diff --git a/source/module_cell/atom_spec.h b/source/module_cell/atom_spec.h index d2deffebf8..00ce14898e 100644 --- a/source/module_cell/atom_spec.h +++ b/source/module_cell/atom_spec.h @@ -22,7 +22,7 @@ class Atom std::vector iw2_new; int nw = 0; // number of local orbitals (l,n,m) of this type - void set_index(void); + void set_index(); int type = 0; // Index of atom type int na = 0; // Number of atoms in this type. @@ -34,8 +34,7 @@ class Atom std::string label = "\0"; // atomic symbol std::vector> tau; // Cartesian coordinates of each atom in this type. - std::vector> - dis; // direct displacements of each atom in this type in current step liuyu modift 2023-03-22 + std::vector> dis; // direct displacements of each atom in this type in current step liuyu modift 2023-03-22 std::vector> taud; // Direct coordinates of each atom in this type. std::vector> vel; // velocities of each atom in this type. std::vector> force; // force acting on each atom in this type. @@ -54,8 +53,8 @@ class Atom void print_Atom(std::ofstream& ofs); void update_force(ModuleBase::matrix& fcs); #ifdef __MPI - void bcast_atom(void); - void bcast_atom2(void); + void bcast_atom(); + void bcast_atom2(); #endif }; diff --git a/source/module_cell/test/support/mock_unitcell.cpp b/source/module_cell/test/support/mock_unitcell.cpp index c335a181a9..c619a1f90a 100644 --- a/source/module_cell/test/support/mock_unitcell.cpp +++ b/source/module_cell/test/support/mock_unitcell.cpp @@ -33,10 +33,7 @@ bool UnitCell::read_atom_positions(std::ifstream& ifpos, std::ofstream& ofs_warning) { return true; } -void UnitCell::update_pos_taud(double* posd_in) {} -void UnitCell::update_pos_taud(const ModuleBase::Vector3* posd_in) {} -void UnitCell::update_vel(const ModuleBase::Vector3* vel_in) {} -void UnitCell::bcast_atoms_tau() {} + bool UnitCell::judge_big_cell() const { return true; } void UnitCell::update_stress(ModuleBase::matrix& scs) {} void UnitCell::update_force(ModuleBase::matrix& fcs) {} diff --git a/source/module_cell/test/unitcell_test.cpp b/source/module_cell/test/unitcell_test.cpp index 90925df62d..738ee8714f 100644 --- a/source/module_cell/test/unitcell_test.cpp +++ b/source/module_cell/test/unitcell_test.cpp @@ -1021,7 +1021,7 @@ TEST_F(UcellTest, UpdateVel) { vel_in[iat].set(iat * 0.1, iat * 0.1, iat * 0.1); } - ucell->update_vel(vel_in); + unitcell::update_vel(vel_in,ucell->ntype,ucell->nat,ucell->atoms); for (int iat = 0; iat < ucell->nat; ++iat) { EXPECT_DOUBLE_EQ(vel_in[iat].x, 0.1 * iat); diff --git a/source/module_cell/test/unitcell_test_para.cpp b/source/module_cell/test/unitcell_test_para.cpp index 11f629d707..a69b7655aa 100644 --- a/source/module_cell/test/unitcell_test_para.cpp +++ b/source/module_cell/test/unitcell_test_para.cpp @@ -153,7 +153,7 @@ TEST_F(UcellTest, UpdatePosTau) } delete[] pos_in; } -TEST_F(UcellTest, UpdatePosTaud) +TEST_F(UcellTest, UpdatePosTaud_pointer) { double* pos_in = new double[ucell->nat * 3]; ModuleBase::Vector3* tmp = new ModuleBase::Vector3[ucell->nat]; @@ -167,7 +167,8 @@ TEST_F(UcellTest, UpdatePosTaud) ucell->iat2iait(iat, &ia, &it); tmp[iat] = ucell->atoms[it].taud[ia]; } - ucell->update_pos_taud(pos_in); + unitcell::update_pos_taud(ucell->lat,pos_in,ucell->ntype, + ucell->nat,ucell->atoms); for (int iat = 0; iat < ucell->nat; ++iat) { int it, ia; @@ -180,6 +181,37 @@ TEST_F(UcellTest, UpdatePosTaud) delete[] pos_in; } +//test update_pos_taud with ModuleBase::Vector3 version +TEST_F(UcellTest, UpdatePosTaud_Vector3) +{ + ModuleBase::Vector3* pos_in = new ModuleBase::Vector3[ucell->nat]; + ModuleBase::Vector3* tmp = new ModuleBase::Vector3[ucell->nat]; + ucell->set_iat2itia(); + for (int iat = 0; iat < ucell->nat; ++iat) + { + for (int ik = 0; ik < 3; ++ik) + { + pos_in[iat][ik] = 0.01; + } + int it=0; + int ia=0; + ucell->iat2iait(iat, &ia, &it); + tmp[iat] = ucell->atoms[it].taud[ia]; + } + unitcell::update_pos_taud(ucell->lat,pos_in,ucell->ntype, + ucell->nat,ucell->atoms); + for (int iat = 0; iat < ucell->nat; ++iat) + { + int it, ia; + ucell->iat2iait(iat, &ia, &it); + for (int ik = 0; ik < 3; ++ik) + { + EXPECT_DOUBLE_EQ(ucell->atoms[it].taud[ia][ik], tmp[iat][ik] + 0.01); + } + } + delete[] tmp; + delete[] pos_in; +} TEST_F(UcellTest, ReadPseudo) { PARAM.input.pseudo_dir = pp_dir; diff --git a/source/module_cell/unitcell.cpp b/source/module_cell/unitcell.cpp index 69ca76df23..3d383c565a 100755 --- a/source/module_cell/unitcell.cpp +++ b/source/module_cell/unitcell.cpp @@ -314,65 +314,6 @@ std::vector> UnitCell::get_constrain() const return constrain; } - - -void UnitCell::update_pos_taud(double* posd_in) { - int iat = 0; - for (int it = 0; it < this->ntype; it++) { - Atom* atom = &this->atoms[it]; - for (int ia = 0; ia < atom->na; ia++) { - for (int ik = 0; ik < 3; ++ik) { - atom->taud[ia][ik] += posd_in[3 * iat + ik]; - atom->dis[ia][ik] = posd_in[3 * iat + ik]; - } - iat++; - } - } - assert(iat == this->nat); - unitcell::periodic_boundary_adjustment(this->atoms,this->latvec, this->ntype); - this->bcast_atoms_tau(); -} - -// posd_in is atomic displacements here liuyu 2023-03-22 -void UnitCell::update_pos_taud(const ModuleBase::Vector3* posd_in) { - int iat = 0; - for (int it = 0; it < this->ntype; it++) { - Atom* atom = &this->atoms[it]; - for (int ia = 0; ia < atom->na; ia++) { - for (int ik = 0; ik < 3; ++ik) { - atom->taud[ia][ik] += posd_in[iat][ik]; - atom->dis[ia][ik] = posd_in[iat][ik]; - } - iat++; - } - } - assert(iat == this->nat); - unitcell::periodic_boundary_adjustment(this->atoms,this->latvec, this->ntype); - this->bcast_atoms_tau(); -} - -void UnitCell::update_vel(const ModuleBase::Vector3* vel_in) { - int iat = 0; - for (int it = 0; it < this->ntype; ++it) { - Atom* atom = &this->atoms[it]; - for (int ia = 0; ia < atom->na; ++ia) { - this->atoms[it].vel[ia] = vel_in[iat]; - ++iat; - } - } - assert(iat == this->nat); -} - - -void UnitCell::bcast_atoms_tau() { -#ifdef __MPI - MPI_Barrier(MPI_COMM_WORLD); - for (int i = 0; i < ntype; i++) { - atoms[i].bcast_atom(); // bcast tau array - } -#endif -} - //============================================================== // Calculate various lattice related quantities for given latvec //============================================================== diff --git a/source/module_cell/unitcell.h b/source/module_cell/unitcell.h index e6f2fa96f0..7b10a18767 100644 --- a/source/module_cell/unitcell.h +++ b/source/module_cell/unitcell.h @@ -200,10 +200,6 @@ class UnitCell { void print_cell(std::ofstream& ofs) const; void print_cell_xyz(const std::string& fn) const; - void update_pos_taud(const ModuleBase::Vector3* posd_in); - void update_pos_taud(double* posd_in); - void update_vel(const ModuleBase::Vector3* vel_in); - void bcast_atoms_tau(); bool judge_big_cell() const; void update_stress(ModuleBase::matrix& scs); // updates stress diff --git a/source/module_cell/update_cell.cpp b/source/module_cell/update_cell.cpp index c4c324ce45..759389b9d8 100644 --- a/source/module_cell/update_cell.cpp +++ b/source/module_cell/update_cell.cpp @@ -374,6 +374,75 @@ void update_pos_tau(const Lattice& lat, bcast_atoms_tau(atoms, ntype); } +void update_pos_taud(const Lattice& lat, + const double* posd_in, + const int ntype, + const int nat, + Atom* atoms) +{ + int iat = 0; + for (int it = 0; it < ntype; it++) + { + Atom* atom = &atoms[it]; + for (int ia = 0; ia < atom->na; ia++) + { + for (int ik = 0; ik < 3; ++ik) + { + atom->taud[ia][ik] += posd_in[3 * iat + ik]; + atom->dis[ia][ik] = posd_in[3 * iat + ik]; + } + iat++; + } + } + assert(iat == nat); + periodic_boundary_adjustment(atoms,lat.latvec,ntype); + bcast_atoms_tau(atoms, ntype); +} + +// posd_in is atomic displacements here liuyu 2023-03-22 +void update_pos_taud(const Lattice& lat, + const ModuleBase::Vector3* posd_in, + const int ntype, + const int nat, + Atom* atoms) +{ + int iat = 0; + for (int it = 0; it < ntype; it++) + { + Atom* atom = &atoms[it]; + for (int ia = 0; ia < atom->na; ia++) + { + for (int ik = 0; ik < 3; ++ik) + { + atom->taud[ia][ik] += posd_in[iat][ik]; + atom->dis[ia][ik] = posd_in[iat][ik]; + } + iat++; + } + } + assert(iat == nat); + periodic_boundary_adjustment(atoms,lat.latvec,ntype); + bcast_atoms_tau(atoms, ntype); +} + +void update_vel(const ModuleBase::Vector3* vel_in, + const int ntype, + const int nat, + Atom* atoms) +{ + int iat = 0; + for (int it = 0; it < ntype; ++it) + { + Atom* atom = &atoms[it]; + for (int ia = 0; ia < atom->na; ++ia) + { + atoms[it].vel[ia] = vel_in[iat]; + ++iat; + } + } + assert(iat == nat); +} + void periodic_boundary_adjustment(Atom* atoms, const ModuleBase::Matrix3& latvec, const int ntype) diff --git a/source/module_cell/update_cell.h b/source/module_cell/update_cell.h index d7105535dc..a13bf58546 100644 --- a/source/module_cell/update_cell.h +++ b/source/module_cell/update_cell.h @@ -48,6 +48,48 @@ namespace unitcell const int ntype, const int nat, Atom* atoms); + + /** + * @brief update the position and tau of the atoms + * + * @param lat: the lattice of the atoms [in] + * @param pos_in: the position of the atoms in direct coordinate system [in] + * @param ntype: the number of types of the atoms [in] + * @param nat: the number of atoms [in] + * @param atoms: the atoms to be updated [out] + */ + void update_pos_taud(const Lattice& lat, + const double* posd_in, + const int ntype, + const int nat, + Atom* atoms); + /** + * @brief update the velocity of the atoms + * + * @param lat: the lattice of the atoms [in] + * @param pos_in: the position of the atoms in direct coordinate system + * in ModuleBase::Vector3 version [in] + * @param ntype: the number of types of the atoms [in] + * @param nat: the number of atoms [in] + * @param atoms: the atoms to be updated [out] + */ + void update_pos_taud(const Lattice& lat, + const ModuleBase::Vector3* posd_in, + const int ntype, + const int nat, + Atom* atoms); + /** + * @brief update the velocity of the atoms + * + * @param vel_in: the velocity of the atoms [in] + * @param ntype: the number of types of the atoms [in] + * @param nat: the number of atoms [in] + * @param atoms: the atoms to be updated [out] + */ + void update_vel(const ModuleBase::Vector3* vel_in, + const int ntype, + const int nat, + Atom* atoms); } // #endif // UPDATE_CELL_H \ No newline at end of file diff --git a/source/module_md/md_base.cpp b/source/module_md/md_base.cpp index 30e344dbe2..8b330927d1 100644 --- a/source/module_md/md_base.cpp +++ b/source/module_md/md_base.cpp @@ -1,11 +1,10 @@ #include "md_base.h" - #include "md_func.h" #ifdef __MPI #include "mpi.h" #endif #include "module_io/print_info.h" - +#include "module_cell/update_cell.h" MD_base::MD_base(const Parameter& param_in, UnitCell& unit_in) : mdp(param_in.mdp), ucell(unit_in) { my_rank = param_in.globalv.myrank; @@ -112,7 +111,7 @@ void MD_base::update_pos() MPI_Bcast(pos, ucell.nat * 3, MPI_DOUBLE, 0, MPI_COMM_WORLD); #endif - ucell.update_pos_taud(pos); + unitcell::update_pos_taud(ucell.lat,pos,ucell.ntype,ucell.nat,ucell.atoms); return; } diff --git a/source/module_md/run_md.cpp b/source/module_md/run_md.cpp index 1f85525979..b82a0c3e69 100644 --- a/source/module_md/run_md.cpp +++ b/source/module_md/run_md.cpp @@ -10,7 +10,7 @@ #include "msst.h" #include "nhchain.h" #include "verlet.h" - +#include "module_cell/update_cell.h" namespace Run_MD { @@ -97,7 +97,7 @@ void md_line(UnitCell& unit_in, ModuleESolver::ESolver* p_esolver, const Paramet if ((mdrun->step_ + mdrun->step_rst_) % param_in.mdp.md_restartfreq == 0) { - unit_in.update_vel(mdrun->vel); + unitcell::update_vel(mdrun->vel,unit_in.ntype,unit_in.nat,unit_in.atoms); std::stringstream file; file << PARAM.globalv.global_stru_dir << "STRU_MD_" << mdrun->step_ + mdrun->step_rst_; // changelog 20240509 diff --git a/source/module_relax/relax_new/relax.cpp b/source/module_relax/relax_new/relax.cpp index 88800c88d8..b6f0560824 100644 --- a/source/module_relax/relax_new/relax.cpp +++ b/source/module_relax/relax_new/relax.cpp @@ -633,7 +633,7 @@ void Relax::move_cell_ions(UnitCell& ucell, const bool is_new_dir) ucell.symm.symmetrize_vec3_nat(move_ion); } - ucell.update_pos_taud(move_ion); + unitcell::update_pos_taud(ucell.lat,move_ion,ucell.ntype,ucell.nat,ucell.atoms); // Print the structure file. ucell.print_tau(); diff --git a/source/module_relax/relax_new/test/relax_test.cpp b/source/module_relax/relax_new/test/relax_test.cpp index 74328026a4..5db3ecde3f 100644 --- a/source/module_relax/relax_new/test/relax_test.cpp +++ b/source/module_relax/relax_new/test/relax_test.cpp @@ -1,4 +1,5 @@ #include "gtest/gtest.h" +#include #define private public #include "module_parameter/parameter.h" #undef private @@ -27,13 +28,13 @@ class Test_SETGRAD : public testing::Test force_in.create(nat,3); stress_in.create(3,3); - force_in(0,0) = 1; force_in(0,1) = 2; force_in(0,2)= 3; - force_in(1,0) = 4; force_in(1,1) = 5; force_in(1,2)= 6; - force_in(2,0) = 7; force_in(2,1) = 8; force_in(2,2)= 9; + force_in(0,0) = 0.1; force_in(0,1) = 0.1; force_in(0,2)= 0.1; + force_in(1,0) = 0; force_in(1,1) = 0.1; force_in(1,2)= 0.1; + force_in(2,0) = 0; force_in(2,1) = 0; force_in(2,2)= 0.1; - stress_in(0,0) = 1; stress_in(0,1) = 2; stress_in(0,2)= 3; - stress_in(1,0) = 4; stress_in(1,1) = 5; stress_in(1,2)= 6; - stress_in(2,0) = 7; stress_in(2,1) = 8; stress_in(2,2)= 9; + stress_in(0,0) = 1; stress_in(0,1) = 1; stress_in(0,2)= 1; + stress_in(1,0) = 0; stress_in(1,1) = 1; stress_in(1,2)= 1; + stress_in(2,0) = 0; stress_in(2,1) = 0; stress_in(2,2)= 1; ucell.ntype = 1; ucell.nat = nat; @@ -46,6 +47,8 @@ class Test_SETGRAD : public testing::Test ucell.iat2ia = new int[nat]; ucell.atoms[0].mbl.resize(nat); ucell.atoms[0].taud.resize(nat); + ucell.atoms[0].tau.resize(nat); + ucell.atoms[0].dis.resize(nat); ucell.lc = new int[3]; ucell.iat2it[0] = 0; @@ -136,14 +139,25 @@ TEST_F(Test_SETGRAD, relax_new) { std::vector result_ref = { - 0,0,0.1709672056,0,0.2849453427,0,0.3989234797,0,0,1.005319517, - 0.01063903455,0.01595855183,0.0212780691,1.026597586,0.03191710366, - 0.03723662093,0.04255613821,1.047875655,1.059181731,0,0,0,1.059181731, - 