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Refactor: move vdw classes to module_vdw and clean up (#1448)
* vdw: move source files from src_pw to module_vdw and clean up * vdw: combine calculate and get * vdw: downgrade to c++11 and clean up * vdw: replace old vdw classes with new ones * vdw: remove old files * vdw: fix deepks test compile
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@@ -393,6 +393,7 @@ target_link_libraries(${ABACUS_BIN_NAME} | |
| hamilt | ||
| psi | ||
| esolver | ||
| vdw | ||
| ) | ||
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| if(ENABLE_LCAO) | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,30 @@ | ||
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| #include "vdw.h" | ||
| #include "vdwd2.h" | ||
| #include "vdwd3.h" | ||
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| namespace vdw | ||
| { | ||
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| std::unique_ptr<Vdw> make_vdw(const UnitCell_pseudo &ucell, const Input &input) | ||
| { | ||
| if (INPUT.vdw_method == "d2") | ||
| { | ||
| std::unique_ptr<Vdwd2> vdw_ptr = make_unique<Vdwd2>(ucell); | ||
| vdw_ptr->parameter().initial_parameters(input); | ||
| vdw_ptr->parameter().initset(ucell); | ||
| return vdw_ptr; | ||
| } | ||
| else if (INPUT.vdw_method == "d3_0" || INPUT.vdw_method == "d3_bj") | ||
| { | ||
| std::unique_ptr<Vdwd3> vdw_ptr = make_unique<Vdwd3>(ucell); | ||
| vdw_ptr->parameter().initial_parameters(input); | ||
| return vdw_ptr; | ||
| } | ||
| else | ||
| { | ||
| return nullptr; | ||
| } | ||
| } | ||
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| } // namespace vdw |
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| @@ -0,0 +1,54 @@ | ||
| #ifndef VDW_H | ||
| #define VDW_H | ||
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| #include <vector> | ||
| #include "module_cell/unitcell_pseudo.h" | ||
| #include "module_vdw/vdw_parameters.h" | ||
| #include "module_vdw/vdwd2_parameters.h" | ||
| #include "module_vdw/vdwd3_parameters.h" | ||
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| namespace vdw | ||
| { | ||
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| template<typename T, typename... Args> | ||
| std::unique_ptr<T> make_unique(Args &&... args) { | ||
| return std::unique_ptr<T>(new T(std::forward<Args>(args)...)); | ||
| } | ||
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| class Vdw | ||
| { | ||
| public: | ||
| Vdw(const UnitCell_pseudo &unit_in) : ucell_(unit_in) {}; | ||
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| virtual ~Vdw(){}; | ||
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| inline double get_energy(bool cal=true) { | ||
| if (cal) { cal_energy(); } | ||
| return energy_; | ||
| } | ||
| inline const std::vector<ModuleBase::Vector3<double>> &get_force(bool cal=true) { | ||
| if (cal) { cal_force(); } | ||
| return force_; | ||
| } | ||
| inline const ModuleBase::Matrix3 &get_stress(bool cal=true) { | ||
| if (cal) { cal_stress(); } | ||
| return stress_; | ||
| } | ||
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| protected: | ||
| const UnitCell_pseudo &ucell_; | ||
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| double energy_ = 0; | ||
| std::vector<ModuleBase::Vector3<double>> force_; | ||
| ModuleBase::Matrix3 stress_; | ||
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| virtual void cal_energy() { throw std::runtime_error("No cal_energy method in base Vdw class"); } | ||
| virtual void cal_force() { throw std::runtime_error("No cal_energy method in base Vdw class"); } | ||
| virtual void cal_stress() { throw std::runtime_error("No cal_energy method in base Vdw class"); } | ||
| }; | ||
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| std::unique_ptr<Vdw> make_vdw(const UnitCell_pseudo &ucell, const Input &input); | ||
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| } // namespace vdw | ||
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| #endif // VDW_H |
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| @@ -0,0 +1,27 @@ | ||
| #ifndef VDW_PARAMETERS_H | ||
| #define VDW_PARAMETERS_H | ||
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| #include "module_base/vector3.h" | ||
