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Merge branch 'develop' into collected-small-changes

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Axel Kohlmeyer
2024-06-19 12:02:56 -04:00
parent d54f38ff62 4e0bf6137d
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1
.github/CODEOWNERS vendored
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@ -38,6 +38,7 @@ src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde src/ML-POD/* @exapde
src/ML-UF3/* @monk-04
src/MOFFF/* @hheenen src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka src/NETCDF/* @pastewka

1
cmake/CMakeLists.txt
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@ -285,6 +285,7 @@ set(STANDARD_PACKAGES
ML-RANN ML-RANN
ML-SNAP ML-SNAP
ML-POD ML-POD
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
MOLFILE MOLFILE

1
cmake/presets/all_off.cmake
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@ -60,6 +60,7 @@ set(ALL_PACKAGES
ML-QUIP ML-QUIP
ML-RANN ML-RANN
ML-SNAP ML-SNAP
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
MOLFILE MOLFILE

1
cmake/presets/all_on.cmake
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@ -62,6 +62,7 @@ set(ALL_PACKAGES
ML-QUIP ML-QUIP
ML-RANN ML-RANN
ML-SNAP ML-SNAP
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
MOLFILE MOLFILE

1
cmake/presets/mingw-cross.cmake
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@ -50,6 +50,7 @@ set(WIN_PACKAGES
ML-POD ML-POD
ML-RANN ML-RANN
ML-SNAP ML-SNAP
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
MOLFILE MOLFILE

1
cmake/presets/most.cmake
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@ -45,6 +45,7 @@ set(ALL_PACKAGES
ML-IAP ML-IAP
ML-POD ML-POD
ML-SNAP ML-SNAP
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
OPENMP OPENMP

1
cmake/presets/windows.cmake
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@ -42,6 +42,7 @@ set(WIN_PACKAGES
ML-IAP ML-IAP
ML-POD ML-POD
ML-SNAP ML-SNAP
ML-UF3
MOFFF MOFFF
MOLECULE MOLECULE
MOLFILE MOLFILE

11
doc/src/Commands_pair.rst
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@ -25,16 +25,16 @@ OPT.
* :doc:`none <pair_none>` * :doc:`none <pair_none>`
* :doc:`zero <pair_zero>` * :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>` * :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>` * :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>` * :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>` * :doc:`kim <pair_kim>`
* :doc:`list <pair_list>` * :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>` * :doc:`tracker <pair_tracker>`
* *
* *
* *
*
* :doc:`adp (ko) <pair_adp>` * :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>` * :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>` * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -269,7 +269,7 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>` * :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>` * :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>` * :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>` * :doc:`soft (gko) <pair_soft>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>` * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>` * :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj (g) <pair_sph_lj>` * :doc:`sph/lj (g) <pair_sph_lj>`
@ -303,6 +303,7 @@ OPT.
* :doc:`tip4p/long/soft (o) <pair_fep_soft>` * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>` * :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>` * :doc:`ufm (got) <pair_ufm>`
* :doc:`uf3 (k) <pair_uf3>`
* :doc:`vashishta (gko) <pair_vashishta>` * :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>` * :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>` * :doc:`wf/cut <pair_wf_cut>`

26
doc/src/Packages_details.rst
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@ -84,6 +84,7 @@ page gives those details.
* :ref:`ML-QUIP <PKG-ML-QUIP>` * :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>` * :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`ML-SNAP <PKG-ML-SNAP>` * :ref:`ML-SNAP <PKG-ML-SNAP>`
* :ref:`ML-UF3 <PKG-ML-UF3>`
* :ref:`MOFFF <PKG-MOFFF>` * :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLECULE <PKG-MOLECULE>` * :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>` * :ref:`MOLFILE <PKG-MOLFILE>`
@ -1925,6 +1926,31 @@ computes which analyze attributes of the potential.
---------- ----------
.. _PKG-ML-UF3:
ML-UF3 package
--------------
**Contents:**
A pair style for the ultra-fast force field potentials (UF3). UF3 is a
methodology for deriving a highly accurate classical potential which is
fast to evaluate and is fitted to a large archives of quantum mechanical
(DFT) data. The use of b-spline basis set in UF3 enables the rapid
evaluation of 2-body and 3-body interactions.
**Authors:** Ajinkya C Hire (University of Florida),
Hendrik Krass (University of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (University of Florida)
**Supporting info:**
* src/ML-UF3: filenames -> commands
* :doc:`pair_style uf3 <pair_uf3>`
* examples/uf3
* https://github.com/uf3/uf3
.. _PKG-MOFFF: .. _PKG-MOFFF:
MOFFF package MOFFF package

5
doc/src/Packages_list.rst
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@ -318,6 +318,11 @@ whether an extra library is needed to build and use the package:
- :doc:`pair_style snap <pair_snap>` - :doc:`pair_style snap <pair_snap>`
- snap - snap
- no - no
* - :ref:`ML-UF3 <PKG-ML-UF3>`
- quantum-fitted ultra fast potentials
- :doc:`pair_style uf3 <pair_uf3>`
- PACKAGES/uf3
- no
* - :ref:`MOFFF <PKG-MOFFF>` * - :ref:`MOFFF <PKG-MOFFF>`
- styles for `MOF-FF <MOFplus_>`_ force field - styles for `MOF-FF <MOFplus_>`_ force field
- :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` - :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`

2
doc/src/fix_deform.rst
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@ -64,6 +64,8 @@ Syntax
effectively an engineering shear strain rate effectively an engineering shear strain rate
*erate* value = R *erate* value = R
R = engineering shear strain rate (1/time units) R = engineering shear strain rate (1/time units)
*erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
R = engineering shear strain rate (1/time units)
*trate* value = R *trate* value = R
R = true shear strain rate (1/time units) R = true shear strain rate (1/time units)
*wiggle* values = A Tp *wiggle* values = A Tp

12
doc/src/fix_wall_gran.rst
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@ -115,6 +115,18 @@ friction and twisting friction supported by the :doc:`pair_style granular <pair_
supported for walls. These are discussed in greater detail on the doc supported for walls. These are discussed in greater detail on the doc
page for :doc:`pair_style granular <pair_granular>`. page for :doc:`pair_style granular <pair_granular>`.
.. note::
When *fstyle* *granular* is specified, the associated *fstyle_params* are taken as
those for a wall/particle interaction. For example, for the *hertz/material* normal
contact model with :math:`E = 960` and :math:`\nu = 0.2`, the effective Young's
modulus for a wall/particle interaction is computed as
:math:`E_{eff} = \frac{960}{2(1-0.2^2)} = 500`. Any pair coefficients defined by
:doc:`pair_style granular <pair_granular>` are not taken into consideration. To
model different wall/particle interactions for particles of different material
types, the user may define multiple fix wall/gran commands operating on separate
groups (e.g. based on particle type) each with a different wall/particle effective
Young's modulus.
Note that you can choose a different force styles and/or different Note that you can choose a different force styles and/or different
values for the wall/particle coefficients than for particle/particle values for the wall/particle coefficients than for particle/particle
interactions. E.g. if you wish to model the wall as a different interactions. E.g. if you wish to model the wall as a different

30
doc/src/pair_granular.rst
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@ -111,7 +111,7 @@ For the *hertz* model, the normal component of force is given by:
\mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} \mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective Here, :math:`R_{eff} = R = \frac{R_i R_j}{R_i + R_j}` is the effective
radius, denoted for simplicity as *R* from here on. For *hertz*, the radius, denoted for simplicity as *R* from here on. For *hertz*, the
units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or
equivalently *pressure*\ . equivalently *pressure*\ .
@ -120,13 +120,14 @@ For the *hertz/material* model, the force is given by:
.. math:: .. math::
\mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R^{1/2}\delta_{ij}^{3/2} \mathbf{n}
Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` is the effective Young's Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}`
modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of is the effective Young's modulus, with :math:`\nu_i, \nu_j` the Poisson ratios
types *i* and *j*\ . Note that if the elastic modulus and the shear of the particles of types *i* and *j*. :math:`E_{eff}` is denoted as *E* from here on.
modulus of the two particles are the same, the *hertz/material* model Note that if the elastic modulus and the shear modulus of the two particles are the
is equivalent to the *hertz* model with :math:`k_n = 4/3 E_{eff}` same, the *hertz/material* model is equivalent to the *hertz* model with
:math:`k_n = 4/3 E`
The *dmt* model corresponds to the The *dmt* model corresponds to the
:ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force :ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
@ -270,7 +271,8 @@ where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since
*coeff_restitution* accounts for the effective mass, effective radius, and *coeff_restitution* accounts for the effective mass, effective radius, and
pairwise overlaps (except when used with the *hooke* normal model) when calculating pairwise overlaps (except when used with the *hooke* normal model) when calculating
the damping coefficient, it accurately reproduces the specified coefficient of the damping coefficient, it accurately reproduces the specified coefficient of
restitution for both monodisperse and polydisperse particle pairs. restitution for both monodisperse and polydisperse particle pairs. This damping
model is not compatible with cohesive normal models such as *JKR* or *DMT*.
The total normal force is computed as the sum of the elastic and The total normal force is computed as the sum of the elastic and
damping components: damping components:
@ -441,11 +443,11 @@ discussion above. To match the Mindlin solution, one should set
G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1} G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1}
where :math:`G` is the shear modulus, related to Young's modulus :math:`E` where :math:`G_i` is the shear modulus of a particle of type :math:`i`, related to Young's
and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be modulus :math:`E_i` and Poisson's ratio :math:`\nu_i` by :math:`G_i = E_i/(2(1+\nu_i))`.
achieved by specifying *NULL* for :math:`k_t`, in which case a This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
normal contact model that specifies material parameters :math:`E` and normal contact model that specifies material parameters :math:`E_i` and
:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this :math:`\nu_i` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this
case, mixing of the shear modulus for different particle types *i* and case, mixing of the shear modulus for different particle types *i* and
*j* is done according to the formula above. *j* is done according to the formula above.
@ -575,7 +577,7 @@ opposite torque on each particle, according to:
.. math:: .. math::
\tau_{roll,i} = R_{eff} \mathbf{n} \times \mathbf{F}_{roll} \tau_{roll,i} = R \mathbf{n} \times \mathbf{F}_{roll}
.. math:: .. math::

