Merge branch 'develop' of https://github.com/deepmodeling/abacus-develop

 into after_scf

docs/advanced/opt.md

@@ -78,3 +78,12 @@ Sometimes we want to do variable-cell relaxation with some of the cell degrees o
 - ISIF = 5 : calculation = "cell-relax", fixed_axes = "volume", fixed_atoms = True
 - ISIF = 6 : calculation = "cell-relax", fixed_atoms = True
 - ISIF = 7 : calculation = "cell-realx", fixed_axes = "shape", fixed_atoms = True
+
+### Stop Geometry Optimization Manually
+
+It is usually difficult to converge when calculating large systems, but people do not want to give up this calculation result.
+Providing a file named `EXIT`:
+```
+stop_ion    true
+```
+ABACUS will end normally and produce a complete file.

source/Makefile.Objects

@@ -171,6 +171,7 @@ OBJS_CELL=atom_pseudo.o\
     atom_spec.o\
     pseudo.o\
     read_pp.o\
+    read_pp_complete.o\
     read_pp_upf100.o\
     read_pp_upf201.o\
     read_pp_blps.o\
@@ -476,6 +477,7 @@ OBJS_IO=input_conv.o\
     read_cube.o\
     read_rho.o\
     read_rhog.o\
+    read_exit_file.o\
     read_wfc_pw.o\
     restart.o\
     binstream.o\

source/module_cell/CMakeLists.txt

@@ -11,6 +11,7 @@ add_library(
     atom_spec.cpp
     pseudo.cpp
     read_pp.cpp
+    read_pp_complete.cpp
     read_pp_upf100.cpp
     read_pp_upf201.cpp
     read_pp_blps.cpp

source/module_cell/pseudo.cpp

@@ -21,36 +21,6 @@ pseudo::~pseudo()
     delete[] lll;
 }
 
-//---------------------------------------------------------------------
-void pseudo::set_pseudo()
-{
-    ModuleBase::TITLE("pseudo", "set_pseudo");
-
-    // call subroutines
-    this->set_pseudo_h();
-	this->set_pseudo_atom();
-	this->set_pseudo_vl();
-
-	if (nbeta == 0) {
-		return;
-}
-
-	if (lll == nullptr)
-	{
-		lll = new int[nbeta];
-		assert(lll != nullptr);
-	}
-
-	nh = 0;
-
-	for (int nb = 0; nb < nbeta;nb++)
-	{
-		nh += 2 * lll [nb] + 1;
-	} 
-
-	return;
-} // end subroutine set_pseudo_upf
-
 void pseudo::print_pseudo(std::ofstream& ofs)
 {
 	print_pseudo_vl(ofs);
@@ -63,161 +33,6 @@ void pseudo::print_pseudo(std::ofstream& ofs)
 	ofs << "\n ----------------------";
 }
 
-
-void pseudo::set_pseudo_h()
-{
-	ModuleBase::TITLE("pseudo","set_pseudo_h");
-
-	// mohan update 2021-02-22
-	//  max number of points in the atomic radial mesh
-	int ndmx = 200000; 
-	if (this->mesh > ndmx)
-	{
-		std::cout << "\n set_pseudo_h, too many grid points,";
-	}
-
-	if (this->els == nullptr)
-	{
-		this->els = new std::string[nchi];
-		assert(this->els != nullptr);
-	}
-
-	if (this->lchi == nullptr)
-	{
-		this->lchi = new int[this->nchi];
-		assert(this->lchi != nullptr);
-	}
-
-	if (this->oc == nullptr)
-	{
-		this->oc = new double[nchi];
-		assert(this->oc != nullptr);
-	}
-
-	if (jjj == nullptr) {
-		this->jjj = new double[nbeta];
-		assert(this->jjj != nullptr);
-		assert(!this->has_so);
-		for (int i=0; i<nbeta; i++)
-		{
-			this->jjj[i]  = 0;
-		}
-	}
-
-	if (nn == nullptr) {
-		this->nn = new int[nchi];
-		assert(this->nn != nullptr);
-		assert(!this->has_so);
-		for (int i=0; i<nchi; i++)
-		{
-			this->nn[i] = 0;
-		}
-	}
-
-	if (jchi == nullptr) {
-		this->jchi = new double[nchi];
-		assert(this->jchi != nullptr);
-		assert(!this->has_so);
-		for (int i=0; i<nchi; i++)
-		{
-			this->jchi[i] = 0;
-		}
-	}
-
-    return;
-} // end subroutine set_pseudo_upf
-
-
-void pseudo::set_pseudo_atom()
-{
-	ModuleBase::TITLE("pseudo","set_pseudo_atom");
-
-	// mohan 2009-12-15
-	// mohan update again 2011-05-23, 
-	// in order to calculate more accurate Vna.
-	this->rcut = GlobalV::PSEUDORCUT;//(a.u.);
-
-// remember to update here if you need it.
-//	rcut = 25.0; 
-
-	ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"PAO radial cut off (Bohr)",rcut);
-	if(rcut <= 0.0)
-	{
-		ModuleBase::WARNING_QUIT("pseudo_atom::set_pseudo_atom","PAO rcut<=0.0");
-	}
-
-	// chi.create(nchi, mesh);
-
-	if (r == nullptr) {
-		r = new double[mesh];
-		assert(r != nullptr);
-		ModuleBase::GlobalFunc::ZEROS(r, mesh);
-	}
-
-	if (rab == nullptr) {
-		rab = new double[mesh];
-		assert(rab != nullptr);
-		ModuleBase::GlobalFunc::ZEROS(rab, mesh);
-	}
-
-	if (rho_at == nullptr) {
-		rho_at = new double[mesh];
-		assert(rho_at != nullptr);
-		ModuleBase::GlobalFunc::ZEROS(rho_at, mesh);
-	}
-
-	if (rho_atc == nullptr) {
-		rho_atc = new double[mesh];
-		assert(rho_atc != nullptr);
-		assert(!nlcc);
-		ModuleBase::GlobalFunc::ZEROS(rho_atc, mesh);
-	}
-
-	bool br = false;
-
-	this->msh = 0;
-
-	for (int ir = 0;ir < mesh;ir++)
-	{
-		if (r [ir] > rcut)
-		{
-			msh = ir + 1;
-			br = true;
-			break;
-		}
-	}
-
-	if (br)
-	{
-		// force msh to be odd for simpson integration
-		msh = 2 * (int)((msh + 1) / 2) - 1;	// 5
-	}
-	else
-	{
-		msh = mesh ;
-	}
-
-	return;
-} // end subroutine set_pseudo
-
-
-
-void pseudo::set_pseudo_vl()
-{
-	ModuleBase::TITLE("pseudo","set_pseudo_vl");
-
-	assert(mesh>0);//mohan add 2021-05-01
-
-	if (vloc_at == nullptr) {
-		vloc_at = new double[mesh];
-		assert(vloc_at != nullptr);
-	}
-
-
-	return;
-} 
-
-
 void pseudo::print_pseudo_atom(std::ofstream &ofs)
 {
 	print_pseudo_h(ofs);

source/module_cell/pseudo.h

@@ -75,11 +75,6 @@ class pseudo
     ModuleBase::realArray qfuncl; // qfuncl(2*lmax+1,nbeta*(nbeta+1)/2,mesh) Q_{mu,nu}(|r|) function for |r|> r_L
     ModuleBase::matrix qqq;       // qqq(nbeta,nbeta) q_{mu,nu}
 
-    void set_pseudo_h();
-    void set_pseudo_atom();
-    void set_pseudo_vl();
-    void set_pseudo();
-
     void print_pseudo_h(std::ofstream& ofs);
     void print_pseudo_atom(std::ofstream& ofs);
     void print_pseudo_vl(std::ofstream& ofs);

source/module_cell/read_cell_pseudopots.cpp

@@ -81,8 +81,7 @@ void UnitCell::read_cell_pseudopots(const std::string& pp_dir, std::ofstream& lo
 
         if (GlobalV::MY_RANK == 0)
         {
-            atoms[i].ncpp.set_pseudo(); // need to refactor, sunliang 20240716
-
+		    upf.complete_default(this->atoms[i].ncpp);
             log << "\n Read in pseudopotential file is " << pseudo_fn[i] << std::endl;
             ModuleBase::GlobalFunc::OUT(log, "pseudopotential type", atoms[i].ncpp.pp_type);
             ModuleBase::GlobalFunc::OUT(log, "exchange-correlation functional", atoms[i].ncpp.xc_func);

source/module_cell/read_pp.cpp

@@ -44,36 +44,36 @@ int Pseudopot_upf::init_pseudo_reader(const std::string &fn, std::string &type,
 	{
 		set_pseudo_type(fn, type);
 	}
+
+	int info = -1;
 	// read in the .UPF type of pseudopotentials
 	// if(GlobalV::global_pseudo_type=="upf")
 	if (type == "upf")
 	{
-		int info = read_pseudo_upf(ifs, pp);
-		return info;
+		info = read_pseudo_upf(ifs, pp);
 	}
 	// read in the .vwr type of pseudopotentials
 	// else if(GlobalV::global_pseudo_type=="vwr")
 	else if (type == "vwr")
 	{
-		int info = read_pseudo_vwr(ifs, pp);
-		return info;
+		info = read_pseudo_vwr(ifs, pp);
 	}
 	// else if(GlobalV::global_pseudo_type=="upf201")
 	else if (type == "upf201")
 	{
-		int info = read_pseudo_upf201(ifs, pp);
-		return info;
+		info = read_pseudo_upf201(ifs, pp);
 	}
 	// else if(GlobalV::global_pseudo_type=="blps") // sunliang added 2021.7
 	else if (type == "blps")
 	{
-		int info = read_pseudo_blps(ifs, pp);
-		return info;
+		info = read_pseudo_blps(ifs, pp);
 	}
     else
     {
         return 4;
     }
+
+	return info;
 }
 
 
@@ -486,4 +486,4 @@ void Pseudopot_upf::setqfnew(const int& nqf,
         }
         rho[ir] *= pow(r[ir], l + n);
     }
-}
+}

source/module_cell/read_pp.h

@@ -72,6 +72,7 @@ class Pseudopot_upf
     int average_p(const double& lambda, Atom_pseudo& pp); // zhengdy add 2020-10-20
     void set_empty_element(Atom_pseudo& pp);            // Peize Lin add for bsse 2022.04.07
     void set_upf_q(Atom_pseudo& pp);                    // liuyu add 2023-09-21
+    void complete_default(Atom_pseudo& pp);
 
   private:
     int set_pseudo_type(const std::string& fn, std::string& type);
@@ -118,6 +119,12 @@ class Pseudopot_upf
                   const double* qfcoef,
                   const double* r,
                   double* rho);
+
+    // complete default
+    // void complete_default(Atom_pseudo& pp);
+    void complete_default_h(Atom_pseudo& pp);
+    void complete_default_atom(Atom_pseudo& pp);
+    void complete_default_vl(Atom_pseudo& pp);
 };
 
 #endif //pseudopot_upf class