Feature : added paw_cell_libpaw and test (#2815)

* added some subroutines for info gathering

* added paw_cell_libpaw and test

* added explanations on unit tests

---------

Co-authored-by: wenfei-li <[email protected]>

Author: wenfei-li

source/module_cell/module_paw/CMakeLists.txt

@@ -4,6 +4,7 @@ add_library(
     paw_element.cpp
     paw_sphbes.cpp
     paw_cell.cpp
+    paw_cell_libpaw.cpp
 )
 
 if(ENABLE_COVERAGE)

source/module_cell/module_paw/paw_cell.h

@@ -12,6 +12,7 @@
 
 #include "paw_element.h"
 #include "paw_atom.h"
+#include "module_base/matrix3.h"
 
 class Paw_Cell
 {
@@ -20,6 +21,8 @@ class Paw_Cell
     Paw_Cell(){};
     ~Paw_Cell(){};
 
+// PART I. Operations in ABACUS
+
     void init_paw_cell(
         const double ecutwfc_in, const double cell_factor_in,
         const double omega_in,
@@ -151,6 +154,63 @@ class Paw_Cell
 
     void set_ylm(const int npw_in, const double ** kpg);
 
+// Part II. Passing infor for the initialization of PAW
+
+    public:
+    // The following gathers information needed by LibPAW, they will be inserted
+    // to proper places in the main program
+
+    // Cutoff energies, sets ecut and ecutpaw
+    void set_libpaw_ecut(const double ecut_in, const double ecutpaw_in);
+    // Sets rprimd, gprimd, gmet and ucvol
+    // Input is latvec and lat0, will calculate the required info
+    void set_libpaw_cell(const ModuleBase::Matrix3 latvec, const double lat0);
+    // FFT grid information, sets ngfft and ngfftdg
+    void set_libpaw_fft(const int nx_in, const int ny_in, const int nz_in,
+        const int nxdg_in, const int nydg_in, const int nzdg_in);
+    // Sets natom, ntypat, typat and xred
+    void set_libpaw_atom(const int natom_in, const int ntypat_in, const int * typat_in, const double * xred_in);
+    // Sets filename_list
+    void set_libpaw_files();
+    
+    // Extract the information
+    double get_libpaw_ecut() {return ecut;}
+    double get_libpaw_ecutpaw() {return ecutpaw;}
+    std::vector<double> get_libpaw_rprimd() {return rprimd;}
+    std::vector<double> get_libpaw_gprimd() {return gprimd;}
+    std::vector<double> get_libpaw_gmet() {return gmet;}
+    double get_libpaw_ucvol() {return ucvol;}
+    std::vector<int> get_libpaw_ngfft() {return ngfft;}
+    std::vector<int> get_libpaw_ngfftdg() {return ngfftdg;}
+    int get_libpaw_natom() {return natom;}
+    int get_libpaw_ntypat() {return ntypat;}
+    std::vector<int> get_libpaw_typat() {return typat;}
+    std::vector<double> get_libpaw_xred() {return xred;}
+    char* get_libpaw_filename_list() {return filename_list;}
+
+    private:
+// Info to be passed to libpaw_interface:
+// 1. ecut, ecutpaw : kinetic energy cutoff of the planewave basis set
+// there will be one coarse grid for density/potential, and a fine grid for PAW
+// the unit is in Hartree
+// 2. rprimd, gprimd : real and reciprocal space lattice vectors, respectively
+// unit for rprimd is in Bohr, and for gprimd is in Bohr^-1
+// 3. gmet : reciprocal space metric (bohr^-2)
+// 4. ucvol : volume of unit cell (Bohr^3)
+// 5. ngfft, ngfftdg : dimension of FFT grids of the corase and fine grids
+// 6. natom, ntypat, typat: #. atoms, #. element types
+// and typat records the type of each atom
+// 7. xred : coordinate of each atom, in terms of rprimd (namely, direct coordinate)
+// 8. filename_list : filename of the PAW xml files for each element
+
+    double ecut, ecutpaw;
+    std::vector<double> rprimd, gprimd, gmet;
+    double ucvol;
+    std::vector<int> ngfft, ngfftdg;
+    int natom, ntypat;
+    std::vector<int> typat;
+    std::vector<double> xred;
+    char* filename_list;
 };
 