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doc/src/pair_hybrid.rst
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@ -1,28 +1,41 @@
.. index:: pair_style hybrid .. index:: pair_style hybrid
.. index:: pair_style hybrid/kk .. index:: pair_style hybrid/kk
.. index:: pair_style hybrid/omp
.. index:: pair_style hybrid/molecular
.. index:: pair_style hybrid/molecular/omp
.. index:: pair_style hybrid/overlay .. index:: pair_style hybrid/overlay
.. index:: pair_style hybrid/overlay/omp
.. index:: pair_style hybrid/overlay/kk .. index:: pair_style hybrid/overlay/kk
.. index:: pair_style hybrid/scaled .. index:: pair_style hybrid/scaled
.. index:: pair_style hybrid/scaled/omp
pair_style hybrid command pair_style hybrid command
========================= =========================
Accelerator Variants: *hybrid/kk* Accelerator Variants: *hybrid/kk*, *hybrid/omp*
pair_style hybrid/molecular command
===================================
Accelerator Variant: *hybrid/molecular/omp*
pair_style hybrid/overlay command pair_style hybrid/overlay command
================================= =================================
Accelerator Variants: *hybrid/overlay/kk* Accelerator Variants: *hybrid/overlay/kk*, *hybrid/overlay/omp*
pair_style hybrid/scaled command pair_style hybrid/scaled command
================================== ==================================
Accelerator Variant: *hybrid/scaled/omp*
Syntax Syntax
"""""" """"""
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style hybrid style1 args style2 args ... pair_style hybrid style1 args style2 args ...
pair_style hybrid/molecular factor1 style1 args factor2 style 2 args
pair_style hybrid/overlay style1 args style2 args ... pair_style hybrid/overlay style1 args style2 args ...
pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ... pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
@ -47,6 +60,10 @@ Examples
pair_coeff * * tersoff Si.tersoff Si pair_coeff * * tersoff Si.tersoff Si
pair_coeff * * sw Si.sw Si pair_coeff * * sw Si.sw Si
pair_style hybrid/molecular lj/cut 2.5 lj/cut 2.5
pair_coeff * * lj/cut 1 1.0 1.0
pair_coeff * * lj/cut 2 1.5 1.0
variable one equal ramp(1.0,0.0) variable one equal ramp(1.0,0.0)
variable two equal 1.0-v_one variable two equal 1.0-v_one
pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5 pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
@ -56,17 +73,26 @@ Examples
Description Description
""""""""""" """""""""""
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled*
use of multiple pair styles in one simulation. With the *hybrid* style, styles enable the use of multiple pair styles in one simulation. With
exactly one pair style is assigned to each pair of atom types. With the the *hybrid* style, exactly one pair style is assigned to each pair of
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one
be assigned to each pair of atom types. The assignment of pair styles or more pair styles can be assigned to each pair of atom types. With
to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command. the hybrid/molecular style, pair styles are assigned to either intra-
The major difference between the *hybrid/overlay* and *hybrid/scaled* or inter-molecular interactions.
styles is that the *hybrid/scaled* adds a scale factor for each
sub-style contribution to forces, energies and stresses. Because of the The assignment of pair styles to type pairs is made via the
added complexity, the *hybrid/scaled* style has more overhead and thus :doc:`pair_coeff <pair_coeff>` command. The major difference between
may be slower than *hybrid/overlay*. the *hybrid/overlay* and *hybrid/scaled* styles is that the
*hybrid/scaled* adds a scale factor for each sub-style contribution to
forces, energies and stresses. Because of the added complexity, the
*hybrid/scaled* style has more overhead and thus may be slower than
*hybrid/overlay*.
The *hybrid/molecular* pair style accepts *only* two sub-styles: the
first is assigned to intra-molecular interactions (i.e. both atoms
have the same molecule ID), the second to inter-molecular interactions
(i.e. interacting atoms have different molecule IDs).
Here are two examples of hybrid simulations. The *hybrid* style could Here are two examples of hybrid simulations. The *hybrid* style could
be used for a simulation of a metal droplet on a LJ surface. The metal be used for a simulation of a metal droplet on a LJ surface. The metal
@ -476,6 +502,8 @@ the same or else LAMMPS will generate an error.
Pair style *hybrid/scaled* currently only works for non-accelerated Pair style *hybrid/scaled* currently only works for non-accelerated
pair styles and pair styles from the OPT package. pair styles and pair styles from the OPT package.
Pair style *hybrid/molecular* is not compatible with manybody potentials.
When using pair styles from the GPU package they must not be listed When using pair styles from the GPU package they must not be listed
multiple times. LAMMPS will detect this and abort. multiple times. LAMMPS will detect this and abort.

3
doc/src/pair_soft.rst
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@ -1,11 +1,12 @@
.. index:: pair_style soft .. index:: pair_style soft
.. index:: pair_style soft/gpu .. index:: pair_style soft/gpu
.. index:: pair_style soft/kk
.. index:: pair_style soft/omp .. index:: pair_style soft/omp
pair_style soft command pair_style soft command
======================= =======================
Accelerator Variants: *soft/gpu*, *soft/omp* Accelerator Variants: *soft/gpu*, *soft/kk*, *soft/omp*
Syntax Syntax
"""""" """"""

2
doc/src/pair_style.rst
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@ -108,6 +108,7 @@ accelerated styles exist.
* :doc:`none <pair_none>` - turn off pairwise interactions * :doc:`none <pair_none>` - turn off pairwise interactions
* :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions * :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
* :doc:`hybrid/molecular <pair_hybrid>` - different pair styles for intra- and inter-molecular interactions
* :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions * :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
* :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions * :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
* :doc:`zero <pair_zero>` - neighbor list but no interactions * :doc:`zero <pair_zero>` - neighbor list but no interactions
@ -382,6 +383,7 @@ accelerated styles exist.
* :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions * :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions
* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles * :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
* :doc:`ufm <pair_ufm>` - * :doc:`ufm <pair_ufm>` -
* :doc:`uf3 <pair_uf3>` - UF3 machine-learning potential
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential * :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
* :doc:`vashishta/table <pair_vashishta>` - * :doc:`vashishta/table <pair_vashishta>` -
* :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions * :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions

213
doc/src/pair_uf3.rst Normal file
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@ -0,0 +1,213 @@
.. index:: pair_style uf3
.. index:: pair_style uf3/kk
pair_style uf3 command
======================
Accelerator Variants: *uf3/kk*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style BodyFlag
* style = *uf3* or *uf3/kk*
.. parsed-literal::
BodyFlag = Indicates whether to calculate only 2-body or 2 and 3-body interactions. Possible values: 2 or 3
Examples
""""""""
.. code-block:: LAMMPS
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
pair_style uf3 2
pair_coeff * * NbSn.uf3 Nb Sn
pair_style uf3 3
pair_coeff * * NbSn.uf3 Nb Sn
Description
"""""""""""
.. versionadded:: TBD
The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3)
<Xie23>` potential, a machine-learning interatomic potential. In UF3,
the total energy of the system is defined via two- and three-body
interactions:
.. math::
E & = \sum_{i,j} V_2(r_{ij}) + \sum_{i,j,k} V_3 (r_{ij},r_{ik},r_{jk}) \\
V_2(r_{ij}) & = \sum_{n=0}^N c_n B_n(r_{ij}) \\
V_3 (r_{ij},r_{ik},r_{jk}) & = \sum_{l=0}^{N_l} \sum_{m=0}^{N_m} \sum_{n=0}^{N_n} c_{l,m,n} B_l(r_{ij}) B_m(r_{ik}) B_n(r_{jk})
where :math:`V_2(r_{ij})` and :math:`V_3 (r_{ij},r_{ik},r_{jk})` are the
two- and three-body interactions, respectively. For the two-body the
summation is over all neighbors J and for the three-body the summation
is over all neighbors J and K of atom I within a cutoff distance
determined from the potential files. :math:`B_n(r_{ij})` are the cubic
b-spline basis, :math:`c_n` and :math:`c_{l,m,n}` are the machine-learned
interaction parameters and :math:`N`, :math:`N_l`, :math:`N_m`, and
:math:`N_n` denote the number of basis functions per spline or tensor
spline dimension.
With *uf3* style only a single pair_coeff command is used to indicate the
UF3 LAMMPS potential file containing all the two- and three-body interactions
followed by N additional arguments specifying the mapping of UF3 elements to
LAMMPS atom types, where N is the number of LAMMPS atom types:
* UF3 LAMMPS potential file
* N elements names = mapping of UF3 elements to atom types
As an example, if a LAMMPS simulation contains 2 atom types (elements
'A' and 'B'), the pair_coeff command will be:
.. code-block:: LAMMPS
pair_style uf3 3
pair_coeff * * AB.uf3 A B
The AB.uf3 file should contain all two-body (A-A, A-B, B-B) and three-body
(A-A-A, A-A-B, A-B-B, B-A-A, B-A-B, B-B-B).
If a value of "2" is specified in the :code:`pair_style uf3` command,
only the two-body potentials are needed. For 3-body interaction the
first atom type is the central atom. We recommend using the
:code:`generate_uf3_lammps_pots.py` script (found `here
<https://github.com/uf3/uf3/tree/develop/lammps_plugin/scripts>`_) for
generating the UF3 LAMMPS potential file from the UF3 JSON potentials.
----------
UF3 LAMMPS potential file in the *potentials* directory of the LAMMPS
distribution have a ".uf3" suffix. The interaction block in UF3 LAMMPS potential
file should start with :code:`#UF3 POT` and end with :code:`#` characters.
Following shows the format of a generic 2-body and 3-body potential block in
UF3 LAMMPS potential file-
.. code-block:: LAMMPS
#UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
2B ELEMENT1 ELEMENT2 LEADING_TRIM TRAILING_TRIM
Rij_CUTOFF NUM_OF_KNOTS
BSPLINE_KNOTS
NUM_OF_COEFF
COEFF
#
#UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
3B ELEMENT1 ELEMENT2 ELEMENT3 LEADING_TRIM TRAILING_TRIM
Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ
BSPLINE_KNOTS_FOR_JK
BSPLINE_KNOTS_FOR_IK
BSPLINE_KNOTS_FOR_IJ
SHAPE_OF_COEFF_MATRIX[I][J][K]
COEFF_MATRIX[0][0][K]
COEFF_MATRIX[0][1][K]
COEFF_MATRIX[0][2][K]
.
.
.
COEFF_MATRIX[1][0][K]
COEFF_MATRIX[1][1][K]
COEFF_MATRIX[1][2][K]
.
.
.
#
The second line indicates whether the block contains data for 2-body
(:code:`2B`) or 3-body (:code:`3B`) interaction. This is followed by element
combination interaction, :code:`LEADING_TRIM` and :code:`TRAILING_TRIM`
number on the same line. The current implementation is only tested for
:code:`LEADING_TRIM=0` and :code:`TRAILING_TRIM=3`.
If other values are used LAMMPS is terminated after issuing an error message.
The :code:`Rij_CUTOFF` sets the 2-body cutoff for the interaction described
by the potential block. :code:`NUM_OF_KNOTS` is the number of knots
(or the length of the knot vector) present on the very next line. The
:code:`BSPLINE_KNOTS` line should contain all the knots in ascending order.
:code:`NUM_OF_COEFF` is the number of coefficients in the :code:`COEFF` line.
All the numbers in the BSPLINE_KNOTS and COEFF line should be space-separated.
Similar to the 2-body potential block, the third line sets the cutoffs and
length of the knots. The cutoff distance between atom-type I and J is
:code:`Rij_CUTOFF`, atom-type I and K is :code:`Rik_CUTOFF` and between
J and K is :code:`Rjk_CUTOFF`.
.. note::
The current implementation only works for UF3 potentials with cutoff
distances for 3-body interactions that follows
:code:`2Rij_CUTOFF=2Rik_CUTOFF=Rjk_CUTOFF` relation.
The :code:`BSPLINE_KNOTS_FOR_JK`, :code:`BSPLINE_KNOTS_FOR_IK`, and
:code:`BSPLINE_KNOTS_FOR_IJ` lines (note the order) contain the knots in
increasing order for atoms J and K, I and K, and atoms I and J
respectively. The number of knots is defined by the
:code:`NUM_OF_KNOTS_*` characters in the previous line. The shape of
the coefficient matrix is defined on the
:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` line followed by the columns of
the coefficient matrix, one per line, as shown above. For example, if
the coefficient matrix has the shape of 8x8x13, then
:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` will be :code:`8 8 13` followed
by 64 (8x8) lines each containing 13 coefficients separated by space.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as described
above from values in the potential file.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
Restrictions
""""""""""""
The 'uf3' pair style is part of the ML-UF3 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 :doc:`newton <newton>` setting to be "on".
The UF3 LAMMPS potential file provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <units>`.
The single() function of 'uf3' pair style only return the 2-body
interaction energy.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none
----------
.. _Xie23:
**(Xie23)** Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7

6
doc/utils/sphinx-config/false_positives.txt
View File

@ -1434,6 +1434,7 @@ Hendrik
Henin Henin
Henkelman Henkelman
Henkes Henkes
Hennig
henrich henrich
Henrich Henrich
Hermitian Hermitian
@ -1595,6 +1596,7 @@ interlayer
intermolecular intermolecular
interoperable interoperable
Interparticle Interparticle
interpretable
interstitials interstitials
intertube intertube
Intr Intr
@ -1817,6 +1819,7 @@ Koziol
Kp Kp
kradius kradius
Kraker Kraker
Krass
Kraus Kraus
Kremer Kremer
Kress Kress
@ -3271,6 +3274,7 @@ Rudranarayan
Rudzinski Rudzinski
Runge Runge
runtime runtime
Rupp
Rutuparna Rutuparna
rx rx
rxd rxd
@ -3820,6 +3824,8 @@ uChem
uCond uCond
uef uef
UEF UEF
uf
uf3
ufm ufm
Uhlenbeck Uhlenbeck
Ui Ui

1
examples/PACKAGES/uf3/Nb.uf3 Symbolic link
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@ -0,0 +1 @@
../../../potentials/Nb.uf3

46
examples/PACKAGES/uf3/in.uf3.Nb Normal file
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@ -0,0 +1,46 @@
# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable ny equal ${nrep}
variable nz equal ${nrep}
boundary p p p
lattice bcc $a
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}

