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[Refactor] Move module_ri to source_lcao/module_ri and module_rdmft to source_lcao/module_rdmft and correct some documents (#6344)
* Move module_ri to source_lcao/module_ri * Modify pathes of file in source_lcao/module_ri * Fix CMakeFiles in test * Move module_rdmft to source_lcao/module_rdmft * Correct documentation * Line up document * Fix document about source_relax
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‎docs/CONTRIBUTING.md

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@@ -71,7 +71,8 @@ For those who are interested in the source code, the following figure shows the
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| |-- module_dftu The module for defining the Hamiltonian in DFT+U calculations.
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| |-- module_gint The module for performing grid integral in LCAO calculations.
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| |-- module_hcontainer The module for storing the Hamiltonian matrix in LCAO calculations.
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| `-- module_tddft The module for defining the Hamiltonian in TDDFT calculations.
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| |-- module_tddft The module for defining the Hamiltonian in TDDFT calculations.
75+
| `-- module_ri The module for performing RI calculations.
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|-- source_pw The module for defining the Hamiltonian in PW calculations.
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| |-- hamilt_ofdft The module for defining the Hamiltonian in OFDFT calculations.
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| |-- hamilt_pwdft The module for defining the Hamiltonian in PW-DFT calculations.
@@ -82,10 +83,7 @@ For those who are interested in the source code, the following figure shows the
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|-- source_io The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
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|-- source_md The module for performing molecular dynamics.
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|-- source_psi The module for defining the wave function and its operations.
85-
|-- source_relax The module for performing structural optimization.
86-
| |-- relax_new The module for performing structural optimization with new algorithm, optimized for cell and ion simultaneously.
87-
| `-- relax_old The module for performing structural optimization with old algorithm, optimized for cell and ion separately.
88-
|-- module_ri The module for performing RI calculations.
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`-- source_relax The module for performing structural optimization, optimized for cell and ion simultaneously.
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```
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## Submitting an Issue

‎source/CMakeLists.txt

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@@ -14,12 +14,12 @@ add_subdirectory(source_esolver)
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add_subdirectory(source_lcao/module_gint)
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add_subdirectory(source_io)
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add_subdirectory(source_relax)
17-
add_subdirectory(module_ri)
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add_subdirectory(source_lcao/module_ri)
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add_subdirectory(module_parameter)
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add_subdirectory(module_lr)
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# add by jghan
22-
add_subdirectory(module_rdmft)
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add_subdirectory(source_lcao/module_rdmft)
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add_library(
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driver

‎source/Makefile.Objects

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@@ -67,15 +67,15 @@ VPATH=./src_global:\
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./source_io:\
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./source_io/json_output:\
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./src_ri:\
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./module_ri:\
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./source_lcao/module_ri:\
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./module_parameter:\
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./module_lr:\
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./module_lr/ao_to_mo_transformer:\
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./module_lr/dm_trans:\
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./module_lr/operator_casida:\
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./module_lr/potentials:\
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./module_lr/utils:\
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./module_rdmft:\
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./source_lcao/module_rdmft:\
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./\
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OBJS_ABACUS_PW=${OBJS_MAIN}\

‎source/module_lr/esolver_lrtd_lcao.h

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@@ -20,7 +20,7 @@
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#include "source_lcao/module_gint/temp_gint/gint_info.h"
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#ifdef __EXX
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// #include <RI/physics/Exx.h>
23-
#include "module_ri/Exx_LRI.h"
23+
#include "source_lcao/module_ri/Exx_LRI.h"
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#endif
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namespace LR
2626
{

‎source/module_lr/hamilt_casida.h

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@@ -9,7 +9,7 @@
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#ifdef __EXX
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#include "module_lr/operator_casida/operator_lr_exx.h"
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#include "module_lr/ri_benchmark/operator_ri_hartree.h"
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#include "module_ri/LRI_CV_Tools.h"
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#include "source_lcao/module_ri/LRI_CV_Tools.h"
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#endif
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namespace LR
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{

