git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11137 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_modify.html

@@ -350,7 +350,7 @@ derived class.  See fix.h for details.
 <TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep (optional)</TD></TR>
 <TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps (optional)</TD></TR>
 <TR><TD >pre_neighbor</TD><TD > called before neighbor list build (optional)</TD></TR>
-<TR><TD >pre_force</TD><TD > called after pair & molecular forces are computed (optional)</TD></TR>
+<TR><TD >pre_force</TD><TD > called before pair & molecular forces are computed (optional)</TD></TR>
 <TR><TD >post_force</TD><TD > called after pair & molecular forces are computed and communicated (optional)</TD></TR>
 <TR><TD >final_integrate</TD><TD > called at end of each timestep (optional)</TD></TR>
 <TR><TD >end_of_step</TD><TD > called at very end of timestep (optional)</TD></TR>

doc/Section_modify.txt

@@ -338,7 +338,7 @@ min_setup: like setup, but for minimizations instead of MD runs (optional)
 initial_integrate: called at very beginning of each timestep (optional)
 pre_exchange: called before atom exchange on re-neighboring steps (optional)
 pre_neighbor: called before neighbor list build (optional)
-pre_force: called after pair & molecular forces are computed (optional)
+pre_force: called before pair & molecular forces are computed (optional)
 post_force: called after pair & molecular forces are computed and communicated (optional)
 final_integrate: called at end of each timestep (optional)
 end_of_step: called at very end of timestep (optional)

doc/fix_pour.html

@@ -27,10 +27,12 @@
 
 <LI>one or more keyword/value pairs may be appended to args 
 
-<LI>keyword = <I>region</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I> 
+<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> 
 
 <PRE>  <I>region</I> value = region-ID
     region-ID = ID of region to use as insertion volume
+  <I>mol</I> value = template-ID
+    template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
   <I>diam</I> values = dstyle args
     dstyle = <I>one</I> or <I>range</I> or <I>poly</I>
       <I>one</I> args = D
@@ -64,14 +66,21 @@ fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Insert particles into a granular run every few timesteps within a
+<P>Insert finite-size particles or molecules into the simulation box
-specified region until N particles have been inserted.  This is useful
+every few timesteps within a specified region until N particles have
-for simulating the pouring of particles into a container under the
+been inserted.  This is typically used to model the pouring of
-influence of gravity.
+granular particles into a container under the influence of gravity.
+For the remainder of this doc page, a single inserted atom or molecule
+is referred to as a "particle".
 </P>
-<P>Inserted particles are assigned the specified atom type and are
+<P>If inserted particles are individual atoms, they are assigned the
-assigned to two groups: the default group "all" and the group
+specified atom type.  For molecules the specified type is ignored, and
-specified in the fix pour command (which can also be "all").
+the type of each atom in the inserted molecule is specified in the
+file read by the <A HREF = "molecule.html">molecule</A> command.
+</P>
+<P>All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix pour command
+(which can also be "all").
 </P>
 <P>This command must use the <I>region</I> keyword to define an insertion
 volume.  The specified region must have been previously defined with a
@@ -79,26 +88,40 @@ volume.  The specified region must have been previously defined with a
 <I>cylinder</I> and must be defined with side = <I>in</I>.  The cylinder style
 of region can only be used with 3d simulations.
 </P>
+<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used.  It
+specifies a <I>template-ID</I> previously defined using the
+<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
+molecule.  The coordinates, atom types, center-of-mass, moments of
+inertia, etc, as well as any bond/angle/etc information for the
+molecule can be specified in the molecule file.  See the
+<A HREF = "molecule.html">molecule</A> command for details.  The only settings
+required to be in this file are the coordinates and types of atoms in
+the molecule.
+</P>
 <P>Each timestep particles are inserted, they are placed randomly inside
-the insertion volume so as to mimic a stream of poured particles.  The
+the insertion volume so as to mimic a stream of poured particles.  If
-larger the volume, the more particles that can be inserted at any one
+they are molecules they are also oriented randomly.  The larger the
-timestep.  Particles are inserted again after enough time has elapsed
+volume, the more particles that can be inserted at any one timestep.
-that the previously inserted particles fall out of the insertion
+Particles are inserted again after enough time has elapsed that the
-volume under the influence of gravity.  Insertions continue every so
+previously inserted particles fall out of the insertion volume under
-many timesteps until the desired # of particles has been inserted.
+the influence of gravity.  Insertions continue every so many timesteps
+until the desired # of particles has been inserted.
 </P>
 <P>All other keywords are optional with defaults as shown below.
 </P>
-<P>The <I>diam</I> option specifes the diameters of inserted particles.  There
+<P>The <I>diam</I> option is only used when inserting atoms and specifes the
-are 3 styles: <I>one</I>, <I>range</I>, or <I>poly</I>.  For <I>one</I>, all particles
+diameters of inserted particles.  For molecule insertion, the
-will have diameter <I>D</I>.  For <I>range</I>, the diameter of each particle
+diameters of individual atoms in the molecule can be specified in the
-will be chosen randomly and uniformly between the specified <I>Dlo</I> and
+file read by the <A HREF = "molecule.html">molecule</A> command.  There are 3
-<I>Dhi</I> bounds.  For <I>poly</I>, a series of <I>Npoly</I> diameters is specified.
+styles: <I>one</I>, <I>range</I>, or <I>poly</I>.  For <I>one</I>, all particles will have
-For each diameter a percentage value from 0.0 to 1.0 is also
+diameter <I>D</I>.  For <I>range</I>, the diameter of each particle will be
-specified.  The <I>Npoly</I> percentages must sum to 1.0.  For the example
+chosen randomly and uniformly between the specified <I>Dlo</I> and <I>Dhi</I>
-shown above with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will
+bounds.  For <I>poly</I>, a series of <I>Npoly</I> diameters is specified.  For
-have a diameter of 0.7 or 1.5.  40% of the particles will be small;
+each diameter a percentage value from 0.0 to 1.0 is also specified.
-60% will be large.
+The <I>Npoly</I> percentages must sum to 1.0.  For the example shown above
+with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a
+diameter of 0.7 or 1.5.  40% of the particles will be small; 60% will
+be large.
 </P>
 <P>The <I>dens</I> and <I>vel</I> options enable inserted particles to have a range
 of densities or xy velocities.  The specific values for a particular
@@ -124,6 +147,8 @@ insertions, it prints a warning.
 or y direction (2d).  This enables pouring particles from a
 successively higher height over time.
 </P>
+<HR>
+
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart

doc/fix_pour.txt

@@ -18,9 +18,11 @@ N = # of atoms to insert :l
 type = atom type to assign to inserted atoms :l
 seed = random # seed (positive integer) :l
 one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} :l
+keyword = {region} or {mol} or {diam} or {dens} or {vol} or {rate} or {vel} :l
   {region} value = region-ID
     region-ID = ID of region to use as insertion volume
+  {mol} value = template-ID
+    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
   {diam} values = dstyle args
     dstyle = {one} or {range} or {poly}
       {one} args = D
@@ -53,14 +55,21 @@ fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6 :pre
 
 [Description:]
 
-Insert particles into a granular run every few timesteps within a
+Insert finite-size particles or molecules into the simulation box
-specified region until N particles have been inserted.  This is useful
+every few timesteps within a specified region until N particles have
-for simulating the pouring of particles into a container under the
+been inserted.  This is typically used to model the pouring of
-influence of gravity.
+granular particles into a container under the influence of gravity.
+For the remainder of this doc page, a single inserted atom or molecule
+is referred to as a "particle".
 
-Inserted particles are assigned the specified atom type and are
+If inserted particles are individual atoms, they are assigned the
-assigned to two groups: the default group "all" and the group
+specified atom type.  For molecules the specified type is ignored, and
-specified in the fix pour command (which can also be "all").
+the type of each atom in the inserted molecule is specified in the
+file read by the "molecule"_molecule.html command.
+
+All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix pour command
+(which can also be "all").
 
 This command must use the {region} keyword to define an insertion
 volume.  The specified region must have been previously defined with a
@@ -68,26 +77,40 @@ volume.  The specified region must have been previously defined with a
 {cylinder} and must be defined with side = {in}.  The cylinder style
 of region can only be used with 3d simulations.
 
+Individual atoms are inserted, unless the {mol} keyword is used.  It
+specifies a {template-ID} previously defined using the
+"molecule"_molecule.html command, which reads a file that defines the
+molecule.  The coordinates, atom types, center-of-mass, moments of
+inertia, etc, as well as any bond/angle/etc information for the
+molecule can be specified in the molecule file.  See the
+"molecule"_molecule.html command for details.  The only settings
+required to be in this file are the coordinates and types of atoms in
+the molecule.
+
 Each timestep particles are inserted, they are placed randomly inside
-the insertion volume so as to mimic a stream of poured particles.  The
+the insertion volume so as to mimic a stream of poured particles.  If
-larger the volume, the more particles that can be inserted at any one
+they are molecules they are also oriented randomly.  The larger the
-timestep.  Particles are inserted again after enough time has elapsed
+volume, the more particles that can be inserted at any one timestep.
-that the previously inserted particles fall out of the insertion
+Particles are inserted again after enough time has elapsed that the
-volume under the influence of gravity.  Insertions continue every so
+previously inserted particles fall out of the insertion volume under
-many timesteps until the desired # of particles has been inserted.
+the influence of gravity.  Insertions continue every so many timesteps
+until the desired # of particles has been inserted.
 
 All other keywords are optional with defaults as shown below.
 
-The {diam} option specifes the diameters of inserted particles.  There
+The {diam} option is only used when inserting atoms and specifes the
-are 3 styles: {one}, {range}, or {poly}.  For {one}, all particles
+diameters of inserted particles.  For molecule insertion, the
-will have diameter {D}.  For {range}, the diameter of each particle
+diameters of individual atoms in the molecule can be specified in the
-will be chosen randomly and uniformly between the specified {Dlo} and
+file read by the "molecule"_molecule.html command.  There are 3
-{Dhi} bounds.  For {poly}, a series of {Npoly} diameters is specified.
+styles: {one}, {range}, or {poly}.  For {one}, all particles will have
-For each diameter a percentage value from 0.0 to 1.0 is also
+diameter {D}.  For {range}, the diameter of each particle will be
-specified.  The {Npoly} percentages must sum to 1.0.  For the example
+chosen randomly and uniformly between the specified {Dlo} and {Dhi}
-shown above with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will
+bounds.  For {poly}, a series of {Npoly} diameters is specified.  For
-have a diameter of 0.7 or 1.5.  40% of the particles will be small;
+each diameter a percentage value from 0.0 to 1.0 is also specified.
-60% will be large.
+The {Npoly} percentages must sum to 1.0.  For the example shown above
+with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a
+diameter of 0.7 or 1.5.  40% of the particles will be small; 60% will
+be large.
 
 The {dens} and {vel} options enable inserted particles to have a range
 of densities or xy velocities.  The specific values for a particular
@@ -113,6 +136,8 @@ The {rate} option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables pouring particles from a
 successively higher height over time.
 
+:line
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart