''

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13811 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/doc2/Section_commands.html

@@ -168,7 +168,7 @@ needed.  For example:
 </P>
 <PRE>print "Volume = $v"
 print 'Volume = $v'
-if "$<I>steps</I> > 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.
 <TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna_atom.html">sna/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_sna_atom.html">snad/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> 
 </TD></TR></TABLE></DIV>

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:
 </P>
-<PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python
+<PRE>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
-setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src 
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
 </PRE>
 <P>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

doc/doc2/Section_start.html

@@ -1138,11 +1138,11 @@ that use it.
 <P>For the csh or tcsh shells, you would add something like this to your
 ~/.cshrc file:
 </P>
-<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src 
+<PRE>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
 </PRE>
 <H5><B>Calling the LAMMPS library:</B> 
 </H5>
-<P>Either flavor of library (static or shared0 allows one or more LAMMPS
+<P>Either flavor of library (static or shared) allows one or more LAMMPS
 objects to be instantiated from the calling program.
 </P>
 <P>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS

doc/doc2/compute.html

@@ -223,9 +223,9 @@ page</A>.
 <LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
 <LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
 <LI><A HREF = "compute_slice.html">slice</A> - extract values from global vector or array
-<LI><A HREF = "compute_sna.html">sna/atom</A> - calculate bispectrum coefficients for each atom
+<LI><A HREF = "compute_sna_atom.html">sna/atom</A> - calculate bispectrum coefficients for each atom
-<LI><A HREF = "compute_sna.html">snad/atom</A> - derivative of bispectrum coefficients for each atom
+<LI><A HREF = "compute_sna_atom.html">snad/atom</A> - derivative of bispectrum coefficients for each atom
-<LI><A HREF = "compute_sna.html">snav/atom</A> - virial contribution from bispectrum coefficients for each atom
+<LI><A HREF = "compute_sna_atom.html">snav/atom</A> - virial contribution from bispectrum coefficients for each atom
 <LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
 <LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
 <LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles

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 $<I>angle1</I> dihedral 3 1 2 9 0.0 5000.0 $<I>angle2</I>
+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 $<I>angle1</I> dihedral 3 1 2 9 5000.0 5000.0 $<I>angle2</I>
+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

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
 <A HREF = "special_bonds.html">special_bonds</A> command.  Different weights can be
 assigned to different pair hybrid sub-styles via the <A HREF = "pair_modify.html">pair_modify
-special</A> command.  This allows multiple force fields
+special</A> command. This allows multiple force fields
-to be used in a model of a hybrid system.  See the
+to be used in a model of a hybrid system, however, there is no consistent
-<A HREF = "pair_modify.html">pair_modify</A> doc page for details.
+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.
 </P>
+<P>Here is an example for mixing CHARMM and AMBER: The global <I>amber</I>
+setting sets the 1-4 interactions to non-zero scaling factors and
+then overrides them with 0.0 only for CHARMM:
+</P>
+<PRE>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 
+</PRE>
+<P>The this input achieves the same effect:
+</P>
+<PRE>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 
+</PRE>
+<P>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 <I>lj/coul 0.0 0.0 0.5</I> as required for OPLS/AA:
+</P>
+<PRE>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 
+</PRE>
+<P>See the <A HREF = "pair_modify.html">pair_modify</A> doc page for details on
+the specific syntax, requirements and restrictions.
+</P>
+<HR>
+
 <P>The potential energy contribution to the overall system due to an
 individual sub-style can be accessed and output via the <A HREF = "compute_pair.html">compute
 pair</A> command.

doc/doc2/pair_modify.html

@@ -17,14 +17,14 @@
 </PRE>
 <UL><LI>one or more keyword/value pairs may be listed 
 
-<LI>keyword = <I>pair</I> or <I>special</I> or <I>shift</I> or <I>mix</I> or <I>table</I> or <I>table/disp</I> or <I>tabinner</I> or <I>tabinner/disp</I> or <I>tail</I> or <I>compute</I> 
+<LI>keyword = <I>pair</I> or <I>shift</I> or <I>mix</I> or <I>table</I> or <I>table/disp</I> or <I>tabinner</I> or <I>tabinner/disp</I> or <I>tail</I> or <I>compute</I> 
 