 #endif

source/module_cell/module_paw/paw_cell_libpaw.cpp

@@ -0,0 +1,206 @@
+#include "module_base/tool_quit.h"
+#include "module_base/tool_title.h"
+#include "paw_cell.h"
+#include "module_base/global_variable.h"
+
+// The subroutines here are used to gather information from the main ABACUS program
+// 1. ecut, ecutpaw : kinetic energy cutoff of the planewave basis set
+// there will be one coarse grid for density/potential, and a fine grid for PAW
+// the unit is in Hartree
+// 2. rprimd, gprimd : real and reciprocal space lattice vectors, respectively
+// unit for rprimd is in Bohr, and for gprimd is in Bohr^-1
+// 3. gmet : reciprocal space metric (bohr^-2)
+// 4. ucvol : volume of unit cell (Bohr^3)
+// 5. ngfft, ngfftdg : dimension of FFT grids of the corase and fine grids
+// 6. natom, ntypat, typat: #. atoms, #. element types
+// and typat records the type of each atom
+// 7. xred : coordinate of each atom, in terms of rprimd (namely, direct coordinate)
+// 8. filename_list : filename of the PAW xml files for each element
+
+// Cutoff energies, sets ecut and ecutpaw
+void Paw_Cell::set_libpaw_ecut(const double ecut_in, const double ecutpaw_in)
+{
+    ModuleBase::TITLE("Paw_Cell", "set_libpaw_ecut");
+    ecut = ecut_in;
+    ecutpaw = ecutpaw_in;
+}
+
+// inverse of 3 by 3 matrix, needed by set_libpaw_cell to calculate gprimd
+// adapted from m_symtk/matr3inv of ABINIT
+
+void matr3inv(std::vector<double>& mat_in, std::vector<double>& mat_out)
+{
+
+    assert(mat_in.size() == 9);
+    assert(mat_out.size() == 9);
+
+    double t1 = mat_in[4] * mat_in[8] - mat_in[7] * mat_in[5];
+    double t2 = mat_in[7] * mat_in[2] - mat_in[1] * mat_in[8];
+    double t3 = mat_in[1] * mat_in[5] - mat_in[4] * mat_in[2];
+    double det = mat_in[0] * t1 + mat_in[3] * t2 + mat_in[6] * t3;
+
+    double dd;
+    if (std::abs(det) > 1e-16)
+    {
+        dd = 1.0 / det;
+    }
+    else
+    {
+        ModuleBase::WARNING_QUIT("matr3inv", "matrix is singular!");
+    }
+
+    mat_out[0] = t1 * dd;
+    mat_out[3] = t2 * dd;
+    mat_out[6] = t3 * dd;
+    mat_out[1] = (mat_in[6] * mat_in[5] - mat_in[3] * mat_in[8]) * dd;
+    mat_out[4] = (mat_in[0] * mat_in[8] - mat_in[6] * mat_in[2]) * dd;
+    mat_out[7] = (mat_in[3] * mat_in[2] - mat_in[0] * mat_in[5]) * dd;
+    mat_out[2] = (mat_in[3] * mat_in[7] - mat_in[6] * mat_in[4]) * dd;
+    mat_out[5] = (mat_in[6] * mat_in[1] - mat_in[0] * mat_in[7]) * dd;
+    mat_out[8] = (mat_in[0] * mat_in[4] - mat_in[3] * mat_in[1]) * dd;
+}
+
+// calculates G = A^T A for 3 by 3 matrix
+// G_ij = sum_k A_ki A_kj
+
+void mattmat(std::vector<double>& mat_in, std::vector<double>& mat_out)
+{
+    mat_out[0] = mat_in[0] * mat_in[0] + mat_in[1] * mat_in[1] + mat_in[2] * mat_in[2];
+    mat_out[1] = mat_in[0] * mat_in[3] + mat_in[1] * mat_in[4] + mat_in[2] * mat_in[5];
+    mat_out[2] = mat_in[0] * mat_in[6] + mat_in[1] * mat_in[7] + mat_in[2] * mat_in[8];
+    mat_out[3] = mat_in[3] * mat_in[0] + mat_in[4] * mat_in[1] + mat_in[5] * mat_in[2];
+    mat_out[4] = mat_in[3] * mat_in[3] + mat_in[4] * mat_in[4] + mat_in[5] * mat_in[5];
+    mat_out[5] = mat_in[3] * mat_in[6] + mat_in[4] * mat_in[7] + mat_in[5] * mat_in[8];
+    mat_out[6] = mat_in[6] * mat_in[0] + mat_in[7] * mat_in[1] + mat_in[8] * mat_in[2];
+    mat_out[7] = mat_in[6] * mat_in[3] + mat_in[7] * mat_in[4] + mat_in[8] * mat_in[5];
+    mat_out[8] = mat_in[6] * mat_in[6] + mat_in[7] * mat_in[7] + mat_in[8] * mat_in[8];
+}
+
+// Sets rprimd, gprimd, gmet and ucvol
+// Only real space lattice vector needed, others are to be calculated
+void Paw_Cell::set_libpaw_cell(const ModuleBase::Matrix3 latvec, const double lat0)
+{
+    ModuleBase::TITLE("Paw_Cell", "set_libpaw_cell");
+
+    rprimd.resize(9);
+    gprimd.resize(9);
+    gmet.resize(9);
+
+    rprimd[0] = latvec.e11 * lat0;
+    rprimd[1] = latvec.e12 * lat0;
+    rprimd[2] = latvec.e13 * lat0;
+    rprimd[3] = latvec.e21 * lat0;
+    rprimd[4] = latvec.e22 * lat0;
+    rprimd[5] = latvec.e23 * lat0;
+    rprimd[6] = latvec.e31 * lat0;
+    rprimd[7] = latvec.e32 * lat0;
+    rprimd[8] = latvec.e33 * lat0;
+
+    // calculating gprimd, gmet and ucvol, adapted from m_geometry/metric of ABINIT
+
+    // Compute first dimensional primitive translation vectors in reciprocal space
+    // gprimd from rprimd
+    // Then, computes metrics for real and recip space rmet and gmet using length
+    // dimensional primitive translation vectors in columns of rprimd(3,3) and gprimd(3,3).
+    //  gprimd is the inverse transpose of rprimd.
+    //  i.e. $ rmet_{i,j}= \sum_k ( rprimd_{k,i}*rprimd_{k,j} )  $
+    //       $ gmet_{i,j}= \sum_k ( gprimd_{k,i}*gprimd_{k,j} )  $
+    // Also computes unit cell volume ucvol in $\textrm{bohr}^3$
+
+    // Compute unit cell volume
+    // ucvol=rprimd(1,1)*(rprimd(2,2)*rprimd(3,3)-rprimd(3,2)*rprimd(2,3))+&
+    //       rprimd(2,1)*(rprimd(3,2)*rprimd(1,3)-rprimd(1,2)*rprimd(3,3))+&
+    //       rprimd(3,1)*(rprimd(1,2)*rprimd(2,3)-rprimd(2,2)*rprimd(1,3))
+    ucvol = rprimd[0] * (rprimd[4] * rprimd[8] - rprimd[7] * rprimd[5])
+            + rprimd[3] * (rprimd[7] * rprimd[2] - rprimd[1] * rprimd[8])
+            + rprimd[6] * (rprimd[1] * rprimd[5] - rprimd[4] * rprimd[2]);
+    // ucvol = det3r(rprimd)
+
+    if (std::abs(ucvol) < 1e-12)
+    {
+        ModuleBase::WARNING_QUIT("set_libpaw_cell", "ucvol vanishingly small");
+    }
+
+    // ABACUS allows negative volume, but it seems ABINIT do not
+    // I am not quite sure why, but to avoid possible complications I will follow ABINIT here
+    // as the user can always just exchange two axis to make it positive
+    if (ucvol < 0)
+    {
+        ModuleBase::WARNING_QUIT("set_libpaw_cell", "ucvol negative, one way to solve is to exchange two cell axis");
+    }
+
+    // Generate gprimd
+    matr3inv(rprimd, gprimd);
+
+    // Compute reciprocal space metric.
+    mattmat(gprimd, gmet);
+}
+
+// FFT grid information, sets ngfft and ngfftdg
+void Paw_Cell::set_libpaw_fft(const int nx_in, const int ny_in, const int nz_in,
+        const int nxdg_in, const int nydg_in, const int nzdg_in)
+{
+    ngfft.resize(3);
+    ngfftdg.resize(3);
+
+    ngfft[0] = nx_in;
+    ngfft[1] = ny_in;
+    ngfft[2] = nz_in;
+    ngfftdg[0] = nxdg_in;
+    ngfftdg[1] = nydg_in;
+    ngfftdg[2] = nzdg_in;
+}
+
+// Sets natom, ntypat, typat and xred
+// !!!!!!!Note : the index stored in typat here will start from 1, not 0 !!!!!!
+void Paw_Cell::set_libpaw_atom(const int natom_in, const int ntypat_in, const int* typat_in, const double* xred_in)
+{
+    natom = natom_in;
+    ntypat = ntypat_in;
+
+    typat.resize(natom);
+    xred.resize(3 * natom);
+    
+    for(int iat = 0; iat < natom; iat ++)
+    {
+        typat[iat] = typat_in[iat];
+        for(int j = 0; j < 3; j ++)
+        {
+          xred[3 * iat + j] = xred_in[3 * iat + j];
+        }
+    }
+}
+
+// Sets filename_list
+// I'm going to read directly from STRU file
+void Paw_Cell::set_libpaw_files()
+{
+    ModuleBase::TITLE("Paw_Cell", "set_libpaw_files");
+
+    if(GlobalV::MY_RANK == 0)
+    {
+        std::ifstream ifa(GlobalV::stru_file.c_str(), std::ios::in);
+        if (!ifa)
+        {
+            ModuleBase::WARNING_QUIT("set_libpaw_files", "can not open stru file");
+        }
+
+        std::string line;
+        while(!ifa.eof())
+        {
+            getline(ifa,line);
+            if (line.find("PAW_FILES") != std::string::npos) break;
+        }
+
+        filename_list = new char[ntypat*264];
+        for(int i = 0; i < ntypat; i++)
+        {
+            std::string filename;
+            ifa >> filename;
+            for(int j = 0; j < filename.size(); j++)
+            {
+                filename_list[264*i+j] = filename[j];
+            }
+        }
+    }
+}

