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sjplimp
parent
29746678ff
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2284dcc452
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@ -127,7 +127,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
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<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>
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<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>
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<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>
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<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "fix_adapt.html">fix adapt/fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
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<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>
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<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>
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<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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@ -119,7 +119,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
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USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
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USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
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USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
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USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "fix adapt/fep"_fix_adapt.html, USER/fep, -, -
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USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
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USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
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USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
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USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
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@ -31,7 +31,7 @@
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I,J = type pair(s) to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter)
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<I>atom</I> args = aparam I v_delta
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aparam = parameter to adapt over time
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aparam = parameter to perturb
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I = type to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter)
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</PRE>
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@ -23,7 +23,7 @@ attribute = {pair} or {atom} :l
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I,J = type pair(s) to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter)
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{atom} args = aparam I v_delta
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aparam = parameter to adapt over time
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aparam = parameter to perturb
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I = type to set parameter for
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v_delta = variable with perturbation to apply (in the units of the parameter) :pre
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zero or more keyword/value pairs may be appended :l
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@ -125,12 +125,12 @@ pair_coeff 1 1 1.0 9.5
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<P>The <I>lj/cut/soft</I> style and substyles compute the 12/6 Lennard-Jones
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and Coulomb potential modified by a soft core, in order to avoid
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singularities during free energy calculations when sites are created
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or anihilated <A HREF = "#Beutler">(Beutler)</A>.
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or anihilated <A HREF = "#Beutler">(Beutler)</A>,
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</P>
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<CENTER><IMG SRC = "Eqs/pair_lj_soft.jpg">
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</CENTER>
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<P>Coulomb interactions are also damped with a soft core at short
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distance as
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distance,
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</P>
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<CENTER><IMG SRC = "Eqs/pair_coul_soft.jpg">
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</CENTER>
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@ -139,11 +139,11 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant
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which can be set by the <A HREF = "dielectric.html">dielectric</A> command.
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</P>
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<P>The coefficient lambda is an activation parameter. When lambda = 1 the
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pair potentiel is identical to a Lennard-Jones term plus a Coulomb
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term. When lambda = 0 the pair interactions are deactivated. The
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transition between these two extrema is smoothed by a repulsive soft
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core in order to avoid singularities in potential energy and forces
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when sites are created or anihilated and can overlap
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pair potentiel is identical to a Lennard-Jones term or a Coulomb term
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or a combination of both. When lambda = 0 the interactions are
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deactivated. The transition between these two extrema is smoothed by a
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soft repulsive core in order to avoid singularities in potential
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energy and forces when sites are created or anihilated and can overlap
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<A HREF = "#Beutler">(Beutler)</A>.
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</P>
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<P>The paratemers n, alpha_LJ and alpha_C are set in the
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@ -151,11 +151,34 @@ when sites are created or anihilated and can overlap
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choices for the exponent are n = 2 or n = 1. For the remaining
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coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
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appropriate choices. Plots of the LJ and Coulomb terms are shown
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below, for lambda ranging from 1 ro 0 every 0.1.
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below, for lambda ranging from 1 to 0 every 0.1.
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</P>
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<CENTER><IMG SRC = "JPG/lj_soft.jpg"><IMG SRC = "JPG/coul_soft.jpg">
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</CENTER>
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<P>The <I>lj/cut/tip4p/long/soft</I> implements a soft-core version of the
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<P>For the <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> pair styles,
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the following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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</P>
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<UL><LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>lambda (activation parameter between 0 and 1)
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<LI>cutoff1 (distance units)
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<LI>cutoff2 (distance units)
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</UL>
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<P>The latter two coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair. You cannot specify 2 cutoffs for style <I>lj/cut/soft</I>,
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since it has no Coulombic terms. For the <I>coul/cut/soft</I> and
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<I>coul/long/soft</I> only lambda and the optional cutoff2 are to be
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specified.
