Merge pull request #3787 from oywg11/ilp-water-graphene
Registry-Dependent Potential for Interfaces of Water with Graphene
This commit is contained in:
Axel Kohlmeyer
@ -37,6 +37,7 @@ OPT.
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*
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* :doc:`adp (ko) <pair_adp>`
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* :doc:`agni (o) <pair_agni>`
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* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
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* :doc:`airebo (io) <pair_airebo>`
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* :doc:`airebo/morse (io) <pair_airebo>`
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* :doc:`amoeba (g) <pair_amoeba>`
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167
doc/src/pair_aip_water_2dm.rst
Normal file
167
doc/src/pair_aip_water_2dm.rst
Normal file
@ -0,0 +1,167 @@
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.. index:: pair_style aip/water/2dm
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.. index:: pair_style aip/water/2dm/opt
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pair_style aip/water/2dm command
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===================================
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Accelerator Variant: *aip/water/2dm/opt*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style [hybrid/overlay ...] aip/water/2dm cutoff tap_flag
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* cutoff = global cutoff (distance units)
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* tap_flag = 0/1 to turn off/on the taper function
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style hybrid/overlay aip/water/2dm 16.0 1
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pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
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pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
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pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
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pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
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Description
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"""""""""""
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.. versionadded:: TBD
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The *aip/water/2dm* style computes the anisotropic interfacial potential
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(AIP) potential for interfaces of water with two-dimensional (2D)
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materials as described in :ref:`(Feng) <Feng>`.
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.. math::
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E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
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V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
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\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
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\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
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\cdot \frac{C_6}{r^6_{ij}} \right \}\\
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\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
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\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
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f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
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{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
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70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
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84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
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35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
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Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
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a continuous cutoff (up to third derivative) for interatomic separations
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larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
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<pair_ilp_graphene_hbn>`.
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.. note::
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This pair style uses the atomic normal vector definition from
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:ref:`(Feng) <Feng>`), where the atomic normal vectors of the
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hydrogen atoms are assumed to lie along the corresponding
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oxygen-hydrogen bonds and the normal vector of the central oxygen
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atom is defined as their average.
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The provided parameter file, ``COH.aip.water.2dm``, is intended for use
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with *metal* :doc:`units <units>`, with energies in meV. Two additional
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parameters, *S*, and *rcut* are included in the parameter file. *S* is
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designed to facilitate scaling of energies; *rcut* is the cutoff for an
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internal, short distance neighbor list that is generated for speeding up
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the calculation of the normals for all atom pairs.
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.. note::
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The parameters presented in the provided parameter file,
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``COH.aip.water.2dm``, are fitted with the taper function enabled by
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setting the cutoff equal to 16.0 Angstrom. Using a different cutoff
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or taper function setting should be carefully checked as they can
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lead to significant errors. These parameters provide a good
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description in both short- and long-range interaction regimes. This
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is essential for simulations in high pressure regime (i.e., the
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interlayer distance is smaller than the equilibrium distance).
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This potential must be used in combination with hybrid/overlay. Other
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interactions can be set to zero using :doc:`pair_coeff settings
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<pair_coeff>` with the pair style set to *none*\ .
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This pair style tallies a breakdown of the total interlayer potential
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energy into sub-categories, which can be accessed via the :doc:`compute
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pair <compute_pair>` command as a vector of values of length 2. The 2
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values correspond to the following sub-categories:
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1. *E_vdW* = vdW (attractive) energy
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2. *E_Rep* = Repulsive energy
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To print these quantities to the log file (with descriptive column
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headings) the following commands could be included in an input script:
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.. code-block:: LAMMPS
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compute 0 all pair aip/water/2dm
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variable Evdw equal c_0[1]
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variable Erep equal c_0[2]
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thermo_style custom step temp epair v_Erep v_Evdw
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----------
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.. include:: accel_styles.rst
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This pair style does not support the pair_modify mix, shift, table, and
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tail options.
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This pair style does not write their information to binary restart
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files, since it is stored in potential files. Thus, you need to
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re-specify the pair_style and pair_coeff commands in an input script
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that reads a restart file.
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Restrictions
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""""""""""""
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This pair style is part of the INTERLAYER package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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This pair style requires the newton setting to be *on* for pair
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interactions.
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The ``COH.aip.water.2dm`` potential file provided with LAMMPS is
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parameterized for *metal* units. You can use this pair style with any
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LAMMPS units, but you would need to create your own potential file with
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parameters in the appropriate units, if your simulation does not use
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*metal* units.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`,
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:doc:`pair_none <pair_none>`,
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:doc:`pair_style hybrid/overlay <pair_hybrid>`,
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:doc:`pair_style drip <pair_drip>`,
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:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
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:doc:`pair_style saip_metal <pair_saip_metal>`,
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:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
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:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
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:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
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:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
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:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
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Default
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"""""""
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tap_flag = 1
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----------
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.. _Feng:
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**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).
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@ -155,8 +155,8 @@ interactions.
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The BNCH.ILP potential file provided with LAMMPS (see the potentials
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directory) are parameterized for *metal* units. You can use this
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potential with any LAMMPS units, but you would need to create your
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BNCH.ILP potential file with coefficients listed in the appropriate
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potential with any LAMMPS units, but you would need to create your own
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custom BNCH.ILP potential file with coefficients listed in the appropriate
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units, if your simulation does not use *metal* units.
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Related commands
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@ -181,6 +181,14 @@ tap_flag = 1
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----------
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.. _Ouyang1:
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**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
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.. _Ouyang2:
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**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
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.. _Leven1:
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**(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
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@ -196,11 +204,3 @@ tap_flag = 1
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.. _Kolmogorov2:
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**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
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.. _Ouyang1:
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**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
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.. _Ouyang2:
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**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
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@ -135,8 +135,8 @@ interactions.
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The TMD.ILP potential file provided with LAMMPS (see the potentials
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directory) are parameterized for *metal* units. You can use this
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potential with any LAMMPS units, but you would need to create your
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BNCH.ILP potential file with coefficients listed in the appropriate
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potential with any LAMMPS units, but you would need to create your own
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custom TMD.ILP potential file with coefficients listed in the appropriate
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units, if your simulation does not use *metal* units.
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Related commands
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@ -129,7 +129,7 @@ interactions.
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The CH.KC potential file provided with LAMMPS (see the potentials
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folder) is parameterized for metal units. You can use this pair style
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with any LAMMPS units, but you would need to create your own custom
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CC.KC potential file with all coefficients converted to the appropriate
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CH.KC potential file with all coefficients converted to the appropriate
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units.
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Related commands
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@ -134,8 +134,8 @@ interactions.
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The CHAu.ILP potential file provided with LAMMPS (see the potentials
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directory) are parameterized for *metal* units. You can use this
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potential with any LAMMPS units, but you would need to create your
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BNCH.ILP potential file with coefficients listed in the appropriate
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potential with any LAMMPS units, but you would need to create your own
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custom CHAu.ILP potential file with coefficients listed in the appropriate
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units, if your simulation does not use *metal* units.
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Related commands
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@ -114,6 +114,7 @@ accelerated styles exist.
