forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11143 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
e1ebfdda1c
commit
4fba6ab25b
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@ -27,12 +27,14 @@
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<LI>one or more keyword/value pairs may be appended to args
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<LI>keyword = <I>region</I> or <I>mol</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I>
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<LI>keyword = <I>region</I> or <I>mol</I> or <I>rigid</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I>
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<PRE> <I>region</I> value = region-ID
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region-ID = ID of region to use as insertion volume
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<I>mol</I> value = template-ID
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template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
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<I>rigid</I> value = fix-ID
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fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
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<I>diam</I> values = dstyle args
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dstyle = <I>one</I> or <I>range</I> or <I>poly</I>
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<I>one</I> args = D
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@ -62,16 +64,17 @@
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</P>
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<PRE>fix 3 all pour 1000 2 29494 region myblock
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fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1
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fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
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fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
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fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Insert finite-size particles or molecules into the simulation box
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every few timesteps within a specified region until N particles have
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been inserted. This is typically used to model the pouring of
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granular particles into a container under the influence of gravity.
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For the remainder of this doc page, a single inserted atom or molecule
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is referred to as a "particle".
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every few timesteps within a specified region until N particles or
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molecules have been inserted. This is typically used to model the
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pouring of granular particles into a container under the influence of
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gravity. For the remainder of this doc page, a single inserted atom
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or molecule is referred to as a "particle".
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</P>
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<P>If inserted particles are individual atoms, they are assigned the
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specified atom type. For molecules the specified type is ignored, and
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@ -98,6 +101,12 @@ molecule can be specified in the molecule file. See the
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required to be in this file are the coordinates and types of atoms in
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the molecule.
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</P>
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<P>If you wish to insert molecules via the <I>mol</I> keyword, that will be
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treated as rigid bodies, you can first specify a <A HREF = "fix_rigid.html">fix
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rigid/small</A> command, and then use the <I>rigid</I> keyword
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with this command, specifying the ID of the fix rigid/small command as
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its value.
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</P>
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<P>Each timestep particles are inserted, they are placed randomly inside
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the insertion volume so as to mimic a stream of poured particles. If
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they are molecules they are also oriented randomly. The larger the
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@ -18,11 +18,13 @@ N = # of atoms to insert :l
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type = atom type to assign to inserted atoms :l
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seed = random # seed (positive integer) :l
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one or more keyword/value pairs may be appended to args :l
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keyword = {region} or {mol} or {diam} or {dens} or {vol} or {rate} or {vel} :l
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keyword = {region} or {mol} or {rigid} or {diam} or {dens} or {vol} or {rate} or {vel} :l
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{region} value = region-ID
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region-ID = ID of region to use as insertion volume
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{mol} value = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
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{rigid} value = fix-ID
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fix-ID = ID of "fix rigid/small"_fix_rigid.html command
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{diam} values = dstyle args
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dstyle = {one} or {range} or {poly}
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{one} args = D
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@ -51,16 +53,17 @@ keyword = {region} or {mol} or {diam} or {dens} or {vol} or {rate} or {vel} :l
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fix 3 all pour 1000 2 29494 region myblock
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fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1
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fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6 :pre
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fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
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fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid :pre
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[Description:]
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Insert finite-size particles or molecules into the simulation box
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every few timesteps within a specified region until N particles have
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been inserted. This is typically used to model the pouring of
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granular particles into a container under the influence of gravity.
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For the remainder of this doc page, a single inserted atom or molecule
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is referred to as a "particle".
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every few timesteps within a specified region until N particles or
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molecules have been inserted. This is typically used to model the
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pouring of granular particles into a container under the influence of
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gravity. For the remainder of this doc page, a single inserted atom
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or molecule is referred to as a "particle".
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If inserted particles are individual atoms, they are assigned the
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specified atom type. For molecules the specified type is ignored, and
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@ -87,6 +90,12 @@ molecule can be specified in the molecule file. See the
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required to be in this file are the coordinates and types of atoms in
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the molecule.
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If you wish to insert molecules via the {mol} keyword, that will be
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treated as rigid bodies, you can first specify a "fix
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rigid/small"_fix_rigid.html command, and then use the {rigid} keyword
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with this command, specifying the ID of the fix rigid/small command as
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its value.
