Removing unneeded feature

This commit is contained in:
jtclemm
2022-09-06 10:13:59 -06:00
parent 71970858cf
commit 8b3c1a20a8
6 changed files with 18 additions and 50 deletions

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@ -65,9 +65,9 @@ Various properties of bonds can be computed using the
:doc:`compute property/bond <compute_property_bond>` command. This
command allows one to access data saved to the bond's history
such as the reference length of the bond. More information on
historical data can be found on the documentation pages for the specific
BPM bond styles. Finally, this data can be output using `dump local <dump>`.
As one may output many columns from the same compute, the
bond history data can be found on the documentation pages for the specific
BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
command. As one may output many columns from the same compute, the
:doc:`dump modify <dump_modify>` *colname* option may be used to provide
more helpful column names. An example of this procedure is found in
/examples/bpm/pour/. External software, such as OVITO, can read these dump
@ -80,13 +80,16 @@ As bonds can be broken between neighbor list builds, the
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can overlay
pair forces with bond forces such that all bonded particles also
feel pair interactions. This can be accomplished by using the *overlay/pair* keyword present in all bpm bond styles and by using the following special bond settings
feel pair interactions. This can be accomplished by using the *overlay/pair*
keyword present in all bpm bond styles and by using the following special
bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
Alternatively, one can turn off all pair interactions between bonded particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
Alternatively, one can turn off all pair interactions between bonded
particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
by subtracting pair forces during the bond computation but rather by
dynamically updating the special bond list. This is the default behavior
of BPM bond styles and is done by updating the 1-2 special bond list as

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@ -179,7 +179,7 @@ This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart file will
properly resume bonds. However, the reference state is NOT
written to data files. Therefore reading a data file will not
restore bonds which will recalculate their reference state.
restore bonds and will cause their reference states to be redefined.
The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
@ -207,11 +207,12 @@ of a bonded interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the bonded interaction force. However, the single() function also
calculates 7 extra bond quantities. The first 4 are data from the
reference state of the bond including the magnitude :math:`r_0`
followed by the :math:`x`, :math:`y`, and :math:`z` components of the
initial unit vector pointing to particle I from particle J. The next 3
(5-7) are the components of the total force, including normal and
tangential contributions, acting on particle I.
reference state of the bond including the initial distance between particles
:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
of the initial unit vector pointing to particle I from particle J. The next 3
quantities (5-7) are the :math:`x`, :math:`y`, and :math:`z` components
of the total force, including normal and tangential contributions, acting
on particle I.
These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
command, as *b1*, *b2*, ..., *b7*\ .

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@ -143,7 +143,7 @@ This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart
file will properly restore bonds. However, the reference state is NOT
written to data files. Therefore reading a data file will not
restore bonds which will recalculate their reference state.
restore bonds and will cause their reference states to be redefined.
The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these

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@ -59,7 +59,7 @@ include this pair interaction and overlay the pair force over the bond
force or to exclude this pair interaction such that the two particles
only interact via the bond force. See discussion of the *overlay/pair*
option for BPM bond styles and the :doc:`special_bonds <special_bonds>`
command in the `:doc: how to <Howto_BPM>` page on BPMs for more details.
command in the :doc:`how to <Howto_BPM>` page on BPMs for more details.
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples

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@ -29,17 +29,11 @@ using namespace LAMMPS_NS;
ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
Compute(_lmp, narg, arg), nbond(nullptr)
{
if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute nbond/atom command");
if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
comm_reverse = 1;
comm_forward = 0;
if (narg == 4) {
if (utils::strmatch(arg[3], "forward")) comm_forward = 1;
else error->all(FLERR, "Illegal compute nbond/atom argument {}", arg[3]);
}
nmax = 0;
}
@ -106,9 +100,6 @@ void ComputeNBondAtom::compute_peratom()
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) nbond[i] = 0.0;
// forward to ghosts if requested
if (comm_forward != 0) comm->forward_comm(this);
}
/* ---------------------------------------------------------------------- */
@ -135,31 +126,6 @@ void ComputeNBondAtom::unpack_reverse_comm(int n, int *list, double *buf)
nbond[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int ComputeNBondAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = nbond[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeNBondAtom::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) nbond[i] = buf[m++];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array

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@ -32,8 +32,6 @@ class ComputeNBondAtom : public Compute {
void compute_peratom() override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
double memory_usage() override;
private: