Update source_cell module and agent governance (deepmodeling#7625)

* resolve the wrong dependency between klist and berryphase

* remove useless things

* replace ucell.lc with vector<int>

* change the name of a variable

* remove dependency of PARAM

* move test of magnetism

* update magnetism

* update agent governance check

* update agent governance check

* refactor(cell): centralize Magnetism::start_mag initialization in setup() and read_atom_positions()

### Why
Previously `Magnetism::start_mag` had no well-defined single owner for memory
allocation.  Even though `UnitCell::setup_cell()` happened to resize it, any
caller that invoked `unitcell::read_atom_positions()` directly (as most unit
tests did) was required to *externally* call
`ucell->magnet.start_mag.resize(ucell->ntype)` first.  This undocumented
implicit contract produced dozens of scattered, copy-paste pre-conditions
throughout the test harness and made the API easy to misuse.

### What
1. Proactive initialization in `UnitCell::setup()`
   - As soon as `ntype` is set, resize `start_mag` to `ntype_in` with value 0.0.
   - This covers every test helper that already goes through `setup()` so the
     callers no longer need to manually size and zero-initialize the vector.

2. Defensive auto-resize inside `unitcell::read_atom_positions()`
   - Before any access to `start_mag[it]`, check that its size matches
     `ucell.ntype` and resize if needed.
   - This guards the remaining code paths that set `ntype` by hand and
     guarantees the consumer owns its pre-conditions.

3. Removed the now-redundant explicit resize in `UnitCell::setup_cell()`.
   Kept the `assert(ntype > 0)` validity check; renumbered the following
   step comment from `(2)` to `(1)`.

4. Cleaned up ~20+ copies of the redundant preparatory lines across the
   test suites:
   - 7 `prepare_unitcell.h` helpers (source_cell, source_cell/module_neighbor,
     source_estate, source_estate/module_dm, source_lcao/module_hcontainer,
     source_io, source_io/test_serial): removed
     `ucell->magnet.start_mag.resize(ntype)` and the loop body
     `start_mag[it] = 0.0`.
   - Unit tests `unitcell_test.cpp`, `unitcell_test_pw.cpp` and
     `unitcell_test_setupcell.cpp`: removed the now-unnecessary "mandatory
     preliminaries" resize block before `read_atom_positions`.

### Files touched (12)
source/source_cell/unitcell.cpp
source/source_cell/read_atoms.cpp
source/source_cell/module_neighbor/test/prepare_unitcell.h
source/source_cell/test/prepare_unitcell.h
source/source_cell/test/unitcell_test.cpp
source/source_cell/test/unitcell_test_setupcell.cpp
source/source_cell/test_pw/unitcell_test_pw.cpp
source/source_estate/test/prepare_unitcell.h
source/source_estate/module_dm/test/prepare_unitcell.h
source/source_io/test/prepare_unitcell.h
source/source_io/test_serial/prepare_unitcell.h
source/source_lcao/module_hcontainer/test/prepare_unitcell.h

Behavior change: none; resize is idempotent and every removed site defaulted
to the same zero value the new helpers already use.

* fix bugs

---------

Co-authored-by: abacus_fixer <mohanchen@pku.eud.cn>

Author: mohanchen

source/source_cell/atom_spec.h

@@ -31,7 +31,7 @@ class Atom
     std::vector<int> l_nchi; // number of chi for each L
     int stapos_wf = 0;       // start position of wave functions
 
