Also note that pair_style eam defines the masses of -atom types in the EAM potential file, in which case the mass command -is normally not used. +
Also note that pair_style eam and pair_style +bop commands define the masses of atom types in their +respective potential files, in which case the mass command is normally +not used.
If you define a hybrid atom style which includes one (or more) sub-styles which require per-type mass and one (or more) diff --git a/doc/mass.txt b/doc/mass.txt index c024da20a9..4b75132ccf 100644 --- a/doc/mass.txt +++ b/doc/mass.txt @@ -56,9 +56,10 @@ Per-atom masses are defined in the data file read by the set to new values by the "set mass"_set.html or "set density"_set.html commands. -Also note that "pair_style eam"_pair_eam.html defines the masses of -atom types in the EAM potential file, in which case the mass command -is normally not used. +Also note that "pair_style eam"_pair_eam.html and "pair_style +bop"_pair_bop.html commands define the masses of atom types in their +respective potential files, in which case the mass command is normally +not used. If you define a "hybrid atom style"_atom_style.html which includes one (or more) sub-styles which require per-type mass and one (or more) diff --git a/doc/pair_bop.html b/doc/pair_bop.html index ec1ff3172b..a8ed6a2f4d 100644 --- a/doc/pair_bop.html +++ b/doc/pair_bop.html @@ -27,7 +27,7 @@
pair_style bop pair_coeff * * ../potentials/CdTe_bop Cd Te -pair_style bop 4.90 save +pair_style bop save pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te comm_modify cutoff 14.70@@ -85,8 +85,18 @@ to either stabilize or destabilize close-packed structures. The pi bond-order includes hopping paths of length 4. This enables the incorporation of dihedral angles effects. -
One option can be specified as a keyword with the -pair_style command. +
IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP +potentials are not set in the pair_style or pair_coeff command; they +are specified in the BOP potential files themselves. Likewise, the +BOP potential files list atomic masses; thus you do not need to use +the mass command to specify them. Note that for BOP +potentials with hydrogen, you will likely want to set the mass of H +atoms to be 10x or 20x larger to avoid having to use a tiny timestep. +You can do this by using the mass command after using the +pair_coeff command to read the BOP potential +file. +
+One option can be specified as a keyword with the pair_style command.
The save keyword gives you the option to calculate in advance and store a set of distances, angles, and derivatives of angles. The @@ -296,11 +306,14 @@ the previous section but is interaction type dependent)
The next section contains a line for each three body interaction type e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
-The rest of the table has the same structure as the previous section (see above). diff --git a/doc/pair_bop.txt b/doc/pair_bop.txt index 11dddb2d86..d1c7e77392 100644 --- a/doc/pair_bop.txt +++ b/doc/pair_bop.txt @@ -21,7 +21,7 @@ keyword = {save} :l pair_style bop pair_coeff * * ../potentials/CdTe_bop Cd Te -pair_style bop 4.90 save +pair_style bop save pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te comm_modify cutoff 14.70 :pre @@ -79,8 +79,18 @@ to either stabilize or destabilize close-packed structures. The pi bond-order includes hopping paths of length 4. This enables the incorporation of dihedral angles effects. -One option can be specified as a keyword with the -pair_style command. +IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP +potentials are not set in the pair_style or pair_coeff command; they +are specified in the BOP potential files themselves. Likewise, the +BOP potential files list atomic masses; thus you do not need to use +the "mass"_mass.html command to specify them. Note that for BOP +potentials with hydrogen, you will likely want to set the mass of H +atoms to be 10x or 20x larger to avoid having to use a tiny timestep. +You can do this by using the "mass"_mass.html command after using the +"pair_coeff"_doc/pair_coeff.html command to read the BOP potential +file. + +One option can be specified as a keyword with the pair_style command. The {save} keyword gives you the option to calculate in advance and store a set of distances, angles, and derivatives of angles. The @@ -268,11 +278,14 @@ the previous section but is interaction type dependent) :l,ule The next section contains a line for each three body interaction type e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -Line 1: g0, g1, g2... (These are coefficients for -the angular spline of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. -The function can contain up to 10 term thus 10 constants. The first line -can contain up to five constants. If the spline has more than five terms -the second g0, g1, g2 (for e_1-e_1-e_2) :l,ule +Line 1: g0, g1, g2... (These are coefficients for the angular spline +of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The +function can contain up to 10 term thus 10 constants. The first line +can contain up to five constants. If the spline has more than five +terms the second line will contain the remaining constants The +following lines will then contain the constants for the remainaing g0, +g1, g2... (for e_1-e_1-e_2) and the other three body +interactions :l,ule The rest of the table has the same structure as the previous section (see above).