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Each timestep particles are inserted, they are placed randomly inside
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the insertion volume so as to mimic a stream of poured particles. If
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they are molecules they are also oriented randomly. The larger the
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@ -39,7 +39,7 @@
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I>
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<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I> or <I>mol</I>
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<PRE> <I>langevin</I> values = Tstart Tstop Tperiod seed
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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@ -70,7 +70,9 @@
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass torque is active
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<I>infile</I> filename
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filename = file with per-body values of mass, center-of-mass, moments of inertia
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filename = file with per-body values of mass, center-of-mass, moments of inertia
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<I>mol</I> value = template-ID
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template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
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</PRE>
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</UL>
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@ -178,6 +180,12 @@ setforce</A> command), and integrating them as usual
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most one rigid body. Which atoms are in which bodies can be defined
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via several options.
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</P>
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<P>IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
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<I>molecule</I>, you can define a system that has no rigid bodies
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initially. This is useful when you are adding rigid bodies on-the-fly
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via commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
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pour</A>.
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</P>
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<P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
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rigid body. This option is only allowed for fix rigid and its
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sub-styles.
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@ -438,6 +446,22 @@ rigid bodies should then effectively thermostat the rigid body
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temperature as well without use of the Langevin or Nose/Hoover options
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associated with the fix rigid commands.
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</P>
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<HR>
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<P>The <I>mol</I> keyword can only be used with fix rigid/small. It should
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be used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
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<A HREF = "fix_pour.html">fix pour</A>, which will add rigid bodies on-the-fly
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during a simulation. You specify a <I>template-ID</I> previously defined
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using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
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defines the molecule. You must use the same <I>template-ID</I> that the
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command adding rigid bodies uses. The coordinates, atom types, atom
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diameters, center-of-mass, and moments of inertia can be specified in
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the molecule file. See the <A HREF = "molecule.html">molecule</A> command for
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details. The only settings required to be in this file are the
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coordinates and types of atoms in the molecule.
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</P>
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<HR>
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<P>The <I>infile</I> keyword allows a file of rigid body attributes to be read
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in from a file, rather then having LAMMPS compute them. There are 3
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such attributes: the total mass of the rigid body, its center-of-mass
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@ -493,6 +517,15 @@ fix using an <I>infile</I> keyword and the appropriate filename. Note that
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the auxiliary file will contain one line for every rigid body, even if
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the original file only listed a subset of the rigid bodies.
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</P>
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<P>IMPORTANT NOTE: If you are using fix rigid/small and defining a system
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that has no rigid bodies initially, because they will be added
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on-the-fly by commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
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pour</A>, you may still wish to use the <I>infile</I> keyword.
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This is so that restart files written during the simulation will
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output an auxiliary restart file as described above with information
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on the new rigid bodies. In this case the initial <I>infile</I> file
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should use N = 0.
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</P>
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<HR>
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<P>If you use a <A HREF = "compute.html">temperature compute</A> with a group that
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@ -27,7 +27,7 @@ bodystyle = {single} or {molecule} or {group} :l
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groupID1, groupID2, ... = list of N group IDs :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
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keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} or {mol} :l
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{langevin} values = Tstart Tstop Tperiod seed
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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@ -57,7 +57,9 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass torque is active
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{infile} filename
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filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
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filename = file with per-body values of mass, center-of-mass, moments of inertia
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{mol} value = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre
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:ule
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[Examples:]
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@ -164,6 +166,12 @@ Each rigid body must have two or more atoms. An atom can belong to at
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most one rigid body. Which atoms are in which bodies can be defined
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via several options.
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IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
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{molecule}, you can define a system that has no rigid bodies
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initially. This is useful when you are adding rigid bodies on-the-fly
|
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via commands such as "fix deposit"_fix_deposit.html or "fix
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pour"_fix_pour.html.
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For bodystyle {single} the entire fix group of atoms is treated as one
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rigid body. This option is only allowed for fix rigid and its
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sub-styles.
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@ -424,6 +432,22 @@ rigid bodies should then effectively thermostat the rigid body
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temperature as well without use of the Langevin or Nose/Hoover options
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associated with the fix rigid commands.