‎source/module_lr/operator_casida/operator_lr_exx.h

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@@ -2,7 +2,7 @@
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#pragma once
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#include "source_hamilt/operator.h"
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#include "source_estate/module_dm/density_matrix.h"
5-
#include "module_ri/Exx_LRI.h"
5+
#include "source_lcao/module_ri/Exx_LRI.h"
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#include "module_lr/utils/lr_util.h"
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namespace LR
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{

‎source/source_base/abfs-vector3_order.h

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@@ -6,7 +6,7 @@
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#ifndef ABFS_VECTOR3_ORDER_H
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#define ABFS_VECTOR3_ORDER_H
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#include "module_ri/abfs.h"
9+
#include "source_lcao/module_ri/abfs.h"
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// mohan comment out 2021-02-06
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//#include <boost/archive/binary_oarchive.hpp>

‎source/source_base/test/abfs-vector3_order_test.cpp

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@@ -1,7 +1,7 @@
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#include "source_base/abfs-vector3_order.h"
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#include "source_base/vector3.h"
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#include "gtest/gtest.h"
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#include "module_ri/abfs.h"
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#include "source_lcao/module_ri/abfs.h"
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/************************************************
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* unit test of functions in class Abfs::vector3_order

‎source/source_cell/bcast_cell.cpp

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@@ -2,7 +2,7 @@
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#include "source_base/parallel_common.h"
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#include "module_parameter/parameter.h"
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#ifdef __EXX
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#include "module_ri/serialization_cereal.h"
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#include "source_lcao/module_ri/serialization_cereal.h"
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#include "source_pw/hamilt_pwdft/global.h"
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#endif
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namespace unitcell

‎source/source_cell/read_atom_species.cpp

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@@ -4,7 +4,7 @@
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#include "source_base/tool_title.h"
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#ifdef __EXX
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#include "source_pw/hamilt_pwdft/global.h"
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#include "module_ri/serialization_cereal.h"
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#include "source_lcao/module_ri/serialization_cereal.h"
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#endif
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namespace unitcell
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{

‎source/source_esolver/esolver_ks_lcao.cpp

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#include "source_hsolver/hsolver_lcao.h"
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// test RDMFT
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#include "module_rdmft/rdmft.h"
62+
#include "source_lcao/module_rdmft/rdmft.h"
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#include "source_lcao/module_gint/temp_gint/gint_info.h"
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‎source/source_esolver/esolver_ks_lcao.h

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// for EXX
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#ifdef __EXX
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#include "module_ri/Exx_LRI_interface.h"
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#include "module_ri/Mix_DMk_2D.h"
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#include "source_lcao/module_ri/Exx_LRI_interface.h"
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#include "source_lcao/module_ri/Mix_DMk_2D.h"
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#endif
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// for RDMFT
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#include "module_rdmft/rdmft.h"
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#include "source_lcao/module_rdmft/rdmft.h"
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#include <memory>
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‎source/source_esolver/esolver_ks_lcaopw.h

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#include "source_hsolver/hsolver_lcaopw.h"
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#ifdef __EXX
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#include "module_ri/exx_lip.h"
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#include "source_lcao/module_ri/exx_lip.h"
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#endif
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namespace ModuleESolver
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{

‎source/source_hamilt/module_xc/exx_info.h

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#ifndef EXX_INFO_H
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#define EXX_INFO_H
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#include "module_ri/conv_coulomb_pot_k.h"
4+
#include "source_lcao/module_ri/conv_coulomb_pot_k.h"
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#include "xc_functional.h"
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#include <vector>

‎source/source_io/ctrl_output_lcao.cpp

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@@ -24,10 +24,10 @@
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#include "source_lcao/module_deepks/LCAO_deepks_interface.h"
2525
#endif
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#ifdef __EXX
27-
#include "module_ri/Exx_LRI_interface.h" // use EXX codes
28-
#include "module_ri/RPA_LRI.h" // use RPA code
27+
#include "source_lcao/module_ri/Exx_LRI_interface.h" // use EXX codes
28+
#include "source_lcao/module_ri/RPA_LRI.h" // use RPA code
2929
#endif
30-
#include "module_rdmft/rdmft.h" // use RDMFT codes
30+
#include "source_lcao/module_rdmft/rdmft.h" // use RDMFT codes
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#include "source_io/to_qo.h" // use toQO
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namespace ModuleIO

‎source/source_io/ctrl_output_lcao.h

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@@ -12,9 +12,9 @@
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#include "source_lcao/module_gint/gint_k.h" // use Gint_k
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#include "source_basis/module_pw/pw_basis_k.h" // use ModulePW::PW_Basis_K and ModulePW::PW_Basis
1414
#include "source_pw/hamilt_pwdft/structure_factor.h" // use Structure_Factor
15-
#include "module_rdmft/rdmft.h" // use RDMFT codes
15+
#include "source_lcao/module_rdmft/rdmft.h" // use RDMFT codes
1616
#ifdef __EXX
17-
#include "module_ri/Exx_LRI_interface.h" // use EXX codes
17+
#include "source_lcao/module_ri/Exx_LRI_interface.h" // use EXX codes
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#endif
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namespace ModuleIO

‎source/source_io/input_conv.cpp

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#include <algorithm>
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#ifdef __EXX
18-
#include "module_ri/exx_abfs-jle.h"
18+
#include "source_lcao/module_ri/exx_abfs-jle.h"
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#endif
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#include "source_lcao/module_dftu/dftu.h"

‎source/source_io/restart_exx_csr.h

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#pragma once
22
#include "source_base/abfs-vector3_order.h"
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#include "source_cell/unitcell.h"
4-
#include "module_ri/serialization_cereal.h"
4+
#include "source_lcao/module_ri/serialization_cereal.h"
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#include <RI/global/Tensor.h>
66
#include <map>
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‎source/source_io/restart_exx_csr.hpp

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#include "source_cell/unitcell.h"
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#include "source_io/csr_reader.h"
55
#include "source_io/write_HS_sparse.h"
6-
#include "module_ri/serialization_cereal.h"
6+
#include "source_lcao/module_ri/serialization_cereal.h"
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#include <RI/global/Tensor.h>
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#include <map>
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‎source/source_io/write_vxc_r.hpp

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#include "source_io/write_HS_sparse.h"
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#ifdef __EXX
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#include "source_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
11-
#include "module_ri/RI_2D_Comm.h"
11+
#include "source_lcao/module_ri/RI_2D_Comm.h"
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#endif
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#ifndef TGINT_H

‎source/source_lcao/hamilt_lcaodft/FORCE_STRESS.h

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#include "source_io/input_conv.h"
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#include "source_psi/psi.h"
1313
#ifdef __EXX
14-
#include "module_ri/Exx_LRI_interface.h"
14+
#include "source_lcao/module_ri/Exx_LRI_interface.h"
1515
#endif
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#include "force_stress_arrays.h"
1717
#include "source_lcao/module_gint/gint_gamma.h"

‎source/source_lcao/hamilt_lcaodft/LCAO_hamilt.hpp

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#include "source_base/global_variable.h"
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#include "source_base/timer.h"
99
#include "source_lcao/hamilt_lcaodft/spar_exx.h"
10-
#include "module_ri/RI_2D_Comm.h"
10+
#include "source_lcao/module_ri/RI_2D_Comm.h"
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#include <RI/global/Global_Func-2.h>
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#include <RI/ri/Cell_Nearest.h>

‎source/source_lcao/hamilt_lcaodft/hamilt_lcao.cpp

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#endif
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#ifdef __EXX
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#include "module_ri/Exx_LRI_interface.h"
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#include "source_lcao/module_ri/Exx_LRI_interface.h"
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#include "operator_lcao/op_exx_lcao.h"
2020
#endif
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‎source/source_lcao/hamilt_lcaodft/hamilt_lcao.h

