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84
doc/Section_howto.html
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@ -31,7 +31,8 @@ certain kinds of LAMMPS simulations.
4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
4.17 <A HREF = "#4_17">Walls</A><BR>
4.18 <A HREF = "#4_18">Elastic constants</A> <BR>
4.18 <A HREF = "#4_18">Elastic constants</A><BR>
4.19 <A HREF = "#4_19">Computing free energies from thermodyanmic integration</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -1609,6 +1610,72 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
</P>
<HR>
<A NAME = "4_19"></A><H4>4.19 Computing free energies from thermodynamic integration
</H4>
<P>Thermodynamic integration is a widely used method to compute free
energies from atomistic simulations. LAMMPS can be used to run
thermodynamic integration calculations using the methods discussed in
this section and the <A HREF = "fix_adapt.html">fix adapt</A> command. Currently,
it is capable of the transformations essential for computing melting
points using the pseudo-supercritical path method developed by <A HREF = "#Eike_Maginn">Eike
and Maginn</A>.
</P>
<P>See the examples/TI directory for more information and sample files
that compute a melting point using the techniques described in this
section. That directory has its own README file. See also the paper
by <A HREF = "#Jayaraman">Jayaraman</A> for an example of using this implementation
of thermodynamic integration in LAMMPS to compute melting points of
alkali nitrate salts, using the steps outlined here.
</P>
<P>In this method, three intermediate "pseudo-supercritical" states are
accessed in the transformation between the liquid and solid
phases. These pseudo-states are a weak liquid, a dense weak liquid,
and an ordered weak phase. The transformation between the liquid and
solid states can also be driven uisng the <A HREF = "fix_adapt.html">fix adapt</A>
command.
</P>
<P>For the transformation from the liquid to the weak phase, the
intermolecular interactions need to be weakened. Appropriate scale
factors, computed by variables you define, and applied to pair styles
by <A HREF = "fix_adapt.html">fix adapt</A>, can be used to do this, as in the
example scripts. The <A HREF = "compute_ti.html">compute ti</A> command can
accumulate the value of dU/d<I>lambda</I>. See <A HREF = "#Jayaraman_Maginn">Jayaraman and
Maginn</A> for more information about calculating a
free energy from dU/d<I>lambda</I>.
</P>
<P>IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
are listed on the <A HREF = "fix_adapt">fix adapt</A> doc page. interaction scaling
is desired. If a pair style is not on that list, it is generally
quite easy to add an extract() method to the pair style, to enable fix
adapt to rescale it.
</P>
<P>Step 2 is the transformation of the simulation box density from the
liquid phase to that of the equilibrated crystal. The parameters for
box1 and box2 should be obtained from equilibrated NPT simulations of
the liquid and crystal phases and used in a <A HREF = "fix_deform.html">fix
deform</A> command to change the box size and/or shape.
It also advisable to use <A HREF = "fix_adapt.html">fix adapt</A> on the pair styles
to prevent overlaps which may occur during the box transformation.
</P>
<P>In step 3, the dense, weak system is transformed to an ordered state,
which has the same ordering as in the equilibrated crystal. Ordering
is achieved by introducing an attractive potential between atoms and
lattice sites. These lattice sites can be calculated as the mean
positions of the atoms in an equilibrium simulation of the
crystal. The <A HREF = "pair_gauss.html">pair/gauss</A> command can be used to
introduce an attractive Gaussian potential between the atoms and their
corresponding lattice sites. The prefactor of the Gaussian pair
potential can be scaled by <A HREF = "fix_adapt.html">fix adapt</A> to turn on the
attractions. Again, the quantity dU/d<I>lambda</I> can be tracked via the
<A HREF = "compute_ti.html">compute ti</A> command.
</P>
<P>Step 4 is the transformation of the ordered state to the final
crystal. In this step, the intermolecular interactions are scaled
back to full strength, while the Gaussian tethers are removed, all via
<A HREF = "fix_adapt.html">fix adapt</A>.
</P>
<HR>
<HR>
<A NAME = "Berendsen"></A>
@ -1644,4 +1711,19 @@ Phys, 79, 926 (1983).
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
<A NAME = "Eike_Maginn"></A>
<P><B>(Eike and Maginn)</B> Eike and Maginn, J Chem Phys, 124,
164503 (2006).