118
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@ -0,0 +1,118 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.3005
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
create_atoms CPU = 0.000 seconds
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
Reading potential file Nb.uf3 with DATE: 2024-04-02
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair uf3, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.376 | 3.376 | 3.376 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.4256832 0 -4.3872081 90756.437
10 294.36659 -4.4249607 0 -4.3872081 91006.427
20 277.9021 -4.422849 0 -4.387208 91716.126
30 251.88303 -4.4195119 0 -4.3872078 92789.12
40 218.42803 -4.4152211 0 -4.3872076 94118.45
50 180.40641 -4.4103445 0 -4.3872073 95579.009
60 141.2326 -4.4053202 0 -4.3872071 97031.816
70 104.54429 -4.4006146 0 -4.3872068 98332.882
80 73.787889 -4.3966699 0 -4.3872066 99351.332
90 51.759956 -4.3938446 0 -4.3872064 99992.934
100 40.209821 -4.3923633 0 -4.3872064 100211.98
Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms
Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38403 | 0.38403 | 0.38403 | 0.0 | 99.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090609 | 0.00090609 | 0.00090609 | 0.0 | 0.23
Output | 0.00017626 | 0.00017626 | 0.00017626 | 0.0 | 0.05
Modify | 0.00018204 | 0.00018204 | 0.00018204 | 0.0 | 0.05
Other | | 0.0002795 | | | 0.07
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1601 ave 1601 max 1601 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 21504 ave 21504 max 21504 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21504
Ave neighs/atom = 168
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

118
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@ -0,0 +1,118 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.3005
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
create_atoms CPU = 0.001 seconds
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
Reading potential file Nb.uf3 with DATE: 2024-04-02
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair uf3, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.351 | 3.351 | 3.351 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.4256832 0 -4.3872081 90756.437
10 294.36659 -4.4249607 0 -4.3872081 91006.427
20 277.9021 -4.422849 0 -4.387208 91716.126
30 251.88303 -4.4195119 0 -4.3872078 92789.12
40 218.42803 -4.4152211 0 -4.3872076 94118.45
50 180.40641 -4.4103445 0 -4.3872073 95579.009
60 141.2326 -4.4053202 0 -4.3872071 97031.816
70 104.54429 -4.4006146 0 -4.3872068 98332.882
80 73.787889 -4.3966699 0 -4.3872066 99351.332
90 51.759956 -4.3938446 0 -4.3872064 99992.934
100 40.209821 -4.3923633 0 -4.3872064 100211.98
Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms
Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10673 | 0.10875 | 0.11236 | 0.7 | 91.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0057324 | 0.0093477 | 0.011375 | 2.4 | 7.87
Output | 0.00016629 | 0.00018236 | 0.00022483 | 0.0 | 0.15
Modify | 9.4948e-05 | 0.00010621 | 0.00012066 | 0.0 | 0.09
Other | | 0.0004263 | | | 0.36
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1049 ave 1049 max 1049 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5376 ave 5376 max 5376 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21504
Ave neighs/atom = 168
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

136
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@ -0,0 +1,136 @@
#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
2B Nb Nb 0 3 nk
8.0 31
0.001 0.001 0.001 0.001 0.33429166666666665 0.66758333333333331 1.000875 1.3341666666666665 1.6674583333333333 2.00075 2.3340416666666663 2.6673333333333331 3.0006249999999999 3.3339166666666666 3.667208333333333 4.0004999999999997 4.3337916666666665 4.6670833333333333 5.000375 5.3336666666666668 5.6669583333333335 6.0002500000000003 6.3335416666666671 6.6668333333333338 7.0001249999999997 7.3334166666666665 7.6667083333333332 8 8 8 8
27
79.140244588519465 79.140244588519465 55.85833391113556 36.597903318706138 21.358952811231141 12.290000872768841 1.9593931914091953 -0.65697974623243804 -0.85177956270573463 -0.68929688239869991 -0.46787243412973262 -0.27624655899523165 -0.11912921944351409 -0.056302369393035338 -0.0049812809608429064 0.0085637634684603507 0.0034716161454604712 -0.0058751075573311978 -0.005453415412748467 -0.0015123194244718201 0.0011577919587182201 0.001583772506713282 -0.00049823976100720228 -0.0013902809146717273 0 0 0
#
#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
3B Nb Nb Nb 0 3 nk
8.0 4.0 4.0 23 15 15
0.001 0.001 0.001 0.001 0.50093749999999992 1.000875 1.5008124999999999 2.00075 2.5006874999999997 3.0006249999999999 3.5005624999999996 4.0004999999999997 4.5004375000000003 5.000375 5.5003124999999997 6.0002500000000003 6.5001875 7.0001249999999997 7.5000625000000003 8 8 8 8
0.001 0.001 0.001 0.001 0.50087499999999996 1.00075 1.5006249999999999 2.0005000000000002 2.500375 3.0002499999999999 3.5001250000000002 4 4 4 4
0.001 0.001 0.001 0.001 0.50087499999999996 1.00075 1.5006249999999999 2.0005000000000002 2.500375 3.0002499999999999 3.5001250000000002 4 4 4 4
11 11 19
-1.1790416072105636e-06 6.589114265858035e-08 2.1094970065385374e-06 4.7014910818419987e-07 8.288423734406254e-06 0.000186151370764668 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
3.2366723157260956e-05 2.6208783380066457e-05 1.0239981836366566e-05 1.8487993936404763e-05 2.1943710009352506e-05 2.6899947783571087e-07 5.002786118380638e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
4.0696915445106504e-05 6.184559535738335e-05 5.870203846064511e-05 -1.112085789465658e-05 -4.7600144351359347e-07 -5.861397594145908e-08 1.4524208784805573e-08 2.300649782987421e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
5.282737863089323e-05 6.328946161646202e-06 1.8329325276370316e-05 1.6423572667388823e-05 1.2653184610977003e-06 7.181714140248046e-06 3.491501462345434e-06 -7.285463619241614e-06 3.2609159022388403e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
6.9413198850914024e-06 2.107626397843018e-05 1.8155172114721186e-05 2.0928626557075606e-06 1.5632037328512312e-06 -2.7335717313450097e-07 -7.2126792356200426e-09 9.213093725547886e-09 4.186629643010996e-08 8.198811769753182e-08 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
1.4231393739579515e-06 3.630746449160232e-07 9.318604659023228e-07 4.92311430374376e-07 -3.701479331898353e-09 2.1280257031614452e-07 1.2240989510544568e-06 5.3432540178806065e-06 2.043230389835189e-06 3.2740024159475547e-07 6.717304982644579e-07 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 5.196157077391817e-07 6.938124100654148e-08 7.597564197383545e-08 1.863740632660483e-07 4.437837629589167e-07 5.453941063185757e-07 1.5602917821833568e-06 3.404289212094662e-07 9.967447994956849e-07 5.8845599651090215e-06 1.5052240335012455e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 3.196534127251379e-06 -1.1872677866681306e-06 -2.5678892066098854e-08 5.139117071436217e-09 1.1142431390092631e-06 2.0605776537608227e-06 5.297265009242829e-06 6.713907186544732e-06 2.7028644452395994e-06 1.149242737988068e-06 2.2449682976927855e-06 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
3.2366723157260956e-05 2.6208783380066457e-05 1.0239981836366566e-05 1.8487993936404763e-05 2.1943710009352506e-05 2.6899947783571087e-07 5.002786118380638e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
9.36844864368356e-06 1.9223644807676324e-05 1.9979026246524356e-05 3.627062812549574e-05 9.775578281629195e-06 -5.894357549683858e-06 6.470814473155067e-07 2.31805322174729e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
2.2218614171918013e-06 5.325319655352672e-06 7.766746363269582e-06 9.361315506075464e-06 5.0417710282874456e-05 9.822946186678772e-05 0.00026400568406806884 0.00033610865151919737 0.00013239814531221768 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
4.4850777249143735e-05 7.094600012126306e-05 0.00030581781354430576 0.00044661036994300023 0.00016699596636619577 1.5860625743775105e-05 9.74250537001798e-07 5.385650613476577e-06 8.091278451728344e-06 1.2460869401480828e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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0.0001650881267658455 6.548635015912796e-05 3.282822556024051e-05 7.205996516588195e-05 0.00030710620226134084 0.0007279352507540159 0.000909918529220897 0.0017257383928761386 0.00047543969768972346 -0.00030462814537952123 2.7321207199326783e-05 0.00010130812246147248 5.4817489360932934e-05 0.00012640103175376577 0.00018995742264027741 0.00023929212126678798 0.0 0.0 0.0
6.489304732024981e-05 0.0011748014116558024 0.014162497237899634 0.024470256017495366 0.046651858009005745 0.46415330969555396 0.6536160620847673 0.38295932353650225 0.39318393240673155 0.2877811024545165 0.03747496490739291 0.2654106688863148 0.074634565935104 0.012330295300167044 -0.0004996457463809098 0.00023089219471653216 0.0 0.0 0.0
-0.00011090752856021898 0.0043805342288213535 0.0016927729283659975 0.012954305343473369 0.4368797400066579 0.7614408833500013 0.10944765261392181 0.0412051224385603 0.15805652281823218 0.2585893276179897 0.05949650977132904 0.30356693149425945 0.19493804255113664 0.5122323478146567 0.35279041052227494 -0.007488446744915854 0.0 0.0 0.0
4.1934884152796484e-05 0.0035902058234846823 0.0005824017329515572 0.01441762880686721 0.6293209695433368 0.09572421881003676 0.08586090788885907 0.031601835145355577 0.06121858995657405 0.07315778164682188 -0.0013308261229131521 0.012882908917780034 0.13273058077548822 0.2035107778991338 0.1961396131043037 -0.04170252478795313 0.0 0.0 0.0
-0.0008465335016788498 -9.208409992139663e-05 -1.1210629044433908e-05 0.004300763141885697 0.1800503541691201 0.016819879476467067 0.060737350690215776 0.042330087306607714 0.0007006095666399378 0.02251352126872946 0.011185142175963118 -0.02716513333374441 0.00952941322650142 0.02210443704516212 0.07011148238258197 0.057840211345517194 0.0 0.0 0.0
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#

1
potentials/README
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@ -118,4 +118,5 @@ sw Stillinger-Weber potential
tersoff Tersoff potential tersoff Tersoff potential
tersoff.mod modified Tersoff potential tersoff.mod modified Tersoff potential
tersoff.zbl Tersoff with ZBL core tersoff.zbl Tersoff with ZBL core
uf3 UF3 potential
vashishta Vashishta 2-body and 3-body potential vashishta Vashishta 2-body and 3-body potential

11
src/.gitignore vendored
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@ -169,6 +169,17 @@
/rann_*.cpp /rann_*.cpp
/rann_*.h /rann_*.h
/pair_uf3.cpp
/pair_uf3.h
/uf3_bspline_basis2.cpp
/uf3_bspline_basis2.h
/uf3_bspline_basis3.cpp
/uf3_bspline_basis3.h
/uf3_pair_bspline.cpp
/uf3_pair_bspline.h
/uf3_triplet_bspline.cpp
/uf3_triplet_bspline.h
/compute_test_nbl.cpp /compute_test_nbl.cpp
/compute_test_nbl.h /compute_test_nbl.h
/pair_multi_lucy.cpp /pair_multi_lucy.cpp

23
src/BPM/bond_bpm.cpp
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@ -352,19 +352,32 @@ void BondBPM::process_broken(int i, int j)
{ {
if (!break_flag) if (!break_flag)
error->one(FLERR, "BPM bond broke with break no option"); error->one(FLERR, "BPM bond broke with break no option");
if (fix_store_local) {
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
int nlocal = atom->nlocal;
if (fix_store_local) {
// If newton off, bond can break on two procs so only record if proc owns lower tag
// (BPM bond styles should sort so i -> atom with lower tag)
if (force->newton_bond || (i < nlocal)) {
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
fix_store_local->add_data(output_data, i, j); fix_store_local->add_data(output_data, i, j);
} }
}
if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j); if (fix_update_special_bonds) {
// If this processor owns two copies of the bond (i.e. if the domain is periodic and 1 proc thick),
// skip instance where larger tag (j) owned
int check = 1;
if (i >= nlocal) {
int imap = atom->map(atom->tag[i]);
if (imap < nlocal) check = 0;
}
if (check) fix_update_special_bonds->add_broken_bond(i, j);
}
// Manually search and remove from atom arrays // Manually search and remove from atom arrays
// need to remove in case special bonds arrays rebuilt // need to remove in case special bonds arrays rebuilt
int m, n;
int nlocal = atom->nlocal;
int m, n;
tagint *tag = atom->tag; tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom; tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type; int **bond_type = atom->bond_type;

