diff --git a/source/api_cc/include/AtomMap.h b/source/api_cc/include/AtomMap.h
index 90b53b3281..0da2eefdcb 100644
--- a/source/api_cc/include/AtomMap.h
+++ b/source/api_cc/include/AtomMap.h
@@ -2,8 +2,6 @@
 
 #include <vector>
 
-// using namespace std;
-
 namespace deepmd {
 class AtomMap {
  public:
diff --git a/source/api_cc/include/version.h.in b/source/api_cc/include/version.h.in
index fa5e358f0b..c6bf6cf491 100644
--- a/source/api_cc/include/version.h.in
+++ b/source/api_cc/include/version.h.in
@@ -1,8 +1,6 @@
 #pragma once
 
 #include <string>
-// using namespace std;
-
 
 const std::string global_install_prefix="@CMAKE_INSTALL_PREFIX@";
 const std::string global_git_summ="@GIT_SUMM@";
diff --git a/source/ipi/include/Convert.h b/source/ipi/include/Convert.h
index f116cc61e9..199498cc7b 100644
--- a/source/ipi/include/Convert.h
+++ b/source/ipi/include/Convert.h
@@ -4,8 +4,6 @@
 #include <string>
 #include <vector>
 
-// using namespace std;
-
 template <typename VALUETYPE>
 class Convert {
  public:
diff --git a/source/ipi/include/XyzFileManager.h b/source/ipi/include/XyzFileManager.h
index aa50e76461..fa27592548 100644
--- a/source/ipi/include/XyzFileManager.h
+++ b/source/ipi/include/XyzFileManager.h
@@ -3,7 +3,6 @@
 
 #include <string>
 #include <vector>
-// using namespace std;
 
 namespace XyzFileManager {
 
diff --git a/source/lib/include/SimulationRegion_Impl.h b/source/lib/include/SimulationRegion_Impl.h
index 8d7807a1e7..c6e34b27c4 100644
--- a/source/lib/include/SimulationRegion_Impl.h
+++ b/source/lib/include/SimulationRegion_Impl.h
@@ -10,8 +10,6 @@
 
 #include "errors.h"
 
-// using namespace std;
-
 template <typename VALUETYPE>
 SimulationRegion<VALUETYPE>::~SimulationRegion() {}
 
diff --git a/source/md/include/AdWeight.h b/source/md/include/AdWeight.h
index e43896e3f9..fffd549fef 100644
--- a/source/md/include/AdWeight.h
+++ b/source/md/include/AdWeight.h
@@ -2,8 +2,6 @@
 
 #include <vector>
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -13,29 +11,29 @@ typedef float VALUETYPE;
 class AdWeight {
  public:
   AdWeight(const VALUETYPE& pl);
-  virtual void zone_tag(vector<int>& tag,
-                        const vector<VALUETYPE>& coord) const = 0;
-  virtual void atom_weight(vector<VALUETYPE>& weight,
-                           vector<VALUETYPE>& weight_x,
-                           const vector<VALUETYPE>& coord) const = 0;
-  virtual vector<VALUETYPE> get_center() const = 0;
-  void sel_nn_atom(vector<VALUETYPE>& nn_coord,
-                   vector<int>& nn_type,
-                   vector<int>& nn_idx,
-                   vector<int>& nn_tag,
-                   const vector<VALUETYPE>& dcoord,
-                   const vector<int>& dtype) const;
-  void force_intpl(vector<VALUETYPE>& of,
-                   const vector<VALUETYPE>& dcoord,
-                   const vector<VALUETYPE>& ff_force,
-                   const vector<VALUETYPE>& nn_force,
-                   const vector<int>& nn_idx) const;
-  void force_intpl(vector<VALUETYPE>& of,
-                   const vector<VALUETYPE>& dcoord,
-                   const vector<VALUETYPE>& ff_bd_force,
-                   const vector<VALUETYPE>& ff_nb_force,
-                   const vector<VALUETYPE>& nn_force,
-                   const vector<int>& nn_idx) const;
+  virtual void zone_tag(std::vector<int>& tag,
+                        const std::vector<VALUETYPE>& coord) const = 0;
+  virtual void atom_weight(std::vector<VALUETYPE>& weight,
+                           std::vector<VALUETYPE>& weight_x,
+                           const std::vector<VALUETYPE>& coord) const = 0;
+  virtual std::vector<VALUETYPE> get_center() const = 0;
+  void sel_nn_atom(std::vector<VALUETYPE>& nn_coord,
+                   std::vector<int>& nn_type,
+                   std::vector<int>& nn_idx,
+                   std::vector<int>& nn_tag,
+                   const std::vector<VALUETYPE>& dcoord,
+                   const std::vector<int>& dtype) const;
+  void force_intpl(std::vector<VALUETYPE>& of,
+                   const std::vector<VALUETYPE>& dcoord,
+                   const std::vector<VALUETYPE>& ff_force,
+                   const std::vector<VALUETYPE>& nn_force,
+                   const std::vector<int>& nn_idx) const;
+  void force_intpl(std::vector<VALUETYPE>& of,
+                   const std::vector<VALUETYPE>& dcoord,
+                   const std::vector<VALUETYPE>& ff_bd_force,
+                   const std::vector<VALUETYPE>& ff_nb_force,
+                   const std::vector<VALUETYPE>& nn_force,
+                   const std::vector<int>& nn_idx) const;
 
