implemented d3 pair style
This commit is contained in:
soniasalomoni
140
doc/src/pair_d3.rst
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140
doc/src/pair_d3.rst
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.. index:: pair_style d3
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..
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.. index:: pair_style d3/kk
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pair_style d3 command
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=====================
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..
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Accelerator Variants: *d3/kk*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style d3 damping functional cutoff cn_cutoff
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* damping = damping function: *zero*, *zerom*, *bj*, or *bjm*
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* functional = XC functional form: *pbe*, *pbe0*, etc.
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* cutoff = global cutoff (distance units)
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* cn_cutoff = coordination number cutoff (distance units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style d3 zero pbe 30.0 20.0
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pair_coeff * * C
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Description
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"""""""""""
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Style *d3* computes the dispersion energy-correction used in the DFT-D3
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method of Grimme :ref:`(Grimme1) <Grimme1>`.
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The energy contribution :math:`E_i` for an atom :math:`i` is given by:
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.. math::
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E_i = \frac{1}{2} \sum_{j \neq i} \big(
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s_6 \frac{C_{6,ij}}{r^6_{ij}} f_6^{damp}(r_{ij}) +
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s_8 \frac{C_{8,ij}}{r^8_{ij}} f_8^{damp}(r_{ij}) \big)
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where :math:`C_n` is the averaged, geometry-dependent nth-order dispersion
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coefficient for atom pair :math:`ij`, :math:`r_{ij}` their internuclear distance,
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:math:`s_n` are XC functional-dependent scaling factor, and :math:`f_n^{damp}` are
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damping functions.
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N.B.: in the current version of the code, it is *not* possible to calculate three-body
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dispersion contributions, according for example to the Axilrod-Teller-Muto model.
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Available damping functions are the original "zero-damping" :ref:`(Grimme1) <Grimme1>`,
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Becke-Johnson damping :ref:`(Grimme2) <Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
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Available XC functional scaling factors are listed in the table below, and depend on
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the selected damping function.
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+------------------+--------------------------------------------------------------------------------+
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| Damping function | XC functional |
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+==================+================================================================================+
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| | | | slater-dirac-exchange, b-lyp, b-p, b97-d, revpbe, pbe, pbesol, rpw86-pbe, |
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| | | | rpbe, tpss, b3-lyp, pbe0, hse06, revpbe38, pw6b95, tpss0, b2-plyp, pwpb95, |
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| | zero | | b2gp-plyp, ptpss, hf, mpwlyp, bpbe, bh-lyp, tpssh, pwb6k, b1b95, bop, o-lyp, |
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| | | | o-pbe, ssb, revssb, otpss, b3pw91, revpbe0, pbe38, mpw1b95, mpwb1k, bmk, |
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| | | | cam-b3lyp, lc-wpbe, m05, m052x, m06l, m06, m062x, m06hf, hcth120 |
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+------------------+--------------------------------------------------------------------------------+
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| zerom | b2-plyp, b3-lyp, b97-d, b-lyp, b-p, pbe, pbe0, lc-wpbe |
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+------------------+--------------------------------------------------------------------------------+
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| | | | b-p, b-lyp, revpbe, rpbe, b97-d, pbe, rpw86-pbe, b3-lyp, tpss, hf, tpss0, |
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| | | | pbe0, hse06, revpbe38, pw6b95, b2-plyp, dsd-blyp, dsd-blyp-fc, bop, mpwlyp, |
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| | bj | | o-lyp, pbesol, bpbe, opbe, ssb, revssb, otpss, b3pw91, bh-lyp, revpbe0, |
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| | | | tpssh, mpw1b95, pwb6k, b1b95, bmk, cam-b3lyp, lc-wpbe, b2gp-plyp, ptpss, |
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| | | | pwpb95, hf/mixed, hf/sv, hf/minis, b3lyp/6-31gd, hcth120, pw1pw, pwgga, |
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| | | | hsesol, hf3c, hf3cv, pbeh3c, pbeh-3c |
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+------------------+--------------------------------------------------------------------------------+
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| bjm | b2-plyp, b3-lyp, b97-d, b-lyp, b-p, pbe, pbe0, lc-wpbe |
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+------------------+--------------------------------------------------------------------------------+
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This style is primarly supposed to be used combined with a machine-learned
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interatomic potential trained on a DFT dataset (the selected XC functional
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should be chosen accordingly) via the *pair_style hybrid* command.
