham"_#MitchellFinchham is a simple method for adding
|
||||
polarizability to a system. In order to mimic the electron shell of
|
||||
an ion, a ghost atom is attached to it. This way the ions are split
|
||||
into a core and a shell where the latter is meant to react to the
|
||||
electrostatic environment inducing polarizability.
|
||||
an ion, a satellite particle is attached to it. This way the ions are
|
||||
split into a core and a shell where the latter is meant to react to
|
||||
the electrostatic environment inducing polarizability.
|
||||
|
||||
Technically, shells are attached to the cores by a spring force f =
|
||||
k*r where k is a parametrized spring constant and r is the distance
|
||||
@ -2583,6 +2660,70 @@ CS-Info # header of additional section :pre
|
||||
8 4
|
||||
(...) :pre
|
||||
|
||||
:line
|
||||
|
||||
6.27 Drude induced dipoles :link(howto_27),h4
|
||||
|
||||
The thermalized Drude model, similarly to the "core-shell"_#howto_26
|
||||
model, representes induced dipoles by a pair of charges (the core atom
|
||||
and the Drude particle) connected by a harmonic spring. The Drude
|
||||
model has a number of features aimed at its use in molecular systems
|
||||
("Lamoureux and Roux"_#Lamoureux):
|
||||
|
||||
Thermostating of the additional degrees of freedom associated with the
|
||||
induced dipoles at very low temperature, in terms of the reduced
|
||||
coordinates of the Drude particles with respect to their cores. This
|
||||
makes the trajectory close to that of relaxed induced dipoles. :ulb,l
|
||||
|
||||
Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
|
||||
pair represents a single (polarizable) atom, so the special screening
|
||||
factors in a covalent structure should be the same for the core and
|
||||
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
|
||||
special neighbor relations from their respective cores. :l
|
||||
|
||||
Stabilization of the interactions between induced dipoles. Drude
|
||||
dipoles on covalently bonded atoms interact too strongly due to the
|
||||
short distances, so an atom may capture the Drude particle of a
|
||||
neighbor, or the induced dipoles within the same molecule may align
|
||||
too much. To avoid this, damping at short range can be done by Thole
|
||||
functions (for which there are physical grounds). This Thole damping
|
||||
is applied to the point charges composing the induced dipole (the
|
||||
charge of the Drude particle and the opposite charge on the core, not
|
||||
to the total charge of the core atom). :l,ule
|
||||
|
||||
A detailed tutorial covering the usage of Drude induced dipoles in
|
||||
LAMMPS is "available here"_tutorial_drude.html.
|
||||
|
||||
As with the core-shell model, the cores and Drude particles should
|
||||
appear in the data file as standard atoms. The same holds for the
|
||||
springs between them, which are described by standard harmonic bonds.
|
||||
The nature of the atoms (core, Drude particle or non-polarizable) is
|
||||
specified via the "fix drude"_fix_drude.html command. The special
|
||||
list of neighbors is automatically refactored to account for the
|
||||
equivalence of core and Drude particles as regards special 1-2 to 1-4
|
||||
screening. It may be necessary to use the {extra} keyword of the
|
||||
"special_bonds"_special_bonds.html command. If using "fix
|
||||
shake"_fix_shake.html, make sure no Drude particle is in this fix
|
||||
group.
|
||||
|
||||
There are two ways to thermostat the Drude particles at a low
|
||||
temperature: use either "fix langevin/drude"_fix_langevin_drude.html
|
||||
for a Langevin thermostat, or "fix
|
||||
drude/transform"_fix_drude_transform.html for a Nose-Hoover
|
||||
thermostat. The former requires use of the command "comm_modify vel
|
||||
yes"_comm_modify.html. The latter requires two separate integration
|
||||
fixes like {nvt} or {npt}. The correct temperatures of the reduced
|
||||
degrees of freedom can be calculated using the "compute
|
||||
temp/drude"_compute_temp_drude.html. This requires also to use the
|
||||
command {comm_modify vel yes}.
|
||||
|
||||
Short-range damping of the induced dipole interactions can be achieved
|
||||
using Thole functions through the the "pair style
|
||||
thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
|
||||
with a Coulomb pair style. It may be useful to use {coul/long/cs} or
|
||||
similar from the CORESHELL package if the core and Drude particle come
|
||||
too close, which can cause numerical issues.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
@ -2623,3 +2764,6 @@ Phys, 79, 926 (1983).