  private:
   VALUETYPE protect_level;
@@ -44,19 +42,20 @@ class AdWeight {
 // slab model, axis x
 class SlabWeight : public AdWeight {
  public:
-  SlabWeight(const vector<VALUETYPE>& box,
+  SlabWeight(const std::vector<VALUETYPE>& box,
              const VALUETYPE& rnn,
              const VALUETYPE& rhy,
              const VALUETYPE& rc,
              const VALUETYPE& protect_level = 1e-3);
-  virtual void zone_tag(vector<int>& tag, const vector<VALUETYPE>& coord) const;
-  virtual void atom_weight(vector<VALUETYPE>& weight,
-                           vector<VALUETYPE>& weight_x,
-                           const vector<VALUETYPE>& coord) const;
-  virtual vector<VALUETYPE> get_center() const { return center; }
+  virtual void zone_tag(std::vector<int>& tag,
+                        const std::vector<VALUETYPE>& coord) const;
+  virtual void atom_weight(std::vector<VALUETYPE>& weight,
+                           std::vector<VALUETYPE>& weight_x,
+                           const std::vector<VALUETYPE>& coord) const;
+  virtual std::vector<VALUETYPE> get_center() const { return center; }
 
  private:
-  vector<VALUETYPE> center;
+  std::vector<VALUETYPE> center;
   VALUETYPE rnn;
   VALUETYPE rhy;
   VALUETYPE rc;
diff --git a/source/md/include/Convert.h b/source/md/include/Convert.h
index 5f6a50bc34..d5a15d09f1 100644
--- a/source/md/include/Convert.h
+++ b/source/md/include/Convert.h
@@ -4,38 +4,36 @@
 #include <string>
 #include <vector>
 
-using namespace std;
-
 template <typename VALUETYPE>
 class Convert {
  public:
-  Convert(const vector<string>& atomname,
-          map<string, int>& name_type_map,
-          map<string, VALUETYPE>& name_mass_map,
-          map<string, VALUETYPE>& name_charge_map,
+  Convert(const std::vector<std::string>& atomname,
+          std::map<std::string, int>& name_type_map,
+          std::map<std::string, VALUETYPE>& name_mass_map,
+          std::map<std::string, VALUETYPE>& name_charge_map,
           const bool sort = true);
-  void gro2nnp(vector<VALUETYPE>& coord,
-               vector<VALUETYPE>& veloc,
-               vector<VALUETYPE>& box,
-               const vector<vector<double> >& posi,
-               const vector<vector<double> >& velo,
-               const vector<double>& box_size) const;
-  void nnp2gro(vector<vector<double> >& posi,
-               vector<vector<double> >& velo,
-               vector<double>& box_size,
-               const vector<VALUETYPE>& coord,
-               const vector<VALUETYPE>& veloc,
-               const vector<VALUETYPE>& box) const;
-  void idx_gro2nnp(vector<int>& out, const vector<int>& in) const;
-  void idx_nnp2gro(vector<int>& out, const vector<int>& in) const;
-  const vector<int>& get_type() const { return atype; }
-  const vector<VALUETYPE>& get_mass() const { return amass; }
-  const vector<VALUETYPE>& get_charge() const { return acharge; }
+  void gro2nnp(std::vector<VALUETYPE>& coord,
+               std::vector<VALUETYPE>& veloc,
+               std::vector<VALUETYPE>& box,
+               const std::vector<std::vector<double> >& posi,
+               const std::vector<std::vector<double> >& velo,
+               const std::vector<double>& box_size) const;
+  void nnp2gro(std::vector<std::vector<double> >& posi,
+               std::vector<std::vector<double> >& velo,
+               std::vector<double>& box_size,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<VALUETYPE>& veloc,
+               const std::vector<VALUETYPE>& box) const;
+  void idx_gro2nnp(std::vector<int>& out, const std::vector<int>& in) const;
+  void idx_nnp2gro(std::vector<int>& out, const std::vector<int>& in) const;
+  const std::vector<int>& get_type() const { return atype; }
+  const std::vector<VALUETYPE>& get_mass() const { return amass; }
+  const std::vector<VALUETYPE>& get_charge() const { return acharge; }
 