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Coefficients
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""""""""""""
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All the required coefficients are already stored internally, in the pair_d3_pars.h file.
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The only information to provide are the chemical symbols of the atoms.
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The number of chemical symbols given must be equal to the number of atom types
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used and should match their ordering.
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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 mixing since all parameters are explicit for each pair.
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This pair style does not support the :doc:`pair_modify` shift, table, and tail options.
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This pair style does not write its information to :doc:`binary restart files <restart>`.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*, *middle*, *outer* keywords.
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Restrictions
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""""""""""""
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Style *d3* is part of the EXTRA-PAIR package. It is only enabled if LAMMPS
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was built with that package.
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See the :doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`
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Default
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"""""""
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none
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----------
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.. _Grimme1:
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**(Grimme1)** S. Grimme, J. Antony, S. Ehrlich, and H. Krieg,
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J. Chem. Phys. 132, 154104 (2010).
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.
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.. _Grimme2:
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**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk,
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J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759.
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.. _Sherrill:
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**(Sherrill)** D. G. A. Smith, L. A. Burns, K. Patkowski, and C. D. Sherrill,
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J. Phys. Chem. Lett., 7, 2197, (2016); DOI: 10.1021/acs.jpclett.6b00780.
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1143
src/EXTRA-PAIR/pair_d3.cpp
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1143
src/EXTRA-PAIR/pair_d3.cpp
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File diff suppressed because it is too large
Load Diff
96
src/EXTRA-PAIR/pair_d3.h
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src/EXTRA-PAIR/pair_d3.h
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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-------------------------------------------------------------------------
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Contributing authors:
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Sonia Salomoni^1,^2
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Arthur France-Lanord^1
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^1: IMPMC, CNRS, Sorbonne Universite, Paris, France
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^2: SCAI, Sorbonne Universite, Paris, France
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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// clang-format off
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PairStyle(d3,PairD3);
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// clang-format on
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#else
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#ifndef LMP_PAIR_D3_H
