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Adding option to doc files, clarifying normal forces in compute pair/bond local

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This commit is contained in:
jtclemm
2023-05-19 13:51:53 -06:00
parent 7ec842d9cb
commit cb5934cbcd
4 changed files with 20 additions and 3 deletions
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6
doc/src/bond_bpm_rotational.rst
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@ -30,6 +30,9 @@ Syntax
*smooth* value = *yes* or *no* *smooth* value = *yes* or *no*
smooths bond forces near the breaking point smooths bond forces near the breaking point
*normalize* value = *yes* or *no*
normalizes normal and shear forces by the reference length
*break/no* *break/no*
indicates that bonds should not break during a run indicates that bonds should not break during a run
@ -136,6 +139,9 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\gamma_r` (force*distance/velocity units) * :math:`\gamma_r` (force*distance/velocity units)
* :math:`\gamma_t` (force*distance/velocity units) * :math:`\gamma_t` (force*distance/velocity units)
However, the *normalize* option will normalize the radial and shear forces
by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
By default, pair forces are not calculated between bonded particles. By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific the *overlay/pair* keyword. These settings require specific

8
doc/src/bond_bpm_spring.rst
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@ -30,6 +30,9 @@ Syntax
*smooth* value = *yes* or *no* *smooth* value = *yes* or *no*
smooths bond forces near the breaking point smooths bond forces near the breaking point
*normalize* value = *yes* or *no*
normalizes bond forces by their reference length
*break/no* *break/no*
indicates that bonds should not break during a run indicates that bonds should not break during a run
@ -66,7 +69,7 @@ particles based on a model described by Clemmer and Robbins
F = k (r - r_0) w F = k (r - r_0) w
where :math:`k_r` is a stiffness, :math:`r` is the current distance where :math:`k` is a stiffness, :math:`r` is the current distance
and :math:`r_0` is the initial distance between the two particles, and and :math:`r_0` is the initial distance between the two particles, and
:math:`w` is an optional smoothing factor discussed below. Bonds will :math:`w` is an optional smoothing factor discussed below. Bonds will
break at a strain of :math:`\epsilon_c`. This is done by setting by break at a strain of :math:`\epsilon_c`. This is done by setting by
@ -102,6 +105,9 @@ the data file or restart files read by the :doc:`read_data
* :math:`\epsilon_c` (unit less) * :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units) * :math:`\gamma` (force/velocity units)
However, the *normalize* option will normalize the elastic bond force by
:math:`r_0` such that :math:`k` is unit less.
By default, pair forces are not calculated between bonded particles. By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific the *overlay/pair* keyword. These settings require specific

5
doc/src/compute_bond_local.rst
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@ -76,7 +76,10 @@ The value *force* is the magnitude of the force acting between the
pair of atoms in the bond. pair of atoms in the bond.
The values *fx*, *fy*, and *fz* are the xyz components of The values *fx*, *fy*, and *fz* are the xyz components of
*force* between the pair of atoms in the bond. *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 remaining properties are all computed for motion of the two atoms The remaining properties are all computed for motion of the two atoms
relative to the center of mass (COM) velocity of the 2 atoms in the relative to the center of mass (COM) velocity of the 2 atoms in the

4
doc/src/compute_pair_local.rst
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@ -66,7 +66,9 @@ 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 The value *force* is the force acting between the pair of atoms, which
is positive for a repulsive force and negative for an attractive 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. The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
*force* on atom I. *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.
A pair style may define additional pairwise quantities which can be 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. accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.