  private:
-  vector<int> idx_map_nnp2gro;
-  vector<int> idx_map_gro2nnp;
-  vector<int> atype;
-  vector<VALUETYPE> amass;
-  vector<VALUETYPE> acharge;
+  std::vector<int> idx_map_nnp2gro;
+  std::vector<int> idx_map_gro2nnp;
+  std::vector<int> atype;
+  std::vector<VALUETYPE> amass;
+  std::vector<VALUETYPE> acharge;
 };
diff --git a/source/md/include/Gaussian.h b/source/md/include/Gaussian.h
index 80a75af204..e3cdecfad1 100644
--- a/source/md/include/Gaussian.h
+++ b/source/md/include/Gaussian.h
@@ -5,8 +5,6 @@
 
 #include "RandomGenerator.h"
 
-using namespace std;
-
 class Gaussian {
  public:
   void set_seed(unsigned long seed);
diff --git a/source/md/include/HarmonicAngle.h b/source/md/include/HarmonicAngle.h
index 84ad5d8fd3..84a2558994 100644
--- a/source/md/include/HarmonicAngle.h
+++ b/source/md/include/HarmonicAngle.h
@@ -4,8 +4,6 @@
 
 #include "SimulationRegion.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -18,12 +16,12 @@ class HarmonicAngle {
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<int>& alist);
+               const std::vector<int>& alist);
 
  private:
   VALUETYPE ka, tt;
diff --git a/source/md/include/HarmonicBond.h b/source/md/include/HarmonicBond.h
index 0c7779db55..48751d85b7 100644
--- a/source/md/include/HarmonicBond.h
+++ b/source/md/include/HarmonicBond.h
@@ -4,8 +4,6 @@
 
 #include "SimulationRegion.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -18,12 +16,12 @@ class HarmonicBond {
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<int>& blist);
+               const std::vector<int>& blist);
 
  private:
   VALUETYPE kk, bb;
diff --git a/source/md/include/Integrator.h b/source/md/include/Integrator.h
index 99f720fc51..caefffbac8 100644
--- a/source/md/include/Integrator.h
+++ b/source/md/include/Integrator.h
@@ -4,7 +4,6 @@
 
 #include "Gaussian.h"
 #include "UnitManager.h"
-using namespace std;
 
 template <typename VALUETYPE>
 class Integrator {
@@ -12,13 +11,13 @@ class Integrator {
   Integrator() : massConst(UnitManager::IntegratorMassConstant){};
 
  public:
-  void stepVeloc(vector<VALUETYPE>& vv,
-                 const vector<VALUETYPE>& ff,
-                 const vector<VALUETYPE>& mass,
+  void stepVeloc(std::vector<VALUETYPE>& vv,
+                 const std::vector<VALUETYPE>& ff,
+                 const std::vector<VALUETYPE>& mass,
                  const double& dt,
-                 const vector<int>& freez = vector<int>()) const;
-  void stepCoord(vector<VALUETYPE>& rr,
-                 const vector<VALUETYPE>& vv,
+                 const std::vector<int>& freez = std::vector<int>()) const;
+  void stepCoord(std::vector<VALUETYPE>& rr,
+                 const std::vector<VALUETYPE>& vv,
                  const double& dt) const;
 
  private:
@@ -34,14 +33,14 @@ class ThermostatLangevin {
   void reinit(const VALUETYPE T = 300.,
               const VALUETYPE tau = 1.,
               const long long int seed = 0);
-  void stepOU(vector<VALUETYPE>& vv,
-              const vector<VALUETYPE>& mass,
+  void stepOU(std::vector<VALUETYPE>& vv,
+              const std::vector<VALUETYPE>& mass,
               const double& dt,
-              const vector<int>& freez = vector<int>()) const;
+              const std::vector<int>& freez = std::vector<int>()) const;
 
  private:
   mutable Gaussian gaussian;
-  string scheme;
+  std::string scheme;
   VALUETYPE temperature;
   VALUETYPE gamma;
   VALUETYPE sigma;
diff --git a/source/md/include/LJInter.h b/source/md/include/LJInter.h
index 267a8367d2..b71453b8a0 100644
--- a/source/md/include/LJInter.h
+++ b/source/md/include/LJInter.h
@@ -4,8 +4,6 @@
 