-    std::string label = "\0";                     // atomic symbol
+    std::string label;                            ///< 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>> taud;  // Direct coordinates of each atom in this type.
@@ -40,7 +40,7 @@ class Atom
     std::vector<ModuleBase::Vector3<double>> force; // force acting on each atom in this type.
     std::vector<ModuleBase::Vector3<double>> lambda; // Lagrange multiplier for each atom in this type. used in deltaspin
     std::vector<ModuleBase::Vector3<int>> constrain; // constrain for each atom in this type. used in deltaspin
-    std::string label_orb = "\0";                    // atomic Element symbol in the orbital file of lcao
+    std::string label_orb;                           ///< atomic element symbol in the orbital file of lcao
 
     std::vector<double> mag;
     std::vector<double> angle1; // spin angle, added by zhengdy-soc

source/source_cell/bcast_cell.cpp

@@ -81,7 +81,7 @@ namespace unitcell
             Parallel_Common::bcast_double(lat.a2[i]);
             Parallel_Common::bcast_double(lat.a3[i]);
             Parallel_Common::bcast_double(lat.latcenter[i]);
-            Parallel_Common::bcast_int(lat.lc[i]);
+            Parallel_Common::bcast_int(lat.lat_axis_free[i]);
         }
 
         // distribute superlattice vectors.
@@ -103,7 +103,11 @@ namespace unitcell
     {
     #ifdef __MPI
         MPI_Barrier(MPI_COMM_WORLD);
-        Parallel_Common::bcast_double(magnet.start_mag, ntype);
+        if (GlobalV::MY_RANK != 0)
+        {
+            magnet.start_mag.resize(ntype, 0.0);
+        }
+        Parallel_Common::bcast_double(magnet.start_mag.data(), ntype);
         if (PARAM.inp.nspin == 4) 
         {
             Parallel_Common::bcast_double(magnet.ux_[0]);

source/source_cell/magnetism.cpp

@@ -1,8 +1,5 @@
 #include "magnetism.h"
-
 #include "source_base/parallel_reduce.h"
-#include "source_io/module_parameter/parameter.h"
-//#include "source_estate/module_charge/charge.h"
 
 Magnetism::Magnetism()
 {
@@ -14,21 +11,23 @@ Magnetism::Magnetism()
 
 Magnetism::~Magnetism()
 {
-    delete[] start_mag;
 }
 
 void Magnetism::compute_mag(const double& omega,
-		const int& nrxx, 
-		const int& nxyz, 
-		const double* const * rho, 
+		const int& nrxx,
+		const int& nxyz,
+		const double* const * rho,
+		const int& nspin,
+		const bool& two_fermi,
+		const double& nelec,
 		double* nelec_spin)
 {
     assert(omega>0.0);
     assert(nxyz>0);
 
     const double fac = omega / nxyz;
 
-    if (PARAM.inp.nspin==2)
+    if (nspin==2)
     {
         this->tot_mag = 0.00;
         this->abs_mag = 0.00;
@@ -51,17 +50,17 @@ void Magnetism::compute_mag(const double& omega,
 
 		//update number of electrons for each spin
 		//if TWO_EFERMI, no need to update
-		if(!PARAM.globalv.two_fermi)
+		if(!two_fermi)
 		{
-			nelec_spin[0] = (PARAM.inp.nelec + this->tot_mag) / 2;
-			nelec_spin[1] = (PARAM.inp.nelec - this->tot_mag) / 2;
+			nelec_spin[0] = (nelec + this->tot_mag) / 2;
+			nelec_spin[1] = (nelec - this->tot_mag) / 2;
 			ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"Electron number for spin up", nelec_spin[0]);
 			ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"Electron number for spin down", nelec_spin[1]);
 		}
     }
 
 	// noncolliear :
-	else if(PARAM.inp.nspin==4)
+	else if(nspin==4)
 	{
 		for(int i=0;i<3;i++) 
 		{

source/source_cell/magnetism.h

@@ -3,6 +3,7 @@
 
 #include "source_base/global_function.h"
 #include "source_base/vector3.h"
+#include <vector>
 
 class Magnetism
 {
@@ -12,7 +13,7 @@ class Magnetism
     ~Magnetism();
 
     // notice : bcast (MPI operation) is done in unitcell
-    double *start_mag=nullptr;
+    std::vector<double> start_mag;
 