|
||||
:link(MitchellFinchham)
|
||||
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
|
||||
:link(Lamoureux)
|
||||
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
|
||||
|
||||
@ -121,12 +121,13 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
|
||||
@ -164,10 +165,14 @@ library from.
|
||||
<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
|
||||
Jon Zimmerman (Sandia).
|
||||
</P>
|
||||
<P>(3) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
||||
<P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
||||
the colvars module library written by Giacomo Fiorin (Temple U) and
|
||||
Jerome Henin (LISM, Marseille, France).
|
||||
</P>
|
||||
<P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
|
||||
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
|
||||
(U Blaise Pascal).
|
||||
</P>
|
||||
<P>The "Doc page" column links to either a portion of the
|
||||
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
|
||||
command implemented as part of the package, or to additional
|
||||
@ -356,6 +361,29 @@ Arkansas. Contact him directly if you have questions.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4>USER-DRUDE package
|
||||
</H4>
|
||||
<P>This package implements methods for simulating polarizable systems
|
||||
in LAMMPS using thermalized Drude oscillators.
|
||||
</P>
|
||||
<P>See these doc pages and their related commands to get started:
|
||||
</P>
|
||||
<P><A HREF = "tutorial_drude.html">Drude tutorial</A>
|
||||
<A HREF = "fix_drude.html">fix drude</A>
|
||||
<A HREF = "compute_temp_drude.html">compute temp/drude</A>
|
||||
<A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
|
||||
<A HREF = "fix_drude_transform.html">fix drude/transform/...</A>
|
||||
<A HREF = "pair_thole.html">pair thole</A>
|
||||
</P>
|
||||
<P>There are auxiliary tools for using this package in tools/drude.
|
||||
</P>
|
||||
<P>The person who created this package is Alain Dequidt at Universite
|
||||
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
|
||||
Contact him directly if you have questions. Co-authors: Julien Devemy,
|
||||
Agilio Padua.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4>USER-EFF package
|
||||
</H4>
|
||||
<P>This package contains a LAMMPS implementation of the electron Force
|
||||
|
||||
@ -113,12 +113,13 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
|
||||
The current list of user-contributed packages is as follows:
|
||||
|
||||
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
|
||||
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
|
||||
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
|
||||
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
|
||||
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
|
||||
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
|
||||
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
|
||||
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
|
||||
USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
|
||||
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
|
||||
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
|
||||
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
|
||||
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
|
||||
@ -151,10 +152,14 @@ library from.
|
||||
(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
|
||||
Jon Zimmerman (Sandia).
|
||||
|
||||
(3) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
||||
(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
||||
the colvars module library written by Giacomo Fiorin (Temple U) and
|
||||
Jerome Henin (LISM, Marseille, France).
|
||||
|
||||
(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
|
||||
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
|
||||
(U Blaise Pascal).
|
||||
|
||||
The "Doc page" column links to either a portion of the
|
||||
"Section_howto"_Section_howto.html of the manual, or an input script
|
||||
command implemented as part of the package, or to additional
|
||||
@ -343,6 +348,29 @@ Arkansas. Contact him directly if you have questions.
|
||||
|
||||
:line
|
||||
|
||||
USER-DRUDE package :h4
|
||||
|
||||
This package implements methods for simulating polarizable systems
|
||||
in LAMMPS using thermalized Drude oscillators.
|
||||
|
||||
See these doc pages and their related commands to get started:
|
||||
|
||||
"Drude tutorial"_tutorial_drude.html
|
||||
"fix drude"_fix_drude.html
|
||||
"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
|
||||
|
||||
There are auxiliary tools for using this package in tools/drude.
|
||||
|
||||
The person who created this package is Alain Dequidt at Universite
|
||||
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
|
||||
Contact him directly if you have questions. Co-authors: Julien Devemy,
|
||||
Agilio Padua.
|
||||
|
||||
:line
|
||||
|
||||
USER-EFF package :h4
|
||||
|
||||
This package contains a LAMMPS implementation of the electron Force
|
||||
|
||||
Reference in New Issue
Block a user