These are pair styles contributed by users, which can be used if @@ -509,19 +509,19 @@ package.
A TIP4P model is run with LAMMPS using two commands:
-Note that only a TIP4P model with long-range Coulombics is currently @@ -554,7 +554,7 @@ cutoff + 2*(OM distance), to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. The OM distance and the LJ and Coulombic cutoffs are set in the pair_style -lj/cut/coul/long/tip4p command. +lj/cut/tip4p/long command.
Wikipedia also has a nice article on water models. diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 00935f3215..044d2c73df 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -493,7 +493,7 @@ angle style of {harmonic} or {charmm} should also be used. A TIP4P model is run with LAMMPS using two commands: -"pair_style lj/cut/coul/long/tip4p"_pair_lj.html +"pair_style lj/cut/tip4p/long"_pair_lj.html "kspace_style pppm/tip4p"_kspace_style.html :ul Note that only a TIP4P model with long-range Coulombics is currently @@ -549,7 +549,7 @@ cutoff + 2*(OM distance), to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. The OM distance and the LJ and Coulombic cutoffs are set in the "pair_style -lj/cut/coul/long/tip4p"_pair_lj.html command. +lj/cut/tip4p/long"_pair_lj.html command. Wikipedia also has a nice article on "water models"_http://en.wikipedia.org/wiki/Water_model. diff --git a/doc/Section_python.html b/doc/Section_python.html index 64889c3d53..6fcc0f0e8b 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -165,7 +165,7 @@ which Python is invoked by root.
Note that if you want Python to be able to load different versions of the LAMMPS shared library (see this section below), you will -need to manually copy files like lmplammps_g++.so into the appropriate +need to manually copy files like liblammps_g++.so into the appropriate system directory. This is not needed if you set the LD_LIBRARY_PATH environment variable as described above.
diff --git a/doc/Section_python.txt b/doc/Section_python.txt index 38fad3451f..872a4c68bf 100644 --- a/doc/Section_python.txt +++ b/doc/Section_python.txt @@ -161,7 +161,7 @@ which Python is invoked by root. Note that if you want Python to be able to load different versions of the LAMMPS shared library (see "this section"_#py_5 below), you will -need to manually copy files like lmplammps_g++.so into the appropriate +need to manually copy files like liblammps_g++.so into the appropriate system directory. This is not needed if you set the LD_LIBRARY_PATH environment variable as described above. diff --git a/doc/kspace_style.html b/doc/kspace_style.html index 28d1978cf8..cc54cb8442 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -127,7 +127,7 @@ or not. Its default value is 1.0e-5.The pppm/tip4p style is identical to the pppm style except that it adds a charge at the massless 4th site in each TIP4P water molecule. It should be used with pair styles with a -long/tip4p in their style name. +tip4p/long in their style name.
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom IDs for the O and 2 H atoms must be consecutive, with the O atom @@ -208,11 +220,12 @@ LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model.
-The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: +
For all of the lj/cut pair styles, the following coefficients must +be defined for each pair of atoms types via the +pair_coeff command as in the examples above, or in +the data file or restart files read by the read_data +or read_restart commands, or by mixing as +described below:
All of the lj/cut pair styles support the +
All of the lj/cut pair styles support the pair_modify shift option for the energy of the Lennard-Jones portion of the pair interaction.
@@ -275,16 +288,16 @@ Lennard-Jones portion of the pair interaction. pair_modify table option since they can tabulate the short-range portion of the long-range Coulombic interaction. -All of the lj/cut pair styles support the +
All of the lj/cut pair styles support the pair_modify tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction.
-All of the lj/cut pair styles write their information to binary
+ All of the lj/cut pair styles write their information to binary
restart files, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/cut and lj/cut/coul/long pair styles support the use of the
+ The lj/cut and lj/cut/coul/long pair styles support the use of the
inner, middle, and outer keywords of the run_style
respa command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
@@ -296,9 +309,11 @@ See the run_style command for details.
Restrictions:
The lj/cut/coul/long and lj/cut/tip4p/long styles are part of the
-KSPACE package. They are only enabled if LAMMPS was built with those
+KSPACE package. The lj/cut/tip4p/cut style is part of the MOLECULE
+package. These styles are only enabled if LAMMPS was built with those
packages. See the Making LAMMPS section
-for more info. Note that the KSPACE package is installed by default.
+for more info. Note that the KSPACE and MOLECULE packages are
+installed by default.
Related commands: