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

Author: wenfei-li

docs/examples/phonopy.md

@@ -3,7 +3,7 @@
 [back to main page](../../README.md)
 
 
-[Phonopy](https://github.com/phonopy/phonopy) is a powerful package to calculate phonon and related properties. It has provided interface with ABACUS. In the following, we take the FCC aluminum as an example:
+[Phonopy](https://github.com/phonopy/phonopy) (Note: please use the `develop` branch, rather than the `master` branch until the abacus interface has been merged into phonopy's `master` branch.) is a powerful package to calculate phonon and related properties. It has provided interface with ABACUS. In the following, we take the FCC aluminum as an example:
 
 
 1. Prepare a 'setting.conf' with following tags:
@@ -39,4 +39,4 @@ PRIMITIVE_AXES = 0 1/2 1/2  1/2 0 1/2  1/2 1/2 0
 BAND= 1 1 1  1/2 1/2 1  3/8 3/8 3/4  0 0 0   1/2 1/2 1/2
 BAND_POINTS = 21
 BAND_CONNECTION = .TRUE.
-```
+```

docs/features.md

@@ -50,9 +50,14 @@ ATOMIC_SPECIES
 Si 28.00 Si_ONCV_PBE-1.0.upf
 ```
 
-The user can download the pseudopotential files from our [website](http://abacus.ustc.edu.cn/pseudo.html).
+You can download the pseudopotential files from our [website](http://abacus.ustc.edu.cn/pseudo/list.htm).
 
-For more information of different types of pseudopotentials, please visit the Quantum espresso [website](http://www.quantum-espresso.org/pseudopotentials/).
+There are pseudopotential files in these websites which are also supported by ABACUS:
+1. [Quantum ESPRESSO](http://www.quantum-espresso.org/pseudopotentials/).
+2. [SG15-ONCV](http://quantum-simulation.org/potentials/sg15_oncv/upf/).
+3. [DOJO](http://www.pseudo-dojo.org/).
+
+If LCAO base is used, the numerical orbital files should match the pseudopotential files. The [official orbitals package](http://abacus.ustc.edu.cn/pseudo/list.htm) only matches SG15-ONCV pseudopotentials.
 
 [back to top](#features)
 

docs/input-main.md

@@ -158,7 +158,10 @@ This part of variables are used to control general system parameters.
 #### symmetry
 
 - **Type**: Integer
-- **Description**: takes value 0 and 1, if set to 1, symmetry analysis will be performed to determine the type of Bravais lattice and associated symmetry operations.
+- **Description**: takes value 1, 0 and -1. 
+  - if set to 1, symmetry analysis will be performed to determine the type of Bravais lattice and associated symmetry operations. (point groups only)
+  - if set to 0, only time reversal symmetry would be considered in symmetry operations, which implied k point and -k point would be treated as one double weight k point.
+  - if set to -1, any symmetry will not be considered.
 - **Default**: 0
 
 #### kpar

source/input.cpp

@@ -177,7 +177,7 @@ void Input::Default(void)
     ks_solver = "default"; // xiaohui add 2013-09-01
     search_radius = -1.0; // unit: a.u. -1.0 has no meaning.
     search_pbc = true;
-    symmetry = false;
+    symmetry = 0;
     init_vel = false;
     symmetry_prec = 1.0e-5; // LiuXh add 2021-08-12, accuracy for symmetry
     cal_force = 0;
@@ -2015,7 +2015,7 @@ void Input::Bcast()
     Parallel_Common::bcast_double(search_radius);
     Parallel_Common::bcast_bool(search_pbc);
     Parallel_Common::bcast_double(search_radius);
-    Parallel_Common::bcast_bool(symmetry);
+    Parallel_Common::bcast_int(symmetry);
     Parallel_Common::bcast_bool(init_vel); // liuyu 2021-07-14
     Parallel_Common::bcast_double(symmetry_prec); // LiuXh add 2021-08-12, accuracy for symmetry
     Parallel_Common::bcast_int(cal_force);