7
src/BPM/compute_nbond_atom.cpp
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@ -65,14 +65,13 @@ void ComputeNBondAtom::compute_peratom()
tagint **bond_atom = atom->bond_atom; tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type; int **bond_type = atom->bond_type;
int ntotal = nlocal;
if (force->newton) ntotal += atom->nghost;
// set local nbond array // set local nbond array
int i, j, k; int i, j, k;
int *num_bond = atom->num_bond; int *num_bond = atom->num_bond;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
int ntotal = nlocal;
if (newton_bond) ntotal += atom->nghost;
for (i = 0; i < ntotal; i++) nbond[i] = 0; for (i = 0; i < ntotal; i++) nbond[i] = 0;
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
@ -88,7 +87,7 @@ void ComputeNBondAtom::compute_peratom()
} }
// communicate ghost nbond between neighbor procs // communicate ghost nbond between neighbor procs
if (force->newton) comm->reverse_comm(this); if (newton_bond) comm->reverse_comm(this);
// zero nbond of atoms not in group // zero nbond of atoms not in group
// only do this after comm since ghost contributions must be included // only do this after comm since ghost contributions must be included

2
src/BPM/fix_update_special_bonds.cpp
View File

@ -100,6 +100,7 @@ void FixUpdateSpecialBonds::pre_exchange()
n1 = nspecial[i][0]; n1 = nspecial[i][0];
for (m = 0; m < n1; m++) for (m = 0; m < n1; m++)
if (slist[m] == tagj) break; if (slist[m] == tagj) break;
if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
for (; m < n1 - 1; m++) slist[m] = slist[m + 1]; for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
nspecial[i][0]--; nspecial[i][0]--;
nspecial[i][1] = nspecial[i][2] = nspecial[i][0]; nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
@ -110,6 +111,7 @@ void FixUpdateSpecialBonds::pre_exchange()
n1 = nspecial[j][0]; n1 = nspecial[j][0];
for (m = 0; m < n1; m++) for (m = 0; m < n1; m++)
if (slist[m] == tagi) break; if (slist[m] == tagi) break;
if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
for (; m < n1 - 1; m++) slist[m] = slist[m + 1]; for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
nspecial[j][0]--; nspecial[j][0]--;
nspecial[j][1] = nspecial[j][2] = nspecial[j][0]; nspecial[j][1] = nspecial[j][2] = nspecial[j][0];

9
src/GRANULAR/gran_sub_mod_damping.cpp
View File

@ -156,6 +156,7 @@ double GranSubModDampingTsuji::calculate_forces()
GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) : GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) :
GranSubModDamping(gm, lmp) GranSubModDamping(gm, lmp)
{ {
allow_cohesion = 0;
} }
void GranSubModDampingCoeffRestitution::init() void GranSubModDampingCoeffRestitution::init()
@ -173,6 +174,12 @@ void GranSubModDampingCoeffRestitution::init()
double GranSubModDampingCoeffRestitution::calculate_forces() double GranSubModDampingCoeffRestitution::calculate_forces()
{ {
damp_prefactor = damp * sqrt(gm->meff * gm->Fnormal / gm->delta); // in case argument <= 0 due to precision issues
double sqrt1;
if (gm->delta > 0.0)
sqrt1 = MAX(0.0, gm->meff * gm->Fnormal / gm->delta);
else
sqrt1 = 0.0;
damp_prefactor = damp * sqrt(sqrt1);
return -damp_prefactor * gm->vnnr; return -damp_prefactor * gm->vnnr;
} }

22
src/INTEL/npair_skip_intel.cpp
View File

@ -74,9 +74,13 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int nlocal = atom->nlocal; const int nlocal = atom->nlocal;
const int e_nall = nlocal + atom->nghost; const int e_nall = nlocal + atom->nghost;
const int * _noalias const type = atom->type; const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist; int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh; int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh; const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -110,7 +114,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) { for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii]; const int i = ilist_skip[ii];
const int itype = type[i]; const int itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
int n = 0; int n = 0;
int *neighptr = ipage.vget(); int *neighptr = ipage.vget();
@ -142,7 +146,11 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int jj = 0; jj < jnum; jj++) { for (int jj = 0; jj < jnum; jj++) {
const int joriginal = jlist[jj]; const int joriginal = jlist[jj];
const int j = joriginal & NEIGHMASK; const int j = joriginal & NEIGHMASK;
if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
neighptr[n++] = joriginal;
} }
} }
@ -269,9 +277,13 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int e_nall = nlocal + atom->nghost; const int e_nall = nlocal + atom->nghost;
const ATOM_T * _noalias const x = buffers->get_x(); const ATOM_T * _noalias const x = buffers->get_x();
const int * _noalias const type = atom->type; const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist; int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh; int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist; const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh; const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -306,7 +318,7 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) { for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii]; const int i = ilist_skip[ii];
const int itype = type[i]; const int itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
const flt_t xtmp = x[i].x; const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y; const flt_t ytmp = x[i].y;
@ -370,7 +382,9 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int j = joriginal & NEIGHMASK; const int j = joriginal & NEIGHMASK;
int addme = 1; int addme = 1;
if (ijskip[itype][type[j]]) addme = 0; if (!molskip && ijskip[itype][type[j]]) addme = 0;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) addme = 0;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) addme = 0;
// trim to shorter cutoff // trim to shorter cutoff

2
src/KOKKOS/Install.sh
View File

@ -365,6 +365,8 @@ action pair_reaxff_kokkos.h pair_reaxff.h
action pair_snap_kokkos_impl.h pair_snap.cpp action pair_snap_kokkos_impl.h pair_snap.cpp
action pair_snap_kokkos.cpp pair_snap.cpp action pair_snap_kokkos.cpp pair_snap.cpp
action pair_snap_kokkos.h pair_snap.h action pair_snap_kokkos.h pair_snap.h
action pair_soft_kokkos.cpp
action pair_soft_kokkos.h
action pair_sw_kokkos.cpp pair_sw.cpp action pair_sw_kokkos.cpp pair_sw.cpp
action pair_sw_kokkos.h pair_sw.h action pair_sw_kokkos.h pair_sw.h
action pair_table_kokkos.cpp action pair_table_kokkos.cpp

255
src/KOKKOS/pair_soft_kokkos.cpp Normal file
View File

@ -0,0 +1,255 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "pair_soft_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "error.h"
#include "force.h"
#include "kokkos.h"
#include "math_const.h"
#include "memory_kokkos.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairSoftKokkos<DeviceType>::PairSoftKokkos(LAMMPS *lmp) : PairSoft(lmp)
{
respa_enable = 0;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairSoftKokkos<DeviceType>::~PairSoftKokkos()
{
if (copymode) return;
if (allocated) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_cutsq,cutsq);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL) no_virial_fdotr_compute = 1;
ev_init(eflag,vflag,0);
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
atomKK->sync(execution_space,datamask_read);
k_cutsq.template sync<DeviceType>();
k_params.template sync<DeviceType>();
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK);
x = atomKK->k_x.view<DeviceType>();
c_x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
special_lj[0] = force->special_lj[0];
special_lj[1] = force->special_lj[1];
special_lj[2] = force->special_lj[2];
special_lj[3] = force->special_lj[3];
// loop over neighbors of my atoms
copymode = 1;
EV_FLOAT ev = pair_compute<PairSoftKokkos<DeviceType>,void >(this,(NeighListKokkos<DeviceType>*)list);
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
virial[1] += ev.v[1];
virial[2] += ev.v[2];
virial[3] += ev.v[3];
virial[4] += ev.v[4];
virial[5] += ev.v[5];
}
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
}
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairSoftKokkos<DeviceType>::
compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
(void) i;
const F_FLOAT r = sqrt(rsq);
const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
const F_FLOAT arg = MY_PI*r/cut_ij;
F_FLOAT fpair = 0.0;
if (r > 0.0) fpair = prefactor_ij *
sin(arg) * MY_PI/cut_ij/r;
return fpair;
}
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairSoftKokkos<DeviceType>::
compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
(void) i;
const F_FLOAT r = sqrt(rsq);
const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
const F_FLOAT arg = MY_PI*r/cut_ij;
return prefactor_ij*(1.0+cos(arg));
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::allocate()
{
PairSoft::allocate();
int n = atom->ntypes;
memory->destroy(cutsq);
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>("PairSoft::params",n+1,n+1);
params = k_params.template view<DeviceType>();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::settings(int narg, char **arg)
{
if (narg > 2) error->all(FLERR,"Illegal pair_style command");
PairSoft::settings(1,arg);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::init_style()
{
PairSoft::init_style();
// error if rRESPA with inner levels
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
// adjust neighbor list request for KOKKOS
neighflag = lmp->kokkos->neighflag;
auto request = neighbor->find_request(this);
request->set_kokkos_host(std::is_same_v<DeviceType,LMPHostType> &&
!std::is_same_v<DeviceType,LMPDeviceType>);
request->set_kokkos_device(std::is_same_v<DeviceType,LMPDeviceType>);
if (neighflag == FULL) request->enable_full();
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
template<class DeviceType>
double PairSoftKokkos<DeviceType>::init_one(int i, int j)
{
double cutone = PairSoft::init_one(i,j);
k_params.h_view(i,j).prefactor = prefactor[i][j];
k_params.h_view(i,j).cut = cutone;
k_params.h_view(i,j).cutsq = cutone*cutone;
k_params.h_view(j,i) = k_params.h_view(i,j);
if (i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
}
k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
k_cutsq.template modify<LMPHostType>();
k_params.template modify<LMPHostType>();
return cutone;
}
namespace LAMMPS_NS {
template class PairSoftKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class PairSoftKokkos<LMPHostType>;
#endif
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(soft/kk,PairSoftKokkos<LMPDeviceType>);
PairStyle(soft/kk/device,PairSoftKokkos<LMPDeviceType>);
PairStyle(soft/kk/host,PairSoftKokkos<LMPHostType>);
// clang-format on
#else
// clang-format off
#ifndef LMP_PAIR_SOFT_KOKKOS_H
#define LMP_PAIR_SOFT_KOKKOS_H
#include "pair_kokkos.h"
#include "pair_soft.h"
#include "neigh_list_kokkos.h"
namespace LAMMPS_NS {
template<class DeviceType>
class PairSoftKokkos : public PairSoft {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
PairSoftKokkos(class LAMMPS *);
~PairSoftKokkos() override;
void compute(int, int) override;
void settings(int, char **) override;
void init_style() override;
double init_one(int, int) override;
struct params_soft{
KOKKOS_INLINE_FUNCTION
params_soft() {cutsq=0,cut=0,prefactor=0;};
KOKKOS_INLINE_FUNCTION
params_soft(int /*i*/) {cutsq=0,cut=0,prefactor=0;};
F_FLOAT cutsq,cut,prefactor;
};
protected:
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_ecoul(const F_FLOAT& /*rsq*/, const int& /*i*/, const int& /*j*/,
const int& /*itype*/, const int& /*jtype*/) const { return 0; }
Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_soft m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 12 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename AT::t_x_array_randomread x;
typename AT::t_x_array c_x;
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
int newton_pair;
double special_lj[4];
typename AT::tdual_ffloat_2d k_cutsq;
typename AT::t_ffloat_2d d_cutsq;
int neighflag;
int nlocal,nall,eflag,vflag;
void allocate() override;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,0>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,1>;
friend struct PairComputeFunctor<PairSoftKokkos,HALF,true>;
friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,true>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,0>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,1>;
friend struct PairComputeFunctor<PairSoftKokkos,HALF,false>;
friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,false>;
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,0>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,1>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALF>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALFTHREAD>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairSoftKokkos>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairSoftKokkos>(PairSoftKokkos*);
};
}
#endif
#endif