     // tot_mag : majority spin - minority spin (nelup - neldw).
     double tot_mag;
@@ -22,16 +23,13 @@ class Magnetism
     double abs_mag;
 
 	void compute_mag(const double& omega,
-			const int& nrxx, 
-			const int& nxyz, 
-			const double* const * rho, 
-			double* nelec_spin = nullptr);
-
-    ModuleBase::Vector3<double> *m_loc_=nullptr; //magnetization for each element along c-axis
-
-	double *angle1_=nullptr;                     //angle between c-axis and real spin std::vector
-
-	double *angle2_=nullptr;                     //angle between a-axis and real spin std::vector projection in ab-plane
+			const int& nrxx,
+			const int& nxyz,
+			const double* const * rho,
+			const int& nspin,
+			const bool& two_fermi,
+			const double& nelec,
+			double* nelec_spin);
 
     double ux_[3]={0.0};
 

source/source_cell/module_neighbor/test/prepare_unitcell.h

@@ -77,13 +77,11 @@ class UcellTestPrepare
 				this->init_vel,
 				this->fixed_axes);
 
-		delete[] ucell->magnet.start_mag; //mag set here
 		ucell->atom_label.resize(ucell->ntype);
 		ucell->atom_mass.resize(ucell->ntype);
 		ucell->pseudo_fn.resize(ucell->ntype);
 		ucell->pseudo_type.resize(ucell->ntype);
 		ucell->orbital_fn.resize(ucell->ntype);
-		ucell->magnet.start_mag = new double[ucell->ntype]; //mag set here
 		ucell->magnet.ux_[0] = 0.0; // ux_ set here
 		ucell->magnet.ux_[1] = 0.0;
 		ucell->magnet.ux_[2] = 0.0;
@@ -94,7 +92,6 @@ class UcellTestPrepare
 			ucell->pseudo_fn[it] = this->pp_files[it];
 			ucell->pseudo_type[it] = this->pp_types[it];
 			ucell->orbital_fn[it] = this->orb_files[it];
-			ucell->magnet.start_mag[it] = 0.0; //mag set here
 		}
 		//lattice info
 		ucell->lat0 = this->lat0;

source/source_cell/module_neighbor/test/sltk_atom_arrange_test.cpp

@@ -28,11 +28,9 @@ Magnetism::Magnetism()
 {
     this->tot_mag = 0.0;
     this->abs_mag = 0.0;
-    this->start_mag = nullptr;
 }
 Magnetism::~Magnetism()
 {
-    delete[] this->start_mag;
 }
 
 /************************************************

source/source_cell/module_neighbor/test/sltk_grid_test.cpp

@@ -25,11 +25,9 @@ Magnetism::Magnetism()
 {
     this->tot_mag = 0.0;
     this->abs_mag = 0.0;
-    this->start_mag = nullptr;
 }
 Magnetism::~Magnetism()
 {
-    delete[] this->start_mag;
 }
 
 /************************************************

source/source_cell/read_atoms.cpp

@@ -25,6 +25,11 @@ bool unitcell::read_atom_positions(UnitCell& ucell,
     const int nspin = PARAM.inp.nspin;
     assert (nspin==1 || nspin==2 || nspin==4);
 
+    if (ucell.magnet.start_mag.size() != static_cast<size_t>(ntype))
+    {
+        ucell.magnet.start_mag.resize(ntype, 0.0);
+    }
+
     if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifpos, "ATOMIC_POSITIONS"))
     {
         ModuleBase::GlobalFunc::READ_VALUE(ifpos, Coordinate);

source/source_cell/test/CMakeLists.txt

@@ -4,6 +4,14 @@ abacus_disable_feature_definitions(__ROCM)
 abacus_disable_feature_definitions(__EXX)
 
