forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4438 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
632eddc43a
commit
c5f9d387d8
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@ -115,11 +115,9 @@ details.
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</P>
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<P>For example, these commands would change the prefactor coefficient of
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the <A HREF = "pair_soft.html">pair_style soft</A> potential from 10.0 to 30.0 in a
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linear fashion over the course of a 1000-step simulation:
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linear fashion over the course of a simulation:
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</P>
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<PRE>variable min equal 10.0
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variable max equal 30.0
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variable prefactor equal min+(max-min)*elapsed/1000
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<PRE>variable prefactor equal ramp(10,30)
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fix 1 all adapt 1 pair soft a * * prefactor
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</PRE>
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<P>The <I>atom</I> keyword enables various atom properties to be changed. The
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@ -103,11 +103,9 @@ details.
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For example, these commands would change the prefactor coefficient of
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the "pair_style soft"_pair_soft.html potential from 10.0 to 30.0 in a
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linear fashion over the course of a 1000-step simulation:
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linear fashion over the course of a simulation:
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variable min equal 10.0
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variable max equal 30.0
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variable prefactor equal min+(max-min)*elapsed/1000
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variable prefactor equal ramp(10,30)
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fix 1 all adapt 1 pair soft a * * prefactor :pre
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The {atom} keyword enables various atom properties to be changed. The
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@ -33,7 +33,7 @@ pair_coeff * *
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</PRE>
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<PRE>pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
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pair_coeff * *
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variable vmu equal 1.0+elapsed/10000
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variable vmu equal ramp(1,2)
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fix 1 all adapt 1 pair lubricate mu * * vmu
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</PRE>
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<P><B>Description:</B>
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@ -30,7 +30,7 @@ pair_coeff * * :pre
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pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
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pair_coeff * *
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variable vmu equal 1.0+elapsed/10000
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variable vmu equal ramp(1,2)
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fix 1 all adapt 1 pair lubricate mu * * vmu :pre
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[Description:]
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@ -25,7 +25,7 @@ pair_coeff 1 1 10.0 3.0
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</PRE>
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<PRE>pair_style soft 2.5
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pair_coeff * * 0.0
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variable prefactor equal 30.0*elapsed/10000
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variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * prefactor
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</PRE>
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<P><B>Description:</B>
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@ -59,9 +59,9 @@ or more pair types over the course of a simulation, in which case
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pair_coeff settings for A must still be specified, but will be
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overridden. For example these commands will vary the prefactor A for
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all pairwise interactions from 0.0 at the beginning to 30.0 at the end
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of a 10,000 step run:
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of a run:
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</P>
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<PRE>variable prefactor equal 30.0*elapsed/10000
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<PRE>variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * prefactor
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</PRE>
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<P>Note that a formula defined by an <A HREF = "variable.html">equal-style variable</A>
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@ -22,7 +22,7 @@ pair_coeff 1 1 10.0 3.0 :pre
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pair_style soft 2.5
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pair_coeff * * 0.0
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variable prefactor equal 30.0*elapsed/10000
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variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * prefactor :pre
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[Description:]
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@ -56,9 +56,9 @@ or more pair types over the course of a simulation, in which case
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pair_coeff settings for A must still be specified, but will be
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overridden. For example these commands will vary the prefactor A for
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all pairwise interactions from 0.0 at the beginning to 30.0 at the end
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of a 10,000 step run:
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of a run:
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variable prefactor equal 30.0*elapsed/10000
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variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * prefactor :pre
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Note that a formula defined by an "equal-style variable"_variable.html
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@ -34,7 +34,7 @@
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x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
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math functions = sqrt(x), exp(x), ln(x), log(x),
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sin(x), cos(x), tan(x), asin(x), acos(x), atan(x),
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ceil(x), floor(x), round(x)
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ceil(x), floor(x), round(x), ramp(x,y)
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group functions = count(group), mass(group), charge(group),
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xcm(group,dim), vcm(group,dim), fcm(group,dim),
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bound(group,xmin), gyration(group), ke(group),
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@ -257,7 +257,7 @@ references to other variables.
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<TR><TD >Number</TD><TD > 0.2, 100, 1.0e20, -15.4, etc</TD></TR>
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<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
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<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y</TD></TR>
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<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x)</TD></TR>
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<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x), ramp(x,y)</TD></TR>
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<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), inertia(ID,dimdim), omega(ID,dim)</TD></TR>
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<TR><TD >Region functions</TD><TD > count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</TD></TR>
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<TR><TD >Atom values</TD><TD > mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]</TD></TR>
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@ -267,16 +267,18 @@ references to other variables.
