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2
doc/Section_howto.html
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@ -2726,7 +2726,7 @@ group.
<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
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

2
doc/Section_howto.txt
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@ -2709,7 +2709,7 @@ 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
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

57
doc/tutorial_drude.html
View File

@ -8,13 +8,13 @@
<H3>Tutorial for Thermalized Drude oscillators in LAMMPS
</H3>
<P>This tutorial explains how to use <A HREF = "drude_oscillators.html">Drude
oscillators</A> in LAMMPS to simulate polarizable
systems. As an illustration, the input files for a simulation of 250
phenol molecules are documented. First of all, LAMMPS has to be
compiled with the USER-DRUDE package activated. Then, the data file
and input scripts have to be modified to include the Drude dipoles and
how to handle them.
<P>This tutorial explains how to use Drude oscillators in LAMMPS to
simulate polarizable systems using the USER-DRUDE package. As an
illustration, the input files for a simulation of 250 phenol molecules
are documented. First of all, LAMMPS has to be compiled with the
USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
</P>
<HR>
@ -155,18 +155,13 @@ script (the use of these lines will be explained below). In order for
LAMMPS to recognize that you are using Drude oscillators, you should
use the fix <I>drude</I>. The command is
</P>
<PRE>fix DRUDE all drude 1 1 1 0 0 2 2 2
</PRE>
<P>or, equivalently
</P>
<PRE>fix DRUDE all drude C C C N N D D D
</PRE>
<P>The 0, 1, 2 (or N, C, D) following the <I>drude</I> keyword have the
following meaning: There is one tag for each atom type. This tag is 1
(or C) for DCs, 2 (or D) for DPs and 0 (or N) for non-polarizable
atoms. Here the atom types 1 to 3 (C and O atoms) are DC, atom types
4 and 5 (H atoms) are non-polarizable and the atom types 6 to 8 are
the newly created DPs.
<P>The N, C, D following the <I>drude</I> keyword have the following meaning:
There is one tag for each atom type. This tag is C for DCs, D for DPs
and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O
atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
the atom types 6 to 8 are the newly created DPs.
</P>
<P>By recognizing the fix <I>drude</I>, LAMMPS will find and store matching
DC-DP pairs and will treat DP as equivalent to their DC in the
@ -245,11 +240,16 @@ dump_modify DUMP element C C O H H D D D
LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as
standard atoms in his default compute. If you want to output the
temperatures of the DC-DP pair centers of mass and of the DPs relative
to their DCs, you should use <I>thermo_style custom</I> with respectively
<I>f_LANG[1]</I> and <I>f_LANG[2]</I>. These should be close to 300. and
1. on average.
to their DCs, you should use the <A HREF = "compute_temp_drude.html">compute
temp_drude</A>
</P>
<PRE>thermo_style custom step temp f_LANG[1] f_LANG[2]
<PRE>compute TDRUDE all temp/drude
</PRE>
<P>And then output the correct temperatures of the Drude oscillators
using <I>thermo_style custom</I> with respectively <I>c_TDRUDE[1]</I> and
<I>c_TDRUDE[2]</I>. These should be close to 300.0 and 1.0 on average.
</P>
<PRE>thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
</PRE>
<HR>
@ -319,21 +319,24 @@ pair_coeff 8 8 thole 0.630 0.670
</PRE>
<P>For the <I>thole</I> pair style the coefficients are
</P>
<OL><LI>the atom polarizability in units of cubic length
<LI>the screening factor of the Thole function (optional, default value specified by the pair_style command)
<LI>the cutoff (optional, default value defined by the pair_style command)
<OL><LI>the atom polarizability in units of cubic length
<LI>the screening factor of the Thole function (optional, default value
specified by the pair_style command)
<LI>the cutoff (optional, default value defined by the pair_style command)
</OL>
<P>The special neighbors have charge-charge and charge-dipole
interactions screened by the <I>coul</I> factors of the <I>special_bonds</I>
command (0., 0., and 0.5 in the example above). Without using the
command (0.0, 0.0, and 0.5 in the example above). Without using the
pair_style <I>thole</I>, dipole-dipole interactions are screened by the
same factor. By using the pair_style <I>thole</I>, dipole-dipole
interactions are screened by Thole's function, whatever their special
relationship (except within each DC-DP pair of course). Consider for
example 1-2 neighbors: using the pair_style <I>thole</I>, their dipoles
will see each other (despite the <I>coul</I> factor being 0.) and the
interactions between these dipoles will be damped by Thole's
function.
interactions between these dipoles will be damped by Thole's function.
</P>
<HR>

