Merge branch 'develop' into refactor

deepmodeling · Jan 5, 2025 · 43a3b8b · 43a3b8b
2 parents d3d5b7c + 4ddec65
commit 43a3b8b
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Showing 14 changed files with 220 additions and 435 deletions.
diff --git a/source/module_cell/atom_spec.h b/source/module_cell/atom_spec.h
@@ -22,7 +22,7 @@ class Atom
     std::vector<bool> 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<ModuleBase::Vector3<double>> tau; // Cartesian coordinates of each atom in this type.
-    std::vector<ModuleBase::Vector3<double>>
-        dis; // direct displacements of each atom in this type in current step  liuyu modift 2023-03-22
+    std::vector<ModuleBase::Vector3<double>> dis; // direct displacements of each atom in this type in current step  liuyu modift 2023-03-22
     std::vector<ModuleBase::Vector3<double>> taud;  // Direct coordinates of each atom in this type.
     std::vector<ModuleBase::Vector3<double>> vel;   // velocities of each atom in this type.
     std::vector<ModuleBase::Vector3<double>> 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
@@ -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<double>* posd_in) {}
-void UnitCell::update_vel(const ModuleBase::Vector3<double>* 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
@@ -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
@@ -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<double>* tmp = new ModuleBase::Vector3<double>[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<double> version
+TEST_F(UcellTest, UpdatePosTaud_Vector3)
+{
+    ModuleBase::Vector3<double>* pos_in = new ModuleBase::Vector3<double>[ucell->nat];
+    ModuleBase::Vector3<double>* tmp = new ModuleBase::Vector3<double>[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
@@ -314,65 +314,6 @@ std::vector<ModuleBase::Vector3<int>> 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<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[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<double>* 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
@@ -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<double>* posd_in);
-    void update_pos_taud(double* posd_in);
-    void update_vel(const ModuleBase::Vector3<double>* 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
@@ -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<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[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<double>* 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
@@ -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<double>* 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<double>* vel_in,
+                    const int ntype,
+                    const int nat,
+                    Atom* atoms);
 }
 //
 #endif // UPDATE_CELL_H
diff --git 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
@@ -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
@@ -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();