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ajinkya Hire (Univ. of Florida),
Hendrik Kraß (Univ. of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (Univ of Florida)
---------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(uf3/kk,PairUF3Kokkos<LMPDeviceType>)
PairStyle(uf3/kk/device,PairUF3Kokkos<LMPDeviceType>)
// clang-format on
#else
#ifndef LMP_PAIR_UF3_KOKKOS_H
#define LMP_PAIR_UF3_KOKKOS_H
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_uf3.h"
template <int NEIGHFLAG, int EVFLAG> struct TagPairUF3ComputeFullA {};
struct TagPairUF3ComputeShortNeigh {};
namespace LAMMPS_NS {
template <class DeviceType> class PairUF3Kokkos : public PairUF3 {
public:
PairUF3Kokkos(class LAMMPS *);
~PairUF3Kokkos() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void allocate();
void init_style() override;
void init_list(int, class NeighList *) override; // needed for ptr to full neigh list
double init_one(int, int) override; // needed for cutoff radius for neighbour list
double single(int, int, int, int, double, double, double, double &) override;
template <typename T, typename V> void copy_2d(V &d, T **h, int m, int n);
template <typename T, typename V> void copy_3d(V &d, T ***h, int m, int n, int o);
template <int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>, const int &,
EV_FLOAT &) const;
template <int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>,
const int &) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairUF3ComputeShortNeigh, const int &) const;
enum { EnabledNeighFlags = FULL };
enum { COUL_FLAG = 0 };
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typedef EV_FLOAT value_type;
protected:
typename AT::tdual_ffloat_2d k_cutsq;//Create a DualView, defination of tdual_ffloat_2d in kokkos_type.h
typename AT::t_ffloat_2d d_cutsq; //t_ffloat_2d = t_dev ==> Creates a new View d_cutsq
//the type of d_cutsq is decided by the Device(not host) type for the DualView k_cutsq
//Meaning the memory location of d_cutsq is the same as the Device(not host) memory location of
//k_cutsq
typedef Kokkos::DualView<F_FLOAT***, Kokkos::LayoutRight, DeviceType> tdual_ffloat_3d;
typedef Kokkos::DualView<F_FLOAT****, Kokkos::LayoutRight, DeviceType> tdual_ffloat_4d;
tdual_ffloat_3d k_cut_3b;
tdual_ffloat_4d k_min_cut_3b;
typename tdual_ffloat_3d::t_dev d_cut_3b;
typename tdual_ffloat_4d::t_dev d_min_cut_3b;
template <typename TYPE> void destroy_3d(TYPE data, typename TYPE::value_type*** &array);
template <typename TYPE> void destroy_4d(TYPE data, typename TYPE::value_type**** &array);
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> /*d_cutsq,*/ d_cut_3b_list;
//Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_cut_3b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_2b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_2b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot;
Kokkos::View<F_FLOAT *, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot_spacings;
Kokkos::View<int **, LMPDeviceType::array_layout, LMPDeviceType> map2b;
Kokkos::View<F_FLOAT[4][4], LMPDeviceType::array_layout, LMPDeviceType> constants;
Kokkos::View<F_FLOAT[3][3], LMPDeviceType::array_layout, LMPDeviceType> dnconstants;
Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix;
Kokkos::View<F_FLOAT ****, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_3b;
Kokkos::View<F_FLOAT *****, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_3b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_spacings;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix_spacings;
Kokkos::View<int ***, LMPDeviceType::array_layout, LMPDeviceType> map3b;
Kokkos::View<F_FLOAT **[16], LMPDeviceType::array_layout, LMPDeviceType> constants_2b;
Kokkos::View<F_FLOAT **[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_2b;
Kokkos::View<F_FLOAT ***[16], LMPDeviceType::array_layout, LMPDeviceType> constants_3b;
Kokkos::View<F_FLOAT ***[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_3b;
std::vector<F_FLOAT> get_constants(double *knots, double coefficient);
std::vector<F_FLOAT> get_dnconstants(double *knots, double coefficient);
int coefficients_created = 0;
void create_coefficients();
void create_3b_coefficients();
void create_2b_coefficients();
std::vector<F_FLOAT> get_coefficients(const double *knots, const double coefficient) const;
std::vector<F_FLOAT> get_dncoefficients(const double *knots, const double coefficient) const;
template <int EVFLAG>
void twobody(const int itype, const int jtype, const F_FLOAT r, F_FLOAT &evdwl,
F_FLOAT &fpair) const;
template <int EVFLAG>
void threebody(const int itype, const int jtype, const int ktype, const F_FLOAT value_rij,
const F_FLOAT value_rik, const F_FLOAT value_rjk, F_FLOAT &evdwl3,
F_FLOAT (&fforce)[3]) const;
template <int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION void
ev_tally(EV_FLOAT &ev, const int &i, const int &j, const F_FLOAT &epair, const F_FLOAT &fpair,
const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const;
template <int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
const F_FLOAT &evdwl, const F_FLOAT &ecoul, F_FLOAT *fj,
F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_tagint_1d tag;
typename AT::t_int_1d_randomread type;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
using ScatterFType = Kokkos::Experimental::ScatterView<F_FLOAT *[3], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterFType fscatter;
using ScatterVType = Kokkos::Experimental::ScatterView<F_FLOAT *[6], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterVType vscatter;
using ScatterCVType = Kokkos::Experimental::ScatterView<F_FLOAT *[9], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterCVType cvscatter;
using ScatterEType = Kokkos::Experimental::ScatterView<E_FLOAT *, LMPDeviceType::array_layout,
typename DeviceType::memory_space>;
ScatterEType escatter;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d_randomread d_ilist;
typename AT::t_int_1d_randomread d_numneigh;
int neighflag, newton_pair;
int nlocal, nall, eflag, vflag;
int inum;
Kokkos::View<int **, DeviceType> d_neighbors_short;
Kokkos::View<int *, DeviceType> d_numneigh_short;
friend void pair_virial_fdotr_compute<PairUF3Kokkos>(PairUF3Kokkos *);
};
KOKKOS_INLINE_FUNCTION int min(int i, int j)
{
return i < j ? i : j;
}
KOKKOS_INLINE_FUNCTION int max(int i, int j)
{
return i > j ? i : j;
}
} // namespace LAMMPS_NS
#endif
#endif

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ajinkya Hire (Univ. of Florida),
Hendrik Kraß (Univ. of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (Univ of Florida)
---------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(uf3,PairUF3);
// clang-format on
#else
#ifndef LMP_PAIR_UF3_H
#define LMP_PAIR_UF3_H
#include "pair.h"
namespace LAMMPS_NS {
class PairUF3 : public Pair {
public:
PairUF3(class LAMMPS *);
~PairUF3() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
void init_list(int, class NeighList *) override; // needed for ptr to full neigh list
double init_one(int, int) override; // needed for cutoff radius for neighbour list
double single(int, int, int, int, double, double, double, double &) override;
double memory_usage() override;
protected:
int ***setflag_3b, **knot_spacing_type_2b, ***knot_spacing_type_3b;
double **cut, ***cut_3b, **cut_3b_list, ****min_cut_3b;
double **knot_spacing_2b, ****knot_spacing_3b;
double ***n2b_knots_array, ***n2b_coeff_array;
int **n2b_knots_array_size, **n2b_coeff_array_size;
double ****cached_constants_2b, ****cached_constants_2b_deri;
int ***map_3b;
double ***n3b_knots_array, ****n3b_coeff_array;
int **n3b_knots_array_size, **n3b_coeff_array_size;
double ****coeff_for_der_jk, ****coeff_for_der_ik,****coeff_for_der_ij;
double ****cached_constants_3b, ****cached_constants_3b_deri;
int *neighshort, maxshort; // short neighbor list array for 3body interaction
void uf3_read_unified_pot_file(char *potf_name);
void communicate();
int bsplines_created;
bool pot_3b;
virtual void allocate();
void create_bsplines();
void create_cached_constants_2b();
void create_cached_constants_3b();
int get_starting_index_uniform_2b(int i, int j, double r);
int get_starting_index_uniform_3b(int i, int j, int k, double r, int knot_dim);
int get_starting_index_nonuniform_2b(int i, int j, double r);
int get_starting_index_nonuniform_3b(int i, int j, int k, double r, int knot_dim);
int (PairUF3::*get_starting_index_2b)(int i, int j, double r);
int (PairUF3::*get_starting_index_3b)(int i, int j, int k, double r, int knot_dim);
int nbody_flag = 3;
int max_num_knots_2b = 0;
int max_num_coeff_2b = 0;
int max_num_knots_3b = 0;
int max_num_coeff_3b = 0;
int tot_interaction_count_3b = 0;
};
} // namespace LAMMPS_NS
#endif
#endif

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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "uf3_bspline_basis2.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using MathSpecial::square;
// Constructor
// Initializes coefficients and knots
// Requires [knots] to have length 4
uf3_bspline_basis2::uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient)
{
lmp = ulmp;
double c0, c1, c2;
c0 = coefficient
* (square(knots[0])
/ (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
c1 = coefficient *
(-2.0 * knots[0] /
(square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
c2 = coefficient *
(1.0 / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[0] = c0;
constants[1] = c1;
constants[2] = c2;
c0 = coefficient *
(-knots[1] * knots[3] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
knots[0] * knots[2] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
c1 = coefficient *
(knots[1] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
knots[3] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
knots[0] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])) +
knots[2] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
c2 = coefficient *
(-1.0 / (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
1.0 / (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[3] = c0;
constants[4] = c1;
constants[5] = c2;
c0 = coefficient *
(square(knots[3]) /
(knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
c1 = coefficient *
(-2.0 * knots[3] /
(knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
c2 = coefficient *
(1.0 / (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[6] = c0;
constants[7] = c1;
constants[8] = c2;
}
uf3_bspline_basis2::~uf3_bspline_basis2() {}
// Evaluate outer-left part of spline
double uf3_bspline_basis2::eval0(double rsq, double r)
{
return rsq * constants[2] + r * constants[1] + constants[0];
}
// Evaluate center-left part of spline
double uf3_bspline_basis2::eval1(double rsq, double r)
{
return rsq * constants[5] + r * constants[4] + constants[3];
}
// Evaluate center-right part of spline
double uf3_bspline_basis2::eval2(double rsq, double r)
{
return rsq * constants[8] + r * constants[7] + constants[6];
}
double uf3_bspline_basis2::memory_usage()
{
double bytes = 0;
bytes += (double)9*sizeof(double);
return bytes;
}

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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "pointers.h"
#include <vector>
#ifndef UF3_BSPLINE_BASIS2_H
#define UF3_BSPLINE_BASIS2_H
namespace LAMMPS_NS {
class uf3_bspline_basis2 {
private:
LAMMPS *lmp;
//std::vector<double> constants;
public:
uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient);
~uf3_bspline_basis2();
//std::vector<double> constants;
double constants[9] = {};
double eval0(double, double);
double eval1(double, double);
double eval2(double, double);
double memory_usage();
};
} // namespace LAMMPS_NS
#endif

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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "uf3_bspline_basis3.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using MathSpecial::cube;
using MathSpecial::square;
// Constructor
// Initializes coefficients and knots
// [knots] needs to have length 4
uf3_bspline_basis3::uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient)
{
lmp = ulmp;
double c0, c1, c2, c3;
c0 = coefficient *
(-cube(knots[0]) /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c1 = coefficient *
(3.0 * square(knots[0]) /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c2 = coefficient *
(-3.0 * knots[0] /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c3 = coefficient *
(1.0 /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[0] = c0;
constants[1] = c1;
constants[2] = c2;
constants[3] = c3;
c0 = coefficient *
(square(knots[1]) * knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
square(knots[0]) * knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[0] * knots[1] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c1 = coefficient *
(-square(knots[1]) /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
2.0 * knots[1] * knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
square(knots[0]) /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
2.0 * knots[0] * knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
knots[0] * knots[1] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
knots[0] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
knots[1] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c2 = coefficient *
(2.0 * knots[1] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
2.0 * knots[0] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[0] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
knots[1] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c3 = coefficient *
(-1.0 /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
1.0 /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
1.0 /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[4] = c0;
constants[5] = c1;
constants[6] = c2;
constants[7] = c3;
c0 = coefficient *
(-knots[0] * square(knots[3]) /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
knots[1] * knots[3] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[2] * square(knots[4]) /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c1 = coefficient *
(2.0 * knots[0] * knots[3] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
square(knots[3]) /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
knots[1] * knots[3] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
knots[1] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
knots[3] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
2.0 * knots[2] * knots[4] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])) +
square(knots[4]) /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c2 = coefficient *
(-knots[0] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
2.0 * knots[3] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
knots[1] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[3] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[2] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])) -
2.0 * knots[4] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c3 = coefficient *
(1.0 /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
1.0 /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
1.0 /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[8] = c0;
constants[9] = c1;
constants[10] = c2;
constants[11] = c3;
c0 = coefficient *
(cube(knots[4]) /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c1 = coefficient *
(-3.0 * square(knots[4]) /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c2 = coefficient *
(3.0 * knots[4] /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c3 = coefficient *
(-1.0 /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[12] = c0;
constants[13] = c1;
constants[14] = c2;
constants[15] = c3;
}
uf3_bspline_basis3::~uf3_bspline_basis3() {}
// Evaluate outer-left part of spline
double uf3_bspline_basis3::eval0(double rth, double rsq, double r)
{
return rth * constants[3] + rsq * constants[2] + r * constants[1] + constants[0];
}
// Evaluate center-left part of spline
double uf3_bspline_basis3::eval1(double rth, double rsq, double r)
{
return rth * constants[7] + rsq * constants[6] + r * constants[5] + constants[4];
}
// Evaluate center-right part of spline
double uf3_bspline_basis3::eval2(double rth, double rsq, double r)
{
return rth * constants[11] + rsq * constants[10] + r * constants[9] + constants[8];
}
// Evaluate outer-right part of spline
double uf3_bspline_basis3::eval3(double rth, double rsq, double r)
{
return rth * constants[15] + rsq * constants[14] + r * constants[13] + constants[12];
}
double uf3_bspline_basis3::memory_usage()
{
double bytes = 0;
bytes += (double)16*sizeof(double);
return bytes;
}