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<TR><TD >Other variables</TD><TD > v_name, v_name[i]
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</TD></TR></TABLE></DIV>
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<P>Most of the formula elements generate scalar values. The exceptions
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are those that represent a per-atom vector of values. These are the
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atom vectors, compute references that represent a per-atom vector, fix
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references that represent a per-atom vector, and variables that are
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atom-style variables.
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<P>Most of the formula elements produce a scalar value. A few produce a
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per-atom vector of values. These are the atom vectors, compute
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references that represent a per-atom vector, fix references that
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represent a per-atom vector, and variables that are atom-style
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variables. Math functions that operate on scalar values produce a
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scalar value; math function that operate on per-atom vectors produce a
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per-atom vector.
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</P>
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<P>A formula for equal-style variables cannot use any formula element
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that generates a per-atom vector. A formula for an atom-style
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variable can use formula elements that produce either scalar values or
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per-atom vectors.
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that produces a per-atom vector. A formula for an atom-style variable
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can use formula elements that produce either a scalar value or a
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per-atom vector.
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</P>
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<P>The thermo keywords allowed in a formula are those defined by the
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<A HREF = "thermo_style.html">thermo_style custom</A> command. Thermo keywords that
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@ -293,10 +295,15 @@ values accessed by the thermo keyword must be current. See the
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discussion below about "Variable Accuracy".
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</P>
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<P>Math operators are written in the usual way, where the "x" and "y" in
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the examples above can be another section of the formula. Operators
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are evaluated left to right and have the usual C-style precedence:
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unary minus before exponentiation ("^"); exponentiation before
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multiplication and division; multiplication and division before
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the examples can themselves be arbitrarily complex formulas, as in the
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examples above. In this syntax, "x" and "y" can be scalar values or
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per-atom vectors. For example, "ke/natoms" is the division of two
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scalars, where "y+z" is the sum of two per-atom vectors of y- and
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z-coordinates.
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</P>
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<P>Operators are evaluated left to right and have the usual C-style
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precedence: unary minus before exponentiation ("^"); exponentiation
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before multiplication and division; multiplication and division before
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addition and subtraction; addition and subtraction before the 4
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relational operators "<", "<=", ">", and ">="; those 4 relational
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operators before the remaining two relational operators "==" and "!=";
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@ -319,19 +326,34 @@ whose properties satisy one or more criteria could be calculated by
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taking the returned per-atom vector of ones and zeroes and passing it
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to the <A HREF = "compute_reduce.html">compute reduce</A> command.
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</P>
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<P>Math functions can be specified as keywords followed by a
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parenthesized argument, e.g. sqrt(v_ke). Note that ln() is the
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natural log; log() is the base 10 log. The ceil(), floor(), and
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<P>Math functions are specified as keywords followed by one or more
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parenthesized arguments "x", "y", etc, each of which can themselves be
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arbitrarily complex formulas. In this syntax, the arguments can
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represent scalar values or per-atom vectors. For example,
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"sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)" is a
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per-atom vector with each element being the sqrt() of the product of
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two atom coordinates.
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</P>
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<P>Most of the math functions perform obvious operations. The ln() is
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the natural log; log() is the base 10 log. The ceil(), floor(), and
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round() operations are those in the C math library. Ceil() is the
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smallest integer not less than its argument. Floor() if the largest
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integer not greater than its argument. Round() is the nearest integer
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to its argument.
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</P>
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<P>Group functions take one or two arguments in a specific format. The
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first argument is the group-ID. The <I>dim</I> argument, if it exists, is
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<I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I> argument, if it exists, is <I>xmin</I>,
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<I>xmax</I>, <I>ymin</I>, <I>ymax</I>, <I>zmin</I>, or <I>zmax</I>. The <I>dimdim</I> argument, if it
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exists, is <I>xx</I> or <I>yy</I> or <I>zz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>.
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<P>Ramp(x,y) uses the current timestep to generate a scalar value:
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</P>
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<PRE>value = x + (y-x) * (timestep - startstep) / (stopstep - startstep)
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</PRE>
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<P>which is a value that ramps linear over the timesteps of a run between
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x and y. The run began on startstep and will end on stopstep.