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* :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
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* :doc:`agni <pair_agni>` - AGNI machine-learning potential
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* :doc:`aip/water/2dm <pair_aip_water_2dm>` - anisotropic interfacial potential for water in 2d geometries
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* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
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* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
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* :doc:`amoeba <pair_amoeba>` -
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@ -55,6 +55,7 @@ Ai
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Aidan
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aij
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aimd
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aip
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airebo
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Aj
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ajaramil
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@ -528,6 +529,7 @@ collisional
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Columic
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colvars
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Colvars
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COH
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COLVARS
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comID
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Commun
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@ -1090,6 +1092,7 @@ Fellinger
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femtosecond
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femtoseconds
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fene
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Feng
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Fennell
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fep
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FEP
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1
examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
Symbolic link
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
Symbolic link
@ -0,0 +1 @@
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../../../../potentials/COH.aip.water.2dm
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2040
examples/PACKAGES/interlayer/aip_water_2dm/gra_water.data
Normal file
2040
examples/PACKAGES/interlayer/aip_water_2dm/gra_water.data
Normal file
File diff suppressed because it is too large
Load Diff
51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
Normal file
51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
Normal file
@ -0,0 +1,51 @@
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./gra_water.data
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mass 1 12.0107 # carbon mass (g/mole)
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mass 2 15.9994 # oxygen mass (g/mole)
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mass 3 1.008 # hydrogen mass (g/mole)
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# Separate atom groups
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group gr molecule 1
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group water molecule 2
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
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####################################################################
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pair_coeff 1 1 none
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
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pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
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pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
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# bond and angle
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bond_style harmonic
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bond_coeff 1 0.0 0.9572
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angle_style harmonic
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angle_coeff 1 0.0 104.52
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# define kspace calculation
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kspace_style pppm/tip4p 1E-5
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1 delay 5 check yes page 1000000 one 100000
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####################################################################
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# Calculate pair energy
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compute 1 all pair lj/cut/tip4p/long
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compute 2 all pair aip/water/2dm
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compute wt water temp
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variable TIP4P equal c_1
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variable EILP equal c_2 # total interlayer energy
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variable temp_wt equal c_wt
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############# Output ##############
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thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
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thermo 100
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thermo_modify lost error
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fix subf gr setforce 0.0 0.0 0.0
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fix 1 water shake 0.0001 20 100 b 1 a 1
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timestep 1e-3
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velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
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fix 2 water nve
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run 1000
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51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
Normal file
51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
Normal file
@ -0,0 +1,51 @@
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./gra_water.data
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mass 1 12.0107 # carbon mass (g/mole)
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mass 2 15.9994 # oxygen mass (g/mole)
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mass 3 1.008 # hydrogen mass (g/mole)
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# Separate atom groups
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group gr molecule 1
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group water molecule 2
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
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pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
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# bond and angle
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bond_style harmonic
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bond_coeff 1 0.0 0.9572
|
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angle_style harmonic
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angle_coeff 1 0.0 104.52
|
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# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
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# Neighbor update settings
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neighbor 2.0 bin
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||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
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# Calculate pair energy
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compute 1 all pair lj/cut/tip4p/long
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compute 2 all pair aip/water/2dm/opt
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compute wt water temp
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variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
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||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
@ -0,0 +1,239 @@
|
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LAMMPS (23 Jun 2022 - Update 4)
|
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
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using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
936 atoms
|
||||
reading velocities ...
|
||||
936 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
96 bonds
|
||||
reading angles ...
|
||||
48 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
792 atoms in group gr
|
||||
group water molecule 2
|
||||
144 atoms in group water
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
48 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||
@Article{Ouyang2018
|
||||
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
|
||||
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||
journal = {Nano Letters},
|
||||
volume = 18,
|
||||
pages = 6009,
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
|
||||
@Article{Ouyang2021
|
||||
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
|
||||
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
|
||||
title = {Anisotropic Interlayer Force Field for Transition
|
||||
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
volume = 17,
|
||||
pages = {7237--7245}
|
||||
year = 2021,
|
||||
}
|
||||
|
||||
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||
@Article{Feng2023
|
||||
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||
journal = {J. Phys. Chem. C},
|
||||
volume = 127,
|
||||
pages = {8704-8713}
|
||||
year = 2023,
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.28684806
|
||||
grid = 25 24 80
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0001640931
|
||||
estimated relative force accuracy = 1.1395635e-05
|
||||
using single precision MKL FFT
|
||||
3d grid and FFT values/proc = 84320 48000
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
|
||||
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 100000, page size: 1000000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 6 5 23
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair aip/water/2dm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 1 0.957201 2.19705e-06 96
|
||||
Angle: 1 104.52 0.000203056 48
|
||||
Per MPI rank memory allocation (min/avg/max) = 32.9 | 32.9 | 32.9 Mbytes
|
||||
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 1 0.9572 9.54949e-07 96
|
||||
Angle: 1 104.52 6.01522e-05 48
|
||||
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 1 0.9572 9.63922e-07 96
|
||||
Angle: 1 104.52 7.7021e-05 48
|
||||
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 1 0.9572 1.4264e-06 96
|
||||
Angle: 1 104.52 6.48393e-05 48
|
||||
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
|
||||
SHAKE stats (type/ave/delta/count) on step 400
|
||||
Bond: 1 0.9572 1.33728e-06 96
|
||||
Angle: 1 104.52 7.6239e-05 48
|
||||
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
Bond: 1 0.9572 1.14685e-06 96
|
||||
Angle: 1 104.52 8.58621e-05 48
|
||||
500 -17.491435 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
|
||||
SHAKE stats (type/ave/delta/count) on step 600
|
||||
Bond: 1 0.9572 9.17601e-07 96
|
||||
Angle: 1 104.52 8.24516e-05 48
|
||||
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
|
||||
SHAKE stats (type/ave/delta/count) on step 700
|
||||
Bond: 1 0.9572 9.50422e-07 96
|
||||
Angle: 1 104.52 5.62423e-05 48
|
||||
700 -17.496703 -21.072663 3.5759596 188.2777 -1.9833956 291.20871
|
||||
SHAKE stats (type/ave/delta/count) on step 800
|
||||
Bond: 1 0.9572 1.15262e-06 96
|
||||
Angle: 1 104.52 7.02157e-05 48
|
||||
800 -17.478623 -20.819504 3.3408809 188.37868 -1.9112996 272.06505
|
||||
SHAKE stats (type/ave/delta/count) on step 900
|
||||
Bond: 1 0.9572 9.14138e-07 96
|
||||
Angle: 1 104.52 6.98742e-05 48
|
||||
900 -17.48086 -20.728495 3.2476349 188.59022 -1.8922102 264.47155
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
Bond: 1 0.9572 1.00586e-06 96
|
||||
Angle: 1 104.52 0.000111712 48
|
||||
1000 -17.498465 -20.331545 2.8330804 188.87473 -1.812177 230.71225
|
||||
Loop time of 20.3334 on 1 procs for 1000 steps with 936 atoms
|
||||
|
||||
Performance: 4.249 ns/day, 5.648 hours/ns, 49.180 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.179 | 16.179 | 16.179 | 0.0 | 79.57
|
||||
Bond | 0.00021103 | 0.00021103 | 0.00021103 | 0.0 | 0.00
|
||||
Kspace | 3.3118 | 3.3118 | 3.3118 | 0.0 | 16.29
|
||||
Neigh | 0.79017 | 0.79017 | 0.79017 | 0.0 | 3.89
|
||||
Comm | 0.026379 | 0.026379 | 0.026379 | 0.0 | 0.13
|
||||
Output | 0.00046496 | 0.00046496 | 0.00046496 | 0.0 | 0.00
|
||||
Modify | 0.017013 | 0.017013 | 0.017013 | 0.0 | 0.08
|
||||
Other | | 0.008835 | | | 0.04
|
||||
|
||||
Nlocal: 936 ave 936 max 936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5242 ave 5242 max 5242 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: 431382 ave 431382 max 431382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 431382
|
||||
Ave neighs/atom = 460.87821
|
||||
Ave special neighs/atom = 0.30769231
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:20
|
||||
@ -0,0 +1,239 @@
|
||||
LAMMPS (23 Jun 2022 - Update 4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
936 atoms
|
||||
reading velocities ...
|
||||
936 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
96 bonds
|
||||
reading angles ...
