From 992d9ff3ea570dac090536623c480ab1e78ca360 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 31 Jul 2015 23:59:10 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13811 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_commands.html | 6 +-- doc/doc2/Section_python.html | 4 +- doc/doc2/Section_start.html | 4 +- doc/doc2/compute.html | 6 +-- doc/doc2/fix_restrain.html | 4 +- doc/doc2/pair_hybrid.html | 39 +++++++++++++++++-- doc/doc2/pair_modify.html | 69 +++++++++++++++------------------- doc/doc2/python.html | 4 +- 8 files changed, 80 insertions(+), 56 deletions(-) diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index ea033b22d8..8a8444e6ad 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -168,7 +168,7 @@ needed. For example: 

print "Volume = $v"
 print 'Volume = $v'
-if "$steps > 1000" then quit
+if "${steps} > 1000" then quit
 variable a string "red green blue &
                    purple orange cyan"
 print """
@@ -462,8 +462,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 heat/fluximproper/localinertia/chunkkeke/atomke/rigid
 msdmsd/chunkmsd/nongaussomega/chunkpairpair/local
 pe (c)pe/atomplasticity/atompressure (c)property/atomproperty/local
-property/chunkrdfreducereduce/regionslicesna/atom
-snad/atomsnav/atomstress/atomtemp (c)temp/aspheretemp/com
+property/chunkrdfreducereduce/regionslicesna/atom
+snad/atomsnav/atomstress/atomtemp (c)temp/aspheretemp/com
 temp/chunktemp/deformtemp/partial (c)temp/profiletemp/ramptemp/region
 temp/spheretitorque/chunkvacfvcm/chunkvoronoi/atom 
 
diff --git a/doc/doc2/Section_python.html b/doc/doc2/Section_python.html
index c895035102..2921bc4c3f 100644
--- a/doc/doc2/Section_python.html
+++ b/doc/doc2/Section_python.html
@@ -225,8 +225,8 @@ described above.
 have to do it once.  For the csh or tcsh shells, add something like
 this to your ~/.cshrc file, one line for each of the two files:
 

-
setenv PYTHONPATH $PYTHONPATH:/home/sjplimp/lammps/python
-setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/home/sjplimp/lammps/src 
+
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
 

 
If you use the python/install.py script, you need to invoke it every
 time you rebuild LAMMPS (as a shared library) or make changes to the
diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html
index 20769a24bb..bc7fa8169c 100644
--- a/doc/doc2/Section_start.html
+++ b/doc/doc2/Section_start.html
@@ -1138,11 +1138,11 @@ that use it.
 
For the csh or tcsh shells, you would add something like this to your
 ~/.cshrc file:
 

-
setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/home/sjplimp/lammps/src 
+
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
 

 
Calling the LAMMPS library: 
 

-
Either flavor of library (static or shared0 allows one or more LAMMPS
+
Either flavor of library (static or shared) allows one or more LAMMPS
 objects to be instantiated from the calling program.
 

 
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
diff --git a/doc/doc2/compute.html b/doc/doc2/compute.html
index c6a3030e53..56709a891b 100644
--- a/doc/doc2/compute.html
+++ b/doc/doc2/compute.html
@@ -223,9 +223,9 @@ page.
 
  • reduce - combine per-atom quantities into a single global value
 
  • reduce/region - same as compute reduce, within a region
 
  • slice - extract values from global vector or array
-
  • sna/atom - calculate bispectrum coefficients for each atom
-
  • snad/atom - derivative of bispectrum coefficients for each atom
-
  • snav/atom - virial contribution from bispectrum coefficients for each atom
+
  • sna/atom - calculate bispectrum coefficients for each atom
+
  • snad/atom - derivative of bispectrum coefficients for each atom
+
  • snav/atom - virial contribution from bispectrum coefficients for each atom
 
