Feature: functions needed by uspp (#3026)

* Refactor: rename pseudo_nc to pseudo

* Fix: read zv from string with scientific notation

* Refactor: rename pseudo_nc to pseudo

* Feature: add smooth FFT grid for uspp

* Feature: renormalize norm of pseudo-wavefunctions

* Test: add unittests for ecutrho/ecutwfc

* Test: add unit tests

* Test: update unit tests

* Fix: mpi bug

* Refactor: update NQX

* Fix: renormalize norm of wavefunctions

Author: YuLiu98

docs/advanced/input_files/input-main.md

@@ -36,7 +36,9 @@
     - [wannier\_card](#wannier_card)
   - [Plane wave related variables](#plane-wave-related-variables)
     - [ecutwfc](#ecutwfc)
+    - [ecutrho](#ecutrho)
     - [nx, ny, nz](#nx-ny-nz)
+    - [nsx, nsy, nsz](#nsx-nsy-nsz)
     - [pw\_seed](#pw_seed)
     - [pw\_diag\_thr](#pw_diag_thr)
     - [pw\_diag\_nmax](#pw_diag_nmax)
@@ -662,10 +664,22 @@ These variables are used to control the plane wave related parameters.
 - **Description**: Energy cutoff for plane wave functions, the unit is **Rydberg**. Note that even for localized orbitals basis, you still need to setup an energy cutoff for this system. Because our local pseudopotential parts and the related force are calculated from plane wave basis set, etc. Also, because our orbitals are generated by matching localized orbitals to a chosen set of wave functions from a certain energy cutoff, this set of localize orbitals is most accurate under this same plane wave energy cutoff.
 - **Default**: 50
 
+### ecutrho
+
+- **Type**: Real
+- **Description**: Energy cutoff for charge density and potential, the unit is **Rydberg**. For norm-conserving pseudopotential you should stick to the default value, you can reduce it by a little but it will introduce noise especially on forces and stress. For ultrasoft pseudopotential a larger value than the default is often desirable (`ecutrho` = 8 to 12 times `ecutwfc`, typically). The use of gradient-corrected functional, especially in cells with vacuum, or for pseudopotential without non-linear core correction, usually requires an higher values of `ecutrho` to be accurately converged.
+- **Default**: 4*ecutwfc
+
 ### nx, ny, nz
 
 - **Type**: Integer
-- **Description**: If set to a positive number, then the three variables specify the numbers of FFT grid points in x, y, z directions, respectively. If set to 0, the number will be calculated from ecutwfc.
+- **Description**: If set to a positive number, then the three variables specify the numbers of FFT grid points in x, y, z directions, respectively. If set to 0, the number will be calculated from ecutrho. Note: you must specify all three dimensions for this setting to be used.
+- **Default**: 0
+
+### nsx, nsy, nsz
+
+- **Type**: Integer
+- **Description**: If set to a positive number, then the three variables specify the numbers of FFT grid (for the smooth part of charge density in ultrasoft pseudopotential) points in x, y, z directions, respectively. If set to 0, the number will be calculated from ecutwfc. Note: you must specify all three dimensions for this setting to be used.
 - **Default**: 0
 
 ### pw_seed

source/Makefile.Objects

@@ -144,7 +144,7 @@ OBJS_BASE=abfs-vector3_order.o\
 
 OBJS_CELL=atom_pseudo.o\
     atom_spec.o\
-    pseudo_nc.o\
+    pseudo.o\
     read_pp.o\
     read_pp_upf100.o\
     read_pp_upf201.o\

source/module_base/global_variable.cpp

@@ -61,6 +61,7 @@ int md_prec_level = 0;
 int SCF_NMAX = 100;
 
 bool use_paw = false;
+bool use_uspp = false;
 
 std::string BASIS_TYPE = "pw"; // xiaohui add 2013-09-01
 std::string KS_SOLVER = "cg"; // xiaohui add 2013-09-01

source/module_base/global_variable.h

@@ -59,6 +59,7 @@ extern double relax_scale_force;
 extern bool relax_new;
 
 extern bool use_paw;
+extern bool use_uspp;
 