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</P>
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<P>Style <I>lj/cut/tip4p/long/soft</I> implements a soft-core version of the
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TIP4P water model. The usage of this pair style is documented in the
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<A HREF = "pair_lj.html">pair_lj</A> styles. The soft-core version introduces the
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lambda parameter to the list of arguments, after epsilon and sigma in
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@ -184,28 +207,18 @@ occur. These substyles are suitable to represent charges embedded in
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the Lennard-Jones radius of another site (for example hydrogen atoms
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in several water models).
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</P>
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<P>For the <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> pair styles,
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the following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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</P>
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<UL><LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>lambda (activation parameter between 0 and 1)
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<LI>cutoff1 (distance units)
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<LI>cutoff2 (distance units)
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</UL>
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<P>The latter two coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair. You cannot specify 2 cutoffs for style <I>lj/cut/soft</I>,
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since it has no Coulombic terms. For the <I>coul/cut/soft</I> and
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<I>coul/long/soft</I> only lambda and the optional cutoff2 are to be
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specified.
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<P>IMPORTANT NOTES: When using the core-softed Coulomb potentials with
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long-range solvers (<I>coul/long/soft</I>, <I>lj/cut/coul/long/soft</I>, etc.)
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in a free energy calculation in which sites holding electrostatic
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charges are being created or anihilated (using
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<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A> and <A HREF = "compute_fep.html">compute_fep</A>)
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it is important to adapt both the lambda activation parameter (from 0
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to 1, or the reverse) and the value of the charge (from 0 to its final
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value, or the reverse). This ensures that long-range electrostatic
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terms (kspace) are correct. It is not necessary to use core-softed
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Coulomb potentials if the van der Waals site is present during the
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free-energy route, thus avoiding overlap of the charges. Examples are
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provided in the LAMMPS source directory tree, under examples/USER/fep.
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</P>
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<HR>
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@ -255,10 +268,15 @@ to be specified in an input script that reads a restart file.
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<P><B>Restrictions:</B>
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</P>
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<P>To avoid division by zero do not set sigma = 0. When sites do not
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interact though the Lennard-Jones term use epsilon = 0 and sigma = 1
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for example, or else use the <I>coul/long/soft</I> or similar substyle.
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<P>To avoid division by zero do not set sigma = 0; use the lambda
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parameter instead to activate/deactivate interactions, or use
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epsilon = 0 and sigma = 1. Alternatively, when sites do not
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interact though the Lennard-Jones term the <I>coul/long/soft</I> or
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similar substyle can be used via the
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command.
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</P>
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<HR>
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<P>All of the plain <I>soft</I> pair styles are part of the USER-FEP package.
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The <I>long</I> styles also requires the KSPACE package to be installed.
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They are only enabled if LAMMPS was built with those packages. See
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@ -106,12 +106,12 @@ pair_coeff 1 1 1.0 9.5 :pre
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The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones
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and Coulomb potential modified by a soft core, in order to avoid
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singularities during free energy calculations when sites are created
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or anihilated "(Beutler)"_#Beutler.
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or anihilated "(Beutler)"_#Beutler,
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:c,image(Eqs/pair_lj_soft.jpg)
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Coulomb interactions are also damped with a soft core at short
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distance as
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distance,
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:c,image(Eqs/pair_coul_soft.jpg)
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@ -120,11 +120,11 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant
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which can be set by the "dielectric"_dielectric.html command.
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The coefficient lambda is an activation parameter. When lambda = 1 the
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pair potentiel is identical to a Lennard-Jones term plus a Coulomb
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term. When lambda = 0 the pair interactions are deactivated. The
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transition between these two extrema is smoothed by a repulsive soft
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core in order to avoid singularities in potential energy and forces
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when sites are created or anihilated and can overlap
|
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pair potentiel is identical to a Lennard-Jones term or a Coulomb term
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or a combination of both. When lambda = 0 the interactions are
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deactivated. The transition between these two extrema is smoothed by a
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soft repulsive core in order to avoid singularities in potential
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energy and forces when sites are created or anihilated and can overlap
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"(Beutler)"_#Beutler.