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:line
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The {mol} keyword can only be used with fix rigid/small. It should
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be used when other commands, such as "fix deposit"_fix_deposit.html or
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"fix pour"_fix_pour.html, which will add rigid bodies on-the-fly
|
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during a simulation. You specify a {template-ID} previously defined
|
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using the "molecule"_molecule.html command, which reads a file that
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defines the molecule. You must use the same {template-ID} that the
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command adding rigid bodies uses. The coordinates, atom types, atom
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diameters, center-of-mass, and moments of inertia can be specified in
|
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the molecule file. See the "molecule"_molecule.html command for
|
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details. The only settings required to be in this file are the
|
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coordinates and types of atoms in the molecule.
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|
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:line
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|
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The {infile} keyword allows a file of rigid body attributes to be read
|
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in from a file, rather then having LAMMPS compute them. There are 3
|
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such attributes: the total mass of the rigid body, its center-of-mass
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|
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@ -479,6 +503,15 @@ fix using an {infile} keyword and the appropriate filename. Note that
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the auxiliary file will contain one line for every rigid body, even if
|
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the original file only listed a subset of the rigid bodies.
|
||||
|
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IMPORTANT NOTE: If you are using fix rigid/small and defining a system
|
||||
that has no rigid bodies initially, because they will be added
|
||||
on-the-fly by commands such as "fix deposit"_fix_deposit.html or "fix
|
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pour"_fix_pour.html, you may still wish to use the {infile} keyword.
|
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This is so that restart files written during the simulation will
|
||||
output an auxiliary restart file as described above with information
|
||||
on the new rigid bodies. In this case the initial {infile} file
|
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should use N = 0.
|
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|
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:line
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|
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If you use a "temperature compute"_compute.html with a group that
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|
|
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@ -54,20 +54,26 @@ lines can be used between sections. Sections can appear in any order,
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with a few exceptions as noted below.
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</P>
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<P>These are the recognized header keywords. Header lines can come in
|
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any order. The value(s) are read from the beginning of the line.
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Thus the keyword <I>atoms</I> should be in a line like "10 atoms"; the
|
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keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
|
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keyword <I>xy xz yz</I> should be in a line like "0.0 5.0 6.0 xy xz yz".
|
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All these settings have a default value of 0, except the lo/hi box
|
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size defaults are -0.5 and 0.5. A line need only appear if the value
|
||||
is different than the default.
|
||||
any order. The numeric value(s) are read from the beginning of the
|
||||
line. The keyword should appear at the end of the line. All these
|
||||
settings have default values, as explained below. A line need only
|
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appear if the value(s) are different than the default.
|
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</P>
|
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<UL><LI><I>atoms</I> = # of atoms in molecule
|
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<LI><I>bonds</I> = # of bonds in molecule
|
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<LI><I>angles</I> = # of angles in molecule
|
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<LI><I>dihedrals</I> = # of dihedrals in molecule
|
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<LI><I>impropers</I> = # of impropers in molecule
|
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<UL><LI>N <I>atoms</I> = # of atoms N in molecule, default = 0
|
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<LI>Nb <I>bonds</I> = # of bonds Nb in molecule, default = 0
|
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<LI>Na <I>angles</I> = # of angles Na in molecule, default = 0
|
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<LI>Nd <I>dihedrals</I> = # of dihedrals Nd in molecule, default = 0
|
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<LI>Ni <I>impropers</I> = # of impropers Ni in molecule, default = 0
|
||||
<LI>Mtotal <I>mass</I> = total mass of molecule
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<LI>Xc Yc Zc <I>com</I> = coordinates of center-of-mass of molecule
|
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<LI>Ixx Iyy Izz Ixy Ixz Iyz <I>inertia</I> = 6 components of inertia tensor of molecule
|
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</UL>
|
||||
<P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
|
||||
calculate this quantity itself if needed, assuming the molecules
|
||||
consists of a set of point particles. You typically only need to
|
||||
specify these values for a rigid body consisting of overlapping
|
||||
finite-size particles.
|
||||
</P>
|
||||
<P>These are the allowed section keywords for the body of the file.
|
||||
</P>
|
||||
<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
|
||||
|
|
@ -75,16 +81,17 @@ is different than the default.
