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Merge branch 'develop' into collected-small-fixes

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Axel Kohlmeyer
2023-06-07 20:05:06 -04:00
parent 491e152289 5fdba37492
commit 9235377b44
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1
doc/src/Commands_pair.rst
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@ -37,6 +37,7 @@ OPT.
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba (g) <pair_amoeba>`

18
doc/src/bond_bpm_rotational.rst
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@ -24,14 +24,17 @@ Syntax
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
*overlay/pair* value = none
*overlay/pair* value = *yes* or *no*
bonded particles will still interact with pair forces
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
*normalize* value = *yes* or *no*
normalizes normal and shear forces by the reference length
*break* value = *yes* or *no*
indicates whether bonds break during a run
Examples
""""""""
@ -136,16 +139,19 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\gamma_r` (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.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific
the *overlay/pair* option. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
If the *break* option is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
@ -251,7 +257,7 @@ Related commands
Default
"""""""
The option defaults are *smooth* = *yes*
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
----------

20
doc/src/bond_bpm_spring.rst
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@ -24,14 +24,17 @@ Syntax
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
*overlay/pair* value = none
*overlay/pair* value = *yes* or *no*
bonded particles will still interact with pair forces
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
*normalize* value = *yes* or *no*
normalizes bond forces by the reference length
*break* value = *yes* or *no*
indicates whether bonds break during a run
Examples
""""""""
@ -66,7 +69,7 @@ particles based on a model described by Clemmer and Robbins
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
: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
@ -102,16 +105,19 @@ the data file or restart files read by the :doc:`read_data
* :math:`\epsilon_c` (unit less)
* :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.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific
the *overlay/pair* option. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
If the *break* option is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
@ -206,7 +212,7 @@ Related commands
Default
"""""""
The option defaults are *smooth* = *yes*
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
----------

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.
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
relative to the center of mass (COM) velocity of the 2 atoms in the

12
doc/src/compute_fabric.rst
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@ -146,13 +146,13 @@ m to :math:`M` (inclusive). A middle asterisk means all types from m to n
Output info
"""""""""""
This compute calculates a local vector of doubles and a scalar. The vector
stores the unique components of the first requested tensor in the order
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`
followed by the same components for all subsequent tensors.
This compute calculates a global vector of doubles and a global scalar. The
vector stores the unique components of the first requested tensor in the
order :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz` followed by the same components for all subsequent tensors.
The length of the vector is therefore six times the number of requested
tensors. The scalar output is the number of pairwise interactions included in
the calculation of the fabric tensor.
tensors. The scalar output is the number of pairwise interactions included
in the calculation of the fabric tensor.
Restrictions
""""""""""""

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
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.
*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
accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

167
doc/src/pair_aip_water_2dm.rst Normal file
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@ -0,0 +1,167 @@
.. index:: pair_style aip/water/2dm
.. index:: pair_style aip/water/2dm/opt
pair_style aip/water/2dm command
===================================
Accelerator Variant: *aip/water/2dm/opt*
Syntax
""""""
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] aip/water/2dm cutoff tap_flag
* cutoff = global cutoff (distance units)
* tap_flag = 0/1 to turn off/on the taper function
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay aip/water/2dm 16.0 1
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
Description
"""""""""""
.. versionadded:: TBD
The *aip/water/2dm* style computes the anisotropic interfacial potential
(AIP) potential for interfaces of water with two-dimensional (2D)
materials as described in :ref:`(Feng) <Feng>`.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
a continuous cutoff (up to third derivative) for interatomic separations
larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
<pair_ilp_graphene_hbn>`.
.. note::
This pair style uses the atomic normal vector definition from
:ref:`(Feng) <Feng>`), where the atomic normal vectors of the
hydrogen atoms are assumed to lie along the corresponding
oxygen-hydrogen bonds and the normal vector of the central oxygen
atom is defined as their average.
The provided parameter file, ``COH.aip.water.2dm``, is intended for use
with *metal* :doc:`units <units>`, with energies in meV. Two additional
parameters, *S*, and *rcut* are included in the parameter file. *S* is
designed to facilitate scaling of energies; *rcut* is the cutoff for an
internal, short distance neighbor list that is generated for speeding up
the calculation of the normals for all atom pairs.
.. note::
The parameters presented in the provided parameter file,
``COH.aip.water.2dm``, are fitted with the taper function enabled by
setting the cutoff equal to 16.0 Angstrom. Using a different cutoff
or taper function setting should be carefully checked as they can
lead to significant errors. These parameters provide a good
description in both short- and long-range interaction regimes. This
is essential for simulations in high pressure regime (i.e., the
interlayer distance is smaller than the equilibrium distance).
This potential must be used in combination with hybrid/overlay. Other
interactions can be set to zero using :doc:`pair_coeff settings
<pair_coeff>` with the pair style set to *none*\ .
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the :doc:`compute
pair <compute_pair>` command as a vector of values of length 2. The 2
values correspond to the following sub-categories:
1. *E_vdW* = vdW (attractive) energy
2. *E_Rep* = Repulsive energy
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute 0 all pair aip/water/2dm
variable Evdw equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step temp epair v_Erep v_Evdw
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support the pair_modify mix, shift, table, and
tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
Restrictions
""""""""""""
This pair style is part of the INTERLAYER package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the newton setting to be *on* for pair
interactions.
The ``COH.aip.water.2dm`` potential file provided with LAMMPS is
parameterized for *metal* units. You can use this pair style with any
LAMMPS units, but you would need to create your own potential file with
parameters in the appropriate units, if your simulation does not use
*metal* units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_none <pair_none>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style drip <pair_drip>`,
:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
:doc:`pair_style saip_metal <pair_saip_metal>`,
:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
Default
"""""""
tap_flag = 1
----------
.. _Feng:
**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).

2
doc/src/pair_granular.rst
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@ -736,7 +736,7 @@ or
.. math::
E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})}
E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij}^2)}
These pair styles write their information to :doc:`binary restart files <restart>`, so a pair_style command does not need to be
specified in an input script that reads a restart file.

20
doc/src/pair_ilp_graphene_hbn.rst
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@ -155,8 +155,8 @@ interactions.
The BNCH.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom BNCH.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands
@ -181,6 +181,14 @@ tap_flag = 1
----------
.. _Ouyang1:
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang2:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
.. _Leven1:
**(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
@ -196,11 +204,3 @@ tap_flag = 1
.. _Kolmogorov2:
**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
.. _Ouyang1:
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang2:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

4
doc/src/pair_ilp_tmd.rst
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@ -135,8 +135,8 @@ interactions.
The TMD.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom TMD.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands

2
doc/src/pair_kolmogorov_crespi_full.rst
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@ -129,7 +129,7 @@ interactions.
The CH.KC potential file provided with LAMMPS (see the potentials
folder) is parameterized for metal units. You can use this pair style
with any LAMMPS units, but you would need to create your own custom
CC.KC potential file with all coefficients converted to the appropriate
CH.KC potential file with all coefficients converted to the appropriate
units.
Related commands

4
doc/src/pair_saip_metal.rst
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@ -134,8 +134,8 @@ interactions.
The CHAu.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom CHAu.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands

1
doc/src/pair_style.rst
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@ -114,6 +114,7 @@ accelerated styles exist.
* :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
* :doc:`agni <pair_agni>` - AGNI machine-learning potential
* :doc:`aip/water/2dm <pair_aip_water_2dm>` - anisotropic interfacial potential for water in 2d geometries
* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`amoeba <pair_amoeba>` -