git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5022 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -41,12 +41,14 @@
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<I>string</I> arg = one string
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<I>equal</I> or <I>atom</I> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
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numbers = 0.0, 100, -5.4, 2.8e-4, etc
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constants = PI
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thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
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math operators = (), -x, x+y, x-y, x*y, x/y, x^y,
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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), atan2(y,x),
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random(lo,hi,seed), normal(mu,sigma,seed), ceil(x), floor(x), round(x)
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random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
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ramp(x,y), stagger(x,y), logfreq(x,y,z), vlinear(x,y), swiggle(x,y,z), cwiggle(x,y,z)
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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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@ -55,7 +57,7 @@
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xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
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bound(group,xmin,region), gyration(group,region), ke(group,reigon),
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angmom(group,dim,region), inertia(group,dimdim,region),omega(group,dim,region)
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special functions = ramp(x,y), stagger(x,y), logfreq(x,y,z), sum(x), min(x), max(x), ave(x), trap(x)
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special functions = sum(x), min(x), max(x), ave(x), trap(x)
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atom value = mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]
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atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
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compute references = c_ID, c_ID[i], c_ID[i][j]
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@ -268,12 +270,13 @@ references to other variables.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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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 >Constant</TD><TD > PI</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), atan2(y,x), random(lo,hi,seed), normal(mu,sigma,seed), 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), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), vlinear(x,y), swiggle(x,y,z), cwiggle(x,y,z)</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 >Special functions</TD><TD > ramp(x,y), stagger(x,y), logfreq(x,y,z), sum(x), min(x), max(x), ave(x), trap(x)</TD></TR>
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<TR><TD >Special functions</TD><TD > sum(x), min(x), max(x), ave(x), trap(x)</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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<TR><TD >Atom vectors</TD><TD > mass, type, x, y, z, vx, vy, vz, fx, fy, fz</TD></TR>
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<TR><TD >Compute references</TD><TD > c_ID, c_ID[i], c_ID[i][j]</TD></TR>
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@ -312,6 +315,8 @@ discussion below about "Variable Accuracy".
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</P>
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<HR>
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<H4>Math Operators
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</H4>
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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 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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@ -344,8 +349,12 @@ whose properties satifsy 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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<HR>
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<H4>Math Functions
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</H4>
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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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parenthesized arguments "x", "y", "z", 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. In the latter case, the
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math operation is performed on each element of the vector. For
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@ -356,31 +365,95 @@ product of one atom's y and z coordinates.
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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.
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</P>
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<P>The random() function generates a uniform random number between lo and
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hi. The normal() function generates a Gaussian variate centered on mu
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with variance sigma^2. In both cases the seed is used the first time
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the internal random number generator is invoked, to initialize it.
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For equal-style variables, every processor uses the same seed so that
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they each generate the same sequence of random numbers. For
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atom-style variables, a unique seed is created for each processor,
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based on the specified seed. This effectively generates a different
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random number for each atom being looped over in the atom-style
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variable.
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<P>The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z =
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seed. It generates a uniform random number between lo and hi. The
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normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and
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z = seed. It generates a Gaussian variate centered on mu with
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variance sigma^2. In both cases the seed is used the first time the
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internal random number generator is invoked, to initialize it. For
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equal-style variables, every processor uses the same seed so that they
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each generate the same sequence of random numbers. For atom-style
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variables, a unique seed is created for each processor, based on the
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specified seed. This effectively generates a different random number
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for each atom being looped over in the atom-style variable.
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</P>
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<P>IMPORTANT NOTE: Internally, there is just one random number generator
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for all equal-style variables and one for all atom-style variables.
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If you define multiple variables (of each style) which use the
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random() or normal() math functions, then the internal random number
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generators will only be initialized once, which means only one of the
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specified seeds will determine the sequence of generated random
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numbers.
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</P>
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<P>The ceil(), floor(), and round() functions are those in the C math
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library. Ceil() is the smallest integer not less than its argument.
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Floor() if the largest integer not greater than its argument. Round()
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is the nearest integer to its argument.
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</P>
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<P>IMPORTANT NOTE: Internally, there is just one random number generator
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for equal-style variables and one for atom-style variables. If you
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define multiple variables (of each style) which use the random() or
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normal() math functions, then the internal random number generators
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will only be initialized once, which means only one of the specified
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seeds will determine the sequence of generated random numbers.
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<P>The ramp(x,y) function uses the current timestep to generate a value
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linearly intepolated between the specified x,y values over the course
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of a run, according to this formula:
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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>The run begins on startstep and ends on stopstep. Startstep and
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stopstep can span multiple runs, using the <I>start</I> and <I>stop</I> keywords
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of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for
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details of how to do this.
