Update dipole.py #2270
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Update dipole.py #2270
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tweak the script to output data of absorption spectra
lyb9812
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Apr 19, 2023
mohanchen
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May 1, 2023
* Merge develop branch to TDDFT branch (#2249) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> * New propagator for better Convergence (#2253) * New propagator for better Convergence * Add files via upload * Add files via upload * Modified the code's implementation approach. I have modified the implementation approach of the code, and this one involves less changes to the original code. It also includes handling for multiple k-points. * Delete module_esolver directory * Delete module_hamilt_general directory * Delete module_hamilt_lcao directory * Add files via upload * Update dipole.py (#2270) * Simplify matrix multiplication and add new propagator method (#2272) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val * simplify matrix multiplication and update new propagator for tddft * add autotests for new propagator * fix bug of ekb in tddft * delete temp output * update ref of new propagator * update CASES --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> * delete td_htype and update ref of tddft autotests * delete td_htype --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]>
dyzheng
pushed a commit
that referenced
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May 17, 2023
* Merge develop branch to TDDFT branch (#2249) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> * New propagator for better Convergence (#2253) * New propagator for better Convergence * Add files via upload * Add files via upload * Modified the code's implementation approach. I have modified the implementation approach of the code, and this one involves less changes to the original code. It also includes handling for multiple k-points. * Delete module_esolver directory * Delete module_hamilt_general directory * Delete module_hamilt_lcao directory * Add files via upload * Update dipole.py (#2270) * Simplify matrix multiplication and add new propagator method (#2272) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val * simplify matrix multiplication and update new propagator for tddft * add autotests for new propagator * fix bug of ekb in tddft * delete temp output * update ref of new propagator * update CASES --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> * delete td_htype and update ref of tddft autotests * delete td_htype * refactor tddft code * move read_paramter of electric field to input_conv.cpp for tddft * sve conflicts * move definition of tag * convert read_parameter * add namespace module_tddft * remove tmp file * move read_paramters of electric field in tddft to input_conv.cpp * add force of tddft efield * add annotations * move read_parameters from H_TDDFT_pw.cpp to input_conv.cpp * add ifdef __LCAO * remove input parameter of read_td_efield * remove input parameter of read_td_efield * fix bug for input UTs * change name of parameters of compute_force in H_TDDFT_pw.h * improve annotation * solve conflicts * solve conflicts * add UT for read_td_efield * add ifdef __LCAO * add ifdef __LCAO * mistake for TEST and TEST_F * fix ReadTdEfieldTest * fix ReadTdEfieldTest * add doublenear() for EXPECT_EQ in ReadEfieldTest * add nampspace for doublenear * add nampspace for doublenear * mistake * replace doublenear with EXPECT_NEAR * TEST_F --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]>
dyzheng
pushed a commit
that referenced
this pull request
Jun 8, 2023
* Merge develop branch to TDDFT branch (#2249) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> * New propagator for better Convergence (#2253) * New propagator for better Convergence * Add files via upload * Add files via upload * Modified the code's implementation approach. I have modified the implementation approach of the code, and this one involves less changes to the original code. It also includes handling for multiple k-points. * Delete module_esolver directory * Delete module_hamilt_general directory * Delete module_hamilt_lcao directory * Add files via upload * Update dipole.py (#2270) * Simplify matrix multiplication and add new propagator method (#2272) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val * simplify matrix multiplication and update new propagator for tddft * add autotests for new propagator * fix bug of ekb in tddft * delete temp output * update ref of new propagator * update CASES --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> * delete td_htype and update ref of tddft autotests * delete td_htype * refactor tddft code * move read_paramter of electric field to input_conv.cpp for tddft * sve conflicts * move definition of tag * convert read_parameter * add namespace module_tddft * remove tmp file * move read_paramters of electric field in tddft to input_conv.cpp * add force of tddft efield * add annotations * move read_parameters from H_TDDFT_pw.cpp to input_conv.cpp * add ifdef __LCAO * remove input parameter of read_td_efield * remove input parameter of read_td_efield * fix bug for input UTs * change name of parameters of compute_force in H_TDDFT_pw.h * improve annotation * solve conflicts * solve conflicts * add UT for read_td_efield * add ifdef __LCAO * add ifdef __LCAO * mistake for TEST and TEST_F * fix ReadTdEfieldTest * fix ReadTdEfieldTest * add doublenear() for EXPECT_EQ in ReadEfieldTest * add nampspace for doublenear * add nampspace for doublenear * mistake * replace doublenear with EXPECT_NEAR * TEST_F * delete nband in propagator * add UT for module tddft * comment add_test * fix bug of prepare() in H_TDDFT_pw.cpp * split tddft_test * fix bug * fix bug of UT for tddft * add tddft prefix * add UT for cblacs_gridinit * fix bug of UT for tddft * fix bug of UT for tddft --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]>
