mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4443 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
6173fcaaab
commit
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@ -26,6 +26,7 @@
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E1,...,EN = element name, e.g. C or Fe or Ga
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<I>every</I> arg = N
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N = dump every this many timesteps
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N can be a variable (see below)
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<I>first</I> arg = <I>yes</I> or <I>no</I>
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<I>format</I> arg = C-style format string for one line of output
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<I>flush</I> arg = <I>yes</I> or <I>no</I>
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@ -50,7 +51,9 @@
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<PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000
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dump_modify xtcdump precision 10000
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dump_modify 1 every 1000
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dump_modify 1 every v_myVar
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -77,9 +80,30 @@ in the simulation. The same element name can be given to multiple
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atom types.
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</P>
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<P>The <I>every</I> keyword changes the dump frequency originally specified by
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the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump <I>dcd</I> style.
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the <A HREF = "dump.html">dump</A> command to a new value. The every keyword can be
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specified in one of two ways. It can be a numeric value in which case
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it must be > 0. Or it can be an <A HREF = "variable.html">equal-style variable</A>,
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which should be specified as v_name, where "name" is the variable
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name. In this case, the variable is evaluated at the beginning of a
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run to determine the next timestep at which a dump snapshot will be
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written out. On that timestep, the variable will be evaluated again
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to determine the next timestep, etc. Thus the variable should return
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timestep values. See the stagger() and logfreq() math functions for
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<A HREF = "variable.html">equal-style variables</A>, as examples of useful functions
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to use in this context. Other similar math functions could easily be
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added as options for <A HREF = "variable.html">equal-style variables</A>. When
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using the variable option with the <I>every</I> keyword, you also need to
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use the <I>first</I> option if you want an initial snapshot written to the
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dump file. The <I>every</I> keyword cannot be used with the dump <I>dcd</I>
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style.
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</P>
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<P>For example, the following commands will
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write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
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</P>
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<PRE>variable s equal logfreq(10,3,10)
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s first yes
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</PRE>
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<P>The <I>first</I> keyword determines whether a dump snapshot is written on
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the very first timestep after the dump command is invoked. This will
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always occur if the current timestep is a multiple of N, the frequency
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@ -20,6 +20,7 @@ keyword = {append} or {every} or {flush} or {format} or {image} or {label} or {p
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E1,...,EN = element name, e.g. C or Fe or Ga
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{every} arg = N
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N = dump every this many timesteps
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N can be a variable (see below)
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{first} arg = {yes} or {no}
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{format} arg = C-style format string for one line of output
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{flush} arg = {yes} or {no}
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@ -43,7 +44,9 @@ keyword = {append} or {every} or {flush} or {format} or {image} or {label} or {p
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dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000 :pre
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dump_modify xtcdump precision 10000
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dump_modify 1 every 1000
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dump_modify 1 every v_myVar :pre
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[Description:]
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@ -70,8 +73,29 @@ in the simulation. The same element name can be given to multiple
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atom types.
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The {every} keyword changes the dump frequency originally specified by
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the "dump"_dump.html command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump {dcd} style.
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the "dump"_dump.html command to a new value. The every keyword can be
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specified in one of two ways. It can be a numeric value in which case
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it must be > 0. Or it can be an "equal-style variable"_variable.html,
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which should be specified as v_name, where "name" is the variable
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name. In this case, the variable is evaluated at the beginning of a
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run to determine the next timestep at which a dump snapshot will be
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written out. On that timestep, the variable will be evaluated again
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to determine the next timestep, etc. Thus the variable should return
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timestep values. See the stagger() and logfreq() math functions for
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"equal-style variables"_variable.html, as examples of useful functions
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to use in this context. Other similar math functions could easily be
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added as options for "equal-style variables"_variable.html. When
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using the variable option with the {every} keyword, you also need to
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use the {first} option if you want an initial snapshot written to the
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dump file. The {every} keyword cannot be used with the dump {dcd}
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style.
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For example, the following commands will
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write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
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variable s equal logfreq(10,3,10)
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dump 1 all atom 100 tmp.dump
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dump_modify 1 every v_s first yes :pre
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The {first} keyword determines whether a dump snapshot is written on
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the very first timestep after the dump command is invoked. This will
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@ -34,7 +34,8 @@
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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), ramp(x,y)
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ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y),
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logfreq(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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@ -257,7 +258,7 @@ 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), ramp(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), ramp(x,y), stagger(x,y), logfreq(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 >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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@ -343,7 +344,7 @@ to its argument.
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</P>
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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>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 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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@ -351,6 +352,25 @@ 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) requires x,y > 0 and x > y and uses the current timestep
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to generate a new timestep, 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 frequency</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) requires x,y,z > 0 and y < z and uses the current
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timestep to generate a new timestep, in a logarithmic fashion, as the
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sequence x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc.
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For any current timestep, the next timestep in the sequence is
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returned. Thus if logfreq(100,4,10) is used in a variable by the
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<A HREF = "dump_modify.html">dump_modify frequency</A> command, it will generate the
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sequence of 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>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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@ -29,7 +29,8 @@ 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), ramp(x,y)
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ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y),
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logfreq(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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@ -250,7 +251,7 @@ 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), ramp(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), ramp(x,y), stagger(x,y), logfreq(x,y,z)
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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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@ -342,7 +343,7 @@ to its argument.
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Ramp(x,y) uses the current timestep to generate a scalar value:
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value = x + (y-x) * (timestep - startstep) / (stopstep - startstep) :pre
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value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre
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which is a value that ramps linear 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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@ -350,6 +351,25 @@ and stopstep can span multiple runs, using the {start} and {stop}
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keywords of the "run"_run.html command. See the "run"_run.html
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command for details of how to do this.
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Stagger(x,y) requires x,y > 0 and x > y and uses the current timestep
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to generate a new timestep, 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 "dump_modify frequency"_dump_modify.html
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command, it will generate the sequence of output timesteps:
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100,1000,1100,2000,2100,3000,etc :pre
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Logfreq(x,y,z) requires x,y,z > 0 and y < z and uses the current
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timestep to generate a new timestep, in a logarithmic fashion, as the
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sequence x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc.
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For any current timestep, the next timestep in the sequence is
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returned. Thus if logfreq(100,4,10) is used in a variable by the
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"dump_modify frequency"_dump_modify.html command, it will generate the
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sequence of output timesteps:
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100,200,300,400,1000,2000,3000,4000,10000,20000,etc :pre
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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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{dim} argument, if it exists, is {x} or {y} or {z}. The {dir}
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