0,0,0,1.059181731,1.034363264,0.01301504537,0.01952256806, - 0.02603009074,1.060393355,0.03904513611,0.0455526588,0.05206018148, - 1.086423445,1,0,0,0,1,0,0,0,1 + 0, 0, 0.24293434145, + 0, 0.242934341453, 0, + 0, 0, 0, + //paramter for taud + 1.2267616333,0.2267616333,0.22676163333, + 0, 1.2267616333 ,0.2267616333, + 0, 0, 1.22676163333, + // paramter for fisrt time after relaxation + 1.3677603495, 0, 0, + 0, 1.36776034956, 0, + 0, 0, 1.36776034956, + // paramter for second time after relaxation + 1.3677603495 ,0.3633367476,0.36333674766, + 0, 1.3677603495 ,0.36333674766, + 0, 0, 1.3677603495 , + // paramter for third time after relaxation + 1,0,0,0,1,0,0,0,1 + // paramter for fourth time after relaxation }; - for(int i=0;i result_ref= + { + 0.5000000586,0.4999998876,0.009364595811, + 0.9999999281,1.901333279e-07,0.5476035454, + 3.782097706e-07,0.4999999285,0.4770375874, + 0.4999997826,2.072311863e-07,0.477037871, + 0.9999998523,0.9999997866,0.9349574003, + // paramter for taud after first relaxation + 4.006349654,-1.93128788e-07,5.793863639e-07, + -1.93128788e-07,4.006354579,-3.86257576e-07, + 6.757962549e-07,-4.505308366e-07,3.966870038, + // paramter for latvec after first relaxation + 0.5000000566,0.4999998916,0.009177239183, + 0.9999999308,1.832935626e-07,0.5467689737, + 3.647769323e-07,0.4999999311,0.4771204124, + 0.4999997903,1.998879545e-07,0.4771206859, + 0.9999998574,0.9999997943,0.9358136888, + // paramter for taud after second relaxation + 3.999761277,-1.656764727e-07,4.97029418e-07, + -1.656764727e-07,3.999765501,-3.313529453e-07, + 5.797351131e-07,-3.864900754e-07,4.010925071, + // paramter for latvec after second relaxation + 0.500000082,0.4999999574,0.01057784352, + 0.9999999149,1.939640249e-07,0.5455830599, + 3.795967781e-07,0.4999998795,0.4765373919, + 0.4999998037,2.756298268e-07,0.4765374602, + 0.9999998196,0.9999996936,0.9367652445, + // paramter for taud after third relaxation + 4.017733155,-1.420363309e-07,2.637046077e-07, + -1.420364243e-07,4.017735987,3.126225134e-07, + 3.479123171e-07,2.578467568e-07,4.011674933 + // paramter for latvec after third relaxation + }; for(int i=0;i> tmp; - EXPECT_NEAR(tmp,result[i],1e-8); + EXPECT_NEAR(result_ref[i],result[i],1e-8); } } \ No newline at end of file diff --git a/source/module_relax/relax_new/test/relax_test.h b/source/module_relax/relax_new/test/relax_test.h index d60d37adf9..d31da75f07 100644 --- a/source/module_relax/relax_new/test/relax_test.h +++ b/source/module_relax/relax_new/test/relax_test.h @@ -2,7 +2,6 @@ namespace GlobalC { - UnitCell ucell; Structure_Factor sf; ModulePW::PW_Basis* rhopw; } @@ -10,22 +9,6 @@ namespace GlobalC UnitCell::UnitCell(){}; UnitCell::~UnitCell(){}; -void UnitCell::update_pos_taud(double* posd_in) -{ - int iat = 0; - for (int it = 0; it < this->ntype; it++) - { - Atom* atom = &this->atoms[it]; - for (int ia = 0; ia < atom->na; ia++) - { - this->atoms[it].taud[ia].x += posd_in[iat*3]; - this->atoms[it].taud[ia].y += posd_in[iat*3 + 1]; - this->atoms[it].taud[ia].z += posd_in[iat*3 + 2]; - iat++; - } - } - assert(iat == this->nat); -} void UnitCell::print_stru_file(const std::string& fn, const int& nspin, diff --git a/source/module_relax/relax_new/test/support/result_ref.txt b/source/module_relax/relax_new/test/support/result_ref.txt deleted file mode 100644 index 26303ffbe7..0000000000 --- a/source/module_relax/relax_new/test/support/result_ref.txt +++ /dev/null @@ -1,317 +0,0 @@ - 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