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#endif
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#ifdef __EXX
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#include "module_ri/Exx_LRI.h"
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#include "source_lcao/module_ri/Exx_LRI.h"
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#endif
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namespace hamilt
2525
{

‎source/source_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.hpp

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#include "op_exx_lcao.h"
66
#include "module_parameter/parameter.h"
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#include "module_ri/RI_2D_Comm.h"
7+
#include "source_lcao/module_ri/RI_2D_Comm.h"
88
#include "source_pw/hamilt_pwdft/global.h"
99
#include "source_hamilt/module_xc/xc_functional.h"
1010
#include "source_io/restart_exx_csr.h"

‎source/module_rdmft/CMakeLists.txt renamed to ‎source/source_lcao/module_rdmft/CMakeLists.txt

File renamed without changes.

‎source/module_rdmft/rdmft.cpp renamed to ‎source/source_lcao/module_rdmft/rdmft.cpp

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//==========================================================
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66
#include "rdmft.h"
7-
#include "module_rdmft/rdmft_tools.h"
7+
#include "source_lcao/module_rdmft/rdmft_tools.h"
88
#include "source_base/timer.h"
99
#include "source_pw/hamilt_pwdft/global.h"
1010
#include "source_base/parallel_reduce.h"

‎source/module_rdmft/rdmft.h renamed to ‎source/source_lcao/module_rdmft/rdmft.h

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#include "source_lcao/hamilt_lcaodft/hs_matrix_k.hpp"
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2525
#ifdef __EXX
26-
#include "module_ri/Exx_LRI.h"
27-
#include "module_ri/module_exx_symmetry/symmetry_rotation.h"
26+
#include "source_lcao/module_ri/Exx_LRI.h"
27+
#include "source_lcao/module_ri/module_exx_symmetry/symmetry_rotation.h"
2828
// there are some operator reload to print data in different formats
2929
#endif
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‎source/module_rdmft/rdmft_pot.cpp renamed to ‎source/source_lcao/module_rdmft/rdmft_pot.cpp

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//==========================================================
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66
#include "rdmft.h"
7-
#include "module_rdmft/rdmft_tools.h"
7+
#include "source_lcao/module_rdmft/rdmft_tools.h"
88
#include "source_psi/psi.h"
99
#include "source_estate/module_dm/cal_dm_psi.h"
1010

1111
#ifdef __EXX
12-
#include "module_ri/RI_2D_Comm.h"
12+
#include "source_lcao/module_ri/RI_2D_Comm.h"
1313
#include "source_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
1414
#endif
1515
#include "source_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.h"

‎source/module_rdmft/rdmft_tools.cpp renamed to ‎source/source_lcao/module_rdmft/rdmft_tools.cpp

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// Author: Jingang Han
33
// DATE : 2024-03-11
44
//==========================================================
5-
#include "module_rdmft/rdmft_tools.h"
5+
#include "source_lcao/module_rdmft/rdmft_tools.h"
66
#include "source_pw/hamilt_pwdft/global.h"
77
// used by class Veff_rdmft
88
#include "source_base/tool_title.h"

‎source/module_rdmft/rdmft_tools.h renamed to ‎source/source_lcao/module_rdmft/rdmft_tools.h

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#ifdef __EXX
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#include "module_ri/RI_2D_Comm.h"
31-
#include "module_ri/Exx_LRI.h"
30+
#include "source_lcao/module_ri/RI_2D_Comm.h"
31+
#include "source_lcao/module_ri/Exx_LRI.h"
3232
// there are some operator reload to print data in different formats
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#endif
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‎source/module_rdmft/update_state_rdmft.cpp renamed to ‎source/source_lcao/module_rdmft/update_state_rdmft.cpp