@@ -2451,7 +2451,7 @@ void Input::Check(void)
     else if (calculation == "md" || calculation == "sto-md") // mohan add 2011-11-04
     {
         GlobalV::CALCULATION = calculation;
-        symmetry = false;
+        symmetry = 0;
         cal_force = 1;
         if (mdp.md_nstep == 0)
         {

source/input.h

@@ -46,7 +46,11 @@ class Input
 
     bool init_vel; // read velocity from STRU or not  liuyu 2021-07-14
 
-    bool symmetry; // turn on symmetry or not
+    /* symmetry level: 
+      -1, no symmetry at all; 
+      0, only basic time reversal would be considered; 
+      1, point group symmetry would be considered*/
+    int symmetry; 
     double symmetry_prec; // LiuXh add 2021-08-12, accuracy for symmetry
     int kpar; // ecch pool is for one k point
 

source/input_conv.cpp

@@ -373,6 +373,7 @@ void Input_Conv::Convert(void)
 
     if (GlobalC::exx_global.info.hybrid_type != Exx_Global::Hybrid_Type::No)
     {
+        //EXX case, convert all EXX related variables 
         GlobalC::exx_global.info.hybrid_alpha = INPUT.exx_hybrid_alpha;
         XC_Functional::get_hybrid_alpha(INPUT.exx_hybrid_alpha);
         GlobalC::exx_global.info.hse_omega = INPUT.exx_hse_omega;
@@ -406,6 +407,9 @@ void Input_Conv::Convert(void)
         Exx_Abfs::Jle::Lmax = INPUT.exx_opt_orb_lmax;
         Exx_Abfs::Jle::Ecut_exx = INPUT.exx_opt_orb_ecut;
         Exx_Abfs::Jle::tolerence = INPUT.exx_opt_orb_tolerence;
+
+        //EXX does not support any symmetry analyse, force symmetry setting to -1
+        ModuleSymmetry::Symmetry::symm_flag = -1;
     }
 #endif
 #endif

source/module_elecstate/elecstate_lcao.cpp

@@ -137,7 +137,9 @@ void ElecStateLCAO::print_psi(const psi::Psi<double>& psi_in)
 
     // output but not do "2d-to-grid" conversion
     double** wfc_grid = nullptr;
+#ifdef __MPI
     this->lowf->wfc_2d_to_grid(ElecStateLCAO::out_wfc_lcao, psi_in.get_pointer(), wfc_grid, this->ekb, this->wg);
+#endif
     return;
 }
 void ElecStateLCAO::print_psi(const psi::Psi<std::complex<double>>& psi_in)
@@ -159,7 +161,7 @@ void ElecStateLCAO::print_psi(const psi::Psi<std::complex<double>>& psi_in)
     {
         for (int iw = 0; iw < GlobalV::NLOCAL; iw++)
         {
-            this->lowf->wfc_k_grid[ik][ib][iw] = psi(ib,iw);
+            this->lowf->wfc_k_grid[ik][ib][iw] = psi_in(ib, iw);
         }
     }
 #endif

source/module_elecstate/test/updaterhok_pw_test.cpp

@@ -120,7 +120,7 @@ struct ENVPrepare
     std::string latname_;
     int ntype_;
     double pseudo_rcut_;
-    bool symm_flag_;
+    int symm_flag_;
     std::string kpoint_card_;
     int nspin_;
     bool gamma_only_;
@@ -155,7 +155,7 @@ struct ENVPrepare
         latname_ = "sc";
         ntype_ = 1;
         pseudo_rcut_ = 15.0;
-        symm_flag_ = false;
+        symm_flag_ = 0;
         kpoint_card_ = "./support/KPT";
         nspin_ = 1;
         gamma_only_ = false;

source/module_elecstate/test/updaterhok_pw_test.h

@@ -27,7 +27,7 @@
 #include "module_pw/pw_basis_k.h"
 #include "src_parallel/parallel_pw.h"
 
-bool ModuleSymmetry::Symmetry::symm_flag;
+int ModuleSymmetry::Symmetry::symm_flag;
 
 LCAO_Orbitals::LCAO_Orbitals(){}
 LCAO_Orbitals::~LCAO_Orbitals(){}

source/module_esolver/esolver_ks_lcao_elec.cpp

@@ -516,7 +516,7 @@ namespace ModuleESolver
         }
 
         // add by jingan
-        if (berryphase::berry_phase_flag && ModuleSymmetry::Symmetry::symm_flag == 0)
+        if (berryphase::berry_phase_flag && ModuleSymmetry::Symmetry::symm_flag != 1)
         {
             berryphase bp(this->LOWF);
             bp.Macroscopic_polarization(this->psi);