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The paratemers n, alpha_LJ and alpha_C are set in the
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@ -132,11 +132,34 @@ The paratemers n, alpha_LJ and alpha_C are set in the
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choices for the exponent are n = 2 or n = 1. For the remaining
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coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
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appropriate choices. Plots of the LJ and Coulomb terms are shown
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below, for lambda ranging from 1 ro 0 every 0.1.
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below, for lambda ranging from 1 to 0 every 0.1.
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:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
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The {lj/cut/tip4p/long/soft} implements a soft-core version of the
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For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
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the following coefficients must be defined for each pair of atoms
|
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
|
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon (energy units)
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sigma (distance units)
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lambda (activation parameter between 0 and 1)
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cutoff1 (distance units)
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cutoff2 (distance units) :ul
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The latter two coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
|
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and Coulombic interactions for this type pair. If both coefficients
|
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
|
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since it has no Coulombic terms. For the {coul/cut/soft} and
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{coul/long/soft} only lambda and the optional cutoff2 are to be
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specified.
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Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
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TIP4P water model. The usage of this pair style is documented in the
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"pair_lj"_pair_lj.html styles. The soft-core version introduces the
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lambda parameter to the list of arguments, after epsilon and sigma in
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|
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@ -165,28 +188,18 @@ occur. These substyles are suitable to represent charges embedded in
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the Lennard-Jones radius of another site (for example hydrogen atoms
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in several water models).
|
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For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
|
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the following coefficients must be defined for each pair of atoms
|
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types via the "pair_coeff"_pair_coeff.html command as in the examples
|
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above, or in the data file or restart files read by the
|
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon (energy units)
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sigma (distance units)
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lambda (activation parameter between 0 and 1)
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cutoff1 (distance units)
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cutoff2 (distance units) :ul
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|
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The latter two coefficients are optional. If not specified, the global
|
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LJ and Coulombic cutoffs specified in the pair_style command are used.
|
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If only one cutoff is specified, it is used as the cutoff for both LJ
|
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and Coulombic interactions for this type pair. If both coefficients
|
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are specified, they are used as the LJ and Coulombic cutoffs for this
|
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type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
|
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since it has no Coulombic terms. For the {coul/cut/soft} and
|
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{coul/long/soft} only lambda and the optional cutoff2 are to be
|
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specified.
|
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IMPORTANT NOTES: When using the core-softed Coulomb potentials with
|
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long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.)
|
||||
in a free energy calculation in which sites holding electrostatic
|
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charges are being created or anihilated (using
|
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"fix_adapt/fep"_fix_adapt_fep.html and "compute_fep"_compute_fep.html)
|
||||
it is important to adapt both the lambda activation parameter (from 0
|
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to 1, or the reverse) and the value of the charge (from 0 to its final
|
||||
value, or the reverse). This ensures that long-range electrostatic
|
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terms (kspace) are correct. It is not necessary to use core-softed
|
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Coulomb potentials if the van der Waals site is present during the
|
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free-energy route, thus avoiding overlap of the charges. Examples are
|
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provided in the LAMMPS source directory tree, under examples/USER/fep.
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:line
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@ -236,9 +249,14 @@ to be specified in an input script that reads a restart file.
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[Restrictions:]
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To avoid division by zero do not set sigma = 0. When sites do not
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interact though the Lennard-Jones term use epsilon = 0 and sigma = 1
|
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for example, or else use the {coul/long/soft} or similar substyle.
|
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To avoid division by zero do not set sigma = 0; use the lambda
|
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parameter instead to activate/deactivate interactions, or use
|
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epsilon = 0 and sigma = 1. Alternatively, when sites do not
|
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interact though the Lennard-Jones term the {coul/long/soft} or
|
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similar substyle can be used via the
|
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"pair_style hybrid/overlay"_pair_hybrid.html command.
|
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|
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:line
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All of the plain {soft} pair styles are part of the USER-FEP package.
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The {long} styles also requires the KSPACE package to be installed.
|
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|
|
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