 #include "SimulationRegion.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -18,12 +16,12 @@ class LJInter {
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<vector<int> >& nlist);
+               const std::vector<std::vector<int> >& nlist);
 
  private:
   VALUETYPE c6, c12, rc, rc2, one_over_6, one_over_12, one_over_rc6,
diff --git a/source/md/include/LJTab.h b/source/md/include/LJTab.h
index 96c8089da0..f56f76510d 100644
--- a/source/md/include/LJTab.h
+++ b/source/md/include/LJTab.h
@@ -4,8 +4,6 @@
 
 #include "Tabulated.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -18,12 +16,12 @@ class LJTab {
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<vector<int> >& nlist) {
+               const std::vector<std::vector<int> >& nlist) {
     lj_tab.compute(ener, force, virial, coord, atype, region, nlist);
   };
 
diff --git a/source/md/include/MaxShift.h b/source/md/include/MaxShift.h
index 65971a7037..d940342d91 100644
--- a/source/md/include/MaxShift.h
+++ b/source/md/include/MaxShift.h
@@ -4,8 +4,6 @@
 
 #include "SimulationRegion.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -14,16 +12,16 @@ typedef float VALUETYPE;
 
 class MaxShift {
  public:
-  MaxShift(const vector<VALUETYPE>& dcoord, const VALUETYPE& shell);
+  MaxShift(const std::vector<VALUETYPE>& dcoord, const VALUETYPE& shell);
 
-  bool rebuild(const vector<VALUETYPE>& coord,
+  bool rebuild(const std::vector<VALUETYPE>& coord,
                const SimulationRegion<VALUETYPE>& region);
 
  private:
   VALUETYPE
-  max_shift2(const vector<VALUETYPE>& coord,
+  max_shift2(const std::vector<VALUETYPE>& coord,
              const SimulationRegion<VALUETYPE>& region);
-  vector<VALUETYPE> record;
+  std::vector<VALUETYPE> record;
   VALUETYPE shell;
   VALUETYPE max_allow2;
 };
diff --git a/source/md/include/Statistics.h b/source/md/include/Statistics.h
index 5dd6bad3e0..66574dbd66 100644
--- a/source/md/include/Statistics.h
+++ b/source/md/include/Statistics.h
@@ -3,16 +3,15 @@
 #include <vector>
 
 #include "SimulationRegion.h"
-using namespace std;
 
 template <typename VALUETYPE>
 class Statistics {
  public:
   Statistics(const VALUETYPE e_corr = 0, const VALUETYPE p_corr = 0);
   void record(const VALUETYPE& ener,
-              const vector<VALUETYPE>& virial,
-              const vector<VALUETYPE>& veloc,
-              const vector<VALUETYPE>& mass,
+              const std::vector<VALUETYPE>& virial,
+              const std::vector<VALUETYPE>& veloc,
+              const std::vector<VALUETYPE>& mass,
               const SimulationRegion<VALUETYPE>& region);
 
  public:
@@ -24,17 +23,17 @@ class Statistics {
   double get_epot() const { return r_pot_ener + e_corr; }
 
  public:
-  void print(ostream& os, const int& step, const double time) const;
-  void print_head(ostream& os) const;
+  void print(std::ostream& os, const int& step, const double time) const;
+  void print_head(std::ostream& os) const;
 
  private:
   int natoms;
   double r_ener;
   double r_pot_ener;
   double r_kin_ener;
-  // vector<double> r_box;
+  // std::vector<double> r_box;
   SimulationRegion<double> region;
-  vector<double> r_vir;
+  std::vector<double> r_vir;
   double e_corr;
   double p_corr;
 };
diff --git a/source/md/include/TF.h b/source/md/include/TF.h
index 7fc1720b87..ac286c89bc 100644
--- a/source/md/include/TF.h
+++ b/source/md/include/TF.h
@@ -6,8 +6,6 @@
 #include "AdWeight.h"
 #include "common.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -16,16 +14,16 @@ typedef float VALUETYPE;
 
 class TF {
  public:
-  TF(const string& filename);
+  TF(const std::string& filename);
 
  public:
-  void apply(vector<VALUETYPE>& force,
-             const vector<VALUETYPE>& coord,
+  void apply(std::vector<VALUETYPE>& force,
+             const std::vector<VALUETYPE>& coord,
              const AdWeight& weight) const;
 
  private:
   VALUETYPE meas(const VALUETYPE& xx) const;
-  vector<double> data;
+  std::vector<double> data;
   double hh;
   double xup;
 };
diff --git a/source/md/include/Tabulated.h b/source/md/include/Tabulated.h
index f74eb6354e..4e81cb620e 100644
--- a/source/md/include/Tabulated.h
+++ b/source/md/include/Tabulated.h
@@ -4,8 +4,6 @@
 