</P>
<A NAME = "Jayaraman_Maginn"></A>
<P><B>(Jayaraman and Maginn)</B> Jayaraman and Maginn, Journal of Chemical Physics,
127, 214504 (2007).
</P>
<A NAME = "Jayaraman"></A>
<P><B>(Jayaraman)</B> Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
and Engineering Chemistry Research, 49, 559-571 (2010).
</P>
</HTML>

81
doc/Section_howto.txt
View File

@ -28,7 +28,8 @@ certain kinds of LAMMPS simulations.
4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#4_15
4.16 "Thermostatting, barostatting and computing temperature"_#4_16
4.17 "Walls"_#4_17
4.18 "Elastic constants"_#4_18 :all(b)
4.18 "Elastic constants"_#4_18
4.19 "Computing free energies from thermodyanmic integration"_#4_19 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -1595,6 +1596,72 @@ tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
4.19 Computing free energies from thermodynamic integration :link(4_19),h4
Thermodynamic integration is a widely used method to compute free
energies from atomistic simulations. LAMMPS can be used to run
thermodynamic integration calculations using the methods discussed in
this section and the "fix adapt"_fix_adapt.html command. Currently,
it is capable of the transformations essential for computing melting
points using the pseudo-supercritical path method developed by "Eike
and Maginn"_#Eike_Maginn.
See the examples/TI directory for more information and sample files
that compute a melting point using the techniques described in this
section. That directory has its own README file. See also the paper
by "Jayaraman"_#Jayaraman for an example of using this implementation
of thermodynamic integration in LAMMPS to compute melting points of
alkali nitrate salts, using the steps outlined here.
In this method, three intermediate "pseudo-supercritical" states are
accessed in the transformation between the liquid and solid
phases. These pseudo-states are a weak liquid, a dense weak liquid,
and an ordered weak phase. The transformation between the liquid and
solid states can also be driven uisng the "fix adapt"_fix_adapt.html
command.
For the transformation from the liquid to the weak phase, the
intermolecular interactions need to be weakened. Appropriate scale
factors, computed by variables you define, and applied to pair styles
by "fix adapt"_fix_adapt.html, can be used to do this, as in the
example scripts. The "compute ti"_compute_ti.html command can
accumulate the value of dU/d{lambda}. See "Jayaraman and
Maginn"_#Jayaraman_Maginn for more information about calculating a
free energy from dU/d{lambda}.
IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
are listed on the "fix adapt"_fix_adapt doc page. interaction scaling
is desired. If a pair style is not on that list, it is generally
quite easy to add an extract() method to the pair style, to enable fix
adapt to rescale it.
Step 2 is the transformation of the simulation box density from the
liquid phase to that of the equilibrated crystal. The parameters for
box1 and box2 should be obtained from equilibrated NPT simulations of
the liquid and crystal phases and used in a "fix
deform"_fix_deform.html command to change the box size and/or shape.
It also advisable to use "fix adapt"_fix_adapt.html on the pair styles
to prevent overlaps which may occur during the box transformation.
In step 3, the dense, weak system is transformed to an ordered state,
which has the same ordering as in the equilibrated crystal. Ordering
is achieved by introducing an attractive potential between atoms and
lattice sites. These lattice sites can be calculated as the mean
positions of the atoms in an equilibrium simulation of the
crystal. The "pair/gauss"_pair_gauss.html command can be used to
introduce an attractive Gaussian potential between the atoms and their
corresponding lattice sites. The prefactor of the Gaussian pair
potential can be scaled by "fix adapt"_fix_adapt.html to turn on the
attractions. Again, the quantity dU/d{lambda} can be tracked via the
"compute ti"_compute_ti.html command.
Step 4 is the transformation of the ordered state to the final
crystal. In this step, the intermolecular interactions are scaled
back to full strength, while the Gaussian tethers are removed, all via
"fix adapt"_fix_adapt.html.
:line
:line
@ -1623,3 +1690,15 @@ Phys, 79, 926 (1983).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
:link(Eike_Maginn)
[(Eike and Maginn)] Eike and Maginn, J Chem Phys, 124,
164503 (2006).
:link(Jayaraman_Maginn)
[(Jayaraman and Maginn)] Jayaraman and Maginn, Journal of Chemical Physics,
127, 214504 (2007).
:link(Jayaraman)
[(Jayaraman)] Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
and Engineering Chemistry Research, 49, 559-571 (2010).