|
||||
48 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.017 seconds
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
792 atoms in group gr
|
||||
group water molecule 2
|
||||
144 atoms in group water
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
48 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||
@Article{Ouyang2018
|
||||
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
|
||||
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||
journal = {Nano Letters},
|
||||
volume = 18,
|
||||
pages = 6009,
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
|
||||
@Article{Ouyang2021
|
||||
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
|
||||
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
|
||||
title = {Anisotropic Interlayer Force Field for Transition
|
||||
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
volume = 17,
|
||||
pages = {7237--7245}
|
||||
year = 2021,
|
||||
}
|
||||
|
||||
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||
@Article{Feng2023
|
||||
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||
journal = {J. Phys. Chem. C},
|
||||
volume = 127,
|
||||
pages = {8704-8713}
|
||||
year = 2023,
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.28684806
|
||||
grid = 25 24 80
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0001640931
|
||||
estimated relative force accuracy = 1.1395635e-05
|
||||
using single precision MKL FFT
|
||||
3d grid and FFT values/proc = 30685 12480
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
|
||||
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 100000, page size: 1000000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 6 5 23
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair aip/water/2dm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 1 0.957201 2.19705e-06 96
|
||||
Angle: 1 104.52 0.000203056 48
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.22 | 25.25 | 25.29 Mbytes
|
||||
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 1 0.9572 9.54949e-07 96
|
||||
Angle: 1 104.52 6.01522e-05 48
|
||||
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 1 0.9572 9.63922e-07 96
|
||||
Angle: 1 104.52 7.7021e-05 48
|
||||
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 1 0.9572 1.4264e-06 96
|
||||
Angle: 1 104.52 6.48393e-05 48
|
||||
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
|
||||
SHAKE stats (type/ave/delta/count) on step 400
|
||||
Bond: 1 0.9572 1.33728e-06 96
|
||||
Angle: 1 104.52 7.6239e-05 48
|
||||
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
Bond: 1 0.9572 1.14685e-06 96
|
||||
Angle: 1 104.52 8.58621e-05 48
|
||||
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
|
||||
SHAKE stats (type/ave/delta/count) on step 600
|
||||
Bond: 1 0.9572 9.17601e-07 96
|
||||
Angle: 1 104.52 8.24517e-05 48
|
||||
600 -17.505683 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
|
||||
SHAKE stats (type/ave/delta/count) on step 700
|
||||
Bond: 1 0.9572 9.50425e-07 96
|
||||
Angle: 1 104.52 5.62422e-05 48
|
||||
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
|
||||
SHAKE stats (type/ave/delta/count) on step 800
|
||||
Bond: 1 0.9572 1.15256e-06 96
|
||||
Angle: 1 104.52 7.02177e-05 48
|
||||
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.06489
|
||||
SHAKE stats (type/ave/delta/count) on step 900
|
||||
Bond: 1 0.9572 9.14163e-07 96
|
||||
Angle: 1 104.52 6.98849e-05 48
|
||||
900 -17.480865 -20.728504 3.2476386 188.5902 -1.8922108 264.47185
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
Bond: 1 0.9572 1.00568e-06 96
|
||||
Angle: 1 104.52 0.000111707 48
|
||||
1000 -17.498474 -20.331607 2.833133 188.87466 -1.8121689 230.71654
|
||||
Loop time of 9.05361 on 4 procs for 1000 steps with 936 atoms
|
||||
|
||||
Performance: 9.543 ns/day, 2.515 hours/ns, 110.453 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.462 | 4.2266 | 7.1075 | 89.3 | 46.68
|
||||
Bond | 0.00018424 | 0.00019878 | 0.00022125 | 0.0 | 0.00
|
||||
Kspace | 1.4698 | 4.338 | 6.1001 | 87.8 | 47.91
|
||||
Neigh | 0.39462 | 0.39489 | 0.39518 | 0.0 | 4.36
|
||||
Comm | 0.043753 | 0.055826 | 0.062746 | 3.1 | 0.62
|
||||
Output | 0.00048755 | 0.00053971 | 0.00062785 | 0.0 | 0.01
|
||||
Modify | 0.027255 | 0.028664 | 0.030278 | 0.7 | 0.32
|
||||
Other | | 0.008904 | | | 0.10
|
||||
|
||||
Nlocal: 234 ave 302 max 198 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 2876.5 ave 3122 max 2632 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 107846 ave 150684 max 82181 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 431382
|
||||
Ave neighs/atom = 460.87821
|
||||
Ave special neighs/atom = 0.30769231
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:09
|
||||
@ -0,0 +1,256 @@
|
||||
LAMMPS (23 Jun 2022 - Update 4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
936 atoms
|
||||
reading velocities ...
|
||||
936 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
96 bonds
|
||||
reading angles ...
|
||||
48 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
792 atoms in group gr
|
||||
group water molecule 2
|
||||
144 atoms in group water
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
48 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||
@Article{Ouyang2018
|
||||
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
|
||||
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||
journal = {Nano Letters},
|
||||
volume = 18,
|
||||
pages = 6009,
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
|
||||
@Article{Ouyang2021
|
||||
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
|
||||
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
|
||||
title = {Anisotropic Interlayer Force Field for Transition
|
||||
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
volume = 17,
|
||||
pages = {7237--7245}
|
||||
year = 2021,
|
||||
}
|
||||
|
||||
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||
@Article{Feng2023
|
||||
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||
journal = {J. Phys. Chem. C},
|
||||
volume = 127,
|
||||
pages = {8704-8713}
|
||||
year = 2023,
|
||||
}
|
||||
|
||||
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
|
||||
@inproceedings{gao2021lmff
|
||||
author = {Gao, Ping and Duan, Xiaohui and Others},
|
||||
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
|
||||
year = {2021},
|
||||
isbn = {9781450384421},
|
||||
publisher = {Association for Computing Machinery},
|
||||
address = {New York, NY, USA},
|
||||
url = {https://doi.org/10.1145/3458817.3476137},
|
||||
doi = {10.1145/3458817.3476137},
|
||||
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
|
||||
articleno = {42},
|
||||
numpages = {14},
|
||||
location = {St. Louis, Missouri},
|
||||
series = {SC'21},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.28684806
|
||||
grid = 25 24 80
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0001640931
|
||||
estimated relative force accuracy = 1.1395635e-05
|
||||
using single precision MKL FFT
|
||||
3d grid and FFT values/proc = 84320 48000
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
|
||||
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 100000, page size: 1000000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 6 5 23
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair aip/water/2dm/opt, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 1 0.957201 2.19705e-06 96
|
||||
Angle: 1 104.52 0.000203056 48
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.27 | 25.27 | 25.27 Mbytes
|
||||
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 1 0.9572 9.54949e-07 96
|
||||
Angle: 1 104.52 6.01522e-05 48
|
||||
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 1 0.9572 9.63922e-07 96
|
||||
Angle: 1 104.52 7.7021e-05 48
|
||||
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 1 0.9572 1.4264e-06 96
|
||||
Angle: 1 104.52 6.48393e-05 48
|
||||
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
|
||||
SHAKE stats (type/ave/delta/count) on step 400
|
||||
Bond: 1 0.9572 1.33728e-06 96
|
||||
Angle: 1 104.52 7.6239e-05 48
|
||||
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
Bond: 1 0.9572 1.14685e-06 96
|
||||
Angle: 1 104.52 8.58621e-05 48
|
||||
500 -17.491436 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
|
||||
SHAKE stats (type/ave/delta/count) on step 600
|
||||
Bond: 1 0.9572 9.17601e-07 96
|
||||
Angle: 1 104.52 8.24516e-05 48
|
||||
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
|
||||
SHAKE stats (type/ave/delta/count) on step 700
|
||||
Bond: 1 0.9572 9.50422e-07 96
|
||||
Angle: 1 104.52 5.62423e-05 48
|
||||
700 -17.496701 -21.07266 3.5759595 188.2777 -1.9833956 291.20871
|
||||
SHAKE stats (type/ave/delta/count) on step 800
|
||||
Bond: 1 0.9572 1.15262e-06 96
|
||||
Angle: 1 104.52 7.02158e-05 48
|
||||
800 -17.478623 -20.819504 3.340881 188.37868 -1.9112996 272.06506
|
||||
SHAKE stats (type/ave/delta/count) on step 900
|
||||
Bond: 1 0.9572 9.14138e-07 96
|
||||
Angle: 1 104.52 6.98742e-05 48
|
||||
900 -17.480864 -20.728498 3.2476343 188.59022 -1.8922102 264.4715
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
Bond: 1 0.9572 1.00586e-06 96
|
||||
Angle: 1 104.52 0.000111711 48
|
||||
1000 -17.498466 -20.331547 2.8330808 188.87473 -1.8121768 230.71228
|
||||
Loop time of 8.11929 on 1 procs for 1000 steps with 936 atoms
|
||||
|
||||
Performance: 10.641 ns/day, 2.255 hours/ns, 123.163 timesteps/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 | 4.6849 | 4.6849 | 4.6849 | 0.0 | 57.70
|
||||
Bond | 0.00017678 | 0.00017678 | 0.00017678 | 0.0 | 0.00
|
||||
Kspace | 3.2098 | 3.2098 | 3.2098 | 0.0 | 39.53
|
||||
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 2.16
|
||||
Comm | 0.024693 | 0.024693 | 0.024693 | 0.0 | 0.30
|
||||
Output | 0.00037798 | 0.00037798 | 0.00037798 | 0.0 | 0.00
|
||||
Modify | 0.015853 | 0.015853 | 0.015853 | 0.0 | 0.20
|
||||
Other | | 0.007983 | | | 0.10
|
||||
|
||||
Nlocal: 936 ave 936 max 936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5242 ave 5242 max 5242 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: 431382 ave 431382 max 431382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 431382
|
||||
Ave neighs/atom = 460.87821
|
||||
Ave special neighs/atom = 0.30769231
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
@ -0,0 +1,256 @@
|
||||
LAMMPS (23 Jun 2022 - Update 4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
936 atoms
|
||||
reading velocities ...
