git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13615 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_intro.html

@@ -101,8 +101,8 @@ favorite interatomic potential, boundary condition, or atom type, see
 <A HREF = "Section_modify.html">Section_modify</A>, which describes how you can add
 it to LAMMPS.
 </P>
-<H4>General features 
+<H5>General features 
-</H4>
+</H5>
 <UL><LI>  runs on a single processor or in parallel
 <LI>  distributed-memory message-passing parallelism (MPI)
 <LI>  spatial-decomposition of simulation domain for parallelism
@@ -118,8 +118,8 @@ it to LAMMPS.
 <LI>  build as library, invoke LAMMPS thru library interface or provided Python wrapper
 <LI>  couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both 
 </UL>
-<H4>Particle and model types 
+<H5>Particle and model types 
-</H4>
+</H5>
 <P>(<A HREF = "atom_style.html">atom style</A> command)
 </P>
 <UL><LI>  atoms
@@ -135,8 +135,8 @@ it to LAMMPS.
 <LI>  rigid collections of particles
 <LI>  hybrid combinations of these 
 </UL>
-<H4>Force fields 
+<H5>Force fields 
-</H4>
+</H5>
 <P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
 <A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
 <A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
@@ -163,8 +163,8 @@ commands)
 <LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
 <LI>  overlaid potentials: superposition of multiple pair potentials 
 </UL>
-<H4>Atom creation 
+<H5>Atom creation 
-</H4>
+</H5>
 <P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
 <A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
 <A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
@@ -175,8 +175,8 @@ commands)
 <LI>  replicate existing atoms multiple times
 <LI>  displace atoms 
 </UL>
-<H4>Ensembles, constraints, and boundary conditions 
+<H5>Ensembles, constraints, and boundary conditions 
-</H4>
+</H5>
 <P>(<A HREF = "fix.html">fix</A> command) 
 </P>
 <UL><LI>  2d or 3d systems
@@ -194,8 +194,8 @@ commands)
 <LI>  non-equilibrium molecular dynamics (NEMD)
 <LI>  variety of additional boundary conditions and constraints 
 </UL>
-<H4>Integrators 
+<H5>Integrators 
-</H4>
+</H5>
 <P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands) 
 </P>
 <UL><LI>  velocity-Verlet integrator
@@ -205,12 +205,12 @@ commands)
 <LI>  rRESPA hierarchical timestepping
 <LI>  rerun command for post-processing of dump files 
 </UL>
-<H4>Diagnostics 
+<H5>Diagnostics 
-</H4>
+</H5>
 <UL><LI>  see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands 
 </UL>
-<H4>Output 
+<H5>Output 
-</H4>
+</H5>
 <P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands) 
 </P>
 <UL><LI>  log file of thermodynamic info
@@ -223,15 +223,15 @@ commands)
 <LI>  time averaging of system-wide quantities
 <LI>  atom snapshots in native, XYZ, XTC, DCD, CFG formats 
 </UL>
-<H4>Multi-replica models 
+<H5>Multi-replica models 
-</H4>
+</H5>
 <P><A HREF = "neb.html">nudged elastic band</A>
 <A HREF = "prd.html">parallel replica dynamics</A>
 <A HREF = "tad.html">temperature accelerated dynamics</A>
 <A HREF = "temper.html">parallel tempering</A>
 </P>
-<H4>Pre- and post-processing 
+<H5>Pre- and post-processing 
-</H4>
+</H5>
 <UL><LI>Various pre- and post-processing serial tools are packaged
 with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>. 
 
@@ -245,8 +245,8 @@ Pizza.py WWW site</A>.
 
 
 
-<H4>Specialized features 
+<H5>Specialized features 
-</H4>
+</H5>
 <P>These are LAMMPS capabilities which you may not think of as typical
 molecular dynamics options:
 </P>

doc/Section_intro.txt

@@ -97,7 +97,7 @@ favorite interatomic potential, boundary condition, or atom type, see
 "Section_modify"_Section_modify.html, which describes how you can add
 it to LAMMPS.
 
