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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11960 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-05-09 16:21:08 +00:00
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10
doc/compute_fep.html
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@ -83,8 +83,8 @@ energy. Therefore, this compute can apply perturbations to interaction
parameters that are not directly proportional to the potential energy
(e.g. σ in Lennard-Jones potentials).
</P>
<P>This command can be combined with <A HREF = "fix_adapt.html">fix adapt</A> to
perform multistage free-energy perturbation calculations along
<P>This command can be combined with <A HREF = "fix_adapt_fep.html">fix adapt/fep</A>
to perform multistage free-energy perturbation calculations along
stepwise alchemical transformations during a simulation run:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_fep.jpg">
@ -96,9 +96,9 @@ perturbation method using a very small &delta;:
</P>
<CENTER><IMG SRC = "Eqs/compute_fep_fdti.jpg">
</CENTER>
<P>where <I>w</I><sub>i</sub> are weights of a numerical quadrature. The <A HREF = "fix_adapt.html">fix
adapt</A> command can be used to define the stages of
&lambda; at which the derivative is calculated and averaged.
<P>where <I>w</I><sub>i</sub> are weights of a numerical quadrature. The <A HREF = "fix_adapt_fep.html">fix
adapt/fep</A> command can be used to define the stages
of &lambda; at which the derivative is calculated and averaged.
</P>
<P>The compute fep calculates the exponential Boltzmann term and also the
potential energy difference <I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>. By

8
doc/compute_fep.txt
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@ -72,8 +72,8 @@ energy. Therefore, this compute can apply perturbations to interaction
parameters that are not directly proportional to the potential energy
(e.g. &sigma; in Lennard-Jones potentials).
This command can be combined with "fix adapt"_fix_adapt.html to
perform multistage free-energy perturbation calculations along
This command can be combined with "fix adapt/fep"_fix_adapt_fep.html
to perform multistage free-energy perturbation calculations along
stepwise alchemical transformations during a simulation run:
:c,image(Eqs/compute_fep_fep.jpg)
@ -86,8 +86,8 @@ perturbation method using a very small &delta;:
:c,image(Eqs/compute_fep_fdti.jpg)
where {w}<sub>i</sub> are weights of a numerical quadrature. The "fix
adapt"_fix_adapt.html command can be used to define the stages of
&lambda; at which the derivative is calculated and averaged.
adapt/fep"_fix_adapt_fep.html command can be used to define the stages
of &lambda; at which the derivative is calculated and averaged.
The compute fep calculates the exponential Boltzmann term and also the
potential energy difference {U}<sub>1</sub>-{U}<sub>0</sub>. By

20
doc/pair_lj_soft.html
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@ -109,20 +109,20 @@ pair_coeff 1 1 1.0 9.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/cut/soft</I> style and substyles compute the 12/6
Lennard-Jones and Coulomb potential modified by a soft core, in order
to avoid singularities during free energy calculations when sites are
created or anihilated <A HREF = "#Beutler">(Beutler)</A>,
<P>The <I>lj/cut/soft</I> style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
or anihilated <A HREF = "#Beutler">(Beutler)</A>.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_soft.jpg">
</CENTER>
<P>Coulomb interactions are also damped with a soft core at short
distance,
distance as
</P>
<CENTER><IMG SRC = "Eqs/pair_coul_soft.jpg">
</CENTER>
<P>In the Coulomb part C is an energy-conversion constant, q_i and q_j are
the charges on the 2 atoms, and epsilon is the dielectric constant
<P>In the Coulomb part C is an energy-conversion constant, q_i and q_j
are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the <A HREF = "dielectric.html">dielectric</A> command.
</P>
<P>The coefficient lambda is an activation parameter. When lambda = 1 the
@ -138,7 +138,7 @@ when sites are created or anihilated and can overlap
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 ro 0 every 0.1.
below, for lambda ranging from 1 ro 0 every 0.1.
</P>
<CENTER><IMG SRC = "JPG/lj_soft.jpg"><IMG SRC = "JPG/coul_soft.jpg">
</CENTER>
@ -236,8 +236,8 @@ for example, or else use the <I>coul/long/soft</I> or similar substyle.
</P>
<P>All of the plain <I>soft</I> pair styles are part of the USER-FEP package.
The <I>long</I> styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with that package.
See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
They are only enabled if LAMMPS was built with those packages. See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

20
doc/pair_lj_soft.txt
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@ -92,20 +92,20 @@ pair_coeff 1 1 1.0 9.5 :pre
[Description:]
The {lj/cut/soft} style and substyles compute the 12/6
Lennard-Jones and Coulomb potential modified by a soft core, in order
to avoid singularities during free energy calculations when sites are
created or anihilated "(Beutler)"_#Beutler,
The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
or anihilated "(Beutler)"_#Beutler.
:c,image(Eqs/pair_lj_soft.jpg)
Coulomb interactions are also damped with a soft core at short
distance,
distance as
:c,image(Eqs/pair_coul_soft.jpg)
In the Coulomb part C is an energy-conversion constant, q_i and q_j are
the charges on the 2 atoms, and epsilon is the dielectric constant
In the Coulomb part C is an energy-conversion constant, q_i and q_j
are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the "dielectric"_dielectric.html command.
The coefficient lambda is an activation parameter. When lambda = 1 the
@ -121,7 +121,7 @@ The paratemers n, alpha_LJ and alpha_C are set in the
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 ro 0 every 0.1.
below, for lambda ranging from 1 ro 0 every 0.1.
:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
@ -219,8 +219,8 @@ for example, or else use the {coul/long/soft} or similar substyle.
All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
They are only enabled if LAMMPS was built with those packages. See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]