61
doc/tutorial_drude.txt
View File

@ -7,13 +7,13 @@
Tutorial for Thermalized Drude oscillators in LAMMPS :h3
This tutorial explains how to use "Drude
oscillators"_drude_oscillators.html in LAMMPS to simulate polarizable
systems. As an illustration, the input files for a simulation of 250
phenol molecules are documented. First of all, LAMMPS has to be
compiled with the USER-DRUDE package activated. Then, the data file
and input scripts have to be modified to include the Drude dipoles and
how to handle them.
This tutorial explains how to use Drude oscillators in LAMMPS to
simulate polarizable systems using the USER-DRUDE package. As an
illustration, the input files for a simulation of 250 phenol molecules
are documented. First of all, LAMMPS has to be compiled with the
USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
:line
@ -100,6 +100,7 @@ may align too much. To avoid this, damping at short of the
interactions between the point charges composing the induced dipole
can be done by "Thole"_#Thole functions. :ole,l
:line
[Preparation of the data file]
@ -142,6 +143,7 @@ Masses :pre
4 1.008 # HA
5 1.008 # HO :pre
:line
[Basic input file]
@ -154,18 +156,13 @@ script (the use of these lines will be explained below). In order for
LAMMPS to recognize that you are using Drude oscillators, you should
use the fix {drude}. The command is
fix DRUDE all drude 1 1 1 0 0 2 2 2 :pre
or, equivalently
fix DRUDE all drude C C C N N D D D :pre
The 0, 1, 2 (or N, C, D) following the {drude} keyword have the
following meaning: There is one tag for each atom type. This tag is 1
(or C) for DCs, 2 (or D) for DPs and 0 (or N) for non-polarizable
atoms. Here the atom types 1 to 3 (C and O atoms) are DC, atom types
4 and 5 (H atoms) are non-polarizable and the atom types 6 to 8 are
the newly created DPs.
The N, C, D following the {drude} keyword have the following meaning:
There is one tag for each atom type. This tag is C for DCs, D for DPs
and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O
atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
the atom types 6 to 8 are the newly created DPs.
By recognizing the fix {drude}, LAMMPS will find and store matching
DC-DP pairs and will treat DP as equivalent to their DC in the
@ -244,11 +241,17 @@ You will notice that the global temperature {thermo_temp} computed by
LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as
standard atoms in his default compute. If you want to output the
temperatures of the DC-DP pair centers of mass and of the DPs relative
to their DCs, you should use {thermo_style custom} with respectively
{f_LANG\[1\]} and {f_LANG\[2\]}. These should be close to 300. and
1. on average.
to their DCs, you should use the "compute
temp_drude"_compute_temp_drude.html
compute TDRUDE all temp/drude :pre
And then output the correct temperatures of the Drude oscillators
using {thermo_style custom} with respectively {c_TDRUDE\[1\]} and
{c_TDRUDE\[2\]}. These should be close to 300.0 and 1.0 on average.
thermo_style custom step temp c_TDRUDE\[1\] c_TDRUDE\[2\] :pre
thermo_style custom step temp f_LANG\[1\] f_LANG\[2\] :pre
:line
@ -318,21 +321,23 @@ pair_coeff 8 8 thole 0.630 0.670 :pre
For the {thole} pair style the coefficients are
the atom polarizability in units of cubic length
the screening factor of the Thole function (optional, default value specified by the pair_style command)
the cutoff (optional, default value defined by the pair_style command) :ol
the atom polarizability in units of cubic length :olb,l
the screening factor of the Thole function (optional, default value
specified by the pair_style command) :l
the cutoff (optional, default value defined by the pair_style command)
:l,ole
The special neighbors have charge-charge and charge-dipole
interactions screened by the {coul} factors of the {special_bonds}
command (0., 0., and 0.5 in the example above). Without using the
command (0.0, 0.0, and 0.5 in the example above). Without using the
pair_style {thole}, dipole-dipole interactions are screened by the
same factor. By using the pair_style {thole}, dipole-dipole
interactions are screened by Thole's function, whatever their special
relationship (except within each DC-DP pair of course). Consider for
example 1-2 neighbors: using the pair_style {thole}, their dipoles
will see each other (despite the {coul} factor being 0.) and the
interactions between these dipoles will be damped by Thole's
function.
interactions between these dipoles will be damped by Thole's function.
:line
@ -391,6 +396,7 @@ fix_modify NPT temp TATOMS press thermo_press
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse :pre
:line
[Rigid bodies]
@ -431,6 +437,7 @@ fix_modify RIGID temp TATOM press thermo_press
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse :pre
:line
:link(Lamoureux)