42
src/ML-UF3/uf3_bspline_basis3.h Normal file
View File

@ -0,0 +1,42 @@
// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "pointers.h"
#include <vector>
#ifndef UF3_BSPLINE_BASIS3_H
#define UF3_BSPLINE_BASIS3_H
namespace LAMMPS_NS {
class uf3_bspline_basis3 {
private:
LAMMPS *lmp;
//std::vector<double> constants;
public:
uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient);
~uf3_bspline_basis3();
double constants[16] = {};
double eval0(double, double, double);
double eval1(double, double, double);
double eval2(double, double, double);
double eval3(double, double, double);
double memory_usage();
};
} // namespace LAMMPS_NS
#endif

1
src/Makefile
View File

@ -104,6 +104,7 @@ PACKAGE = \
ml-quip \ ml-quip \
ml-rann \ ml-rann \
ml-snap \ ml-snap \
ml-uf3 \
mofff \ mofff \
molfile \ molfile \
netcdf \ netcdf \

8
src/OPENMP/fix_omp.cpp
View File

@ -229,7 +229,13 @@ void FixOMP::init()
check_hybrid = 0; \ check_hybrid = 0; \
if (force->name) { \ if (force->name) { \
if ( (strcmp(force->name ## _style,"hybrid") == 0) || \ if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \ (strcmp(force->name ## _style,"hybrid/overlay") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular") == 0) || \
(strcmp(force->name ## _style,"hybrid/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular/omp") == 0) ) \
check_hybrid=1; \ check_hybrid=1; \
if (force->name->suffix_flag & Suffix::OMP) { \ if (force->name->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \ last_force_name = (const char *) #name; \

34
src/OPENMP/npair_skip_omp.h
View File

@ -19,14 +19,12 @@
NPairStyle(skip/omp, NPairStyle(skip/omp,
NPairSkip, NPairSkip,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/respa/omp, NPairStyle(skip/half/respa/omp,
NPairSkipRespa, NPairSkipRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/size/omp, NPairStyle(skip/half/size/omp,
@ -36,32 +34,27 @@ NPairStyle(skip/half/size/omp,
NPairStyle(skip/size/off2on/omp, NPairStyle(skip/size/off2on/omp,
NPairSkipSizeOff2on, NPairSkipSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/size/off2on/oneside/omp, NPairStyle(skip/size/off2on/oneside/omp,
NPairSkipSizeOff2onOneside, NPairSkipSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/ghost/omp, NPairStyle(skip/ghost/omp,
NPairSkip, NPairSkip,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST);
NPairStyle(skip/trim/omp, NPairStyle(skip/trim/omp,
NPairSkipTrim, NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/respa/omp, NPairStyle(skip/trim/half/respa/omp,
NPairSkipTrimRespa, NPairSkipTrimRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/size/omp, NPairStyle(skip/trim/half/size/omp,
@ -71,20 +64,17 @@ NPairStyle(skip/trim/half/size/omp,
NPairStyle(skip/trim/size/off2on/omp, NPairStyle(skip/trim/size/off2on/omp,
NPairSkipTrimSizeOff2on, NPairSkipTrimSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/size/off2on/oneside/omp, NPairStyle(skip/trim/size/off2on/oneside/omp,
NPairSkipTrimSizeOff2onOneside, NPairSkipTrimSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/ghost/omp, NPairStyle(skip/trim/ghost/omp,
NPairSkipTrim, NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL | NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST);
// clang-format off // clang-format off
#endif #endif

10
src/delete_atoms.cpp
View File

@ -22,6 +22,7 @@
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "error.h" #include "error.h"
#include "fix_bond_history.h"
#include "force.h" #include "force.h"
#include "group.h" #include "group.h"
#include "input.h" #include "input.h"
@ -754,6 +755,10 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
int nlocal = daptr->atom->nlocal; int nlocal = daptr->atom->nlocal;
// find instances of bond history to delete data
auto histories = daptr->modify->get_fix_by_style("BOND_HISTORY");
int n_histories = histories.size();
// cbuf = list of N deleted atom IDs from other proc, put them in hash // cbuf = list of N deleted atom IDs from other proc, put them in hash
hash->clear(); hash->clear();
@ -771,6 +776,11 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
if (hash->find(bond_atom[i][m]) != hash->end()) { if (hash->find(bond_atom[i][m]) != hash->end()) {
bond_type[i][m] = bond_type[i][n - 1]; bond_type[i][m] = bond_type[i][n - 1];
bond_atom[i][m] = bond_atom[i][n - 1]; bond_atom[i][m] = bond_atom[i][n - 1];
if (n_histories > 0)
for (auto &ihistory: histories) {
dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i,m,n-1);
dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,n-1);
}
n--; n--;
} else } else
m++; m++;

1
src/fix_bond_history.h
View File

@ -44,6 +44,7 @@ class FixBondHistory : public Fix {
void update_atom_value(int, int, int, double); void update_atom_value(int, int, int, double);
double get_atom_value(int, int, int); double get_atom_value(int, int, int);
int get_ndata() const { return ndata; }
// methods to reorder/delete elements of atom->bond_atom // methods to reorder/delete elements of atom->bond_atom
void delete_history(int, int); void delete_history(int, int);

3
src/neigh_list.cpp
View File

@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq)
copy = nq->copy; copy = nq->copy;
trim = nq->trim; trim = nq->trim;
id = nq->id; id = nq->id;
molskip = nq->molskip;
if (nq->copy) { if (nq->copy) {
listcopy = neighbor->lists[nq->copylist]; listcopy = neighbor->lists[nq->copylist];
@ -157,6 +158,7 @@ void NeighList::post_constructor(NeighRequest *nq)
if (nq->skip) { if (nq->skip) {
listskip = neighbor->lists[nq->skiplist]; listskip = neighbor->lists[nq->skiplist];
if (!molskip) {
int ntypes = atom->ntypes; int ntypes = atom->ntypes;
iskip = new int[ntypes+1]; iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip"); memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
@ -166,6 +168,7 @@ void NeighList::post_constructor(NeighRequest *nq)
for (j = 1; j <= ntypes; j++) for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j]; ijskip[i][j] = nq->ijskip[i][j];
} }
}
if (nq->halffull) if (nq->halffull)
listfull = neighbor->lists[nq->halffulllist]; listfull = neighbor->lists[nq->halffulllist];

1
src/neigh_list.h
View File

@ -46,6 +46,7 @@ class NeighList : protected Pointers {
int kk2cpu; // 1 if this list is copied from Kokkos to CPU int kk2cpu; // 1 if this list is copied from Kokkos to CPU
int copymode; // 1 if this is a Kokkos on-device copy int copymode; // 1 if this is a Kokkos on-device copy
int id; // copied from neighbor list request int id; // copied from neighbor list request
int molskip; // 1/2 if this is an intra-/inter-molecular skip list
// data structs to store neighbor pairs I,J and associated values // data structs to store neighbor pairs I,J and associated values

9
src/neigh_request.cpp
View File

@ -76,6 +76,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
skip = 0; skip = 0;
iskip = nullptr; iskip = nullptr;
ijskip = nullptr; ijskip = nullptr;
molskip = REGULAR;
// only set when command = 1; // only set when command = 1;
@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other)
int NeighRequest::same_skip(NeighRequest *other) int NeighRequest::same_skip(NeighRequest *other)
{ {
if (molskip != other->molskip) return 0;
const int ntypes = atom->ntypes; const int ntypes = atom->ntypes;
int same = 1; int same = 1;
@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip)
ijskip = _ijskip; ijskip = _ijskip;
} }
void NeighRequest::set_molskip(int _molskip)
{
skip = 1;
molskip = _molskip;
}
void NeighRequest::enable_full() void NeighRequest::enable_full()
{ {
half = 0; half = 0;

5
src/neigh_request.h
View File

@ -29,6 +29,9 @@ class NeighRequest : protected Pointers {
friend class NPairSkipTrimIntel; friend class NPairSkipTrimIntel;
friend class FixIntel; friend class FixIntel;
public:
enum { REGULAR, INTRA, INTER };
protected: protected:
void *requestor; // class that made request void *requestor; // class that made request
int requestor_instance; // instance of that class (only Fix, Compute, Pair) int requestor_instance; // instance of that class (only Fix, Compute, Pair)
@ -88,6 +91,7 @@ class NeighRequest : protected Pointers {
int skip; // 1 if this list skips atom types from another list int skip; // 1 if this list skips atom types from another list
int *iskip; // iskip[i] if atoms of type I are not in list int *iskip; // iskip[i] if atoms of type I are not in list
int **ijskip; // ijskip[i][j] if pairs of type I,J are not in list int **ijskip; // ijskip[i][j] if pairs of type I,J are not in list
int molskip; // 0 reqular list, 1 keep only intra-molecular entries, 2 keep inter-molecular
// command_style only set if command = 1 // command_style only set if command = 1
// allows print_pair_info() to access command name // allows print_pair_info() to access command name
@ -137,6 +141,7 @@ class NeighRequest : protected Pointers {
void set_kokkos_device(int); void set_kokkos_device(int);
void set_kokkos_host(int); void set_kokkos_host(int);
void set_skip(int *, int **); void set_skip(int *, int **);
void set_molskip(int);
void enable_full(); void enable_full();
void enable_ghost(); void enable_ghost();
void enable_intel(); void enable_intel();

7
src/neighbor.cpp
View File

@ -1800,11 +1800,18 @@ void Neighbor::print_pairwise_info()
else else
out += fmt::format(", half/full from ({})",rq->halffulllist+1); out += fmt::format(", half/full from ({})",rq->halffulllist+1);
} else if (rq->skip) { } else if (rq->skip) {
if (rq->molskip) {
if (rq->trim)
out += fmt::format(", molskip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", molskip from ({})",rq->skiplist+1);
} else {
if (rq->trim) if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1); out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else else
out += fmt::format(", skip from ({})",rq->skiplist+1); out += fmt::format(", skip from ({})",rq->skiplist+1);
} }
}
out += "\n"; out += "\n";
// list of neigh list attributes // list of neigh list attributes

10
src/npair_skip.cpp
View File

@ -17,6 +17,7 @@
#include "error.h" #include "error.h"
#include "my_page.h" #include "my_page.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -41,11 +42,13 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
int *type = atom->type; int *type = atom->type;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
tagint *molecule = atom->molecule;
int *ilist = list->ilist; int *ilist = list->ilist;
int *numneigh = list->numneigh; int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh; int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage; MyPage<int> *ipage = list->ipage;
int molskip = list->molskip;
int *ilist_skip = list->listskip->ilist; int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh; int *numneigh_skip = list->listskip->numneigh;
@ -71,7 +74,8 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
for (ii = 0; ii < num_skip; ii++) { for (ii = 0; ii < num_skip; ii++) {
i = ilist_skip[ii]; i = ilist_skip[ii];
itype = type[i]; itype = type[i];
if (iskip[itype]) continue;
if (!molskip && iskip[itype]) continue;
if (TRIM) { if (TRIM) {
xtmp = x[i][0]; xtmp = x[i][0];
@ -90,7 +94,9 @@ void NPairSkipTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue; if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
if (TRIM) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];