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#define LMP_PAIR_D3_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairD3 : public Pair {
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public:
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PairD3(class LAMMPS *);
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~PairD3() override;
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void compute(int, int) override;
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void settings(int, char **) override;
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void coeff(int, char **) override;
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void init_style() override;
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double init_one(int, int) override;
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int pack_forward_comm(int, int *, double *, int, int *) override;
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int pack_reverse_comm(int, int, double *) override;
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void unpack_forward_comm(int, int, double *) override;
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void unpack_reverse_comm(int, int *, double *) override;
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protected:
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int nmax;
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double evdwl;
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double rthr; // R^2 distance to cutoff for D3_calculation
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double cn_thr; // R^2 distance to cutoff for CN_calculation
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std::string damping_type; // damping function type
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double s6, s8, s18, rs6, rs8, rs18; // XC parameters
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double a1, a2, alpha, alpha6, alpha8;
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double* r2r4 = nullptr; // scale r4/r2 values of the atoms by sqrt(Z)
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double* rcov = nullptr; // covalent radii
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int* mxci = nullptr; // How large the grid for c6 interpolation
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double** r0ab = nullptr; // cut-off radii for all element pairs
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double***** c6ab = nullptr; // C6 for all element pairs
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double* cn = nullptr; // Coordination numbers
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double* dc6 = nullptr; // dC6i(iat) saves dE_dsp/dCN(iat)
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int communicationStage; // communication stage
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void allocate();
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virtual void set_funcpar(std::string&);
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void calc_coordination_number();
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int find_atomic_number(std::string&);
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std::vector<int> is_int_in_array(int*, int, int);
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void read_r0ab(int*, int);
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void set_limit_in_pars_array(int&, int&, int&, int&);
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void read_c6ab(int*, int);
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double* get_dC6(int, int, double, double);
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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32483
src/EXTRA-PAIR/pair_d3_pars.h
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32483
src/EXTRA-PAIR/pair_d3_pars.h
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File diff suppressed because it is too large
Load Diff
155
unittest/force-styles/tests/manybody-pair-d3.yaml
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155
unittest/force-styles/tests/manybody-pair-d3.yaml
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---
