Removing unneeded feature
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@ -65,9 +65,9 @@ Various properties of bonds can be computed using the
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:doc:`compute property/bond <compute_property_bond>` command. This
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command allows one to access data saved to the bond's history
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such as the reference length of the bond. More information on
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historical data can be found on the documentation pages for the specific
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BPM bond styles. Finally, this data can be output using `dump local <dump>`.
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As one may output many columns from the same compute, the
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bond history data can be found on the documentation pages for the specific
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BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
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command. As one may output many columns from the same compute, the
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:doc:`dump modify <dump_modify>` *colname* option may be used to provide
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more helpful column names. An example of this procedure is found in
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/examples/bpm/pour/. External software, such as OVITO, can read these dump
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@ -80,13 +80,16 @@ As bonds can be broken between neighbor list builds, the
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bond styles. There are two possible settings which determine how pair
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interactions work between bonded particles. First, one can overlay
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pair forces with bond forces such that all bonded particles also
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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
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feel pair interactions. This can be accomplished by using the *overlay/pair*
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keyword present in all bpm bond styles and by using the following special
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bond settings
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.. code-block:: LAMMPS
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special_bonds lj/coul 1 1 1
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Alternatively, one can turn off all pair interactions between bonded particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
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Alternatively, one can turn off all pair interactions between bonded
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particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
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by subtracting pair forces during the bond computation but rather by
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dynamically updating the special bond list. This is the default behavior
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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
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:doc:`binary restart files <restart>`. Loading a restart file will
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properly resume bonds. However, the reference state is NOT
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written to data files. Therefore reading a data file will not
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restore bonds which will recalculate their reference state.
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restore bonds and will cause their reference states to be redefined.
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The single() function of these pair styles returns 0.0 for the energy
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of a pairwise interaction, since energy is not conserved in these
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@ -207,11 +207,12 @@ of a bonded interaction, since energy is not conserved in these
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dissipative potentials. It also returns only the normal component of
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the bonded interaction force. However, the single() function also
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calculates 7 extra bond quantities. The first 4 are data from the
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reference state of the bond including the magnitude :math:`r_0`
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followed by the :math:`x`, :math:`y`, and :math:`z` components of the
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initial unit vector pointing to particle I from particle J. The next 3
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(5-7) are the components of the total force, including normal and
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tangential contributions, acting on particle I.
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reference state of the bond including the initial distance between particles
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:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
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of the initial unit vector pointing to particle I from particle J. The next 3
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quantities (5-7) are the :math:`x`, :math:`y`, and :math:`z` components
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of the total force, including normal and tangential contributions, acting
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on particle I.
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These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
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command, as *b1*, *b2*, ..., *b7*\ .
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@ -143,7 +143,7 @@ This bond style writes the reference state of each bond to
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:doc:`binary restart files <restart>`. Loading a restart
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file will properly restore bonds. However, the reference state is NOT
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written to data files. Therefore reading a data file will not
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restore bonds which will recalculate their reference state.
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restore bonds and will cause their reference states to be redefined.
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The single() function of these pair styles returns 0.0 for the energy
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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
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force or to exclude this pair interaction such that the two particles
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only interact via the bond force. See discussion of the *overlay/pair*
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option for BPM bond styles and the :doc:`special_bonds <special_bonds>`
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command in the `:doc: how to <Howto_BPM>` page on BPMs for more details.
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command in the :doc:`how to <Howto_BPM>` page on BPMs for more details.
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The following coefficients must be defined for each pair of atom types
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via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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@ -29,17 +29,11 @@ using namespace LAMMPS_NS;
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ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
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Compute(_lmp, narg, arg), nbond(nullptr)
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{
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if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute nbond/atom command");
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if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command");
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peratom_flag = 1;
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size_peratom_cols = 0;
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comm_reverse = 1;
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comm_forward = 0;
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if (narg == 4) {
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if (utils::strmatch(arg[3], "forward")) comm_forward = 1;
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else error->all(FLERR, "Illegal compute nbond/atom argument {}", arg[3]);
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}
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nmax = 0;
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}
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@ -106,9 +100,6 @@ void ComputeNBondAtom::compute_peratom()
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for (i = 0; i < nlocal; i++)
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if (!(mask[i] & groupbit)) nbond[i] = 0.0;
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// forward to ghosts if requested
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if (comm_forward != 0) comm->forward_comm(this);
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}
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/* ---------------------------------------------------------------------- */
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@ -135,31 +126,6 @@ void ComputeNBondAtom::unpack_reverse_comm(int n, int *list, double *buf)
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nbond[j] += buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeNBondAtom::pack_forward_comm(int n, int *list, double *buf,
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int /*pbc_flag*/, int * /*pbc*/)
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{
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int i,j,m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = nbond[j];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeNBondAtom::unpack_forward_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) nbond[i] = buf[m++];
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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@ -32,8 +32,6 @@ class ComputeNBondAtom : public Compute {
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void compute_peratom() override;
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int pack_reverse_comm(int, int, double *) override;
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void unpack_reverse_comm(int, int *, double *) override;
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int pack_forward_comm(int, int *, double *, int, int *) override;
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void unpack_forward_comm(int, int, double *) override;
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double memory_usage() override;
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private:
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