6
src/npair_skip.h
View File

@ -30,7 +30,8 @@ NPairStyle(skip/ghost,
typedef NPairSkipTemp<0> NPairSkipSize; typedef NPairSkipTemp<0> NPairSkipSize;
NPairStyle(skip/half/size, NPairStyle(skip/half/size,
NPairSkipSize, NPairSkipSize,
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_SKIP | NP_SIZE | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairSkipTemp<1> NPairSkipTrim; typedef NPairSkipTemp<1> NPairSkipTrim;
@ -50,7 +51,8 @@ NPairStyle(skip/ghost/trim,
typedef NPairSkipTemp<1> NPairSkipTrimSize; typedef NPairSkipTemp<1> NPairSkipTrimSize;
NPairStyle(skip/trim/half/size, NPairStyle(skip/trim/half/size,
NPairSkipTrimSize, NPairSkipTrimSize,
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_SKIP | NP_SIZE | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM); NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM);
// clang-format on // clang-format on

17
src/npair_skip_respa.cpp
View File

@ -18,6 +18,7 @@
#include "error.h" #include "error.h"
#include "my_page.h" #include "my_page.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -39,11 +40,13 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
int *neighptr, *jlist, *neighptr_inner, *neighptr_middle; int *neighptr, *jlist, *neighptr_inner, *neighptr_middle;
int *type = atom->type; int *type = atom->type;
tagint *molecule = atom->molecule;
int *ilist = list->ilist; int *ilist = list->ilist;
int *numneigh = list->numneigh; int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh; int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage; MyPage<int> *ipage = list->ipage;
int molskip = list->molskip;
int *ilist_skip = list->listskip->ilist; int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh; int *numneigh_skip = list->listskip->numneigh;
@ -90,7 +93,7 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (ii = 0; ii < inum_skip; ii++) { for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii]; i = ilist_skip[ii];
itype = type[i]; itype = type[i];
if (iskip[itype]) continue; if (!molskip && iskip[itype]) continue;
if (TRIM) { if (TRIM) {
xtmp = x[i][0]; xtmp = x[i][0];
@ -114,7 +117,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue; if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
if (TRIM) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];
@ -135,7 +140,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue; if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
if (TRIM) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];
@ -157,7 +164,9 @@ void NPairSkipRespaTemp<TRIM>::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj]; joriginal = jlist[jj];
j = joriginal & NEIGHMASK; j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue; if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
if (TRIM) { if (TRIM) {
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];

11
src/pair_hybrid.cpp
View File

@ -321,11 +321,12 @@ void PairHybrid::settings(int narg, char **arg)
iarg = 0; iarg = 0;
nstyles = 0; nstyles = 0;
const std::string mystyle = force->pair_style;
while (iarg < narg) { while (iarg < narg) {
if (utils::strmatch(arg[iarg],"^hybrid")) if (utils::strmatch(arg[iarg],"^hybrid"))
error->all(FLERR,"Pair style hybrid cannot have hybrid as a sub-style"); error->all(FLERR,"Pair style {} cannot have hybrid as a sub-style", mystyle);
if (strcmp(arg[iarg],"none") == 0) if (strcmp(arg[iarg],"none") == 0)
error->all(FLERR,"Pair style hybrid cannot have none as a sub-style"); error->all(FLERR,"Pair style {} cannot have none as a sub-style", mystyle);
styles[nstyles] = force->new_pair(arg[iarg],1,dummy); styles[nstyles] = force->new_pair(arg[iarg],1,dummy);
keywords[nstyles] = force->store_style(arg[iarg],0); keywords[nstyles] = force->store_style(arg[iarg],0);
@ -345,6 +346,9 @@ void PairHybrid::settings(int narg, char **arg)
nstyles++; nstyles++;
} }
if (utils::strmatch(mystyle,"^hybrid/molecular") && (nstyles != 2))
error->all(FLERR, "Pair style {} must have exactly two sub-styles", mystyle);
delete[] cutmax_style; delete[] cutmax_style;
cutmax_style = new double[nstyles]; cutmax_style = new double[nstyles];
memset(cutmax_style, 0, nstyles*sizeof(double)); memset(cutmax_style, 0, nstyles*sizeof(double));
@ -394,8 +398,7 @@ void PairHybrid::flags()
for (m = 0; m < nstyles; m++) { for (m = 0; m < nstyles; m++) {
if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward); if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse); if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,styles[m]->comm_reverse_off);
styles[m]->comm_reverse_off);
} }
// single_enable = 1 if all sub-styles are set // single_enable = 1 if all sub-styles are set

1
src/pair_hybrid.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid,PairHybrid); PairStyle(hybrid,PairHybrid);
PairStyle(hybrid/omp,PairHybrid);
// clang-format on // clang-format on
#else #else

162
src/pair_hybrid_molecular.cpp Normal file
View File

@ -0,0 +1,162 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "pair_hybrid_molecular.h"
#include "atom.h"
#include "error.h"
#include "neigh_request.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairHybridMolecular::PairHybridMolecular(LAMMPS *lmp) : PairHybridOverlay(lmp) {}
/* ----------------------------------------------------------------------
modify neighbor list requests
------------------------------------------------------------------------- */
void PairHybridMolecular::init_style()
{
if (!atom->molecule_flag)
error->all(FLERR, "Pair style hybrid/molecular requires atom attribute molecule");
if (manybody_flag)
error->all(FLERR, "Pair style hybrid/molecular is not compatible with manybody potentials");
PairHybridOverlay::init_style();
// modify neighbor list requests
bool first = true;
for (auto &request : neighbor->get_pair_requests()) {
if (first) {
request->set_molskip(NeighRequest::INTRA);
first = false;
} else {
request->set_molskip(NeighRequest::INTER);
}
}
born_matrix_enable = 0;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairHybridMolecular::init_one(int i, int j)
{
// if I,J is not set explicitly:
// perform mixing only if I,I sub-style = J,J sub-style
// plus I,I and J,J need the same number of substyles
if (setflag[i][j] == 0) {
if (nmap[i][i] != nmap[j][j])
error->one(FLERR,"All pair coeffs are not set");
int num = 0;
for (int k = 0; k < nmap[i][i]; ++k) {
for (int l = 0; l < nmap[j][j]; ++l) {
if (map[i][i][k] == map[j][j][l]) {
map[i][j][num] = map[i][i][k];
++num;
nmap[i][j] = num;
}
}
}
if (nmap[i][i] != nmap[i][j])
error->one(FLERR,"All pair coeffs are not set");
}
nmap[j][i] = nmap[i][j];
// call init/mixing for all sub-styles of I,J
// set cutsq in sub-style just as Pair::init() does via call to init_one()
// set cutghost for I,J and J,I just as sub-style does
// sum tail corrections for I,J
// return max cutoff of all sub-styles assigned to I,J
// if no sub-styles assigned to I,J (pair_coeff none), cutmax = 0.0 returned
double cutmax = 0.0;
cutghost[i][j] = cutghost[j][i] = 0.0;
if (tail_flag) etail_ij = ptail_ij = 0.0;
for (int k = 0; k < nmap[i][j]; k++) {
map[j][i][k] = map[i][j][k];
double cut = styles[map[i][j][k]]->init_one(i,j);
if (styles[map[i][j][k]]->did_mix) did_mix = true;
styles[map[i][j][k]]->cutsq[i][j] = styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
if (styles[map[i][j][k]]->ghostneigh)
cutghost[i][j] = cutghost[j][i] = MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
if (tail_flag) {
etail_ij += styles[map[i][j][k]]->etail_ij;
ptail_ij += styles[map[i][j][k]]->ptail_ij;
}
cutmax = MAX(cutmax,cut);
int istyle;
for (istyle = 0; istyle < nstyles; istyle++)
if (styles[istyle] == styles[map[i][j][k]]) break;
if (styles[istyle]->trim_flag) {
if (cut > cutmax_style[istyle]) {
cutmax_style[istyle] = cut;
for (auto &request : neighbor->get_pair_requests()) {
if (styles[istyle] == request->get_requestor()) {
request->set_cutoff(cutmax_style[istyle]);
break;
}
}
}
}
}
return cutmax;
}
/* ----------------------------------------------------------------------
call sub-style to compute single interaction
error if sub-style does not support single() call
since overlay could have multiple sub-styles, sum results explicitly
------------------------------------------------------------------------- */
double PairHybridMolecular::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &fforce)
{
if (nmap[itype][jtype] == 0)
error->one(FLERR,"Invoked pair single() on sub-style none");
double fone;
fforce = 0.0;
double esum = 0.0;
if (nmap[itype][jtype] == 2) {
int m = 0;
if (atom->molecule[i] != atom->molecule[j]) m = 1;
const int mystyle = map[itype][jtype][m];
if (rsq < styles[mystyle]->cutsq[itype][jtype]) {
if (styles[mystyle]->single_enable == 0)
error->one(FLERR,"Pair hybrid/molecular sub-style {} does not support single() call",
keywords[mystyle]);
if ((special_lj[mystyle] != nullptr) || (special_coul[mystyle] != nullptr))
error->one(FLERR,"Pair hybrid/molecular single() calls do not support per sub-style "
"special bond values");
esum += styles[mystyle]->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone);
fforce += fone;
}
}
if (single_extra) copy_svector(itype,jtype);
return esum;
}

41
src/pair_hybrid_molecular.h Normal file
View File

@ -0,0 +1,41 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(hybrid/molecular,PairHybridMolecular);
PairStyle(hybrid/molecular/omp,PairHybridMolecular);
// clang-format on
#else
#ifndef LMP_PAIR_HYBRID_MOLECULAR_H
#define LMP_PAIR_HYBRID_MOLECULAR_H
#include "pair_hybrid_overlay.h"
namespace LAMMPS_NS {
class PairHybridMolecular : public PairHybridOverlay {
public:
PairHybridMolecular(class LAMMPS *);
void init_style() override;
double init_one(int, int) override;
double single(int, int, int, int, double, double, double, double &) override;
};
} // namespace LAMMPS_NS
#endif
#endif

1
src/pair_hybrid_overlay.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid/overlay,PairHybridOverlay); PairStyle(hybrid/overlay,PairHybridOverlay);
PairStyle(hybrid/overlay/omp,PairHybridOverlay);
// clang-format on // clang-format on
#else #else

1
src/pair_hybrid_scaled.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
// clang-format off // clang-format off
PairStyle(hybrid/scaled,PairHybridScaled); PairStyle(hybrid/scaled,PairHybridScaled);
PairStyle(hybrid/scaled/omp,PairHybridScaled);
// clang-format on // clang-format on
#else #else

2
src/pair_soft.cpp
View File

@ -39,6 +39,8 @@ PairSoft::PairSoft(LAMMPS *lmp) : Pair(lmp)
PairSoft::~PairSoft() PairSoft::~PairSoft()
{ {
if (copymode) return;
if (allocated) { if (allocated) {
memory->destroy(setflag); memory->destroy(setflag);
memory->destroy(cutsq); memory->destroy(cutsq);

2
src/pair_soft.h
View File

@ -49,7 +49,7 @@ class PairSoft : public Pair {
double **prefactor; double **prefactor;
double **cut; double **cut;
void allocate(); virtual void allocate();
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS

37
tools/fep/fep.py
View File

@ -2,23 +2,40 @@
# fep.py - calculate free energy from compute fep results # fep.py - calculate free energy from compute fep results
import sys import sys
from argparse import ArgumentParser
import math import math
if len(sys.argv) < 2: def compute_fep():
print("Free Energy Perturbation")
print("usage: fep.py temperature < out.fep")
sys.exit()
rt = 0.008314 / 4.184 * float(sys.argv[1]) # in kcal/mol parser = ArgumentParser(description='A python script to calculate free energy from compute fep results')
v = 1.0 parser.add_argument("units", help="unit system can be lj, real or si")
sum = 0.0 parser.add_argument("Temperature", type=float, help="The temperature of the system")
for line in sys.stdin: parser.add_argument("InputFile", help="The name of the file with the data from compute fep.")
args = parser.parse_args()
r_value = {'lj': 1.0, 'real': 0.0019872036, 'si': 8.31446}
if args.units in r_value:
rt = r_value[args.units] * args.Temperature
else:
sys.exit("The provided units keyword is not valid")
v = 1.0
mysum = 0.0
with open(args.InputFile, "r") as input_file:
for line in input_file:
if line.startswith("#"): if line.startswith("#"):
continue continue
tok = line.split() tok = line.split()
if len(tok) == 4: if len(tok) == 4:
v = float(tok[3]) v = float(tok[3])
sum += math.log(float(tok[2]) / v) mysum += math.log(float(tok[2]) / v)
print(-rt * mysum)
if __name__ == "__main__":
compute_fep()
print(-rt * sum)