 #include "SimulationRegion.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -17,31 +15,31 @@ class Tabulated {
   Tabulated(){};
   Tabulated(const VALUETYPE rc,
             const VALUETYPE hh,
-            const vector<VALUETYPE>& tab);
+            const std::vector<VALUETYPE>& tab);
   void reinit(const VALUETYPE rc,
               const VALUETYPE hh,
-              const vector<VALUETYPE>& tab);
+              const std::vector<VALUETYPE>& tab);
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<vector<int> >& nlist);
+               const std::vector<std::vector<int> >& nlist);
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<VALUETYPE>& charge,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<VALUETYPE>& charge,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<vector<int> >& nlist);
+               const std::vector<std::vector<int> >& nlist);
   void tb_inner(VALUETYPE& ae, VALUETYPE& af, const VALUETYPE& r2);
 
  private:
   VALUETYPE rc2, hi;
-  vector<VALUETYPE> data;
+  std::vector<VALUETYPE> data;
   void compute_posi(int& idx, VALUETYPE& eps, const VALUETYPE& rr);
 };
diff --git a/source/md/include/Trajectory.h b/source/md/include/Trajectory.h
index 85b73ba9dd..9e773713af 100644
--- a/source/md/include/Trajectory.h
+++ b/source/md/include/Trajectory.h
@@ -8,8 +8,6 @@
 #include "xdrfile/xdrfile_trr.h"
 #include "xdrfile/xdrfile_xtc.h"
 
-using namespace std;
-
 class XtcSaver {
  public:
   XtcSaver() : inited(false), prec(1000){};
@@ -20,8 +18,8 @@ class XtcSaver {
  public:
   void save(const int &step,
             const double &time,
-            const vector<vector<double> > &frame,
-            const vector<double> &box);
+            const std::vector<std::vector<double> > &frame,
+            const std::vector<double> &box);
 
  private:
   XDRFILE *xd;
@@ -42,10 +40,10 @@ class TrrSaver {
  public:
   void save(const int &step,
             const double &time,
-            const vector<vector<double> > &ixx,
-            const vector<vector<double> > &ivv,
-            const vector<vector<double> > &iff,
-            const vector<double> &box);
+            const std::vector<std::vector<double> > &ixx,
+            const std::vector<std::vector<double> > &ivv,
+            const std::vector<std::vector<double> > &iff,
+            const std::vector<double> &box);
 
  private:
   XDRFILE *xd;
diff --git a/source/md/include/UnitManager.h b/source/md/include/UnitManager.h
index 977505b5ee..f1db76d1a0 100644
--- a/source/md/include/UnitManager.h
+++ b/source/md/include/UnitManager.h
@@ -1,7 +1,6 @@
 #pragma once
 
 #include <string>
-using namespace std;
 
 class UnitManager {
  protected:
@@ -19,8 +18,8 @@ class UnitManager {
   static double DefaultTableUpperLimit;
   static double DefaultTableStep;
   static double DefaultTableExtension;
-  static void set(const string& name_of_system);
+  static void set(const std::string& name_of_system);
 
  private:
-  static string unit_names[];
+  static std::string unit_names[];
 };
diff --git a/source/md/include/XyzFileManager.h b/source/md/include/XyzFileManager.h
index 5ffbb847be..2759807190 100644
--- a/source/md/include/XyzFileManager.h
+++ b/source/md/include/XyzFileManager.h
@@ -2,18 +2,17 @@
 #define __XyzFileManager_h_wanghan__
 
 #include <vector>
-using namespace std;
 
 namespace XyzFileManager {
 
-void read(const string& file,
-          vector<string>& atom_name,
-          vector<vector<double> >& posi,
-          vector<vector<double> >& velo,
-          vector<vector<double> >& forc,
-          vector<double>& boxsize);
+void read(const std::string& file,
+          std::vector<std::string>& atom_name,
+          std::vector<std::vector<double> >& posi,
+          std::vector<std::vector<double> >& velo,
+          std::vector<std::vector<double> >& forc,
+          std::vector<double>& boxsize);
 