 find_program(BASH bash)
+file(COPY support DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+configure_file(bcast_atom_pseudo_test.sh ${CMAKE_CURRENT_BINARY_DIR}/bcast_atom_pseudo_test.sh COPYONLY)
+configure_file(bcast_atom_spec_test.sh ${CMAKE_CURRENT_BINARY_DIR}/bcast_atom_spec_test.sh COPYONLY)
+configure_file(parallel_kpoints_test.sh ${CMAKE_CURRENT_BINARY_DIR}/parallel_kpoints_test.sh COPYONLY)
+configure_file(klist_test_para.sh ${CMAKE_CURRENT_BINARY_DIR}/klist_test_para.sh COPYONLY)
+configure_file(unitcell_test_parallel.sh ${CMAKE_CURRENT_BINARY_DIR}/unitcell_test_parallel.sh COPYONLY)
+configure_file(bcast_read_sep_test.sh ${CMAKE_CURRENT_BINARY_DIR}/bcast_read_sep_test.sh COPYONLY)
+configure_file(bcast_sep_cell_test.sh ${CMAKE_CURRENT_BINARY_DIR}/bcast_sep_cell_test.sh COPYONLY)
 install(DIRECTORY support DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 install(FILES bcast_atom_pseudo_test.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 install(FILES bcast_atom_spec_test.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
@@ -193,3 +201,9 @@ add_test(NAME MODULE_CELL_sep_cell_parallel
       COMMAND ${BASH} bcast_sep_cell_test.sh
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 )
+
+AddTest(
+  TARGET MODULE_CELL_magnetism
+  LIBS base device
+  SOURCES magnetism_test.cpp ../magnetism.cpp
+)

…estate/test/elecstate_magnetism_test.cpp …urce/source_cell/test/magnetism_test.cppsource/source_estate/test/elecstate_magnetism_test.cpp renamed to source/source_cell/test/magnetism_test.cpp source/source_estate/test/elecstate_magnetism_test.cpp renamed to source/source_cell/test/magnetism_test.cpp

@@ -6,10 +6,6 @@
 // mohan add 2025-04-12
 #include "source_estate/module_charge/charge.h"
 
-#define private public
-#include "source_io/module_parameter/parameter.h"
-#undef private
-
 /************************************************
  *  unit test of magnetism.cpp
  ***********************************************/
@@ -20,8 +16,8 @@
  *   - Magnetism::~Magnetism()
  *   - Magnetism::judge_parallel()
  *   - Magnetism::compute_mag()
- *      - compute mag for spin-polarized system when PARAM.input.nspin = 2
- *      - and non-collinear case with PARAM.input.nspin = 4 
+ *      - compute mag for spin-polarized system when nspin = 2
+ *      - and non-collinear case with nspin = 4
 */
 
 #define private public
@@ -53,7 +49,7 @@ TEST_F(MagnetismTest, Magnetism)
 {
     EXPECT_EQ(0.0, magnetism->tot_mag);
     EXPECT_EQ(0.0, magnetism->abs_mag);
-    EXPECT_EQ(nullptr, magnetism->start_mag);
+    EXPECT_TRUE(magnetism->start_mag.empty());
 }
 
 TEST_F(MagnetismTest, JudgeParallel)
@@ -67,15 +63,15 @@ TEST_F(MagnetismTest, JudgeParallel)
 
 TEST_F(MagnetismTest, ComputeMagnetizationS2)
 {
-	PARAM.input.nspin = 2;
-	PARAM.sys.two_fermi = false;
-	PARAM.input.nelec = 10.0;
+	const int nspin = 2;
+	const bool two_fermi = false;
+	const double nelec = 10.0;
 
