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@ -25,6 +25,10 @@
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</H3>
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<H3>pair_style lj/cut/tip4p/long/soft/omp command
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</H3>
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<H3>pair_style lj/charmm/coul/long/soft command
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</H3>
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<H3>pair_style lj/charmm/coul/long/soft/omp command
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</H3>
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<H3>pair_style coul/cut/soft command
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</H3>
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<H3>pair_style coul/cut/soft/omp command
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@ -41,7 +45,7 @@
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</P>
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<PRE>pair_style style args
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</PRE>
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<UL><LI>style = <I>lj/cut/soft</I> or <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> or <I>lj/cut/tip4p/long/soft</I> or <I>coul/cut/soft</I> or <I>coul/long/soft</I> or <I>tip4p/long/soft</I>
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<UL><LI>style = <I>lj/cut/soft</I> or <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> or <I>lj/cut/tip4p/long/soft</I> or <I>lj/charmm/coul/long/soft</I> or <I>coul/cut/soft</I> or <I>coul/long/soft</I> or <I>tip4p/long/soft</I>
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<LI>args = list of arguments for a particular style
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</UL>
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<PRE> <I>lj/cut/soft</I> args = n alpha_lj cutoff
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@ -52,27 +56,31 @@
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>lj/cut/coul/long/soft</I> args = n alpha_LJ alpha_C cutoff
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>lj/cut/tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>lj/charmm/coul/long/soft</I> args = n alpha_LJ alpha_C inner outer (cutoff)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
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<I>coul/cut/soft</I> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<I>coul/long/soft</I> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<I>tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_C cutoff
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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</PRE>
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@ -99,6 +107,11 @@ pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
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pair_coeff * * 0.155 3.1536 1.0
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pair_coeff 1 1 0.155 3.1536 1.0 9.5
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</PRE>
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<PRE>pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
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pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
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</PRE>
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<PRE>pair_style coul/long/soft 1.0 10.0 9.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5
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@ -150,6 +163,17 @@ the <A HREF = "pair_coeff.html">pair_coeff</A> command. The paratemers n, alpha_
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and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A> command,
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before the cutoffs.
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</P>
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<P>Style <I>lj/charmm/coul/long/soft</I> implements a soft-core version of the
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CHARMM version of LJ interactions with an additional switching
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function S(r) that ramps the energy and force smoothly to zero between
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an inner and outer cutoff. The usage of this pair style is documented
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in the <A HREF = "pair_charmm.html">pair_charmm</A> styles. The soft-core version
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introduces the lambda parameter to the list of arguments, after
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epsilon and sigma in the <A HREF = "pair_coeff.html">pair_coeff</A> command (and
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before the optional eps14 and sigma14). The paratemers n,
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alpha_LJ and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A>
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command, before the cutoffs.
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</P>
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<P>The <I>coul/cut/soft</I>, <I>coul/long/soft</I> and <I>tip4p/long/soft</I> substyles
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are designed to be combined with other pair potentials via the
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command. This is because
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@ -14,6 +14,8 @@ pair_style lj/cut/coul/long/soft command :h3
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pair_style lj/cut/coul/long/soft/omp command :h3
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pair_style lj/cut/tip4p/long/soft command :h3
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pair_style lj/cut/tip4p/long/soft/omp command :h3
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pair_style lj/charmm/coul/long/soft command :h3
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pair_style lj/charmm/coul/long/soft/omp command :h3
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pair_style coul/cut/soft command :h3
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pair_style coul/cut/soft/omp command :h3
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pair_style coul/long/soft command :h3
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@ -25,7 +27,7 @@ pair_style tip4p/long/soft/omp command :h3
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pair_style style args :pre
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style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft}
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style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft}
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args = list of arguments for a particular style :ul
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{lj/cut/soft} args = n alpha_lj cutoff
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n, alpha_LJ = parameters of soft-core potential
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@ -35,27 +37,31 @@ args = list of arguments for a particular style :ul
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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{lj/cut/coul/long/soft} args = n alpha_LJ alpha_C cutoff
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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{lj/cut/tip4p/long/soft} args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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{lj/charmm/coul/long/soft} args = n alpha_LJ alpha_C inner outer (cutoff)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
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{coul/cut/soft} args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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{coul/long/soft} args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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{tip4p/long/soft} args = otype htype btype atype qdist n alpha_C cutoff
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_C = parameters of the soft-core potential
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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:pre
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@ -81,7 +87,12 @@ pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
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pair_coeff * * 0.155 3.1536 1.0
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pair_coeff 1 1 0.155 3.1536 1.0 9.5 :pre
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pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
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pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre
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pair_style coul/long/soft 1.0 10.0 9.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5 :pre
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@ -133,6 +144,17 @@ the "pair_coeff"_pair_coeff.html command. The paratemers n, alpha_LJ
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and alpha_C are set in the "pair_style"_pair_style.html command,
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before the cutoffs.
