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remove directionCorrection and update docs for compute pair/local and compute bond/local

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This commit is contained in:
Axel Kohlmeyer
2025-05-15 23:15:26 -04:00
parent c3c0180649
commit 5fd4d6bb87
4 changed files with 46 additions and 31 deletions
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32
doc/src/compute_bond_local.rst
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@ -64,22 +64,32 @@ All these properties are computed for the pair of atoms in a bond,
whether the two atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value *dist* is the current length of the bond.
The values *dx*, *dy*, and *dz* are the xyz components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of lower to the one with the higher id.
.. versionchanged:: TBD
The sign of *dx*, *dy*, *dz* is no longer determined by the atom IDs
of the bonded atoms but by their order in the bond list to be
consistent with *fx*, *fy*, and *fz*.
The value *dist* is the current length of the bond. The values *dx*,
*dy*, and *dz* are the :math:`(x,y,z)` components of the distance vector
:math:`\vec{x_i} - \vec{x_j}` between the atoms in the bond. The order
of the atoms is determined by the bond list and the respective atom-IDs
can be output with :doc:`compute property/local
<compute_property_local>`.
The value *engpot* is the potential energy for the bond,
based on the current separation of the pair of atoms in the bond.
The value *force* is the magnitude of the force acting between the
pair of atoms in the bond.
The value *force* is the magnitude of the force acting between the pair
of atoms in the bond, which is positive for a repulsive force and
negative for an attractive force.
The values *fx*, *fy*, and *fz* are the xyz components of
*force* between the pair of atoms in the bond. For bond styles that apply
non-central forces, such as :doc:`bond_style bpm/rotational
<bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
components of the normal force component.
The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
the force vector on atom *i* obtained by projecting *force* on the
distance vector. For bond styles that apply non-central forces, such as
:doc:`bond_style bpm/rotational <bond_bpm_rotational>`, these values
only include the :math:`(x,y,z)` components of the normal force
component.
The remaining properties are all computed for motion of the two atoms
relative to the center of mass (COM) velocity of the two atoms in the

27
doc/src/compute_pair_local.rst
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@ -56,19 +56,30 @@ force cutoff distance for that interaction, as defined by the
:doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
commands.
The value *dist* is the distance between the pair of atoms.
The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of higher to the one with the lower atom ID.
.. versionchanged:: TBD
The sign of *dx*, *dy*, *dz* is no longer determined by the value of
their atom-IDs but by their order in the neighbor list to be
consistent with *fx*, *fy*, and *fz*.
The value *dist* is the distance between the pair of atoms. The values
*dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the distance
vector :math:`\vec{x_i} - \vec{x_j}` between the pair of atoms. The
order of the atoms is determined by the neighbor list and the respective
atom-IDs can be output with :doc:`compute property/local
<compute_property_local>`.
The value *eng* is the interaction energy for the pair of atoms.
The value *force* is the force acting between the pair of atoms, which
is positive for a repulsive force and negative for an attractive
force. The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
*force* on atom I. For pair styles that apply non-central forces,
such as :doc:`granular pair styles <pair_gran>`, these values only include
the :math:`(x,y,z)` components of the normal force component.
force.
The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
the force vector on atom *i* obtained by projecting *force* on the
distance vector. For pair styles that apply non-central forces, such as
:doc:`granular pair styles <pair_gran>`, these values only include the
:math:`(x,y,z)` components of the normal force component.
A pair style may define additional pairwise quantities which can be
accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

9
src/compute_bond_local.cpp
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@ -428,22 +428,19 @@ int ComputeBondLocal::compute_bonds(int flag)
if (dstr) input->variable->internal_set(dvar, sqrt(rsq));
}
// to make sure dx, dy and dz are always from the lower to the higher id
double directionCorrection = tag[atom1] > tag[atom2] ? -1.0 : 1.0;
for (int n = 0; n < nvalues; n++) {
switch (bstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case DX:
ptr[n] = dx * directionCorrection;
ptr[n] = dx;
break;
case DY:
ptr[n] = dy * directionCorrection;
ptr[n] = dy;
break;
case DZ:
ptr[n] = dz * directionCorrection;
ptr[n] = dz;
break;
case ENGPOT:
ptr[n] = engpot;

9
src/compute_pair_local.cpp
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@ -277,22 +277,19 @@ int ComputePairLocal::compute_pairs(int flag)
else
ptr = alocal[m];
// to make sure dx, dy and dz are always from the lower to the higher id
double directionCorrection = itag > jtag ? -1.0 : 1.0;
for (n = 0; n < nvalues; n++) {
switch (pstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case DX:
ptr[n] = delx * directionCorrection;
ptr[n] = delx;
break;
case DY:
ptr[n] = dely * directionCorrection;
ptr[n] = dely;
break;
case DZ:
ptr[n] = delz * directionCorrection;
ptr[n] = delz;
break;
case ENG:
ptr[n] = eng;