 	Charge* chr = new Charge;
 	chr->nrxx = 100;
 	chr->nxyz = 1000;
-	chr->rho = new double*[PARAM.input.nspin];
-	for (int i=0; i< PARAM.input.nspin; i++)
+	chr->rho = new double*[nspin];
+	for (int i=0; i< nspin; i++)
 	{
 		chr->rho[i] = new double[chr->nrxx];
 	}
@@ -85,13 +81,14 @@ TEST_F(MagnetismTest, ComputeMagnetizationS2)
 		chr->rho[1][ir] = 1.01;
 	}
 	double* nelec_spin = new double[2];
-	magnetism->compute_mag(500.0,chr->nrxx, chr->nxyz, chr->rho, nelec_spin);
+	magnetism->compute_mag(500.0,chr->nrxx, chr->nxyz, chr->rho,
+	                       nspin, two_fermi, nelec, nelec_spin);
 	EXPECT_DOUBLE_EQ(-0.5, magnetism->tot_mag);
 	EXPECT_DOUBLE_EQ(0.5, magnetism->abs_mag);
 	EXPECT_DOUBLE_EQ(4.75, nelec_spin[0]);
 	EXPECT_DOUBLE_EQ(5.25, nelec_spin[1]);
 	delete[] nelec_spin;
-	for (int i=0; i< PARAM.input.nspin; i++)
+	for (int i=0; i< nspin; i++)
 	{
 		delete[] chr->rho[i];
 	}
@@ -101,13 +98,13 @@ TEST_F(MagnetismTest, ComputeMagnetizationS2)
 
 TEST_F(MagnetismTest, ComputeMagnetizationS4)
 {
-	PARAM.input.nspin = 4;
+	const int nspin = 4;
 
 	Charge* chr = new Charge;
-	chr->rho = new double*[PARAM.input.nspin];
+	chr->rho = new double*[nspin];
 	chr->nrxx = 100;
 	chr->nxyz = 1000;
-	for (int i=0; i< PARAM.input.nspin; i++)
+	for (int i=0; i< nspin; i++)
 	{
 		chr->rho[i] = new double[chr->nrxx];
 	}
@@ -119,13 +116,14 @@ TEST_F(MagnetismTest, ComputeMagnetizationS4)
 		chr->rho[3][ir] = 1.00;
 	}
 	double* nelec_spin = new double[4];
-	magnetism->compute_mag(500.0,chr->nrxx, chr->nxyz, chr->rho, nelec_spin);
+	magnetism->compute_mag(500.0,chr->nrxx, chr->nxyz, chr->rho,
+	                       nspin, false, 0.0, nelec_spin);
 	EXPECT_DOUBLE_EQ(100.0, magnetism->abs_mag);
 	EXPECT_DOUBLE_EQ(50.0*std::sqrt(2.0), magnetism->tot_mag_nc[0]);
 	EXPECT_DOUBLE_EQ(50.0, magnetism->tot_mag_nc[1]);
 	EXPECT_DOUBLE_EQ(50.0, magnetism->tot_mag_nc[2]);
 	delete[] nelec_spin;
-	for (int i=0; i< PARAM.input.nspin; i++)
+	for (int i=0; i< nspin; i++)
 	{
 		delete[] chr->rho[i];
 	}
@@ -135,18 +133,20 @@ TEST_F(MagnetismTest, ComputeMagnetizationS4)
 
 #ifdef __MPI
 #include <mpi.h>
+#include "source_base/parallel_comm.h"
 int main(int argc, char **argv)
 {
-
     MPI_Init(&argc, &argv);
-    MPI_Comm_size(MPI_COMM_WORLD,&GlobalV::NPROC);
-    MPI_Comm_rank(MPI_COMM_WORLD,&GlobalV::MY_RANK);
+    MPI_Comm_size(MPI_COMM_WORLD, &GlobalV::NPROC);
+    MPI_Comm_rank(MPI_COMM_WORLD, &GlobalV::MY_RANK);
+    MPI_Comm_dup(MPI_COMM_WORLD, &POOL_WORLD);
 
     testing::InitGoogleTest(&argc, argv);
     int result = RUN_ALL_TESTS();
 
+    MPI_Comm_free(&POOL_WORLD);
     MPI_Finalize();
-
     return result;
 }
 #endif
+