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| #include <string> | ||
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| namespace vdw | ||
| { | ||
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| class VdwParameters | ||
| { | ||
| public: | ||
| VdwParameters() = default; | ||
| virtual ~VdwParameters() = default; | ||
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| inline const std::string &model() const { return model_; } | ||
| inline const ModuleBase::Vector3<int> &period() const { return period_; }; | ||
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| protected: | ||
| std::string model_; | ||
| ModuleBase::Vector3<int> period_; | ||
| }; | ||
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| } // namespace vdw | ||
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| #endif // VDW_PARAMETERS_H |
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| @@ -0,0 +1,88 @@ | ||
| //========================================================== | ||
| // AUTHOR : Peize Lin | ||
| // DATE : 2014-04-25 | ||
| // UPDATE : 2019-04-26 | ||
| //========================================================== | ||
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| #include "module_vdw/vdwd2.h" | ||
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| namespace vdw | ||
| { | ||
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| void Vdwd2::cal_energy() | ||
| { | ||
| ModuleBase::TITLE("Vdwd2", "energy"); | ||
| para_.initset(ucell_); | ||
| energy_ = 0; | ||
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| auto energy = [&](double r, | ||
| double R0_sum, | ||
| double C6_product, | ||
| double r_sqr, | ||
| int, | ||
| int, | ||
| const ModuleBase::Vector3<double> &, | ||
| const ModuleBase::Vector3<double> &) { | ||
| const double tmp_damp_recip = 1 + exp(-para_.damping() * (r / R0_sum - 1)); | ||
| energy_ -= C6_product / pow(r_sqr, 3) / tmp_damp_recip / 2; | ||
| }; | ||
| index_loops(energy); | ||
| energy_ *= para_.scaling(); | ||
| } | ||
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| void Vdwd2::cal_force() | ||
| { | ||
| ModuleBase::TITLE("Vdwd2", "force"); | ||
| para_.initset(ucell_); | ||
| force_.clear(); | ||
| force_.resize(ucell_.nat); | ||
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| auto force = [&](double r, | ||
| double R0_sum, | ||
| double C6_product, | ||
| double r_sqr, | ||
| int it1, | ||
| int ia1, | ||
| const ModuleBase::Vector3<double> &tau1, | ||
| const ModuleBase::Vector3<double> &tau2) { | ||
| const double tmp_exp = exp(-para_.damping() * (r / R0_sum - 1)); | ||
| const double tmp_factor = C6_product / pow(r_sqr, 3) / r / (1 + tmp_exp) | ||
| * (-6 / r + tmp_exp / (1 + tmp_exp) * para_.damping() / R0_sum); | ||
| force_[ucell_.itia2iat(it1, ia1)] += tmp_factor * (tau1 - tau2); | ||
| }; | ||
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| index_loops(force); | ||
| std::for_each(force_.begin(), force_.end(), [&](ModuleBase::Vector3<double> &f) { | ||
| f *= para_.scaling() / ucell_.lat0; | ||
| }); | ||
| } | ||
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| void Vdwd2::cal_stress() | ||
| { | ||
| ModuleBase::TITLE("Vdwd2", "stress"); | ||
| para_.initset(ucell_); | ||
| stress_.Zero(); | ||
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| auto stress = [&](double r, | ||
| double R0_sum, | ||
| double C6_product, | ||
| double r_sqr, | ||
| int it1, | ||
| int ia1, | ||
| const ModuleBase::Vector3<double> &tau1, | ||
| const ModuleBase::Vector3<double> &tau2) { | ||
| const double tmp_exp = exp(-para_.damping() * (r / R0_sum - 1)); | ||
| const double tmp_factor = C6_product / pow(r_sqr, 3) / r / (1 + tmp_exp) | ||
| * (-6 / r + tmp_exp / (1 + tmp_exp) * para_.damping() / R0_sum); | ||
| const ModuleBase::Vector3<double> dr = tau2 - tau1; | ||
| stress_ += tmp_factor / 2 | ||
| * ModuleBase::Matrix3(dr.x * dr.x, dr.x * dr.y, dr.x * dr.z, | ||
| dr.y * dr.x, dr.y * dr.y, dr.y * dr.z, | ||
| dr.z * dr.x, dr.z * dr.y, dr.z * dr.z); | ||
| }; | ||
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| index_loops(stress); | ||
| stress_ *= para_.scaling() / ucell_.omega; | ||
| } | ||
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| } // namespace vdw |
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