  • stress/atom - stress tensor for each atom
 
  • temp - temperature of group of atoms
 
  • temp/asphere - temperature of aspherical particles
diff --git a/doc/doc2/fix_restrain.html b/doc/doc2/fix_restrain.html
index 6c0f498fab..ae650575a3 100644
--- a/doc/doc2/fix_restrain.html
+++ b/doc/doc2/fix_restrain.html
@@ -93,11 +93,11 @@ as the following may be useful:
 velocity all create 600.0 8675309 mom yes rot yes dist gaussian
 fix NVE all nve
 fix TFIX all langevin 600.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $angle1 dihedral 3 1 2 9 0.0 5000.0 $angle2
+fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
 fix_modify REST energy yes
 run 10000
 fix TFIX all langevin 0.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $angle1 dihedral 3 1 2 9 5000.0 5000.0 $angle2
+fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
 fix_modify REST energy yes
 run 10000
 # sanity check for convergence
diff --git a/doc/doc2/pair_hybrid.html b/doc/doc2/pair_hybrid.html
index 0403530f02..4782685fe1 100644
--- a/doc/doc2/pair_hybrid.html
+++ b/doc/doc2/pair_hybrid.html
@@ -196,10 +196,43 @@ interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
 neighbors in the molecular bond topology, as normally set by the
 special_bonds command.  Different weights can be
 assigned to different pair hybrid sub-styles via the pair_modify
-special command.  This allows multiple force fields
-to be used in a model of a hybrid system.  See the
-pair_modify doc page for details.
+special command. This allows multiple force fields
+to be used in a model of a hybrid system, however, there is no consistent
+approach to determine parameters automatically for the interactions
+between the two force fields, this is only recommended when particles
+described by the different force fields do not mix.
 
    
+
    Here is an example for mixing CHARMM and AMBER: The global amber
+setting sets the 1-4 interactions to non-zero scaling factors and
+then overrides them with 0.0 only for CHARMM:
+
    
+
    special_bonds amber
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 
+
    
+
    The this input achieves the same effect:
+
    
+
    special_bonds 0.0 0.0 0.1
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 
+
    
+
    Here is an example for mixing Tersoff with OPLS/AA based on
+a data file that defines bonds for all atoms where for the
+Tersoff part of the system the force constants for the bonded
+interactions have been set to 0. Note the global settings are
+effectively lj/coul 0.0 0.0 0.5 as required for OPLS/AA:
+
    
+
    special_bonds lj/coul 1e-20 1e-20 0.5
+pair_hybrid tersoff lj/cut/coul/long 12.0
+pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 
+
    
+
    See the pair_modify doc page for details on
+the specific syntax, requirements and restrictions.
+
    
+
    
+
 
    The potential energy contribution to the overall system due to an
 individual sub-style can be accessed and output via the compute
 pair command.
diff --git a/doc/doc2/pair_modify.html b/doc/doc2/pair_modify.html
index f6013a430e..726f292286 100644
--- a/doc/doc2/pair_modify.html
+++ b/doc/doc2/pair_modify.html
@@ -17,14 +17,14 @@
 
    • 
 
    • one or more keyword/value pairs may be listed 
 
-
    • keyword = pair or special or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute 
+
    • keyword = pair or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute 
 
-
        pair values = sub-style N special which w1 wt2 wt3
+
        pair values = sub-style N special which wt1 wt2 wt3
     sub-style = sub-style of pair hybrid
     N = which instance of sub-style (only if sub-style is used multiple times)
-  special values = flavor w1 w2 w3
-    flavor = lj/coul or lj or coul
-    w1,w2,w3 = weights from 0.0 to 1.0 inclusive
+    special which wt1 wt2 wt3 = override special_bonds settings (optional)
+    which = lj/coul or lj or coul
+    w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
   mix value = geometric or arithmetic or sixthpower
   shift value = yes or no
   table value = N
@@ -42,10 +42,12 @@
 
    
 
    Examples:
 
    
-
    pair_modify shift yes mix geometric
+
    pair_modify shift yes mix geometric
 pair_modify tail yes
-pair_modify table 12 
-
    
+pair_modify table 12
+pair_modify pair lj/cut compute no
+pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre
+
    
 
    Description:
 
    
 
    Modify the parameters of the currently defined pair style.  Not all
@@ -64,13 +66,10 @@ keywords will be applied to.  Note that if the pair keyword is not
 used, and the pair style is hybrid or hybrid/overlay, then all the
 specified keywords will be applied to all sub-styles.
 