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lammps_version: 17 Apr 2024
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tags: generated
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date_generated: Mon Dec 9 17:36:37 2024
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epsilon: 1e-11
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skip_tests: single
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prerequisites: ! |
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pair d3
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pre_commands: ! ""
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post_commands: ! ""
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input_file: in.manybody
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pair_style: d3 zero pbe 12.0 12.0
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pair_coeff: ! |
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* * Si Si Si Si Si Si Si Si
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extract: ! ""
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natoms: 64
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init_vdwl: -9.262365243925203
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init_coul: 0
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init_stress: ! |-
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-1.8070680187151131e+00 -1.8151671933941584e+00 -1.9214651828014326e+00 -4.1552461934576006e-02 -7.1708481007728198e-01 -1.3638435806044302e-01
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init_forces: ! |2
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1 4.5901745485403295e-04 -5.8645004074280530e-03 -2.6408414312694140e-03
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2 4.1982212100084848e-02 7.7916988681057701e-03 4.1558505657116980e-03
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3 -1.0599537920220059e-03 -1.5284351930588387e-03 1.3250226337933743e-03
|
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4 1.2952849248662775e-02 -1.2730397233111836e-02 6.4718612422628536e-03
|
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5 1.9307066713768282e-03 3.1031437418921910e-03 3.5451961493820740e-03
|
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6 6.0636534459212882e-03 -3.4538157278896163e-02 -1.5549038115507513e-02
|
||||
7 -5.5478612765789935e-03 9.7600792853363150e-03 -2.1450928858953930e-02
|
||||
8 1.7128888892908867e-05 -1.3865910341446424e-04 8.9170060388590313e-04
|
||||
9 -5.8527207667384923e-02 8.5011601448529789e-02 7.9837310968768324e-02
|
||||
10 -9.9174557740649288e-03 1.3163286903593812e-02 1.2367199081011528e-02
|
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11 -2.0922976094767239e-02 1.7815876096389776e-02 -3.2459912597209782e-02
|
||||
12 9.4039240797152590e-02 3.7466484050302624e-02 -9.4966824527940915e-03
|
||||
13 -4.3611820849020655e-02 -7.5650463282748284e-02 4.1545920231526583e-02
|
||||
14 1.3914348002543740e-02 -9.8186445921730793e-03 -1.5039026972733623e-02
|
||||
15 9.8798529625617471e-02 -9.6939234781371439e-02 -3.5897115913423899e-02
|
||||
16 -1.8828449808052237e-02 1.0084992428372604e-02 -1.6621409829588641e-02
|
||||
17 1.8867454991507823e-02 -3.3410341394944157e-02 5.8649656809196309e-02
|
||||
18 -5.7757244225337357e-03 3.7525864843647697e-03 -1.7465564584510023e-02
|
||||
19 7.3146350316925512e-03 -5.0979152014509572e-03 -5.7918363022845080e-03
|
||||
20 1.2526948567372337e-01 3.4964179752050586e-02 -4.0345565596353550e-02
|
||||
21 -7.9108983380917194e-02 -7.4234491595904575e-02 7.8298798238034567e-02
|
||||
22 3.3256958028948028e-02 -3.5876634770494304e-03 -5.5658445829460078e-03
|
||||
23 -9.4983041889442843e-02 -1.6190744701130849e-01 6.5979264487847342e-02
|
||||
24 -3.9837469553195448e-02 2.5364084068168865e-02 -2.8343465970054268e-02
|
||||
25 -7.3424056488810893e-03 -1.1672660197222877e-02 -4.2413533422096137e-03
|
||||
26 7.1482435753173978e-02 7.9794866671089565e-02 -1.2051822894855302e-01
|
||||
27 -1.2443813759872715e-02 -4.4129787717125659e-03 -4.9977234669242657e-03
|
||||
28 -5.0454676860651063e-03 -4.8367643809983244e-03 -9.7359590837120241e-03
