From d1cbced715705e27c75ef80c6c07b8997b437277 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 8 Dec 2015 23:15:41 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14292 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Manual.html.html | 4 +-- doc/doc2/compute_msd.html | 46 +++++++++++++++++++++----- doc/doc2/compute_orientorder_atom.html | 8 +++-- doc/doc2/fix_atom_swap.html | 2 +- doc/doc2/fix_ave_atom.html | 4 +-- doc/doc2/fix_ave_chunk.html | 4 +-- doc/doc2/fix_ave_histo.html | 6 ++-- doc/doc2/fix_ave_spatial.html | 4 +-- doc/doc2/fix_ave_spatial_sphere.html | 7 ++-- doc/doc2/fix_ave_time.html | 4 +-- doc/doc2/fix_indent.html | 7 ++-- doc/doc2/fix_reaxc_species.html | 7 ++-- doc/doc2/fix_saed_vtk.html | 7 ++-- 13 files changed, 72 insertions(+), 38 deletions(-) diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html index 6d859f8ad0..7a99a28735 100644 --- a/doc/doc2/Manual.html.html +++ b/doc/doc2/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

17 Nov 2015 version +

20 Nov 2015 version

Version info:

diff --git a/doc/doc2/compute_msd.html b/doc/doc2/compute_msd.html index 137e89cb60..5c01e1a716 100644 --- a/doc/doc2/compute_msd.html +++ b/doc/doc2/compute_msd.html @@ -21,16 +21,17 @@
  • zero or more keyword/value pairs may be appended -
  • keyword = com +
  • keyword = com or average -
      com value = yes or no 
+
      com value = yes or no
+  average value = yes or no 
 
    
 
 
 
    Examples:
 
    
 
    compute 1 all msd
-compute 1 upper msd com yes 
+compute 1 upper msd com yes average yes 
 
    
 
    Description:
 
    
@@ -49,13 +50,34 @@ averaged over atoms in the group.
 
    The slope of the mean-squared displacement (MSD) versus time is
 proportional to the diffusion coefficient of the diffusing atoms.
 
    
-
    The displacement of an atom is from its original position at the time
-the compute command was issued.  The value of the displacement will be
+
    The displacement of an atom is from its reference position. This is
+normally the original position at the time
+the compute command was issued, unless the average keyword is set to yes.  
+The value of the displacement will be
 0.0 for atoms not in the specified compute group.
 
    
 
    If the com option is set to yes then the effect of any drift in
-the center-of-mass of the group of atoms is subtracted out before xhe
-displacment of each atom is calcluated.
+the center-of-mass of the group of atoms is subtracted out before the
+displacment of each atom is calculated.
+
    
+
    If the average option is set to yes then the reference position of 
+an atom is based on the average position of that atom, 
+corrected for center-of-mass motion if requested.
+The average position
+is a running average over all previous calls to the compute, including the
+current call. So on the first call 
+it is current position, on the second call it is the arithmetic average of the 
+current position and the position on the first call, and so on.
+Note that when using this option, the precise value of the mean square
+displacement will depend on the number of times the compute is 
+called. So, for example, changing the frequency of thermo output may
+change the computed displacement. Also, the precise values will be 
+changed if a single simulation is broken up into two parts, using
+either multiple run commands or a restart file. It only makes
+sense to use this option if the atoms are not diffusing, so that
+their average positions relative to the center of mass of the system
+are stationary. The most common case is crystalline solids undergoing
+thermal motion.
 
    
 
    IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
 using the image flags associated with each atom.  See the dump
@@ -70,7 +92,13 @@ to be continuous when running from a restart file<
 then you should use the same ID for this compute, as in the original
 run.  This is so that the fix this compute creates to store per-atom
 quantities will also have the same ID, and thus be initialized
-correctly with time=0 atom coordinates from the restart file.
+correctly with atom reference positions from the restart file.
+When average is set to yes, then the atom reference positions 
+are restored correctly, but not the number of samples used
+obtain them. As a result, the reference positions from the restart
+file are combined with subsequent positions as if they were from a 
+single sample, instead of many, which will change the values of msd
+somewhat.
 
    
 
    Output info:
 
    
@@ -94,6 +122,6 @@ msd/chunk    
 
    
 
    Default:
 
    
-
    The option default is com = no.
+
    The option default are com = no, average = no.
 
    
 
diff --git a/doc/doc2/compute_orientorder_atom.html b/doc/doc2/compute_orientorder_atom.html
index d3f28d7c36..70b64f978e 100644
--- a/doc/doc2/compute_orientorder_atom.html
+++ b/doc/doc2/compute_orientorder_atom.html
@@ -71,9 +71,11 @@ parameters. This is followed by that number of integers giving the
 degree of each order parameter. Because Q2 and all odd-degree 
 order parameters are zero for atoms in cubic crystals 
 (see Steinhardt), the default order parameters
-are Q4, Q6, Q8, Q10, and Q12. The correct 
-numerical values for commonly encountered high-symmetry 
-structures are given by Mickel et al.
+are Q4, Q6, Q8, Q10, and Q12. For the
+FCC crystal with nnn=12, Q4 = sqrt(7/3)/8 = 0.19094....
+The numerical values of all order parameters up to Q12
+for a range of commonly encountered high-symmetry structures are given 
+in Table I of Mickel et al..
 
