git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11144 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_deposit.html

@@ -144,14 +144,15 @@ particles is less than the <I>delta</I> setting.
 </P>
 <P>Once a trial x,y,z position has been selected, the insertion is only
 performed if no current atom in the simulation is within a distance R
-of any atom in the new particle.  Note that the default value for R is
-0.0, which will allow atoms to strongly overlap if you are inserting
-where other atoms are present.  This distance test is performed
-independently for each atom in an inserted molecule, based on the
-randomly rotated configuration of the molecule.  If this test fails, a
-new random position within the insertion volume is chosen and another
-trial is made.  Up to Q attempts are made.  If the particle is not
-successfully inserted, LAMMPS prints a warning message.
+of any atom in the new particle, including the effect of periodic
+boundary conditions if applicable.  Note that the default value for R
+is 0.0, which will allow atoms to strongly overlap if you are
+inserting where other atoms are present.  This distance test is
+performed independently for each atom in an inserted molecule, based
+on the randomly rotated configuration of the molecule.  If this test
+fails, a new random position within the insertion volume is chosen and
+another trial is made.  Up to Q attempts are made.  If the particle is
+not successfully inserted, LAMMPS prints a warning message.
 </P>
 <P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables particles to be inserted from a

doc/fix_deposit.txt

@@ -132,14 +132,15 @@ particles is less than the {delta} setting.
 
 Once a trial x,y,z position has been selected, the insertion is only
 performed if no current atom in the simulation is within a distance R
-of any atom in the new particle.  Note that the default value for R is
-0.0, which will allow atoms to strongly overlap if you are inserting
-where other atoms are present.  This distance test is performed
-independently for each atom in an inserted molecule, based on the
-randomly rotated configuration of the molecule.  If this test fails, a
-new random position within the insertion volume is chosen and another
-trial is made.  Up to Q attempts are made.  If the particle is not
-successfully inserted, LAMMPS prints a warning message.
+of any atom in the new particle, including the effect of periodic
+boundary conditions if applicable.  Note that the default value for R
+is 0.0, which will allow atoms to strongly overlap if you are
+inserting where other atoms are present.  This distance test is
+performed independently for each atom in an inserted molecule, based
+on the randomly rotated configuration of the molecule.  If this test
+fails, a new random position within the insertion volume is chosen and
+another trial is made.  Up to Q attempts are made.  If the particle is
+not successfully inserted, LAMMPS prints a warning message.
 
 The {rate} option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables particles to be inserted from a

doc/fix_pour.html

@@ -109,12 +109,16 @@ its value.
 </P>
 <P>Each timestep particles are inserted, they are placed randomly inside
 the insertion volume so as to mimic a stream of poured particles.  If
-they are molecules they are also oriented randomly.  The larger the
-volume, the more particles that can be inserted at any one timestep.
-Particles are inserted again after enough time has elapsed that the
-previously inserted particles fall out of the insertion volume under
-the influence of gravity.  Insertions continue every so many timesteps
-until the desired # of particles has been inserted.
+they are molecules they are also oriented randomly.  Each atom in the
+particle is tested for overlaps with existing particles, including
+effects due to periodic boundary conditions if applicable.  If an
+overlap is detected, another random insertion attempt is made; see the
+<I>vol</I> keyword discussion below.  The larger the volume of the
+insertion region, the more particles that can be inserted at any one
+timestep.  Particles are inserted again after enough time has elapsed
+that the previously inserted particles fall out of the insertion
+volume under 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>

doc/fix_pour.txt

@@ -98,12 +98,16 @@ its value.
 
 Each timestep particles are inserted, they are placed randomly inside
 the insertion volume so as to mimic a stream of poured particles.  If
-they are molecules they are also oriented randomly.  The larger the
-volume, the more particles that can be inserted at any one timestep.
-Particles are inserted again after enough time has elapsed that the
-previously inserted particles fall out of the insertion volume under
-the influence of gravity.  Insertions continue every so many timesteps
-until the desired # of particles has been inserted.
+they are molecules they are also oriented randomly.  Each atom in the
+particle is tested for overlaps with existing particles, including
+effects due to periodic boundary conditions if applicable.  If an
+overlap is detected, another random insertion attempt is made; see the
+{vol} keyword discussion below.  The larger the volume of the
+insertion region, the more particles that can be inserted at any one
+timestep.  Particles are inserted again after enough time has elapsed
+that the previously inserted particles fall out of the insertion
+volume under 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.