-void getBoxSize(const string& name, vector<double>& boxsize);
+void getBoxSize(const std::string& name, std::vector<double>& boxsize);
 
 };  // namespace XyzFileManager
 
diff --git a/source/md/include/ZM.h b/source/md/include/ZM.h
index 1c2647a555..fd83ff0240 100644
--- a/source/md/include/ZM.h
+++ b/source/md/include/ZM.h
@@ -6,8 +6,6 @@
 #include "Tabulated.h"
 #include "ZMFunctions.h"
 
-using namespace std;
-
 #ifdef HIGH_PREC
 typedef double VALUETYPE;
 #else
@@ -20,24 +18,24 @@ class ZM {
 
  public:
   void compute(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<VALUETYPE>& charge,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<VALUETYPE>& charge,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<vector<int> >& nlist) {
+               const std::vector<std::vector<int> >& nlist) {
     zm_tab.compute(ener, force, virial, coord, charge, atype, region, nlist);
   };
   void exclude(VALUETYPE& ener,
-               vector<VALUETYPE>& force,
-               vector<VALUETYPE>& virial,
-               const vector<VALUETYPE>& coord,
-               const vector<VALUETYPE>& charge,
-               const vector<int>& atype,
+               std::vector<VALUETYPE>& force,
+               std::vector<VALUETYPE>& virial,
+               const std::vector<VALUETYPE>& coord,
+               const std::vector<VALUETYPE>& charge,
+               const std::vector<int>& atype,
                const SimulationRegion<VALUETYPE>& region,
-               const vector<int>& elist);
-  VALUETYPE e_corr(const vector<VALUETYPE>& charge) const;
+               const std::vector<int>& elist);
+  VALUETYPE e_corr(const std::vector<VALUETYPE>& charge) const;
 
  private:
   Tabulated zm_tab;
diff --git a/source/md/include/ZMFunctions.h b/source/md/include/ZMFunctions.h
index 9d4206a0a0..755a093ba5 100644
--- a/source/md/include/ZMFunctions.h
+++ b/source/md/include/ZMFunctions.h
@@ -2,7 +2,6 @@
 #define __Functions_h_ZM_wanghan__
 
 #include <vector>
-using namespace std;
 
 namespace ZeroMultipole {
 double funcV(const double& alpha, const double& r);
@@ -14,12 +13,12 @@ double funcD4V(const double& alpha, const double& r);
 void calCoefficients(const int& ll,
                      const double& alpha,
                      const double& rc,
-                     vector<double>& coeff);
+                     std::vector<double>& coeff);
 
 class Potential {
   double alpha, rc;
   int ll;
-  vector<double> coeff;
+  std::vector<double> coeff;
 
  public:
   Potential();
@@ -31,7 +30,7 @@ class Potential {
   double mulpotp(const double& rr);
 
  public:
-  double energyCorr(const vector<double>& charges) const;
+  double energyCorr(const std::vector<double>& charges) const;
 };
 }  // namespace ZeroMultipole
 
diff --git a/source/md/include/common.h b/source/md/include/common.h
index 54d19880d7..c58b3fa2b3 100644
--- a/source/md/include/common.h
+++ b/source/md/include/common.h
@@ -3,22 +3,21 @@
 #include <vector>
 
 #include "SimulationRegion.h"
-using namespace std;
 
 const double b2m_l = 10;
 const double b2m_e = 1.660539040e-21 / 1.602176621e-19;
 
 template <typename VALUETYPE>
 void clear(VALUETYPE& ener,
-           vector<VALUETYPE>& force,
-           vector<VALUETYPE>& virial) {
+           std::vector<VALUETYPE>& force,
+           std::vector<VALUETYPE>& virial) {
   ener = 0;
-  fill(force.begin(), force.end(), 0.);
-  fill(virial.begin(), virial.end(), 0.);
+  std::fill(force.begin(), force.end(), 0.);
+  std::fill(virial.begin(), virial.end(), 0.);
 }
 
 template <typename VALUETYPE>
-void normalize_coord(vector<VALUETYPE>& coord,
+void normalize_coord(std::vector<VALUETYPE>& coord,
                      const SimulationRegion<VALUETYPE>& region) {
   int natoms = coord.size() / 3;
   for (int ii = 0; ii < natoms; ++ii) {