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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| // Copyright (c) 2009-2024 The Regents of the University of Michigan. | ||
| // Part of HOOMD-blue, released under the BSD 3-Clause License. | ||
|
|
||
| #include "PairPotentialExpandedGaussian.h" | ||
|
|
||
| namespace hoomd | ||
| { | ||
| namespace hpmc | ||
| { | ||
|
|
||
| PairPotentialExpandedGaussian::PairPotentialExpandedGaussian( | ||
| std::shared_ptr<SystemDefinition> sysdef) | ||
| : PairPotential(sysdef), m_params(m_type_param_index.getNumElements()) | ||
| { | ||
| } | ||
|
|
||
| LongReal PairPotentialExpandedGaussian::energy(const LongReal r_squared, | ||
| const vec3<LongReal>& r_ij, | ||
| const unsigned int type_i, | ||
| const quat<LongReal>& q_i, | ||
| const LongReal charge_i, | ||
| const unsigned int type_j, | ||
| const quat<LongReal>& q_j, | ||
| const LongReal charge_j) const | ||
| { | ||
| unsigned int param_index = m_type_param_index(type_i, type_j); | ||
| const auto& param = m_params[param_index]; | ||
|
|
||
| LongReal r = fast::sqrt(r_squared); | ||
| LongReal rmd_2 = (r - param.delta) * (r - param.delta); | ||
| LongReal rmd_over_sigma_2 = rmd_2 / param.sigma_2; | ||
| LongReal exp_val = fast::exp(-LongReal(1.0) / LongReal(2.0) * rmd_over_sigma_2); | ||
| LongReal energy = param.epsilon * exp_val; | ||
|
|
||
| if (m_mode == shift || (m_mode == xplor && param.r_on_squared >= param.r_cut_squared)) | ||
| { | ||
| LongReal r_cut = fast::sqrt(param.r_cut_squared); | ||
| LongReal rcutmd_2 = (r_cut - param.delta) * (r_cut - param.delta); | ||
| LongReal rcutmd_over_sigma_2 = rcutmd_2 / param.sigma_2; | ||
| energy -= param.epsilon * fast::exp(-LongReal(1.0) / LongReal(2.0) * rcutmd_over_sigma_2); | ||
| } | ||
|
|
||
| if (m_mode == xplor && r_squared > param.r_on_squared) | ||
| { | ||
| LongReal a = param.r_cut_squared - param.r_on_squared; | ||
| LongReal denominator = a * a * a; | ||
|
|
||
| LongReal b = param.r_cut_squared - r_squared; | ||
| LongReal numerator = b * b | ||
| * (param.r_cut_squared + LongReal(2.0) * r_squared | ||
| - LongReal(3.0) * param.r_on_squared); | ||
| energy *= numerator / denominator; | ||
| } | ||
|
|
||
| return energy; | ||
| } | ||
|
|
||
| void PairPotentialExpandedGaussian::setParamsPython(pybind11::tuple typ, pybind11::dict params) | ||
| { | ||
| auto pdata = m_sysdef->getParticleData(); | ||
| auto type_i = pdata->getTypeByName(typ[0].cast<std::string>()); | ||
| auto type_j = pdata->getTypeByName(typ[1].cast<std::string>()); | ||
| unsigned int param_index_1 = m_type_param_index(type_i, type_j); | ||
| m_params[param_index_1] = ParamType(params); | ||
| unsigned int param_index_2 = m_type_param_index(type_j, type_i); | ||
| m_params[param_index_2] = ParamType(params); | ||
|
|
||
| notifyRCutChanged(); | ||
| } | ||
|
|
||
| pybind11::dict PairPotentialExpandedGaussian::getParamsPython(pybind11::tuple typ) | ||
| { | ||
| auto pdata = m_sysdef->getParticleData(); | ||
| auto type_i = pdata->getTypeByName(typ[0].cast<std::string>()); | ||
| auto type_j = pdata->getTypeByName(typ[1].cast<std::string>()); | ||
| unsigned int param_index = m_type_param_index(type_i, type_j); | ||
| return m_params[param_index].asDict(); | ||
| } | ||
|
|
||
| namespace detail | ||
| { | ||
| void exportPairPotentialExpandedGaussian(pybind11::module& m) | ||
| { | ||
| pybind11::class_<PairPotentialExpandedGaussian, | ||
| PairPotential, | ||
| std::shared_ptr<PairPotentialExpandedGaussian>>( | ||
| m, | ||
| "PairPotentialExpandedGaussian") | ||
| .def(pybind11::init<std::shared_ptr<SystemDefinition>>()) | ||
| .def("setParams", &PairPotentialExpandedGaussian::setParamsPython) | ||
| .def("getParams", &PairPotentialExpandedGaussian::getParamsPython) | ||
| .def_property("mode", | ||
| &PairPotentialExpandedGaussian::getMode, | ||
| &PairPotentialExpandedGaussian::setMode); | ||
| } | ||
| } // end namespace detail | ||
| } // end namespace hpmc | ||
| } // end namespace hoomd |
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