add update_vel for ucell

Author: A-006

source/module_cell/atom_spec.h

@@ -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.

source/module_cell/test/support/mock_unitcell.cpp

@@ -34,7 +34,6 @@ bool UnitCell::read_atom_positions(std::ifstream& ifpos,
     return true;
 }
 
-void UnitCell::update_vel(const ModuleBase::Vector3<double>* vel_in) {}
 bool UnitCell::judge_big_cell() const { return true; }
 void UnitCell::update_stress(ModuleBase::matrix& scs) {}
 void UnitCell::update_force(ModuleBase::matrix& fcs) {}

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);

source/module_cell/unitcell.cpp

@@ -314,18 +314,6 @@ std::vector<ModuleBase::Vector3<int>> UnitCell::get_constrain() const
 	return constrain;
 }
 
-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);
-}
-
 //==============================================================
 // Calculate various lattice related quantities for given latvec
 //==============================================================

source/module_cell/unitcell.h

@@ -200,7 +200,6 @@ class UnitCell {
     void print_cell(std::ofstream& ofs) const;
     void print_cell_xyz(const std::string& fn) const;
 
-    void update_vel(const ModuleBase::Vector3<double>* vel_in);
     bool judge_big_cell() const;
 
     void update_stress(ModuleBase::matrix& scs); // updates stress

source/module_cell/update_cell.cpp

@@ -425,6 +425,24 @@ void update_pos_taud(const Lattice& lat,
     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) 

source/module_cell/update_cell.h

@@ -73,11 +73,23 @@ namespace unitcell
      * @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);
+    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

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