|
||||
936 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
96 bonds
|
||||
reading angles ...
|
||||
48 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.014 seconds
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
792 atoms in group gr
|
||||
group water molecule 2
|
||||
144 atoms in group water
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
48 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||
@Article{Ouyang2018
|
||||
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
|
||||
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||
journal = {Nano Letters},
|
||||
volume = 18,
|
||||
pages = 6009,
|
||||
year = 2018,
|
||||
}
|
||||
|
||||
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
|
||||
@Article{Ouyang2021
|
||||
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
|
||||
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
|
||||
title = {Anisotropic Interlayer Force Field for Transition
|
||||
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
volume = 17,
|
||||
pages = {7237--7245}
|
||||
year = 2021,
|
||||
}
|
||||
|
||||
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||
@Article{Feng2023
|
||||
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||
journal = {J. Phys. Chem. C},
|
||||
volume = 127,
|
||||
pages = {8704-8713}
|
||||
year = 2023,
|
||||
}
|
||||
|
||||
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
|
||||
@inproceedings{gao2021lmff
|
||||
author = {Gao, Ping and Duan, Xiaohui and Others},
|
||||
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
|
||||
year = {2021},
|
||||
isbn = {9781450384421},
|
||||
publisher = {Association for Computing Machinery},
|
||||
address = {New York, NY, USA},
|
||||
url = {https://doi.org/10.1145/3458817.3476137},
|
||||
doi = {10.1145/3458817.3476137},
|
||||
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
|
||||
articleno = {42},
|
||||
numpages = {14},
|
||||
location = {St. Louis, Missouri},
|
||||
series = {SC'21},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||
G vector (1/distance) = 0.28684806
|
||||
grid = 25 24 80
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0001640931
|
||||
estimated relative force accuracy = 1.1395635e-05
|
||||
using single precision MKL FFT
|
||||
3d grid and FFT values/proc = 30685 12480
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
|
||||
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 100000, page size: 1000000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 6 5 23
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair aip/water/2dm/opt, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 1 0.957201 2.19705e-06 96
|
||||
Angle: 1 104.52 0.000203056 48
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 Mbytes
|
||||
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 1 0.9572 9.54949e-07 96
|
||||
Angle: 1 104.52 6.01522e-05 48
|
||||
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 1 0.9572 9.63922e-07 96
|
||||
Angle: 1 104.52 7.7021e-05 48
|
||||
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 1 0.9572 1.4264e-06 96
|
||||
Angle: 1 104.52 6.48393e-05 48
|
||||
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
|
||||
SHAKE stats (type/ave/delta/count) on step 400
|
||||
Bond: 1 0.9572 1.33728e-06 96
|
||||
Angle: 1 104.52 7.6239e-05 48
|
||||
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
Bond: 1 0.9572 1.14685e-06 96
|
||||
Angle: 1 104.52 8.58621e-05 48
|
||||
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
|
||||
SHAKE stats (type/ave/delta/count) on step 600
|
||||
Bond: 1 0.9572 9.17601e-07 96
|
||||
Angle: 1 104.52 8.24517e-05 48
|
||||
600 -17.505682 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
|
||||
SHAKE stats (type/ave/delta/count) on step 700
|
||||
Bond: 1 0.9572 9.50425e-07 96
|
||||
Angle: 1 104.52 5.62423e-05 48
|
||||
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
|
||||
SHAKE stats (type/ave/delta/count) on step 800
|
||||
Bond: 1 0.9572 1.15256e-06 96
|
||||
Angle: 1 104.52 7.02177e-05 48
|
||||
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.0649
|
||||
SHAKE stats (type/ave/delta/count) on step 900
|
||||
Bond: 1 0.9572 9.14163e-07 96
|
||||
Angle: 1 104.52 6.98849e-05 48
|
||||
900 -17.480868 -20.728506 3.2476383 188.5902 -1.8922108 264.47182
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
Bond: 1 0.9572 1.00568e-06 96
|
||||
Angle: 1 104.52 0.000111707 48
|
||||
1000 -17.498472 -20.331605 2.8331335 188.87466 -1.8121689 230.71657
|
||||
Loop time of 4.24862 on 4 procs for 1000 steps with 936 atoms
|
||||
|
||||
Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.25749 | 1.1806 | 2.6872 | 89.0 | 27.79
|
||||
Bond | 0.00018656 | 0.00020786 | 0.00025377 | 0.0 | 0.00
|
||||
Kspace | 1.4259 | 2.9204 | 3.8414 | 56.3 | 68.74
|
||||
Neigh | 0.057504 | 0.057852 | 0.05818 | 0.1 | 1.36
|
||||
Comm | 0.041952 | 0.053593 | 0.05876 | 3.0 | 1.26
|
||||
Output | 0.0004296 | 0.00046809 | 0.00055317 | 0.0 | 0.01
|
||||
Modify | 0.026204 | 0.027251 | 0.028382 | 0.6 | 0.64
|
||||
Other | | 0.008209 | | | 0.19
|
||||
|
||||
Nlocal: 234 ave 302 max 198 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 2876.5 ave 3122 max 2632 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 107846 ave 150684 max 82181 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 431382
|
||||
Ave neighs/atom = 460.87821
|
||||
Ave special neighs/atom = 0.30769231
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
28
potentials/COH.DMC.aip.water.2dm
Normal file
28
potentials/COH.DMC.aip.water.2dm
Normal file
@ -0,0 +1,28 @@
|
||||
# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
|
||||
# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
|
||||
# The parameters below are fitted against the DMC reference data that rescaled from PBE+MBD-NL.
|
||||
#
|
||||
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
|
||||
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
|
||||
# For graphene and hydrocarbons
|
||||
C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0
|
||||
H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2
|
||||
C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
|
||||
H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
|
||||
|
||||
# For water-graphene
|
||||
C Ow 4.03686677 15.09817069 1.00000323 1.03838111 0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222 1.0 2.0
|
||||
C Hw 3.08246994 6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099 4652.78021666 1.0 2.0
|
||||
Ow C 4.03686677 15.09817069 1.00000323 1.03838111 0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222 1.0 1.2
|
||||
Hw C 3.08246994 6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099 4652.78021666 1.0 1.2
|
||||
|
||||
# # The ILPs for other systems are set to zero
|
||||
H Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
H Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Ow H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