 extern bool fixed_atoms;
 

source/module_cell/CMakeLists.txt

@@ -9,7 +9,7 @@ add_library(
     OBJECT
     atom_pseudo.cpp
     atom_spec.cpp
-    pseudo_nc.cpp
+    pseudo.cpp
     read_pp.cpp
     read_pp_upf100.cpp
     read_pp_upf201.cpp

source/module_cell/atom_pseudo.cpp

@@ -239,7 +239,7 @@ void Atom_pseudo::bcast_atom_pseudo(void)
 	Parallel_Common::bcast_double( vloc_at, mesh);
 // == end of pseudo_vl ==
 
-// == pseudo_nc ==
+// == pseudo ==
 	if(GlobalV::MY_RANK != 0)
 	{
 		delete[] lll;

source/module_cell/atom_pseudo.h

@@ -7,10 +7,10 @@
 #include "../module_io/output.h"
 #include "../module_base/complexarray.h"
 #include "../module_base/complexmatrix.h"
-#include "pseudo_nc.h"
+#include "pseudo.h"
 
 
-class Atom_pseudo : public pseudo_nc
+class Atom_pseudo : public pseudo
 {
 public:
 

source/module_cell/module_symmetry/test/symmetry_test_analysis.cpp

@@ -20,8 +20,12 @@
  ***********************************************/
 // mock the useless functions
 void output::printM3(std::ofstream &ofs, const std::string &description, const ModuleBase::Matrix3 &m){}
-pseudo_nc::pseudo_nc(){}
-pseudo_nc::~pseudo_nc(){}
+pseudo::pseudo()
+{
+}
+pseudo::~pseudo()
+{
+}
 Atom::Atom(){}
 Atom::~Atom(){}
 Atom_pseudo::Atom_pseudo(){}

source/module_cell/module_symmetry/test/symmetry_test_symtrz.cpp

@@ -8,8 +8,8 @@
 ***********************************************/
 // mock the useless functions
 void output::printM3(std::ofstream& ofs, const std::string& description, const ModuleBase::Matrix3& m) {}
-pseudo_nc::pseudo_nc() {}
-pseudo_nc::~pseudo_nc() {}
+pseudo::pseudo() {}
+pseudo::~pseudo() {}
 Atom::Atom() {}
 Atom::~Atom() {}
 Atom_pseudo::Atom_pseudo() {}

source/module_cell/pseudo_nc.cpp renamed to source/module_cell/pseudo.cpp

@@ -1,6 +1,6 @@
-#include "pseudo_nc.h"
+#include "pseudo.h"
 
-pseudo_nc::pseudo_nc()
+pseudo::pseudo()
 {
 // pseudo_h
 	els = new std::string[1];
@@ -21,11 +21,11 @@ pseudo_nc::pseudo_nc()
 	rho_at = nullptr;
 	rho_atc = nullptr;
 
-// pseudo_nc
+// pseudo
 	lll = nullptr;
 }
 
-pseudo_nc::~pseudo_nc()
+pseudo::~pseudo()
 {
 // pseudo_h
 	delete[] els;
@@ -44,19 +44,19 @@ pseudo_nc::~pseudo_nc()
 	delete[] rho_at;
 	delete[] rho_atc;
 
-// pseudo_nc
+// pseudo
 	delete[] lll;
 }
 
 
 
 //---------------------------------------------------------------------
-void pseudo_nc::set_pseudo_nc(const Pseudopot_upf &upf)
+void pseudo::set_pseudo(const Pseudopot_upf& upf)
 {
-	ModuleBase::TITLE("pseudo_nc","set_pseudo_nc");
+    ModuleBase::TITLE("pseudo", "set_pseudo");
 
-	// call subroutines
-	this->set_pseudo_h(upf);
+    // call subroutines
+    this->set_pseudo_h(upf);
 	this->set_pseudo_atom(upf);
 	this->set_pseudo_vl(upf);
 
@@ -70,14 +70,9 @@ void pseudo_nc::set_pseudo_nc(const Pseudopot_upf &upf)
 		lll[i] = upf.lll[i];
 	}
 
