\(\renewcommand{\AA}{\text{Å}}\)
3.7. Bond, angle, dihedral, improper styles
Classes that compute molecular interactions are derived from the Bond, Angle, Dihedral, and Improper classes. New styles can be created to add new potentials to LAMMPS.
Bond_harmonic.cpp is the simplest example of a bond style. Ditto for the harmonic forms of the angle, dihedral, and improper style commands.
Here is a brief description of common methods you define in your new derived class. See bond.h, angle.h, dihedral.h, and improper.h for details and specific additional methods.
Required |
“pure” methods that must be overridden in a derived class |
---|---|
compute |
compute the molecular interactions for all listed items |
coeff |
set coefficients for one type |
equilibrium_distance |
length of bond, used by SHAKE (bond styles only) |
equilibrium_angle |
opening of angle, used by SHAKE (angle styles only) |
write & read_restart |
writes/reads coeffs to restart files |
single |
force/r (bond styles only) and energy of a single bond or angle |
Optional |
methods that have a default or dummy implementation |
---|---|
init |
check if all coefficients are set, calls init_style() |
init_style |
check if style specific conditions are met |
settings |
apply global settings for all types |
write & read_restart_settings |
writes/reads global style settings to restart files |
write_data |
write corresponding Coeffs section(s) in data file |
memory_usage |
tally memory allocated by the style |
extract |
provide access to internal data (bond or angle styles only) |
reinit |
reset all type-based parameters, called by fix adapt (bonds only) |
pack & unpack_forward_comm |
copy data to and from buffer in forward communication (bonds only) |
pack & unpack_reverse_comm |
copy data to and from buffer in reverse communication (bonds only) |
Here is a list of flags or settings that should be set in the constructor of the derived class when they differ from the default setting.
Name of flag |
Description |
default |
---|---|---|
writedata |
1 if write_data() is implemented |
1 |
single_extra |
number of extra single values calculated (bond styles only) |
0 |
partial_flag |
1 if bond type can be set to 0 and deleted (bond styles only) |
0 |
reinitflag |
1 if style has reinit() and is compatible with fix adapt |
1 |
comm_forward |
size of buffer (in doubles) for forward communication (bond styles only) |
0 |
comm_reverse |
size of buffer (in doubles) for reverse communication (bond styles only) |
0 |
comm_reverse_off |
size of buffer for reverse communication with newton off (bond styles only) |
0 |