|
||||
Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
28
potentials/COH.aip.water.2dm
Normal file
28
potentials/COH.aip.water.2dm
Normal file
@ -0,0 +1,28 @@
|
||||
# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
|
||||
# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
|
||||
# The parameters below are fitted against the PBE + MBD-NL DFT reference data from 2.5 A to 15 A.
|
||||
#
|
||||
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
|
||||
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
|
||||
# For graphene and hydrocarbons
|
||||
C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0
|
||||
H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2
|
||||
C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
|
||||
H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
|
||||
|
||||
# For water-graphene
|
||||
C Ow 5.45369612 6.18172364 1.25025450 3.34909245 0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127 1.0 2.0
|
||||
C Hw 2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571 7409.12856378 1.0 2.0
|
||||
Ow C 5.45369612 6.18172364 1.25025450 3.34909245 0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127 1.0 1.2
|
||||
Hw C 2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571 7409.12856378 1.0 1.2
|
||||
|
||||
# # The ILPs for other systems are set to zero
|
||||
H Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
H Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Ow H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
|
||||
Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
|
||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -1058,6 +1058,10 @@
|
||||
/pair_adp.h
|
||||
/pair_agni.cpp
|
||||
/pair_agni.h
|
||||
/pair_aip_water_2dm.cpp
|
||||
/pair_aip_water_2dm.h
|
||||
/pair_aip_water_2dm_opt.cpp
|
||||
/pair_aip_water_2dm_opt.h
|
||||
/pair_airebo.cpp
|
||||
/pair_airebo.h
|
||||
/pair_airebo_morse.cpp
|
||||
|
||||
72
src/INTERLAYER/pair_aip_water_2dm.cpp
Normal file
72
src/INTERLAYER/pair_aip_water_2dm.cpp
Normal file
@ -0,0 +1,72 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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: Wengen Ouyang (Wuhan University)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
This is a full version of the potential described in
|
||||
[Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_aip_water_2dm.h"
|
||||
|
||||
#include "citeme.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
#define PGDELTA 1
|
||||
|
||||
static const char cite_aip_water[] =
|
||||
"aip/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
|
||||
"@Article{Feng2023\n"
|
||||
" author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
|
||||
" title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"
|
||||
" journal = {J. Phys. Chem. C},\n"
|
||||
" volume = 127,\n"
|
||||
" pages = {8704-8713}\n"
|
||||
" year = 2023,\n"
|
||||
"}\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairAIPWATER2DM::PairAIPWATER2DM(LAMMPS *lmp) : PairILPGrapheneHBN(lmp), PairILPTMD(lmp)
|
||||
{
|
||||
variant = AIP_WATER_2DM;
|
||||
single_enable = 0;
|
||||
|
||||
// for TMD, each atom have six neighbors
|
||||
Nnei = 6;
|
||||
|
||||
if (lmp->citeme) lmp->citeme->add(cite_aip_water);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairAIPWATER2DM::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
|
||||
if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
|
||||
error->all(FLERR, "Pair style aip/water/2dm must be used as sub-style with hybrid/overlay");
|
||||
|
||||
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
|
||||
if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
}
|
||||
39
src/INTERLAYER/pair_aip_water_2dm.h
Normal file
39
src/INTERLAYER/pair_aip_water_2dm.h
Normal file
@ -0,0 +1,39 @@
|
||||
/* -*- 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(aip/water/2dm,PairAIPWATER2DM);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_AIP_WATER_2DM_H
|
||||
#define LMP_PAIR_AIP_WATER_2DM_H
|
||||
|
||||
#include "pair_ilp_tmd.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairAIPWATER2DM : virtual public PairILPTMD {
|
||||
public:
|
||||
PairAIPWATER2DM(class LAMMPS *);
|
||||
|
||||
protected:
|
||||
void settings(int, char **) override;
|
||||
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -11,7 +11,7 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Wengen Ouyang (Tel Aviv University)
|
||||
Contributing author: Wengen Ouyang (Wuhan University)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
This is a Coulomb potential described in
|
||||
|
||||
@ -11,13 +11,11 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Wengen Ouyang (Tel Aviv University)
|
||||
Contributing author: Wengen Ouyang (Wuhan University)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
This is a full version of the potential described in
|
||||
[Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
|
||||
The definition of normals are the same as that in
|
||||
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
|
||||
[Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_ilp_graphene_hbn.h"
|
||||
@ -59,6 +57,7 @@ static const char cite_ilp[] =
|
||||
static std::map<int, std::string> variant_map = {
|
||||
{PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
|
||||
{PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
|
||||
{PairILPGrapheneHBN::AIP_WATER_2DM, "aip/water/2dm"},
|
||||
{PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -632,7 +631,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
|
||||
|
||||
void PairILPGrapheneHBN::ILP_neigh()
|
||||
{
|
||||
int i, j, ii, jj, n, allnum, jnum, itype, jtype;
|
||||
int i, j, ii, jj, n, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
int *neighptr;
|
||||
@ -649,7 +648,7 @@ void PairILPGrapheneHBN::ILP_neigh()
|
||||
(int **) memory->smalloc(maxlocal * sizeof(int *), "ILPGrapheneHBN:firstneigh");
|
||||
}
|
||||
|
||||
allnum = list->inum + list->gnum;
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
@ -659,7 +658,7 @@ void PairILPGrapheneHBN::ILP_neigh()
|
||||
|
||||
ipage->reset();
|
||||
|
||||
for (ii = 0; ii < allnum; ii++) {
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
|
||||
n = 0;
|
||||
|
||||
@ -39,7 +39,7 @@ class PairILPGrapheneHBN : public Pair {
|
||||
|
||||
static constexpr int NPARAMS_PER_LINE = 13;
|
||||
|
||||
enum { ILP_GrhBN, ILP_TMD, SAIP_METAL }; // for telling class variants apart in shared code
|
||||
enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, AIP_WATER_2DM }; // for telling class variants apart in shared code
|
||||
|
||||
protected:
|
||||
int me;
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
This is a full version of the potential described in
|
||||
[Ouyang et al, J. Chem. Theory Comput. 17, 7237 (2021).]
|
||||
[Ouyang et al., J. Chem. Theory Comput. 17, 7237 (2021).]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_ilp_tmd.h"
|
||||
@ -35,10 +35,6 @@
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace InterLayer;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
#define PGDELTA 1
|
||||
|
||||
static const char cite_ilp_tmd[] =
|
||||
"ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
|
||||
"@Article{Ouyang2021\n"
|
||||
@ -232,7 +228,7 @@ void PairILPTMD::calc_FRep(int eflag, int /* vflag */)
|
||||
|
||||
void PairILPTMD::ILP_neigh()
|
||||
{
|
||||
int i, j, l, ii, jj, ll, n, allnum, jnum, itype, jtype, ltype, imol, jmol, count;
|
||||
int i, j, l, ii, jj, ll, n, inum, jnum, itype, jtype, ltype, imol, jmol, count;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, deljx, deljy, deljz, rsq, rsqlj;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
int *neighsort;
|
||||
@ -249,7 +245,7 @@ void PairILPTMD::ILP_neigh()
|
||||
ILP_firstneigh = (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPTMD:firstneigh");
|
||||
}
|
||||
|
||||
allnum = list->inum + list->gnum;
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
@ -259,7 +255,7 @@ void PairILPTMD::ILP_neigh()
|
||||
|
||||
ipage->reset();
|
||||
|
||||
for (ii = 0; ii < allnum; ii++) {
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
|
||||
//initialize varibles
|
||||
@ -288,21 +284,21 @@ void PairILPTMD::ILP_neigh()
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
// check if the atom i is TMD, i.e., Mo/S/W/Se
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
|
||||
// check if the atom i is a TMD atom, i.e., Mo/S/W/Se
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
|
||||
strcmp(elements[itype], "Te") == 0) {
|
||||
if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol && type[i] == type[j]) {
|
||||
neighptr[n++] = j;
|
||||
}
|
||||
} else { // atom i is C, B, N or H.
|
||||
} else { // atom i can be P, C, B, N or H.