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</P>
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<P>Group functions are specified as keywords followed by one or two
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parenthesized arguments. The first argument is the group-ID. The
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<I>dim</I> argument, if it exists, is <I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I>
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argument, if it exists, is <I>xmin</I>, <I>xmax</I>, <I>ymin</I>, <I>ymax</I>, <I>zmin</I>, or
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<I>zmax</I>. The <I>dimdim</I> argument, if it exists, is <I>xx</I> or <I>yy</I> or <I>zz</I>
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or <I>xy</I> or <I>yz</I> or <I>xz</I>.
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</P>
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<P>The group function count() is the number of atoms in the group. The
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group functions mass() and charge() are the total mass and charge of
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@ -347,11 +369,11 @@ one of 6 components of the inertia tensor of the group of atoms around
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its center of mass. Omega() returns components of the angular
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velocity of the group of atoms around its center of mass.
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</P>
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<P>Region functions are exactly the same as group functions except they
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take an extra argument which is the region ID. The function is
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computed for all atoms that are in both the group and the region. If
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the group is "all", then the only criteria for atom inclusion is that
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it be in the region.
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<P>Region functions are specified exactly the same way as group functions
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except they take an extra argument which is the region ID. The
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function is computed for all atoms that are in both the group and the
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region. If the group is "all", then the only criteria for atom
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inclusion is that it be in the region.
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</P>
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<P>Atom values take a single integer argument I from 1 to N, where I is
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the an atom-ID, e.g. x[243], which means use the x coordinate of the
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@ -29,7 +29,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
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x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
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math functions = sqrt(x), exp(x), ln(x), log(x),
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sin(x), cos(x), tan(x), asin(x), acos(x), atan(x),
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ceil(x), floor(x), round(x)
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ceil(x), floor(x), round(x), ramp(x,y)
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group functions = count(group), mass(group), charge(group),
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xcm(group,dim), vcm(group,dim), fcm(group,dim),
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bound(group,xmin), gyration(group), ke(group),
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@ -250,7 +250,7 @@ references to other variables.
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Number: 0.2, 100, 1.0e20, -15.4, etc
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Thermo keywords: vol, pe, ebond, etc
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Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
|
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Math functions: sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x)
|
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Math functions: sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x), ramp(x,y)
|
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Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \
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vcm(ID,dim), fcm(ID,dim), bound(ID,dir), \
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gyration(ID), ke(ID), angmom(ID,dim), \
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@ -266,16 +266,18 @@ Compute references: c_ID, c_ID\[i\], c_ID\[i\]\[j\]
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Fix references: f_ID, f_ID\[i\], f_ID\[i\]\[j\]
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Other variables: v_name, v_name\[i\] :tb(s=:)
|
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|
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Most of the formula elements generate scalar values. The exceptions
|
||||
are those that represent a per-atom vector of values. These are the
|
||||
atom vectors, compute references that represent a per-atom vector, fix
|
||||
references that represent a per-atom vector, and variables that are
|
||||
atom-style variables.
|
||||
Most of the formula elements produce a scalar value. A few produce a
|
||||
per-atom vector of values. These are the atom vectors, compute
|
||||
references that represent a per-atom vector, fix references that
|
||||
represent a per-atom vector, and variables that are atom-style
|
||||
variables. Math functions that operate on scalar values produce a
|
||||
scalar value; math function that operate on per-atom vectors produce a
|
||||
per-atom vector.
|
||||
|
||||
A formula for equal-style variables cannot use any formula element
|
||||
that generates a per-atom vector. A formula for an atom-style
|
||||
variable can use formula elements that produce either scalar values or
|
||||
per-atom vectors.
|
||||
that produces a per-atom vector. A formula for an atom-style variable
|
||||
can use formula elements that produce either a scalar value or a
|
||||
per-atom vector.
|
||||
|
||||
The thermo keywords allowed in a formula are those defined by the
|
||||
"thermo_style custom"_thermo_style.html command. Thermo keywords that
|
||||
|
|
@ -292,10 +294,15 @@ values accessed by the thermo keyword must be current. See the
|
|||
discussion below about "Variable Accuracy".
|
||||
|
||||
Math operators are written in the usual way, where the "x" and "y" in
|
||||
the examples above can be another section of the formula. Operators
|
||||
are evaluated left to right and have the usual C-style precedence:
|
||||
unary minus before exponentiation ("^"); exponentiation before
|
||||
multiplication and division; multiplication and division before
|
||||
the examples can themselves be arbitrarily complex formulas, as in the
|
||||
examples above. In this syntax, "x" and "y" can be scalar values or
|
||||
per-atom vectors. For example, "ke/natoms" is the division of two
|
||||
scalars, where "y+z" is the sum of two per-atom vectors of y- and
|
||||
z-coordinates.