    
 
    The value of Ql is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than 
diff --git a/doc/doc2/fix_atom_swap.html b/doc/doc2/fix_atom_swap.html
index b6f9192562..1d01b66043 100644
--- a/doc/doc2/fix_atom_swap.html
+++ b/doc/doc2/fix_atom_swap.html
@@ -48,7 +48,7 @@
 
    
 
    fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
 fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6 
-fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0 
+fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 
 
    
 
    Description:
 
    
diff --git a/doc/doc2/fix_ave_atom.html b/doc/doc2/fix_ave_atom.html
index f80025c8f9..88a6b22cfe 100644
--- a/doc/doc2/fix_ave_atom.html
+++ b/doc/doc2/fix_ave_atom.html
@@ -81,8 +81,8 @@ that are a multiple of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
 Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
diff --git a/doc/doc2/fix_ave_chunk.html b/doc/doc2/fix_ave_chunk.html
index c71b9a6e0a..5440b74530 100644
--- a/doc/doc2/fix_ave_chunk.html
+++ b/doc/doc2/fix_ave_chunk.html
@@ -161,8 +161,8 @@ that are a multiples of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
 Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
diff --git a/doc/doc2/fix_ave_histo.html b/doc/doc2/fix_ave_histo.html
index 96e16bd57b..7fd6291e6d 100644
--- a/doc/doc2/fix_ave_histo.html
+++ b/doc/doc2/fix_ave_histo.html
@@ -143,9 +143,9 @@ histogram.  The final histogram is generated on timesteps that are
 multiple of Nfreq.  It is averaged over Nrepeat histograms,
 computed in the preceding portion of the simulation every Nevery
 timesteps.  Nfreq must be a multiple of Nevery and Nevery must
-be non-zero even if Nrepeat is 1.  Also, the timesteps contributing
-to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
-required.
+be non-zero even if Nrepeat is 1.  Also, the timesteps
+contributing to the histogram value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
 on timesteps 90,92,94,96,98,100 will be used to compute the final
diff --git a/doc/doc2/fix_ave_spatial.html b/doc/doc2/fix_ave_spatial.html
index 9d41f243ac..747ca62946 100644
--- a/doc/doc2/fix_ave_spatial.html
+++ b/doc/doc2/fix_ave_spatial.html
@@ -157,8 +157,8 @@ that are a multiples of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
 Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
diff --git a/doc/doc2/fix_ave_spatial_sphere.html b/doc/doc2/fix_ave_spatial_sphere.html
index d7d55d7257..671c48318a 100644
--- a/doc/doc2/fix_ave_spatial_sphere.html
+++ b/doc/doc2/fix_ave_spatial_sphere.html
@@ -127,9 +127,10 @@ the average.  The final averaged quantities are generated on timesteps
 that are a multiples of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
-Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+Nevery must be non-zero even if Nrepeat is 1.  
+Also, the timesteps
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
diff --git a/doc/doc2/fix_ave_time.html b/doc/doc2/fix_ave_time.html
index 7705b36c70..4f2af2095d 100644
--- a/doc/doc2/fix_ave_time.html
+++ b/doc/doc2/fix_ave_time.html
@@ -131,8 +131,8 @@ that are a mlutiple of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
 Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
diff --git a/doc/doc2/fix_indent.html b/doc/doc2/fix_indent.html
index 4e77d2e948..701a576664 100644
--- a/doc/doc2/fix_indent.html
+++ b/doc/doc2/fix_indent.html
@@ -57,9 +57,10 @@ fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
 
    Description:
 
    
 
    Insert an indenter within a simulation box.  The indenter repels all
-atoms that touch it, so it can be used to push into a material or as
-an obstacle in a flow.  Or it can be used as a constraining wall
-around a simulation; see the discussion of the side keyword below.
+atoms in the group that touch it, so it can be used to push into a
+material or as an obstacle in a flow.  Or it can be used as a
+constraining wall around a simulation; see the discussion of the
+side keyword below.
 
    
 
    The indenter can either be spherical or cylindrical or planar.  You
 must set one of those 3 keywords.
diff --git a/doc/doc2/fix_reaxc_species.html b/doc/doc2/fix_reaxc_species.html
index a507564a2d..2fadd7e7f7 100644
--- a/doc/doc2/fix_reaxc_species.html
+++ b/doc/doc2/fix_reaxc_species.html
@@ -102,9 +102,10 @@ order.  The species analysis is performed using the average bond-order
 on timesteps that are a multiple of Nfreq.  The average is over
 Nrepeat bond-order samples, computed in the preceding portion of the
 simulation every Nevery timesteps.  Nfreq must be a multiple of
-Nevery and Nevery must be non-zero even if Nrepeat is 1.  Also,
-the timesteps contributing to the average bond-order cannot overlap,
-i.e. Nfreq > (Nrepeat-1)*Nevery is required.
+Nevery and Nevery must be non-zero even if Nrepeat is 1.
+Also, the timesteps
+contributing to the average bond-order cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
 values on timesteps 90,92,94,96,98,100 will be used to compute the
diff --git a/doc/doc2/fix_saed_vtk.html b/doc/doc2/fix_saed_vtk.html
index 25b281cb2c..c9367708a8 100644
--- a/doc/doc2/fix_saed_vtk.html
+++ b/doc/doc2/fix_saed_vtk.html
@@ -82,9 +82,10 @@ average.  The final averaged quantities are generated on timesteps
 that are a multiple of Nfreq.  The average is over Nrepeat
 quantities, computed in the preceding portion of the simulation every
 Nevery timesteps.  Nfreq must be a multiple of Nevery and
-Nevery must be non-zero even if Nrepeat is 1.  Also, the timesteps
-contributing to the average value cannot overlap, i.e. Nfreq >
-(Nrepeat-1)*Nevery is required.
+Nevery must be non-zero even if Nrepeat is 1.
+Also, the timesteps
+contributing to the average value cannot overlap, 
+i.e. Nrepeat*Nevery can not exceed Nfreq. 
 
    
 
    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average