-<PRE>  <I>pair</I> values = sub-style N special which w1 wt2 wt3
+<PRE>  <I>pair</I> values = sub-style N <I>special</I> which wt1 wt2 wt3
     sub-style = sub-style of <A HREF = "pair_hybrid.html">pair hybrid</A>
     N = which instance of sub-style (only if sub-style is used multiple times)
-  <I>special</I> values = flavor w1 w2 w3
+    <I>special</I> which wt1 wt2 wt3 = override <I>special_bonds</I> settings (optional)
-    flavor = <I>lj/coul</I> or <I>lj</I> or <I>coul</I>
+    which = <I>lj/coul</I> or <I>lj</I> or <I>coul</I>
-    w1,w2,w3 = weights from 0.0 to 1.0 inclusive
+    w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
   <I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
   <I>shift</I> value = <I>yes</I> or <I>no</I>
   <I>table</I> value = N
@@ -42,10 +42,12 @@
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>pair_modify shift yes mix geometric
+<P>pair_modify shift yes mix geometric
 pair_modify tail yes
-pair_modify table 12 
+pair_modify table 12
-</PRE>
+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
+</P>
 <P><B>Description:</B>
 </P>
 <P>Modify the parameters of the currently defined pair style.  Not all
@@ -64,13 +66,10 @@ keywords will be applied to.  Note that if the <I>pair</I> keyword is not
 used, and the pair style is <I>hybrid</I> or <I>hybrid/overlay</I>, then all the
 specified keywords will be applied to all sub-styles.
 </P>
-<P>If used, the <I>special</I> keyword must appear second in the list of
+<P>The <I>special</I> keyword can only be used in conjunction with the <I>pair</I>
-keywords, and must follow the <I>pair</I> keyword.  Like the <I>pair</I>
+keyword and must directly follow it. It allows to override the
-keyword, it also can only be used with the <A HREF = "pair_hybrid.html">hybrid and
+<A HREF = "special_bonds.html">special_bonds</A> settings for the specified sub-style.
-hybrid/overlay</A> pair styles.  Its parameters are
+More details are given below.
-similar to the <A HREF = "special_bonds.html">special_bonds</A> command, and it
-overrides the special_bond settings for the specified sub-style.  More
-details are given below.
 </P>
 <P>The <I>mix</I> 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.
 
 <H5>Use of <I>special</I> keyword 
 </H5>
-<P>The <I>special</I> keyword requires 4 values similar to those specified
+<P>The <I>special</I> keyword allows to override the 1-2, 1-3, and 1-4
-with the <A HREF = "special_bonds.html">special_bonds</A> command, <I>flavor</I> and
+exclusion settings for individual sub-styles of a
-w1,w2,w3.  The <I>flavor</I> argument can be <I>lj</I> to change the
+<A HREF = "pair_hybrid.html">hybrid pair style</A>. It requires 4 arguments similar
-Lennard-Jones settings, <I>coul</I> to change the Coulombic settings, or
+to the <A HREF = "special_bonds.html">special_bonds</A> command, <I>which</I> and
-<I>lj/coul</I> to change both to the same set of 3 values.  The w1,w2,w3
+wt1,wt2,wt3.  The <I>which</I> argument can be <I>lj</I> to change the
+Lennard-Jones settings, <I>coul</I> to change the Coulombic settings,
+or <I>lj/coul</I> 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
+1-3, and 1-4 bond topology neighbors, respectively. The <I>special</I>
-</P>
+keyword can only be used in conjunction with the <I>pair</I> keyword
-<PRE>special_bonds lj/coul 0.0 0.0 0.1
+and has to directly follow it.
-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 
-</PRE>
-<P>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.
 </P>
 <P>IMPORTANT NOTE: The global settings specified by the
 <A HREF = "special_bonds.html">special_bonds</A> 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
+store the neighbor with no weighting applied. Thus only global values
-neighbor list cannot be changed by setting a sub-style weight to a
+different from exactly 0.0 or 1.0 can be overridden and an error
-non-zero or non-one value.  Thus an error is generated if the new
+is generated if the requested setting is not compatible with the
-sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
+global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for
-1.0).  Note that as in the example above, the global factor can simply
+1.0 is usually a sufficient workaround in this case without causing
-be set a value other than 0.0 or 1.0, then overridden by any of the
+a significant error.
-sub-styles with a value that is 0.0 or 1.0.
 </P>
 <HR>
 

doc/doc2/python.html

@@ -64,7 +64,7 @@ def loop(lmpptr,N,cut0):
 <PRE>  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 $<I>cut</I>")   # 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 
 </PRE>
 <PRE>    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut $<I>cut</I>")     # LAMMPS command
+    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
     #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option 
 </PRE>
 <PRE>    lmp.command("pair_coeff * * 1.0 1.0")       # ditto