|
||||
|
||||
Operators are evaluated left to right and have the usual C-style
|
||||
precedence: unary minus before exponentiation ("^"); exponentiation
|
||||
before multiplication and division; multiplication and division before
|
||||
addition and subtraction; addition and subtraction before the 4
|
||||
relational operators "<", "<=", ">", and ">="; those 4 relational
|
||||
operators before the remaining two relational operators "==" and "!=";
|
||||
|
|
@ -318,19 +325,34 @@ whose properties satisy one or more criteria could be calculated by
|
|||
taking the returned per-atom vector of ones and zeroes and passing it
|
||||
to the "compute reduce"_compute_reduce.html command.
|
||||
|
||||
Math functions can be specified as keywords followed by a
|
||||
parenthesized argument, e.g. sqrt(v_ke). Note that ln() is the
|
||||
natural log; log() is the base 10 log. The ceil(), floor(), and
|
||||
Math functions are specified as keywords followed by one or more
|
||||
parenthesized arguments "x", "y", etc, each of which can themselves be
|
||||
arbitrarily complex formulas. In this syntax, the arguments can
|
||||
represent scalar values or per-atom vectors. For example,
|
||||
"sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)" is a
|
||||
per-atom vector with each element being the sqrt() of the product of
|
||||
two atom coordinates.
|
||||
|
||||
Most of the math functions perform obvious operations. The ln() is
|
||||
the natural log; log() is the base 10 log. The ceil(), floor(), and
|
||||
round() operations are those in the C math library. Ceil() is the
|
||||
smallest integer not less than its argument. Floor() if the largest
|
||||
integer not greater than its argument. Round() is the nearest integer
|
||||
to its argument.
|
||||
|
||||
Group functions take one or two arguments in a specific format. The
|
||||
first argument is the group-ID. The {dim} argument, if it exists, is
|
||||
{x} or {y} or {z}. The {dir} argument, if it exists, is {xmin},
|
||||
{xmax}, {ymin}, {ymax}, {zmin}, or {zmax}. The {dimdim} argument, if it
|
||||
exists, is {xx} or {yy} or {zz} or {xy} or {yz} or {xz}.
|
||||
Ramp(x,y) uses the current timestep to generate a scalar value:
|
||||
|
||||
value = x + (y-x) * (timestep - startstep) / (stopstep - startstep) :pre
|
||||
|
||||
which is a value that ramps linear over the timesteps of a run between
|
||||
x and y. The run began on startstep and will end on stopstep.
|
||||
|
||||
Group functions are specified as keywords followed by one or two
|
||||
parenthesized arguments. The first argument is the group-ID. The
|
||||
{dim} argument, if it exists, is {x} or {y} or {z}. The {dir}
|
||||
argument, if it exists, is {xmin}, {xmax}, {ymin}, {ymax}, {zmin}, or
|
||||
{zmax}. The {dimdim} argument, if it exists, is {xx} or {yy} or {zz}
|
||||
or {xy} or {yz} or {xz}.
|
||||
|
||||
The group function count() is the number of atoms in the group. The
|
||||
group functions mass() and charge() are the total mass and charge of
|
||||
|
|
@ -346,11 +368,11 @@ one of 6 components of the inertia tensor of the group of atoms around
|
|||
its center of mass. Omega() returns components of the angular
|
||||
velocity of the group of atoms around its center of mass.
|
||||
|
||||
Region functions are exactly the same as group functions except they
|
||||
take an extra argument which is the region ID. The function is
|
||||
computed for all atoms that are in both the group and the region. If
|
||||
the group is "all", then the only criteria for atom inclusion is that
|
||||
it be in the region.
|
||||
Region functions are specified exactly the same way as group functions
|
||||
except they take an extra argument which is the region ID. The
|
||||
function is computed for all atoms that are in both the group and the
|
||||
region. If the group is "all", then the only criteria for atom
|
||||
inclusion is that it be in the region.
|
||||
|
||||
Atom values take a single integer argument I from 1 to N, where I is
|
||||
the an atom-ID, e.g. x\[243\], which means use the x coordinate of the
|
||||
|
|
|
|||
Loading…
Reference in New Issue