Note that the when using the TIP4P pair style, the neighobr list +cutoff for Coulomb interactions is effectively extended by a distance +2 * (OM distance), to account for the offset distance of the +fictitious charges on O atoms in water molecules. Thus it is +typically best in an efficiency sense to use a LJ cutoff >= Coulomb +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. +
Wikipedia also has a nice article on water models.
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 83465e5895..0044f50d77 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -540,6 +540,17 @@ LJ epsilon of O-O = 0.16275 LJ sigma of O-O = 3.16435 LJ epsilon, sigma of OH, HH = 0.0 :all(b),p +Note that the when using the TIP4P pair style, the neighobr list +cutoff for Coulomb interactions is effectively extended by a distance +2 * (OM distance), to account for the offset distance of the +fictitious charges on O atoms in water molecules. Thus it is +typically best in an efficiency sense to use a LJ cutoff >= Coulomb +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. + Wikipedia also has a nice article on "water models"_http://en.wikipedia.org/wiki/Water_model. diff --git a/doc/create_atoms.html b/doc/create_atoms.html index 30ae86cb05..9496f56688 100644 --- a/doc/create_atoms.html +++ b/doc/create_atoms.html @@ -31,11 +31,12 @@ basis values = M itype
M = which basis atom
itype = atom type (1-N) to assign to this basis atom
+ remap value = yes or no
units value = lattice or box
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
@@ -110,6 +111,12 @@ specific basis atoms as they are created. See the
defined for the unit cell of the lattice. By default, all created
atoms are assigned the argument type as their atom type.
+The remap keyword only applies to the single style. If it is set
+to yes, then if the specified position is outside the simulation
+box, it will mapped back into the box, assuming the relevant
+dimensions are periodic. If it is set to no, no remapping is done
+and no atom is created if its position is outside the box.
+
The units keyword determines the meaning of the distance units used
to specify the coordinates of the one atom created by the single
style. A box value selects standard distance units as defined by
@@ -183,8 +190,8 @@ command.
Default:
-The default for the basis keyword, is all created atoms are assigned
-the argument type as their atom type. The default for the
-units keyword is lattice.
+
The default for the basis keyword is that all created atoms are
+assigned the argument type as their atom type. The default for
+remap = no and for units = lattice.