source/module_cell/module_paw/test/CMakeLists.txt

@@ -6,6 +6,7 @@ install(FILES sphbes_ref.dat func.dat qlist.dat fq_ref.dat
   eigts.dat ca.dat rhoij.dat vkb_ref.dat
   Si_test.xml gnorm.dat ptilde_ref.dat psi.dat rhoij1.dat
   H.LDA_PW-JTH.xml Fe.GGA_PBE-JTH.xml O.GGA_PBE-JTH.xml Si.GGA_PBE-JTH.xml
+  STRU
   DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
 AddTest(
@@ -24,4 +25,10 @@ AddTest(
   TARGET Test_Paw2
   LIBS ${math_libs} base device
   SOURCES test_paw2.cpp ../paw_atom.cpp
+)
+
+AddTest(
+  TARGET Test_Paw3
+  LIBS ${math_libs} base device
+  SOURCES test_paw3.cpp ../paw_atom.cpp ../paw_cell_libpaw.cpp
 )

source/module_cell/module_paw/test/STRU

@@ -0,0 +1,3 @@
+PAW_FILES
+C.xml
+H.xml

source/module_cell/module_paw/test/test_paw.cpp

@@ -3,6 +3,19 @@
 
 #include "../paw_element.h"
 
+/*
+Subroutines related to the processing of PAW xml files:
+
+1. init_paw_element, which prepares some related values
+2. read_paw_xml, which reads the xml file and stores the information
+
+plus subroutines related to the processing of projector functions:
+1. spherical_bessel_function: helper functions, returns values of spherical bessel functions
+2. spherical_bessel_transform: carries out spherical bessel transform
+3. splint and spline: performs cubic spline interpolation
+
+*/
+
 class Test_Read_Paw : public testing::Test
 {
     protected:

source/module_cell/module_paw/test/test_paw1.cpp

@@ -3,6 +3,19 @@
 
 #include "../paw_cell.h"
 
+/*
+Unit Test for subroutines related to the calculation of rhoij,
+where reciprocal space wavefunctions are passed from outside, and rhoij is calculated:
+
+1. init_paw_cell and set_paw_k, which collects necessary information
+2. accumulate_rhoij, which calculates sum_n <psi_n|p_i><p_j|psi_n>
+
+plus two mathematical subroutines:
+3. calc_ylm, which gives values of spherical harmonics
+4. ass_leg_pol, which gives values of legendre polynomials
+
+*/
+
 class Test_Paw_Cell : public testing::Test
 {
     protected:

source/module_cell/module_paw/test/test_paw2.cpp

@@ -3,6 +3,15 @@
 #include <iostream>
 
 #include "../paw_atom.h"
+/*
+
+Unit Test for subroutines related to the processing of rhoij,
+the on-site density matrix to be used for PAW:
+1. set_ca, which passes <psi|ptilde> from outside and saves it
+2. accumulate_rhoij, which accumulates the contribution of one band
+3. convert_rhoij, which converts rhoij to format required by PAW
+
+*/
 
 class Test_Paw_Atom : public testing::Test
 {