|
||||
29 5.0973790723890279e-02 -3.5296812999801377e-02 -1.5607922719867863e-02
|
||||
30 6.9152527688984819e-02 -1.5810831588146963e-03 3.8412598769159367e-02
|
||||
31 2.4462929866513206e-02 -3.5045453885110815e-02 -1.9154039469347770e-02
|
||||
32 2.9037764603397378e-02 -6.8595457740301298e-03 -3.2736895683665988e-03
|
||||
33 -2.3571014332676696e-02 7.4043101417658073e-03 -2.8705289221235150e-02
|
||||
34 -1.4606618276415169e-02 -9.1068958189810610e-04 -8.5624378212242527e-03
|
||||
35 -3.2510043399847137e-02 -2.8006234735108673e-02 -4.6845303267092589e-02
|
||||
36 6.2991561292220326e-03 2.3238393611931946e-02 -5.8116057373416774e-03
|
||||
37 2.6891579367550652e-02 -1.3896976667148994e-02 3.1371675516263159e-02
|
||||
38 2.0868635137082342e-02 5.0357172401113842e-03 -5.3296214166774630e-03
|
||||
39 -8.0127916540051650e-02 -3.7084303700723187e-02 1.2218320413894672e-01
|
||||
40 -3.9584086175377592e-02 1.4186027995495971e-02 -1.1786983668096024e-02
|
||||
41 -2.4078556291313152e-02 2.3979806393375630e-02 3.9808779679609198e-02
|
||||
42 1.2092253594061965e-01 7.0237820535165529e-02 -6.7634093707697934e-02
|
||||
43 -4.7905857362083089e-02 1.7234517679588787e-01 6.1081728343859443e-02
|
||||
44 -8.9268222626455868e-02 1.0935256562868768e-01 4.9391188697389531e-02
|
||||
45 -1.0932468616629654e-02 -1.1437973175510943e-02 2.2070666035021818e-02
|
||||
46 -3.6031863619124846e-02 2.6734739237702171e-02 -3.3611450622333013e-02
|
||||
47 1.4499510937770043e-03 -1.4213296755659972e-02 -2.3112798778515177e-04
|
||||
48 -1.3767091667320651e-02 -3.0136222295009791e-03 1.3113656018437793e-02
|
||||
49 -9.7091853089158325e-03 3.6127847100198028e-02 1.4509648101942035e-02
|
||||
50 8.4557962872537848e-02 -1.0736631874106438e-01 9.9597088995020677e-02
|
||||
51 -1.0386138512337374e-02 -2.0257306344291497e-02 -3.3076970021155658e-02
|
||||
52 -4.6611247598267555e-02 6.5689772896870391e-02 1.9370639128294540e-02
|
||||
53 -5.5610674299579610e-03 -1.4027210047753987e-02 8.7210863654412565e-03
|
||||
54 -4.3167807436909698e-02 5.3419018642258016e-02 -1.5968205469941175e-02
|
||||
55 2.1005445039043447e-03 1.5540888556331189e-02 3.0653660866053294e-02
|
||||
56 -2.0590128155749919e-04 -4.1762635052692443e-03 1.7714423658216408e-02
|
||||
57 1.0284475500160662e-02 4.9815307652019795e-03 1.2436353037813486e-02
|
||||
58 -1.0342665677846569e-01 -1.9280058549113892e-02 -7.4866501787840767e-02
|
||||
59 -2.3544588144277776e-03 3.6121601436188973e-03 -4.6871795309287806e-03
|
||||
60 -5.4150709547244186e-03 5.8612714168733107e-02 1.4839344483422201e-02
|
||||
61 2.7954413595536829e-03 -5.0942788273584158e-02 7.2754423090722080e-03
|
||||
62 1.1252409113821953e-01 -8.8720719845166385e-02 5.4683231088491491e-02
|
||||
63 -3.1773161310039773e-02 3.6061405688573842e-02 -3.8399113603086052e-02
|
||||
64 -1.4722975703867254e-02 -2.6147363467761031e-02 -2.1059016257482918e-01
|
||||
run_vdwl: -9.262826276442015
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-1.8014717164118095e+00 -1.8087390491573838e+00 -1.9142638713109481e+00 -3.9974176680151442e-02 -7.1417886608373016e-01 -1.3759726037342584e-01
|
||||
run_forces: ! |2
|
||||
1 4.7667962897357161e-04 -5.8467702637711484e-03 -2.6991867527471512e-03
|
||||
2 4.1869408756652363e-02 8.4979875395407335e-03 3.4984717622547718e-03
|
||||
3 -9.9160928359434165e-04 -1.4869879159063026e-03 1.2223462368831279e-03
|
||||
4 1.3147106330966834e-02 -1.2926544725178195e-02 6.7789603915220410e-03
|
||||
5 1.9770775494690725e-03 3.1765296745866244e-03 3.5629842560420720e-03
|
||||
6 5.7506960289548086e-03 -3.4699407410875724e-02 -1.5506043491316254e-02
|
||||
7 -5.3406567968898640e-03 9.4551314879620617e-03 -2.0752905865024943e-02
|
||||
8 8.7145147977422260e-05 -2.8842759092264801e-05 8.0207322297105345e-04
|
||||
9 -5.8415508752186096e-02 8.4979266053546693e-02 7.9622715915771303e-02
|
||||
10 -9.9578406937796439e-03 1.3145690562643045e-02 1.2350278010619288e-02
|
||||
11 -2.0970548283965822e-02 1.7641558318643526e-02 -3.3050100269831226e-02
|
||||
12 9.5891788552647905e-02 3.8024542707268488e-02 -9.8061835208236598e-03
|
||||
13 -4.4952222762057452e-02 -7.6842596097771221e-02 4.2613909344784678e-02