|
||||
if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol) { neighptr[n++] = j; }
|
||||
}
|
||||
} // loop over jj
|
||||
|
||||
// if atom i is Mo/W/S/Se/Te, then sorting the orders of neighbors
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
|
||||
strcmp(elements[itype], "Te") == 0) {
|
||||
// initialize neighsort
|
||||
for (ll = 0; ll < n; ll++) {
|
||||
@ -336,9 +332,6 @@ void PairILPTMD::ILP_neigh()
|
||||
}
|
||||
} // end of idenfying the first neighbor
|
||||
} else if (n > Nnei) {
|
||||
fprintf(screen, "Molecule ID = %d\n", imol);
|
||||
fprintf(screen, "Atom Type = %d\n", type[i]);
|
||||
fprintf(screen, "Neinum = %d\n", n);
|
||||
error->one(FLERR,
|
||||
"There are too many neighbors for TMD atoms, please check your configuration");
|
||||
}
|
||||
@ -367,11 +360,11 @@ void PairILPTMD::ILP_neigh()
|
||||
ll++;
|
||||
}
|
||||
} // end of sorting the order of neighbors
|
||||
} else { // for B/N/C/H atoms
|
||||
} else { // for P/B/N/C/H atoms
|
||||
if (n > 3)
|
||||
error->one(
|
||||
FLERR,
|
||||
"There are too many neighbors for B/N/C/H atoms, please check your configuration");
|
||||
"There are too many neighbors for P/B/N/C/H atoms, please check your configuration");
|
||||
for (ll = 0; ll < n; ll++) { neighsort[ll] = neighptr[ll]; }
|
||||
}
|
||||
|
||||
@ -390,12 +383,14 @@ void PairILPTMD::calc_normal()
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum;
|
||||
int cont, id, ip, m, k, itype;
|
||||
double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
|
||||
int *ilist, *jlist;
|
||||
int iH1,iH2,jH1,jH2;
|
||||
double Nave[3], dni[3], dpvdri[3][3];
|
||||
double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
|
||||
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
memory->destroy(dnn);
|
||||
memory->destroy(vect);
|
||||
@ -479,9 +474,60 @@ void PairILPTMD::calc_normal()
|
||||
for (m = 0; m < Nnei; m++) { dnormal[i][id][m][ip] = 0.0; }
|
||||
}
|
||||
}
|
||||
// for hydrogen in water molecule
|
||||
if (strcmp(elements[itype], "Hw") == 0) {
|
||||
if(cont == 0) {
|
||||
jH1 = atom->map(tag[i] - 1);
|
||||
jH2 = atom->map(tag[i] - 2);
|
||||
iH1 = map[type[jH1]];
|
||||
iH2 = map[type[jH2]];
|
||||
if (strcmp(elements[iH1], "Ow") == 0 ) {
|
||||
vect[0][0] = x[jH1][0] - xtp;
|
||||
vect[0][1] = x[jH1][1] - ytp;
|
||||
vect[0][2] = x[jH1][2] - ztp;
|
||||
} else if (strcmp(elements[iH2], "Ow") == 0 ) {
|
||||
vect[0][0] = x[jH2][0] - xtp;
|
||||
vect[0][1] = x[jH2][1] - ytp;
|
||||
vect[0][2] = x[jH2][2] - ztp;
|
||||
} else {
|
||||
error->one(FLERR, "The order of atoms in water molecule should be O H H !");
|
||||
}
|
||||
}
|
||||
Nave[0] = vect[0][0];
|
||||
Nave[1] = vect[0][1];
|
||||
Nave[2] = vect[0][2];
|
||||
// the magnitude of the normal vector
|
||||
nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
|
||||
nn = sqrt(nn2);
|
||||
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
|
||||
// the unit normal vector
|
||||
normal[i][0] = Nave[0] / nn;
|
||||
normal[i][1] = Nave[1] / nn;
|
||||
normal[i][2] = Nave[2] / nn;
|
||||
|
||||
// Calculte dNave/dri, defined as dpvdri
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
if (ip == id) { dpvdri[id][ip] = -1.0;}
|
||||
else {dpvdri[id][ip] = 0.0;}
|
||||
}
|
||||
}
|
||||
|
||||
// derivatives of nn, dnn:3x1 vector
|
||||
dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
|
||||
dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
|
||||
dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
|
||||
// derivatives of unit vector ni respect to ri, the result is 3x3 matrix
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
|
||||
dnormal[i][id][0][ip] = -dnormdri[i][id][ip];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
//############################ For the edge atoms of TMD ################################
|
||||
else if (cont < Nnei) {
|
||||
else if (cont > 1 && cont < Nnei) {
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0) {
|
||||
// derivatives of Ni[l] respect to the cont neighbors
|
||||
@ -557,8 +603,7 @@ void PairILPTMD::calc_normal()
|
||||
for (m = 0; m < cont; m++) {
|
||||
for (id = 0; id < 3; id++) {
|
||||
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
|
||||
Nave[2] * dNave[2][m][id]) /
|
||||
nn;
|
||||
Nave[2] * dNave[2][m][id]) / nn;
|
||||
}
|
||||
}
|
||||
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
|
||||
@ -589,12 +634,99 @@ void PairILPTMD::calc_normal()
|
||||
}
|
||||
}
|
||||
} // for TMD
|
||||
//############################ For Oxygen in the water molecule #######################
|
||||
else if (strcmp(elements[itype], "Ow") == 0) {
|
||||
if(cont == 0) {
|
||||
jH1 = atom->map(tag[i] + 1);
|
||||
jH2 = atom->map(tag[i] + 2);
|
||||
iH1 = map[type[jH1]];
|
||||
iH2 = map[type[jH2]];
|
||||
if (strcmp(elements[iH1], "Hw") == 0 && strcmp(elements[iH2], "Hw") == 0) {
|
||||
vect[0][0] = x[jH1][0] - xtp;
|
||||
vect[0][1] = x[jH1][1] - ytp;
|
||||
vect[0][2] = x[jH1][2] - ztp;
|
||||
|
||||
vect[1][0] = x[jH2][0] - xtp;
|
||||
vect[1][1] = x[jH2][1] - ytp;
|
||||
vect[1][2] = x[jH2][2] - ztp;
|
||||
|
||||
cont = 2;
|
||||
} else {
|
||||
error->one(FLERR, "The order of atoms in water molecule should be O H H !");
|
||||
}
|
||||
}
|
||||
if (cont == 2) {
|
||||
Nave[0] = (vect[0][0] + vect[1][0])/cont;
|
||||
Nave[1] = (vect[0][1] + vect[1][1])/cont;
|
||||
Nave[2] = (vect[0][2] + vect[1][2])/cont;
|
||||
// the magnitude of the normal vector
|
||||
nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
|
||||
nn = sqrt(nn2);
|
||||
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
|
||||
// the unit normal vector
|
||||
normal[i][0] = Nave[0] / nn;
|
||||
normal[i][1] = Nave[1] / nn;
|
||||
normal[i][2] = Nave[2] / nn;
|
||||
|
||||
// derivatives of non-normalized normal vector, dNave:3xcontx3 array
|
||||
// dNave[id][m][ip]: the derivatve of the id component of Nave
|
||||
// respect to the ip component of atom m
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
for (m = 0; m < cont; m++) {
|
||||
if (ip == id) { dNave[id][m][ip] = 0.5;}
|
||||
else {dNave[id][m][ip] = 0.0;}
|
||||
}
|
||||
}
|
||||
}
|
||||
// derivatives of nn, dnn:contx3 vector
|
||||
// dnn[m][id]: the derivative of nn respect to r[m][id], m=0,...Nnei-1; id=0,1,2
|
||||
// r[m][id]: the id's component of atom m
|
||||
for (m = 0; m < cont; m++) {
|
||||
for (id = 0; id < 3; id++) {
|
||||
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