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Style {lj/charmm/coul/long/soft} implements a soft-core version of the
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CHARMM version of LJ interactions with an additional switching
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function S(r) that ramps the energy and force smoothly to zero between
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an inner and outer cutoff. The usage of this pair style is documented
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in the "pair_charmm"_pair_charmm.html styles. The soft-core version
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introduces the lambda parameter to the list of arguments, after
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epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and
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before the optional eps14 and sigma14). The paratemers n,
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alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html
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command, before the cutoffs.
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The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} substyles
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are designed to be combined with other pair potentials via the
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"pair_style hybrid/overlay"_pair_hybrid.html command. This is because
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@ -137,6 +137,17 @@ another machine. In this case, you can use the <A HREF = "Section_start.html#st
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switch</A> to convert a restart file to a data
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file.
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</P>
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<P>IMPORTANT NOTE: Although the purpose of restart files is to enable
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restarting a simulation from where it left off, not all information
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about a simulation is stored in the file. For example, the list of
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fixes that were specified during the initial run is not stored, which
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means the new input script must specify any fixes you want to use.
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Even when restart information is stored in the file, as it is for some
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fixes, commands may need to be re-specified in the new input script,
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in order to re-use that information. See the
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<A HREF = "read_restart.html">read_restart</A> command for information about what is
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stored in a restart file.
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</P>
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<HR>
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<P>The optional <I>nfile</I> or <I>fileper</I> keywords can be used in conjunction
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@ -127,6 +127,17 @@ another machine. In this case, you can use the "-r command-line
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switch"_Section_start.html#start_7 to convert a restart file to a data
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file.
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IMPORTANT NOTE: Although the purpose of restart files is to enable
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restarting a simulation from where it left off, not all information
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about a simulation is stored in the file. For example, the list of
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fixes that were specified during the initial run is not stored, which
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means the new input script must specify any fixes you want to use.
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Even when restart information is stored in the file, as it is for some
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fixes, commands may need to be re-specified in the new input script,
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in order to re-use that information. See the
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"read_restart"_read_restart.html command for information about what is
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stored in a restart file.
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:line
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The optional {nfile} or {fileper} keywords can be used in conjunction
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@ -143,17 +143,17 @@ invoked. If only a single command is specified as NULL, then no
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command is invoked. Thus these lines:
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</P>
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<PRE>variable q equal x[100]
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run 6000 every 2000 "print Coord = $q"
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run 6000 every 2000 "print 'Coord = $q'"
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</PRE>
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<P>are the equivalent of:
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</P>
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<PRE>variable q equal x[100]
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run 2000
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print Coord = $q
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print "Coord = $q"
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run 2000
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print Coord = $q
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print "Coord = $q"
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run 2000
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print Coord = $q
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print "Coord = $q"
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</PRE>
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<P>which does 3 runs of 2000 steps and prints the x-coordinate of a
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particular atom between runs. Note that the variable "$q" will
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@ -136,17 +136,17 @@ invoked. If only a single command is specified as NULL, then no
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command is invoked. Thus these lines:
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variable q equal x\[100\]
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run 6000 every 2000 "print Coord = $q" :pre
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run 6000 every 2000 "print 'Coord = $q'" :pre
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are the equivalent of:
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variable q equal x\[100\]
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run 2000
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print Coord = $q
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print "Coord = $q"
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run 2000
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print Coord = $q
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print "Coord = $q"
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run 2000
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print Coord = $q :pre
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print "Coord = $q" :pre
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which does 3 runs of 2000 steps and prints the x-coordinate of a
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particular atom between runs. Note that the variable "$q" will
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Reference in New Issue