    
-
    If used, the special keyword must appear second in the list of
-keywords, and must follow the pair keyword.  Like the pair
-keyword, it also can only be used with the hybrid and
-hybrid/overlay pair styles.  Its parameters are
-similar to the special_bonds command, and it
-overrides the special_bond settings for the specified sub-style.  More
-details are given below.
+
    The special keyword can only be used in conjunction with the pair
+keyword and must directly follow it. It allows to override the
+special_bonds settings for the specified sub-style.
+More details are given below.
 
    
 
    The mix keyword affects pair coefficients for interactions between
 atoms of type I and J, when I != J and the coefficients are not
@@ -216,36 +215,28 @@ pair style be defined.
 
 
    Use of special keyword 
 
    
-
    The special keyword requires 4 values similar to those specified
-with the special_bonds command, flavor and
-w1,w2,w3.  The flavor argument can be lj to change the
-Lennard-Jones settings, coul to change the Coulombic settings, or
-lj/coul to change both to the same set of 3 values.  The w1,w2,w3
+
    The special keyword allows to override the 1-2, 1-3, and 1-4
+exclusion settings for individual sub-styles of a
+hybrid pair style. It requires 4 arguments similar
+to the special_bonds command, which and
+wt1,wt2,wt3.  The which argument can be lj to change the
+Lennard-Jones settings, coul to change the Coulombic settings,
+or lj/coul to change both to the same set of 3 values.  The wt1,wt2,wt3
 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
-1-3, and 1-4 bond topology neighbors.  For example, these commands
-
    
-
    special_bonds lj/coul 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333 
-
    
-
    show how to use both the CHARMM and AMBER force fields in a single
-simulation.  The first pair modify command sets the special bonds to
-CHARMM values (all 0.0).  The last 2 pair modify commands set the
-standard AMBER values for LJ and Coulombic weights.
+1-3, and 1-4 bond topology neighbors, respectively. The special
+keyword can only be used in conjunction with the pair keyword
+and has to directly follow it.
 
    
 
    IMPORTANT NOTE: The global settings specified by the
 special_bonds command affect the construction of
 neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
 exclude those pairs from the neighbor list entirely.  Weights of 1.0
-store the neighbor with no weighting applied.  The format of the
-neighbor list cannot be changed by setting a sub-style weight to a
-non-zero or non-one value.  Thus an error is generated if the new
-sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
-1.0).  Note that as in the example above, the global factor can simply
-be set a value other than 0.0 or 1.0, then overridden by any of the
-sub-styles with a value that is 0.0 or 1.0.
+store the neighbor with no weighting applied. Thus only global values
+different from exactly 0.0 or 1.0 can be overridden and an error
+is generated if the requested setting is not compatible with the
+global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for
+1.0 is usually a sufficient workaround in this case without causing
+a significant error.
 
    
 
    
 
diff --git a/doc/doc2/python.html b/doc/doc2/python.html
index 02193dd770..9d0aa9868e 100644
--- a/doc/doc2/python.html
+++ b/doc/doc2/python.html
@@ -64,7 +64,7 @@ def loop(lmpptr,N,cut0):
 
      for i in range(N):
     cut = cut0 + i*0.1
     lmp.set_variable("cut",cut)               # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut $cut")   # LAMMPS commands
+    lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
     lmp.command("pair_coeff * * 1.0 1.0")
     lmp.command("run 100")
  """ 
@@ -332,7 +332,7 @@ which loads and runs the following function from examples/python/funcs.py:
     cut = cut0 + i*0.1 
 
    
 
        lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut $cut")     # LAMMPS command
+    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
     #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option 
 
    
 
        lmp.command("pair_coeff * * 1.0 1.0")       # ditto