|
||||
Nave[2] * dNave[2][m][id]) / nn;
|
||||
}
|
||||
}
|
||||
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
|
||||
// for atom m, which is a neighbor atom of atom i, m = 0,...,Nnei-1
|
||||
for (m = 0; m < cont; m++) {
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
dnormal[i][id][m][ip] = dNave[id][m][ip] / nn - Nave[id] * dnn[m][ip] / nn2;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Calculte dNave/dri, defined as dpvdri
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
dpvdri[id][ip] = 0.0;
|
||||
for (k = 0; k < cont; k++) { dpvdri[id][ip] -= dNave[id][k][ip]; }
|
||||
}
|
||||
}
|
||||
|
||||
// derivatives of nn, dnn:3x1 vector
|
||||
dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
|
||||
dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
|
||||
dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
|
||||
// derivatives of unit vector ni respect to ri, the result is 3x3 matrix
|
||||
for (id = 0; id < 3; id++) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
|
||||
}
|
||||
}
|
||||
}
|
||||
else if (cont >= 3) {
|
||||
error->one(FLERR,
|
||||
"There are too many neighbors for calculating normals of water molecules");
|
||||
}
|
||||
}
|
||||
//############################ For the edge & bulk atoms of GrhBN ################################
|
||||
else {
|
||||
if (cont == 2) {
|
||||
for (ip = 0; ip < 3; ip++) {
|
||||
pvet[0][ip] = vect[0][modulo(ip + 1, 3)] * vect[1][modulo(ip + 2, 3)] -
|
||||
vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
|
||||
vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
|
||||
}
|
||||
// dpvet1[k][l][ip]: the derivatve of the k (=0,...cont-1)th Nik respect to the ip component of atom l
|
||||
// derivatives respect to atom l
|
||||
@ -657,8 +789,7 @@ void PairILPTMD::calc_normal()
|
||||
for (m = 0; m < cont; m++) {
|
||||
for (id = 0; id < 3; id++) {
|
||||
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
|
||||
Nave[2] * dNave[2][m][id]) /
|
||||
nn;
|
||||
Nave[2] * dNave[2][m][id]) / nn;
|
||||
}
|
||||
}
|
||||
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Wengen Ouyang (Tel Aviv University)
|
||||
Contributing author: Wengen Ouyang (Wuhan University)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
based on previous versions by Jaap Kroes
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
This is a full version of the potential described in
|
||||
[Ouyang et al, J. Chem. Theory Comput. 17, 7215-7223 (2021)]
|
||||
[Ouyang et al., J. Chem. Theory Comput. 17, 7215-7223 (2021)]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_saip_metal.h"
|
||||
|
||||
@ -14,7 +14,7 @@
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
|
||||
Wengen Ouyang (TAU) - Shift addition
|
||||
Wengen Ouyang (WHU) - Shift addition
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_tersoff.h"
|
||||
|
||||
63
src/OPT/pair_aip_water_2dm_opt.cpp
Normal file
63
src/OPT/pair_aip_water_2dm_opt.cpp
Normal file
@ -0,0 +1,63 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
This is an optimized version of aip/water/2dm based on the contribution of:
|
||||
author: Wengen Ouyang (Wuhan University)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
Optimizations are done by:
|
||||
author1: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
|
||||
e-mail: sunrise_duan at 126 dot com
|
||||
|
||||
author2: Ping Gao (National Supercomputing Center in Wuxi, China)
|
||||
e-mail: qdgaoping at gmail dot com
|
||||
|
||||
Optimizations are described in:
|
||||
Gao, Ping and Duan, Xiaohui, et al.:
|
||||
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
|
||||
DOI: 10.1145/3458817.3476137
|
||||
|
||||
Potential is described by:
|
||||
[Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
|
||||
*/
|
||||
#include "pair_aip_water_2dm_opt.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "memory.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
PairAIPWATER2DMOpt::PairAIPWATER2DMOpt(LAMMPS *lmp) :
|
||||
PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairAIPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)
|
||||
{
|
||||
}
|
||||
|
||||
void PairAIPWATER2DMOpt::coeff(int narg, char **args)
|
||||
{
|
||||
PairILPTMD::coeff(narg, args);
|
||||
memory->create(special_type, atom->ntypes + 1, "PairAIPWATER2DMOpt:check_sublayer");
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
int itype = map[i];
|
||||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
|
||||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
|
||||
strcmp(elements[itype], "Te") == 0) {
|
||||
special_type[i] = TMD_METAL;
|
||||
} else if (strcmp(elements[itype], "Hw") == 0 || strcmp(elements[itype], "Ow") == 0) {
|
||||
special_type[i] = WATER;
|
||||
} else {
|
||||
special_type[i] = NOT_SPECIAL;
|
||||
}
|
||||
}
|
||||
}
|
||||
38
src/OPT/pair_aip_water_2dm_opt.h
Normal file
38
src/OPT/pair_aip_water_2dm_opt.h
Normal file
@ -0,0 +1,38 @@
|
||||
/* -*- 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(aip/water/2dm/opt,PairAIPWATER2DMOpt);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_AIP_WATER_2DM_OPT_H
|
||||
#define LMP_PAIR_AIP_WATER_2DM_OPT_H
|
||||
|
||||
#include "pair_ilp_graphene_hbn_opt.h"
|
||||
#include "pair_aip_water_2dm.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairAIPWATER2DMOpt : public PairAIPWATER2DM, public PairILPGrapheneHBNOpt {
|
||||
public:
|
||||
PairAIPWATER2DMOpt(class LAMMPS *);
|
||||
void coeff(int narg, char **args) override;
|
||||
|
||||
protected:
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
@ -11,12 +11,24 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Optimization author1: Ping Gao (National Supercomputing Center in Wuxi, China)
|
||||
This is an optimized version of ilp/graphene/hbn based on the contirubtion of:
|
||||
author: Wengen Ouyang (Wuhan University, China)
|
||||
e-mail: w.g.ouyang at gmail dot com
|
||||
|
||||
Optimizations are done by:
|
||||
author1: Ping Gao (National Supercomputing Center in Wuxi, China) implements the base ILP potential.
|
||||
e-mail: qdgaoping at gmail dot com
|
||||
Optimization author2: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
|
||||
|
||||
author2: Xiaohui Duan (Shandong University, China) adjusts the framework to adopt SAIP, TMD, WATER2DM, etc.
|
||||
e-mail: sunrise_duan at 126 dot com
|
||||
|
||||
Provides some bugfixes and performance optimizations in this potential.