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//==========================================================
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#include "rdmft.h"
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#include "module_rdmft/rdmft_tools.h"
7+
#include "source_lcao/module_rdmft/rdmft_tools.h"
88
#include "source_estate/module_dm/cal_dm_psi.h"
99
#include "source_estate/module_dm/density_matrix.h"
1010
#include "source_estate/module_charge/symmetry_rho.h"

‎source/module_ri/ABFs_Construct-PCA.cpp renamed to ‎source/source_lcao/module_ri/ABFs_Construct-PCA.cpp

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#include "ABFs_Construct-PCA.h"
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#include "exx_abfs-abfs_index.h"
4-
#include "../source_base/lapack_connector.h"
5-
#include "../source_base/global_function.h"
6-
#include "../source_base/element_basis_index.h"
7-
#include "../source_base/matrix.h"
8-
#include "../module_ri/Matrix_Orbs11.h"
9-
#include "../module_ri/Matrix_Orbs21.h"
4+
#include "../../source_base/lapack_connector.h"
5+
#include "../../source_base/global_function.h"
6+
#include "../../source_base/element_basis_index.h"
7+
#include "../../source_base/matrix.h"
8+
#include "../../source_lcao/module_ri/Matrix_Orbs11.h"
9+
#include "../../source_lcao/module_ri/Matrix_Orbs21.h"
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#include <cassert>
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#include <limits>

‎source/module_ri/ABFs_Construct-PCA.h renamed to ‎source/source_lcao/module_ri/ABFs_Construct-PCA.h

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#ifndef ABFS_CONSTRUCT_PCA_H
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#define ABFS_CONSTRUCT_PCA_H
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4-
#include "../source_basis/module_ao/ORB_read.h"
4+
#include "../../source_basis/module_ao/ORB_read.h"
55
#include "source_cell/unitcell.h"
66
#include <vector>
77
#include <RI/global/Tensor.h>

‎source/module_ri/CMakeLists.txt renamed to ‎source/source_lcao/module_ri/CMakeLists.txt

File renamed without changes.

‎source/module_ri/Exx_LRI.h renamed to ‎source/source_lcao/module_ri/Exx_LRI.h

File renamed without changes.

‎source/module_ri/Exx_LRI.hpp renamed to ‎source/source_lcao/module_ri/Exx_LRI.hpp

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#include "Exx_LRI.h"
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#include "RI_2D_Comm.h"
1212
#include "RI_Util.h"
13-
#include "module_ri/exx_abfs-construct_orbs.h"
14-
#include "module_ri/exx_abfs-io.h"
15-
#include "module_ri/conv_coulomb_pot_k.h"
13+
#include "source_lcao/module_ri/exx_abfs-construct_orbs.h"
14+
#include "source_lcao/module_ri/exx_abfs-io.h"
15+
#include "source_lcao/module_ri/conv_coulomb_pot_k.h"
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#include "source_base/tool_title.h"
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#include "source_base/timer.h"
18-
#include "module_ri/serialization_cereal.h"
19-
#include "module_ri/Mix_DMk_2D.h"
18+
#include "source_lcao/module_ri/serialization_cereal.h"
19+
#include "source_lcao/module_ri/Mix_DMk_2D.h"
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#include "source_basis/module_ao/parallel_orbitals.h"
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#include <RI/distribute/Distribute_Equally.h>

‎source/module_ri/Exx_LRI_interface.h renamed to ‎source/source_lcao/module_ri/Exx_LRI_interface.h

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
#define EXX_LRI_INTERFACE_H
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#include "Exx_LRI.h"
5-
#include "module_ri/Mix_DMk_2D.h"
6-
#include "module_ri/module_exx_symmetry/symmetry_rotation.h"
5+
#include "source_lcao/module_ri/Mix_DMk_2D.h"
6+
#include "source_lcao/module_ri/module_exx_symmetry/symmetry_rotation.h"
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#include <memory>
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class LCAO_Matrix;

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