-General features :h4
+General features :h5
 
   runs on a single processor or in parallel
   distributed-memory message-passing parallelism (MPI)
@@ -114,7 +114,7 @@ General features :h4
   build as library, invoke LAMMPS thru library interface or provided Python wrapper
   couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
 
-Particle and model types :h4
+Particle and model types :h5
 ("atom style"_atom_style.html command)
 
   atoms
@@ -130,7 +130,7 @@ Particle and model types :h4
   rigid collections of particles
   hybrid combinations of these :ul
 
-Force fields :h4
+Force fields :h5
 ("pair style"_pair_style.html, "bond style"_bond_style.html,
 "angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
 "improper style"_improper_style.html, "kspace style"_kspace_style.html
@@ -166,7 +166,7 @@ commands)
     potentials can be used in one simulation
   overlaid potentials: superposition of multiple pair potentials :ul
 
-Atom creation :h4
+Atom creation :h5
 ("read_data"_read_data.html, "lattice"_lattice.html,
 "create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
 "displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
@@ -177,7 +177,7 @@ Atom creation :h4
   replicate existing atoms multiple times
   displace atoms :ul
 
-Ensembles, constraints, and boundary conditions :h4
+Ensembles, constraints, and boundary conditions :h5
 ("fix"_fix.html command) 
 
   2d or 3d systems
@@ -195,7 +195,7 @@ Ensembles, constraints, and boundary conditions :h4
   non-equilibrium molecular dynamics (NEMD)
   variety of additional boundary conditions and constraints :ul
 
-Integrators :h4
+Integrators :h5
 ("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) 
 
   velocity-Verlet integrator
@@ -205,11 +205,11 @@ Integrators :h4
   rRESPA hierarchical timestepping
   rerun command for post-processing of dump files :ul
 
-Diagnostics :h4
+Diagnostics :h5
 
   see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
 
-Output :h4
+Output :h5
 ("dump"_dump.html, "restart"_restart.html commands) 
 
   log file of thermodynamic info
@@ -222,14 +222,14 @@ Output :h4
   time averaging of system-wide quantities
   atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
 
-Multi-replica models :h4
+Multi-replica models :h5
 
 "nudged elastic band"_neb.html
 "parallel replica dynamics"_prd.html
 "temperature accelerated dynamics"_tad.html
 "parallel tempering"_temper.html
 
-Pre- and post-processing :h4
+Pre- and post-processing :h5
 
 Various pre- and post-processing serial tools are packaged
 with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
@@ -243,7 +243,7 @@ Pizza.py WWW site"_pizza. :l,ule
 :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
 :link(python,http://www.python.org)
 
-Specialized features :h4
+Specialized features :h5
 
 These are LAMMPS capabilities which you may not think of as typical
 molecular dynamics options:

doc/write_data.html

@@ -19,9 +19,10 @@
 
 <LI>zero or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>pair</I> 
+<LI>keyword = <I>pair</I> or <I>nocoeff</I> 
 
-<PRE>  <I>pair</I> value = <I>ii</I> or <I>ij</I>
+<PRE>  <I>nocoeff</I> = do not write out force field info
+  <I>pair</I> value = <I>ii</I> or <I>ij</I>
     <I>ii</I> = write one line of pair coefficient info per atom type
     <I>ij</I> = write one line of pair coefficient info per IJ atom type pair 
 </PRE>
@@ -84,6 +85,11 @@ data file is read.
 </P>
 <HR>
 
+<P>The <I>nocoeff</I> keyword requests that no force field parameters should
+be written to the data file. This can be very helpful, if one wants
+to make significant changes to the force field or if the parameters
+are read in separately anyway, e.g. from an include file.
+</P>
 <P>The <I>pair</I> keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value
 is specified as <I>ii</I>, then one line per atom type is written, to

doc/write_data.txt

@@ -14,7 +14,8 @@ write_data file keyword value ... :pre
 
 file = name of data file to write out :ulb,l
 zero or more keyword/value pairs may be appended :l
-keyword = {pair} :l
+keyword = {pair} or {nocoeff} :l
+  {nocoeff} = do not write out force field info
   {pair} value = {ii} or {ij}
     {ii} = write one line of pair coefficient info per atom type
     {ij} = write one line of pair coefficient info per IJ atom type pair :pre
@@ -77,6 +78,11 @@ data file is read.
 
 :line
 
+The {nocoeff} keyword requests that no force field parameters should
+be written to the data file. This can be very helpful, if one wants
+to make significant changes to the force field or if the parameters
+are read in separately anyway, e.g. from an include file.
+
 The {pair} keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value
 is specified as {ii}, then one line per atom type is written, to