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</P>
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<P>The stagger(x,y) function uses the current timestep to generate a new
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timestep. X,y > 0 and x > y is required. The generated timesteps
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increase in a staggered fashion, as the sequence
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x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
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timestep in the sequence is returned. Thus if stagger(1000,100) is
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used in a variable by the <A HREF = "dump_modify.html">dump_modify every</A>
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command, it will generate the sequence of output timesteps:
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</P>
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<PRE>100,1000,1100,2000,2100,3000,etc
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</PRE>
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<P>The logfreq(x,y,z) function uses the current timestep to generate a
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new timestep. X,y,z > 0 and y < z is required. The generated
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timesteps increase in a logarithmic fashion, as the sequence
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x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc. For any
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current timestep, the next timestep in the sequence is returned. Thus
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if logfreq(100,4,10) is used in a variable by the <A HREF = "dump_modify.html">dump_modify
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every</A> command, it will generate the sequence of
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output timesteps:
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</P>
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<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
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</PRE>
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<P>The vlinear(x,y) function takes 2 arguments: x = coord0 and y =
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velocity, and uses the elapsed time to change the coordinate value by
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a linear displacement due to the applied velocity over the course of a
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run, according to this formula:
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</P>
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<PRE>value = coord0 + velocity*(timestep-startstep)*dt
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</PRE>
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<P>where dt = the timestep size.
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</P>
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<P>The run begins on startstep. Startstep can span multiple runs, using
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the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
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<A HREF = "run.html">run</A> command for details of how to do this.
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</P>
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<P>The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
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x = coord0, y = amplitude, z = period. They use the elapsed time to
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oscillate the coordinate value by a sin() or cos() function over the
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course of a run, according to one of these formulas, where
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omega = 2 PI / period:
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</P>
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<PRE>value = coord0 + Amplitude * sin(omega*(timestep-startstep)*dt)
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value = coord0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
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</PRE>
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<P>where dt = the timestep size.
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</P>
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<P>The run begins on startstep. Startstep can span multiple runs, using
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the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
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<A HREF = "run.html">run</A> command for details of how to do this.
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</P>
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<HR>
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<H4>Group and Region Functions
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</H4>
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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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@ -410,42 +483,11 @@ inclusion is that it be in the region.
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</P>
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<HR>
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<H4>Special Functions
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</H4>
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<P>Special functions take specific kinds of arguments, meaning their
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arguments cannot be formulas themselves. For example ramp(10.0,100.0)
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is valid, but ramp(2*5,sqrt(10000)) is not.
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arguments cannot be formulas themselves.
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</P>
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<P>Ramp(x,y) takes two integer or floating point values and uses the
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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 linearly between x and y over the course of
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a run. The run begins on startstep and ends on stopstep. Startstep
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and stopstep can span multiple runs, using the <I>start</I> and <I>stop</I>
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keywords of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A>
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command for details of how to do this.
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</P>
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<P>Stagger(x,y) takes two integer values and uses the current timestep to
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generate a new timestep. X,y > 0 and x > y is required. The
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generated timesteps increase in a staggered fashion, as the sequence
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x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
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timestep in the sequence is returned. Thus if stagger(1000,100) is
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used in a variable by the <A HREF = "dump_modify.html">dump_modify every</A>
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command, it will generate the sequence of output timesteps:
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</P>
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<PRE>100,1000,1100,2000,2100,3000,etc
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</PRE>
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<P>Logfreq(x,y,z) takes 3 integer values and uses the current timestep to
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generate a new timestep. X,y,z > 0 and y < z is required. The
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generated timesteps increase in a logarithmic fashion, as the sequence
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x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc. For any
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current timestep, the next timestep in the sequence is returned. Thus
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if logfreq(100,4,10) is used in a variable by the <A HREF = "dump_modify.html">dump_modify
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every</A> command, it will generate the sequence of
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output timesteps:
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</P>
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<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
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</PRE>
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<P>The sum(x), min(x), max(x), ave(x), and trap(x) functions each take 1
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argument which is of the form "c_ID" or "c_ID[N]" or "f_ID" or
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"f_ID[N]". The first two are computes and the second two are fixes;
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@ -479,6 +521,8 @@ ave/correlate</A> command.
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</P>
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<HR>
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<H4>Atom Values and Vectors
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</H4>
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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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atom with ID = 243.
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@ -492,6 +536,8 @@ a quantity from that compute.
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</P>
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<HR>
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<H4>Compute References
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</H4>
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<P>Compute references access quantities calculated by a
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<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
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the ID of a compute defined elsewhere in the input script. As
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@ -523,6 +569,8 @@ about "Variable Accuracy".
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</P>
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<HR>
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<H4>Fix References
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</H4>
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<P>Fix references access quantities calculated by a <A HREF = "compute.html">fix</A>.
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The ID in the reference should be replaced by the ID of a fix defined
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elsewhere in the input script. As discussed in the doc page for the
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@ -559,6 +607,8 @@ the doc pages for individual fix commands for details.
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</P>
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<HR>
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<H4>Variable References
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</H4>
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<P>Variable references access quantities calulated by other variables,
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which will cause those variables to be evaluated. The name in the
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reference should be replaced by the name of a variable defined
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Reference in New Issue
Block a user