-	kkbeta = 0;
+    kkbeta = upf.kkbeta;
 
-	for (int nb = 0;nb < nbeta;nb++)
-	{
-        kkbeta = (upf.kbeta[nb] > kkbeta) ? upf.kbeta[nb] : kkbeta;
-    }
-
-	betar.create(upf.beta.nr, upf.beta.nc);
+    betar.create(upf.beta.nr, upf.beta.nc);
 
 //	OUT("betar.nr",upf.beta.nr); // nbeta
 //	OUT("betar.nc",upf.beta.nc); // mesh
@@ -98,11 +93,10 @@ void pseudo_nc::set_pseudo_nc(const Pseudopot_upf &upf)
 	return;
 } // end subroutine set_pseudo_upf
 
-
-void pseudo_nc::print_pseudo_nc(std::ofstream &ofs)
+void pseudo::print_pseudo(std::ofstream& ofs)
 {
 	print_pseudo_vl(ofs);
-	ofs << "\n pseudo_nc : ";
+	ofs << "\n pseudo : ";
 	ofs << "\n kkbeta	" << kkbeta;
 	ofs << "\n nh  " << nh;
 	output::printr1_d(ofs, " lll : ", lll, nbeta);
@@ -112,9 +106,9 @@ void pseudo_nc::print_pseudo_nc(std::ofstream &ofs)
 }
 
 
-void pseudo_nc::set_pseudo_h(const Pseudopot_upf &upf)
+void pseudo::set_pseudo_h(const Pseudopot_upf &upf)
 {
-	ModuleBase::TITLE("pseudo_nc","set_pseudo_h");
+	ModuleBase::TITLE("pseudo","set_pseudo_h");
 	// set pseudopotential for each atom type
 	// by using the Unified Pseudopotential Format
 
@@ -221,9 +215,9 @@ void pseudo_nc::set_pseudo_h(const Pseudopot_upf &upf)
 } // end subroutine set_pseudo_upf
 
 
-void pseudo_nc::set_pseudo_atom(const Pseudopot_upf &upf)
+void pseudo::set_pseudo_atom(const Pseudopot_upf &upf)
 {
-	ModuleBase::TITLE("pseudo_nc","set_pseudo_atom");
+	ModuleBase::TITLE("pseudo","set_pseudo_atom");
 
 	// mohan 2009-12-15
 	// mohan update again 2011-05-23, 
@@ -323,9 +317,9 @@ void pseudo_nc::set_pseudo_atom(const Pseudopot_upf &upf)
 
 
 
-void pseudo_nc::set_pseudo_vl(const Pseudopot_upf &upf)
+void pseudo::set_pseudo_vl(const Pseudopot_upf &upf)
 {
-	ModuleBase::TITLE("pseudo_nc","set_pseudo_vl");
+	ModuleBase::TITLE("pseudo","set_pseudo_vl");
 
 	assert(mesh>0);//mohan add 2021-05-01
 
@@ -342,7 +336,7 @@ void pseudo_nc::set_pseudo_vl(const Pseudopot_upf &upf)
 } 
 
 
-void pseudo_nc::print_pseudo_atom(std::ofstream &ofs)
+void pseudo::print_pseudo_atom(std::ofstream &ofs)
 {
 	print_pseudo_h(ofs);
 	ofs << "\n pseudo_atom : ";
@@ -358,15 +352,15 @@ void pseudo_nc::print_pseudo_atom(std::ofstream &ofs)
 }
 
 
-void pseudo_nc::print_pseudo_vl(std::ofstream &ofs)
+void pseudo::print_pseudo_vl(std::ofstream &ofs)
 {
 	ofs << "\n pseudo_vl:";
 	print_pseudo_atom(ofs);
 	output::printr1_d(ofs, "vloc_at : ", vloc_at, mesh);
 	ofs << "\n ----------------------------------- ";
 }
 
-void pseudo_nc::print_pseudo_h(std::ofstream &ofs)
+void pseudo::print_pseudo_h(std::ofstream &ofs)
 {
     ofs << "\n pseudo_info :";
     ofs << "\n nv       " << nv;