diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 9b8d624556..f635732571 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -101,8 +101,8 @@ favorite interatomic potential, boundary condition, or atom type, see Section_modify, which describes how you can add it to LAMMPS.
-(atom style command)
(pair style, bond style, angle style, dihedral style, improper style, kspace style @@ -163,8 +163,8 @@ commands)
(read_data, lattice, create_atoms, delete_atoms, displace_atoms, replicate commands) @@ -175,8 +175,8 @@ commands)
(fix command)
(run, run_style, minimize commands)
nudged elastic band parallel replica dynamics temperature accelerated dynamics parallel tempering
-These are LAMMPS capabilities which you may not think of as typical molecular dynamics options:
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index b2ced6bed6..bd64e80326 100644 --- a/doc/Section_intro.txt +++ b/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: diff --git a/doc/write_data.html b/doc/write_data.html index 64ecc40b42..426b0a2068 100644 --- a/doc/write_data.html +++ b/doc/write_data.html @@ -19,9 +19,10 @@pair value = ii or ij +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@@ -84,6 +85,11 @@ data file is read.
+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 diff --git a/doc/write_data.txt b/doc/write_data.txt index d914fe4b6c..b22a42c49c 100644 --- a/doc/write_data.txt +++ b/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