|
||||
14 1.4295961616915508e-02 -1.0328974978549363e-02 -1.5428512523395358e-02
|
||||
15 9.9943438549559324e-02 -9.7907452663447983e-02 -3.6257259204324190e-02
|
||||
16 -1.8390119036231254e-02 9.7159754167479712e-03 -1.6211888958432827e-02
|
||||
17 1.8981263201349942e-02 -3.3819017834167138e-02 5.9290153984855036e-02
|
||||
18 -5.6513870203370861e-03 3.7641108670888137e-03 -1.7558647302694921e-02
|
||||
19 7.4901241602777988e-03 -4.9270563652220887e-03 -5.9132694166840003e-03
|
||||
20 1.2404887106132249e-01 3.4634285209304783e-02 -4.0135253432049663e-02
|
||||
21 -7.8277898322380690e-02 -7.3279299053891203e-02 7.8010388044320325e-02
|
||||
22 3.3238064217446656e-02 -3.5092881124568851e-03 -5.5130499474961214e-03
|
||||
23 -9.5777464813086854e-02 -1.6270801791195924e-01 6.6577987309083805e-02
|
||||
24 -4.0548984396490580e-02 2.6001318437117903e-02 -2.8710977732994785e-02
|
||||
25 -7.2079783094212008e-03 -1.1551923848041689e-02 -3.9390884716931050e-03
|
||||
26 7.2339414718789685e-02 7.9165643726239313e-02 -1.2169899192698079e-01
|
||||
27 -1.2311213314223447e-02 -4.3068558469614186e-03 -4.9048891096525275e-03
|
||||
28 -5.1134183165409582e-03 -4.9743298117876514e-03 -9.7660849582700982e-03
|
||||
29 5.0646655326840248e-02 -3.5366362317264768e-02 -1.5821692477208313e-02
|
||||
30 6.8872718304629946e-02 -2.6404120131308211e-04 3.9973810776214556e-02
|
||||
31 2.4365821184347394e-02 -3.5211120753030921e-02 -1.9277907381945410e-02
|
||||
32 2.9047476663902016e-02 -6.6602395044956511e-03 -3.0527687948843541e-03
|
||||
33 -2.3100260653032955e-02 7.7806328406423821e-03 -2.8840665483715618e-02
|
||||
34 -1.4082353101335789e-02 -1.2664441844283637e-03 -8.7897343649273926e-03
|
||||
35 -3.2837748483424821e-02 -2.8259033655048716e-02 -4.7109045095735221e-02
|
||||
36 6.3043838063683473e-03 2.2728472759162045e-02 -5.6021644135329923e-03
|
||||
37 2.6212204686130034e-02 -1.3029975561842381e-02 3.1750286301194183e-02
|
||||
38 2.0139944495106622e-02 4.3293211982739187e-03 -6.1649221929395912e-03
|
||||
39 -7.8960492061368320e-02 -3.6406243903921401e-02 1.2184492984680016e-01
|
||||
40 -3.9632145335340999e-02 1.3535049462025148e-02 -1.1321798674348533e-02
|
||||
41 -2.4388307314468449e-02 2.3366329744906832e-02 3.8928089365769816e-02
|
||||
42 1.1996964454673913e-01 6.9851097788973082e-02 -6.7069886963212297e-02
|
||||
43 -4.8078980460622062e-02 1.7214309659743252e-01 6.1467794063077237e-02
|
||||
44 -9.0284549182458221e-02 1.1015441455438249e-01 5.0331470972200497e-02
|
||||
45 -1.0780088805510608e-02 -1.1270483123892882e-02 2.2080179359507665e-02
|
||||
46 -3.6837588908592935e-02 2.7230340588058007e-02 -3.4349458876726219e-02
|
||||
47 1.9027883758890351e-03 -1.3952420712156162e-02 -8.4498460315278066e-04
|
||||
48 -1.3553909305246262e-02 -3.5297267660297201e-03 1.3635814385290735e-02
|
||||
49 -9.5576836166616046e-03 3.6186064165354859e-02 1.4320944961491736e-02
|
||||
50 8.5217870424105446e-02 -1.0799325877459537e-01 1.0051859972453785e-01
|
||||
51 -1.0113063819708310e-02 -2.0226413845647481e-02 -3.3234528125131467e-02
|
||||
52 -4.6943693419275380e-02 6.5649633276221267e-02 1.9270389824586502e-02
|
||||
53 -5.4874429234138388e-03 -1.4030397181841880e-02 8.5032803277714855e-03
|
||||
54 -4.2513762110625415e-02 5.3134910653632295e-02 -1.5583625457217259e-02
|
||||
55 2.2355622337947943e-03 1.5758808063886333e-02 3.0512038080609420e-02
|
||||
56 2.6470325853502827e-04 -3.6590608029393578e-03 1.7588493434887068e-02
|
||||
57 1.0304091828004703e-02 5.7001837787072690e-03 1.2617318639445109e-02
|
||||
58 -1.0367740873897520e-01 -1.9270956096739674e-02 -7.4383753859322305e-02
|
||||
59 -2.4598814289387631e-03 3.6232140002483829e-03 -4.7141806923593913e-03
|
||||
60 -5.0750993143057026e-03 5.8880547695610790e-02 1.4800121802056596e-02
|
||||
61 2.7189101908894160e-03 -5.1306885575781225e-02 7.3310325603516196e-03
|
||||
62 1.1256471950631124e-01 -8.8211823459006702e-02 5.4263270936498222e-02
|
||||
63 -3.2228752476757563e-02 3.6691295193583467e-02 -3.8707049961821866e-02
|
||||
64 -1.5804472791648257e-02 -2.5887199342735968e-02 -2.1134763353880526e-01
|
||||
...
|
||||
Reference in New Issue
Block a user