158
unittest/force-styles/tests/manybody-pair-uf3.yaml Normal file
View File

@ -0,0 +1,158 @@
---
lammps_version: 24 Mar 2022
tags:
date_generated: Tue Nov 28 14:51:03 2023
epsilon: 1e-09
skip_tests:
prerequisites: ! |
pair uf3
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
variable newton_bond delete
post_commands: ! ""
input_file: in.manybody
pair_style: uf3 3
pair_coeff: ! |
* * Nb.uf3 Nb Nb Nb Nb Nb Nb Nb Nb
extract: ! ""
natoms: 64
init_vdwl: -76.14388662099438
init_coul: 0
init_stress: ! |2-
3.1223073343802071e+02 3.1503555484293474e+02 3.2087032195384182e+02 -5.2677023646012433e+00 4.1046361968856566e+01 -2.2705704820012654e-01
init_forces: ! |2
1 -1.0963106297354930e+00 1.9921565797217811e+00 2.0176595423650685e+00
2 -2.5744974244934786e+00 8.6065313692841872e-01 -1.3343920771683084e+00
3 -7.5762202587571881e-01 -5.1086473746213934e-01 1.7774798100697495e+00
4 -1.2651178900120015e+00 2.5481168050091734e+00 1.0332353551246649e+00
5 -3.3301075059618213e-02 -8.6936885426915711e-01 -8.0361144939346540e-01
6 5.9576544655966956e-02 -5.7569733665007693e-02 -2.5260577270195245e-01
7 -7.8223973805485159e-01 -1.5872724248886485e+00 -4.0690678808175756e-01
8 1.2837377243355602e-01 6.8616887866365453e-02 3.9279992110159728e-02
9 1.3013607224018784e+00 -2.2234802020121042e-01 -2.5820065882172409e+00
10 -3.5389541898719123e-01 1.0418734269769769e+00 -6.7534263859128518e-01
11 1.5048713773196754e+00 -1.1607474819622305e+00 -4.1343086960946002e-01
12 -3.8382036374205457e+00 -1.8953194768009614e+00 -1.5975045274049304e+00
13 -5.1243974635480005e-01 2.8005048190722506e+00 -8.5188627697957486e-01
14 -4.3260615266171099e-01 1.7104546503175775e+00 4.8896255947620082e-01
15 -2.1729171109783061e+00 1.9610148525080886e+00 -1.7550881080125238e+00
16 1.3063694982664014e+00 4.0801741093678640e-01 3.3816303090167859e+00
17 1.0103076935514768e+00 1.3062727533124225e+00 -3.0591856171743643e+00
18 6.6364797168941592e-01 1.3269858177825717e+00 1.0859880651465830e+00
19 -4.3237772669504843e-01 1.5179601478654310e+00 -8.9399081937433889e-01
20 -4.1109776137187977e+00 4.8942123015814726e-01 3.0324705210921541e-02
21 1.0443613152888414e+00 -2.7611218991110009e-01 -3.2334333893456133e+00
22 -3.8840635954358733e+00 1.8543888965122868e+00 -2.7044170995178298e+00
23 6.4824470795616951e-01 1.1930964693491897e+00 2.3472683895454201e+00
24 5.6518885203578750e-01 8.9024666222906623e-01 9.9558410495963645e-01
25 -2.3884920507811258e-01 -1.2236748552119361e-01 9.6166740424011798e-04
26 -9.4060753459907698e-01 -2.9688412181022056e-01 6.7007032584453752e-01
27 5.0390685311588923e-01 -5.8477364114704944e-01 1.6320689076693460e+00
28 -8.1564347181637331e-01 1.9951358496458818e-01 3.2879220126777038e+00
29 -1.6141037582891811e+00 3.7621933923780954e-01 5.6865013193370151e-01
30 -1.2051389982059610e+00 6.5471000907223187e-02 4.6548238063076404e-02
31 -8.3799333021355227e-01 -4.3387478264068147e-01 -3.4488785440063413e-01
32 -1.8712481645378094e+00 3.1431436055998407e-02 1.1920833582466677e+00
33 2.1132311819974756e+00 -7.8762333052322075e-01 2.9319369786200289e+00
34 -7.4212669325944880e-01 1.5089695276247311e-01 6.4837671979385259e-01
35 4.7876606586762549e-01 -5.2894027298845681e-01 6.5312176822087242e-01
36 9.4335406181387005e-01 -7.7270400013223828e-01 4.8506498341757304e-01
37 -6.9776523536821422e-01 1.5814045923629079e+00 -1.7145687025150753e+00
38 8.3390581678419395e-01 -2.3460369438656256e-01 -8.1845978792256724e-01
39 7.9082785819764490e-01 -1.4014821253885934e+00 -3.6171284136791626e+00
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run_stress: ! |2-
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64 2.1263589729936818e+00 1.8281740261598369e+00 5.2543331430537403e+00
...

100
unittest/force-styles/tests/mol-pair-hybrid_molecular.yaml Normal file
View File

@ -0,0 +1,100 @@
---
lammps_version: 17 Apr 2024
tags:
date_generated: Sun Jun 9 11:41:13 2024
epsilon: 1e-13
skip_tests:
prerequisites: ! |
atom full
pair lj/cut
pair hybrid/molecular
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify shift yes
input_file: in.fourmol
pair_style: hybrid/molecular lj/cut 8.0 lj/cut 8.0
pair_coeff: ! |
1 1 lj/cut 1 0.02 2.5
2 2 lj/cut 1 0.005 1.0
2 4 lj/cut 1 0.005 0.5
3 3 lj/cut 1 0.02 3.2
4 4 lj/cut 1 0.015 3.1
5 5 lj/cut 1 0.015 3.1
1 1 lj/cut 2 0.02 2.5
2 2 lj/cut 2 0.005 1.0
2 4 lj/cut 2 0.005 0.5
3 3 lj/cut 2 0.02 3.2
4 4 lj/cut 2 0.015 3.1
5 5 lj/cut 2 0.015 3.1
extract: ! ""
natoms: 29
init_vdwl: 749.2470096189497
init_coul: 0
init_stress: ! |2-
2.1793857186503237e+03 2.1988957679770601e+03 4.6653994738862348e+03 -7.5956544622684351e+02 2.4751393539193327e+01 6.6652061873806679e+02
init_forces: ! |2
1 -2.3333390274530565e+01 2.6994567613591136e+02 3.3272827850621587e+02
2 1.5828554630423909e+02 1.3025008843536872e+02 -1.8629682358915150e+02
3 -1.3528903744071786e+02 -3.8704313350789641e+02 -1.4568978426110147e+02
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5 -2.5176757267276137e+00 -4.0521510680612876e+00 1.2152704057983799e+01
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7 5.8203416066164465e+01 -3.3609013622052356e+02 -1.7179626006587687e+03
8 1.4451392646293456e+02 -1.0927476052490437e+02 3.9990594285329479e+02
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20 -9.9760831169755002e-04 -1.0209184785886856e-03 3.6910973051849135e-04
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22 -1.0808840769631149e+02 -2.6193799449067580e+01 -1.6957912849816358e+02
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29 1.2861063251415737e+02 1.4952718246094852e+02 3.1216040111076957e+01
run_vdwl: 719.4532389988315
run_coul: 0
run_stress: ! |2-
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run_forces: ! |2
1 -2.0299419744961813e+01 2.6686193379336868e+02 3.2358785871037435e+02
2 1.5298617928501707e+02 1.2596516341411086e+02 -1.7961292655320207e+02
3 -1.3353630670276331e+02 -3.7923748676909099e+02 -1.4291839777232488e+02
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5 -2.5014258629959465e+00 -4.0250131424457543e+00 1.2103512372172734e+01
6 -8.0681466162480240e+02 9.2165651041424792e+02 1.0270802401119468e+03
7 5.5780302775854636e+01 -3.1117544157318952e+02 -1.5746997989226002e+03
8 1.3452983973683914e+02 -1.0064660034658647e+02 3.8851792520911863e+02
9 7.6746213900459239e+01 8.2501469902247337e+01 3.3944351209160595e+02
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27 5.0800867695850577e+01 -2.2296598219372004e+02 8.8607407764830413e+01
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29 1.2614900659680345e+02 1.4694257504728049e+02 3.0893400701043564e+01
...

119
unittest/force-styles/tests/mol-pair-hybrid_molecular_lj_morse.yaml Normal file
View File

@ -0,0 +1,119 @@
---
lammps_version: 17 Apr 2024
tags:
date_generated: Sun Jun 9 11:41:13 2024
epsilon: 1e-13
skip_tests:
prerequisites: ! |
atom full
pair lj/cut
pair morse
pair hybrid/molecular
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify shift yes
input_file: in.fourmol
pair_style: hybrid/molecular lj/cut 8.0 morse 8.0
pair_coeff: ! |
1 1 lj/cut 0.02 2.5
1 2 lj/cut 0.01 1.75
1 3 lj/cut 0.02 2.85
1 4 lj/cut 0.01732050807568877293 2.8
1 5 lj/cut 0.01732050807568877293 2.8
2 2 lj/cut 0.005 1.0
2 3 lj/cut 0.01 2.1
2 4 lj/cut 0.005 0.5
2 5 lj/cut 0.00866025403784438646 2.05
3 3 lj/cut 0.02 3.2
3 4 lj/cut 0.01732050807568877293 3.15
3 5 lj/cut 0.01732050807568877293 3.15
4 4 lj/cut 0.015 3.1
4 5 lj/cut 0.015 3.1
5 5 lj/cut 0.015 3.1
1 1 morse 0.0202798941614106 2.78203488021395 2.725417159299
1 2 morse 0.0101167811264648 3.9793050302425 1.90749569018897
1 3 morse 0.0202934330695928 2.43948720203264 3.10711749999622
1 4 morse 0.0175731334238374 2.48316585521317 3.05258880102438
1 5 morse 0.0175731334238374 2.48316585521317 3.05258880102438
2 2 morse 0.00503064360487288 6.98433077606902 1.08960295117864
2 3 morse 0.0101296013842819 3.31380153807866 2.28919067558352
2 4 morse 0.00497405122588691 14.0508902925745 0.544416409093563
2 5 morse 0.00877114211614446 3.39491256196178 2.23466262511073
3 3 morse 0.0203039874239943 2.17204344301477 3.48881895084762
3 4 morse 0.0175825321440736 2.20660439192238 3.43428999287994
3 5 morse 0.0175825321440736 2.20660439192238 3.43428999287994
4 4 morse 0.0152259201379927 2.24227873774009 3.37976131582396
4 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396
5 5 morse 0.0152259201379927 2.24227873774009 3.37976131582396
extract: ! ""
natoms: 29
init_vdwl: 642.2857035487534
init_coul: 0
init_stress: ! |2-
1.5446101412530770e+03 1.7762864877230827e+03 4.3406629723991382e+03 -2.4168966825090698e+02 -4.2399281241000449e+02 1.0313398732648857e+03
init_forces: ! |2
1 -2.3337658999820331e+01 2.6994849929388920e+02 3.3272731927204762e+02
2 1.5828475525620013e+02 1.3025198646645657e+02 -1.8629727921784635e+02
3 -1.3530883593401191e+02 -3.8702990176780906e+02 -1.4568955729804821e+02
4 -7.8720974048138279e+00 2.1357285334450031e+00 -5.5956697614574145e+00
5 -2.5179872246085657e+00 -4.0521698308193113e+00 1.2152426584580066e+01
6 -1.0627539753780246e+02 3.7096636535889553e+02 1.6577829288882351e+03
7 6.2545311732649182e+01 -3.3857732069504033e+02 -1.7085638850072914e+03
8 -5.8544805218664203e+02 4.8619364551174579e+02 -1.1637016110669298e+02
9 7.9157108381891348e+01 8.5271268694585373e+01 3.5031950365280102e+02
10 5.3119792393751504e+02 -6.1042010285634149e+02 -1.8355328074325874e+02
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run_coul: 0
run_stress: ! |2-
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...