|
|||
<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
|
||||
</UL>
|
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<P>IMPORTANT NOTE: Whether a section is required depends on how the
|
||||
molecule definition is used by other LAMMPS commands. For example, to
|
||||
molecule template is used by other LAMMPS commands. For example, to
|
||||
add a molecule via the <A HREF = "fix_deposit.html">fix deposit</A> command, the
|
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Coords and Types sections are required. To add a rigid body via the
|
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<A HREF = "fix_pout.html">fix pour</A> command, the Bonds (Angles, etc) sections are
|
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not required, since the molecule will be treated as a rigid body.
|
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Some sections are optional. For example, the <A HREF = "fix_pour.html">fix pour</A>
|
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command can add finite-size granular particles. If the Diameters
|
||||
section is not specified, added particles will have a default diameter
|
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of 1.0. See the doc pages for LAMMPS commands that use read-in
|
||||
molecules for more details.
|
||||
command can be used to add "molecules" which are clusters of
|
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finite-size granular particles. If the Diameters section is not
|
||||
specified, each particle in the molecule will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use molecule
|
||||
templates for more details.
|
||||
</P>
|
||||
<P>Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
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|
|
|
|||
|
|
@ -51,19 +51,25 @@ lines can be used between sections. Sections can appear in any order,
|
|||
with a few exceptions as noted below.
|
||||
|
||||
These are the recognized header keywords. Header lines can come in
|
||||
any order. The value(s) are read from the beginning of the line.
|
||||
Thus the keyword {atoms} should be in a line like "10 atoms"; the
|
||||
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
|
||||
keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz".
|
||||
All these settings have a default value of 0, except the lo/hi box
|
||||
size defaults are -0.5 and 0.5. A line need only appear if the value
|
||||
is different than the default.
|
||||
any order. The numeric value(s) are read from the beginning of the
|
||||
line. The keyword should appear at the end of the line. All these
|
||||
settings have default values, as explained below. A line need only
|
||||
appear if the value(s) are different than the default.
|
||||
|
||||
{atoms} = # of atoms in molecule
|
||||
{bonds} = # of bonds in molecule
|
||||
{angles} = # of angles in molecule
|
||||
{dihedrals} = # of dihedrals in molecule
|
||||
{impropers} = # of impropers in molecule :ul
|
||||
N {atoms} = # of atoms N in molecule, default = 0
|
||||
Nb {bonds} = # of bonds Nb in molecule, default = 0
|
||||
Na {angles} = # of angles Na in molecule, default = 0
|
||||
Nd {dihedrals} = # of dihedrals Nd in molecule, default = 0
|
||||
Ni {impropers} = # of impropers Ni in molecule, default = 0
|
||||
Mtotal {mass} = total mass of molecule
|
||||
Xc Yc Zc {com} = coordinates of center-of-mass of molecule
|
||||
Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :ul
|
||||
|
||||
For {mass}, {com}, and {inertia}, the default is for LAMMPS to
|
||||
calculate this quantity itself if needed, assuming the molecules
|
||||
consists of a set of point particles. You typically only need to
|
||||
specify these values for a rigid body consisting of overlapping
|
||||
finite-size particles.
|
||||
|
||||
These are the allowed section keywords for the body of the file.
|
||||
|
||||
|
|
@ -72,16 +78,17 @@ These are the allowed section keywords for the body of the file.
|
|||
{Special Bond Counts, Special Bonds} = special neighbor info :ul
|
||||
|
||||
IMPORTANT NOTE: Whether a section is required depends on how the
|
||||
molecule definition is used by other LAMMPS commands. For example, to
|
||||
molecule template is used by other LAMMPS commands. For example, to
|
||||
add a molecule via the "fix deposit"_fix_deposit.html command, the
|
||||
Coords and Types sections are required. To add a rigid body via the
|
||||
"fix pour"_fix_pout.html command, the Bonds (Angles, etc) sections are
|
||||
not required, since the molecule will be treated as a rigid body.
|
||||
Some sections are optional. For example, the "fix pour"_fix_pour.html
|
||||
command can add finite-size granular particles. If the Diameters
|
||||
section is not specified, added particles will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use read-in
|
||||
molecules for more details.
|
||||
command can be used to add "molecules" which are clusters of
|
||||
finite-size granular particles. If the Diameters section is not
|
||||
specified, each particle in the molecule will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use molecule
|
||||
templates for more details.
|
||||
|
||||
Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
||||
|
|
|
|||
Loading…
Reference in New Issue