|
||||
Optimizations are described in:
|
||||
Gao, Ping and Duan, Xiaohui, et al:
|
||||
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
|
||||
DOI: 10.1145/3458817.3476137
|
||||
|
||||
Potential is described by:
|
||||
[Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
|
||||
*/
|
||||
|
||||
#include "pair_ilp_graphene_hbn_opt.h"
|
||||
@ -28,19 +40,21 @@
|
||||
#include "interlayer_taper.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "neighbor.h"
|
||||
#include "pointers.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <utility>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace InterLayer;
|
||||
|
||||
static const char cite_ilp_cur[] =
|
||||
"ilp/graphene/hbn/opt potential: doi:10.1145/3458817.3476137\n"
|
||||
"ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137\n"
|
||||
"@inproceedings{gao2021lmff\n"
|
||||
" author = {Gao, Ping and Duan, Xiaohui and others},\n"
|
||||
" title = {{LMFF}: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
|
||||
" author = {Gao, Ping and Duan, Xiaohui and Others},\n"
|
||||
" title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
|
||||
"Many-Core Processors},\n"
|
||||
" year = {2021},\n"
|
||||
" isbn = {9781450384421},\n"
|
||||
@ -50,14 +64,12 @@ static const char cite_ilp_cur[] =
|
||||
" doi = {10.1145/3458817.3476137},\n"
|
||||
" booktitle = {Proceedings of the International Conference for High Performance Computing, "
|
||||
"Networking, Storage and Analysis},\n"
|
||||
" pages = {42},\n"
|
||||
" articleno = {42},\n"
|
||||
" numpages = {14},\n"
|
||||
" location = {St.~Louis, Missouri},\n"
|
||||
" location = {St. Louis, Missouri},\n"
|
||||
" series = {SC'21},\n"
|
||||
"}\n\n";
|
||||
|
||||
static bool check_vdw(tagint itag, tagint jtag, double *xi, double *xj);
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairILPGrapheneHBNOpt::PairILPGrapheneHBNOpt(LAMMPS *lmp) :
|
||||
@ -168,6 +180,36 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if (variant == AIP_WATER_2DM) {
|
||||
if (eflag_global || eflag_atom) {
|
||||
if (vflag_either) {
|
||||
if (tap_flag) {
|
||||
eval<6, 1, 1, 1, AIP_WATER_2DM>();
|
||||
} else {
|
||||
eval<6, 1, 1, 0, AIP_WATER_2DM>();
|
||||
}
|
||||
} else {
|
||||
if (tap_flag) {
|
||||
eval<6, 1, 0, 1, AIP_WATER_2DM>();
|
||||
} else {
|
||||
eval<6, 1, 0, 0, AIP_WATER_2DM>();
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if (vflag_either) {
|
||||
if (tap_flag) {
|
||||
eval<6, 0, 1, 1, AIP_WATER_2DM>();
|
||||
} else {
|
||||
eval<6, 0, 1, 0, AIP_WATER_2DM>();
|
||||
}
|
||||
} else {
|
||||
if (tap_flag) {
|
||||
eval<6, 0, 0, 1, AIP_WATER_2DM>();
|
||||
} else {
|
||||
eval<6, 0, 0, 0, AIP_WATER_2DM>();
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if (variant == SAIP_METAL) {
|
||||
if (eflag_global || eflag_atom) {
|
||||
if (vflag_either) {
|
||||
@ -255,7 +297,7 @@ void PairILPGrapheneHBNOpt::eval()
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
|
||||
if (VARIANT == ILP_TMD && special_type[itype] && itype != type[j]) continue;
|
||||
if ((VARIANT == ILP_TMD || VARIANT == AIP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
|
||||
if (ILP_nneigh >= MAX_NNEIGH) {
|
||||
error->one(FLERR, "There are too many neighbors for calculating normals");
|
||||
}
|
||||
@ -269,7 +311,8 @@ void PairILPGrapheneHBNOpt::eval()
|
||||
dproddni[2] = 0.0;
|
||||
|
||||
double norm[3], dnormdxi[3][3], dnormdxk[MAX_NNEIGH][3][3];
|
||||
calc_normal<MAX_NNEIGH>(i, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
|
||||
|
||||
calc_atom_normal<MAX_NNEIGH>(i, itype, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
|
||||
|
||||
for (jj = 0; jj < jnum_inter; jj++) {
|
||||
j = jlist_inter[jj];
|
||||
@ -298,7 +341,7 @@ void PairILPGrapheneHBNOpt::eval()
|
||||
Tap = 1.0;
|
||||
dTap = 0.0;
|
||||
}
|
||||
if (VARIANT != SAIP_METAL || !special_type[itype]) {
|
||||
if (VARIANT != SAIP_METAL || special_type[itype] != SAIP_BNCH) {
|
||||
// Calculate the transverse distance
|
||||
prodnorm1 = norm[0] * delx + norm[1] * dely + norm[2] * delz;
|
||||
rhosq1 = rsq - prodnorm1 * prodnorm1; // rho_ij
|
||||
@ -310,7 +353,7 @@ void PairILPGrapheneHBNOpt::eval()
|
||||
|
||||
frho1 = exp1 * p.C;
|
||||
Erep = 0.5 * p.epsilon + frho1;
|
||||
if (VARIANT == SAIP_METAL && special_type[jtype]) { Erep += 0.5 * p.epsilon + p.C; }
|
||||
if (VARIANT == SAIP_METAL && special_type[jtype] == SAIP_BNCH) { Erep += 0.5 * p.epsilon + p.C; }
|
||||
Vilp = exp0 * Erep;
|
||||
|
||||
// derivatives
|
||||
@ -428,6 +471,18 @@ inline void deriv_normal(double dndr[3][3], double *del, double *n, double rnnor
|
||||
dndr[1][2] = (del[1] * n[0] * n[1] + del[0] * (n[0] * n[0] + n[2] * n[2])) * rnnorm;
|
||||
dndr[2][2] = (del[1] * n[0] * n[2] - del[0] * n[1] * n[2]) * rnnorm;
|
||||
}
|
||||
inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double factor){
|
||||
double cfactor = rnnorm * factor;
|
||||
dnhatdn[0][0] = (n[1]*n[1]+n[2]*n[2])*cfactor;
|
||||
dnhatdn[1][0] = -n[1]*n[0]*cfactor;
|
||||
dnhatdn[2][0] = -n[2]*n[0]*cfactor;
|
||||
dnhatdn[0][1] = -n[0]*n[1]*cfactor;
|
||||
dnhatdn[1][1] = (n[0]*n[0]+n[2]*n[2])*cfactor;
|
||||
dnhatdn[2][1] = -n[2]*n[1]*cfactor;
|
||||
dnhatdn[0][2] = -n[0]*n[2]*cfactor;
|
||||
dnhatdn[1][2] = -n[1]*n[2]*cfactor;
|
||||
dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
|
||||
}
|
||||
inline double normalize_factor(double *n)
|
||||
{
|
||||
double nnorm = sqrt(n[0] * n[0] + n[1] * n[1] + n[2] * n[2]);
|
||||
@ -441,7 +496,7 @@ inline double normalize_factor(double *n)
|
||||
Yet another normal calculation method for simpiler code.
|
||||
*/
|
||||
template <int MAX_NNEIGH>
|
||||
void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, double *n,
|
||||
void PairILPGrapheneHBNOpt::calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *n,
|
||||
double (*dnormdri)[3], double (*dnormdrk)[3][3])
|
||||
{
|
||||
double **x = atom->x;
|
||||
@ -475,6 +530,32 @@ void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, doubl
|
||||
vet[jj][2] = x[j][2] - x[i][2];
|
||||
}
|
||||
|
||||
//specialize for AIP_WATER_2DM for hydrogen has special normal vector rule
|
||||
if (variant == AIP_WATER_2DM && special_type[itype] == WATER) {
|
||||
if (nneigh == 1){
|
||||
n[0] = vet[0][0];
|
||||
n[1] = vet[0][1];
|
||||
n[2] = vet[0][2];
|
||||
|
||||
double rnnorm = normalize_factor(n);
|
||||
|
||||
deriv_hat(dnormdri, n, rnnorm, -1.0);
|
||||
deriv_hat(dnormdrk[0], n, rnnorm, 1.0);
|
||||
|
||||
} else if (nneigh == 2){
|
||||
n[0] = (vet[0][0] + vet[1][0])*0.5;
|
||||
n[1] = (vet[0][1] + vet[1][1])*0.5;
|
||||
n[2] = (vet[0][2] + vet[1][2])*0.5;
|
||||
double rnnorm = normalize_factor(n);
|
||||
|
||||
deriv_hat(dnormdri, n, rnnorm, -1.0);
|
||||
deriv_hat(dnormdrk[0], n, rnnorm, 0.5);
|
||||
deriv_hat(dnormdrk[1], n, rnnorm, 0.5);
|
||||
} else {
|
||||
error->one(FLERR, "malformed water");
|
||||
}
|
||||
return;
|
||||
}
|
||||
if (nneigh <= 1) {
|
||||
n[0] = 0.0;
|
||||
n[1] = 0.0;
|
||||
|
||||
@ -35,7 +35,7 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
|
||||
protected:
|
||||
void update_internal_list();
|
||||
template <int MAX_NNEIGH>
|
||||
void calc_normal(int i, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
|
||||
void calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
|
||||
double (*dnormdrk)[3][3]);
|
||||
template <int MAX_NNEIGH, int EFLAG, int VFLAG_EITHER, int TAP_FLAG, int VARIANT = ILP_GrhBN>
|
||||
void eval();
|
||||
@ -44,6 +44,14 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
|
||||
int *special_type;
|
||||
int *num_intra, *num_inter, *num_vdw;
|
||||
int inum_max, jnum_max;
|
||||
|
||||
enum special_type_const {
|
||||
NOT_SPECIAL = 0,
|
||||
TMD_METAL,
|
||||
SAIP_BNCH,
|
||||
WATER,
|
||||
};
|
||||
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -23,7 +23,7 @@
|
||||
e-mail: qdgaoping at gmail dot com
|
||||
|
||||
Optimizations are described in:
|
||||
Gao, Ping and Duan, Xiaohui, et al:
|
||||
Gao, Ping and Duan, Xiaohui, et al.:
|
||||
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
|
||||
DOI: 10.1145/3458817.3476137
|
||||
|
||||
|
||||
Reference in New Issue
Block a user