jinzx10
pushed a commit
to jinzx10/abacus-develop
that referenced
this pull request
Jun 10, 2023
* Merge develop branch to TDDFT branch (deepmodeling#2249) * Add the dipole and spectrum post-processing script. (deepmodeling#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (deepmodeling#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (deepmodeling#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> * New propagator for better Convergence (deepmodeling#2253) * New propagator for better Convergence * Add files via upload * Add files via upload * Modified the code's implementation approach. I have modified the implementation approach of the code, and this one involves less changes to the original code. It also includes handling for multiple k-points. * Delete module_esolver directory * Delete module_hamilt_general directory * Delete module_hamilt_lcao directory * Add files via upload * Update dipole.py (deepmodeling#2270) * Simplify matrix multiplication and add new propagator method (deepmodeling#2272) * Add the dipole and spectrum post-processing script. (deepmodeling#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (deepmodeling#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (deepmodeling#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val * simplify matrix multiplication and update new propagator for tddft * add autotests for new propagator * fix bug of ekb in tddft * delete temp output * update ref of new propagator * update CASES --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> * delete td_htype and update ref of tddft autotests * delete td_htype * refactor tddft code * move read_paramter of electric field to input_conv.cpp for tddft * sve conflicts * move definition of tag * convert read_parameter * add namespace module_tddft * remove tmp file * move read_paramters of electric field in tddft to input_conv.cpp * add force of tddft efield * add annotations * move read_parameters from H_TDDFT_pw.cpp to input_conv.cpp * add ifdef __LCAO * remove input parameter of read_td_efield * remove input parameter of read_td_efield * fix bug for input UTs * change name of parameters of compute_force in H_TDDFT_pw.h * improve annotation * solve conflicts * solve conflicts * add UT for read_td_efield * add ifdef __LCAO * add ifdef __LCAO * mistake for TEST and TEST_F * fix ReadTdEfieldTest * fix ReadTdEfieldTest * add doublenear() for EXPECT_EQ in ReadEfieldTest * add nampspace for doublenear * add nampspace for doublenear * mistake * replace doublenear with EXPECT_NEAR * TEST_F * delete nband in propagator * add UT for module tddft * comment add_test * fix bug of prepare() in H_TDDFT_pw.cpp * split tddft_test * fix bug * fix bug of UT for tddft * add tddft prefix * add UT for cblacs_gridinit * fix bug of UT for tddft * fix bug of UT for tddft --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]>
mohanchen
pushed a commit
that referenced
this pull request
Jun 10, 2023
…ao (#2610) * remove unnecessary "this" * allow copy of RadialSet & calculate rcut_max on demand * clean up * add "RadialCollection", the top-level container for radial functions * enable MPI test for module_nao & bug fix for reading orbital file * clean up * BetaRadials implemented * Fix: compiling warning by both Intel and GNU compilers (#2609) * Fix: warning detected by intel compiler * Fix: compiling warning detected by GNU compiler * Fix: error --------- Co-authored-by: dyzheng <[email protected]> * Fix: optimized printing of start magnetization (#2605) * Fix: optimized printing of start magnetization * Fix: update refs in examples --------- Co-authored-by: dyzheng <[email protected]> * Test: UnitTest for module_tddft (#2580) * Merge develop branch to TDDFT branch (#2249) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> * New propagator for better Convergence (#2253) * New propagator for better Convergence * Add files via upload * Add files via upload * Modified the code's implementation approach. I have modified the implementation approach of the code, and this one involves less changes to the original code. It also includes handling for multiple k-points. * Delete module_esolver directory * Delete module_hamilt_general directory * Delete module_hamilt_lcao directory * Add files via upload * Update dipole.py (#2270) * Simplify matrix multiplication and add new propagator method (#2272) * Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. * Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang <[email protected]> * solve conflicts * solve conflicts * solve conflicts * solve conflicts * solve conflicts * Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft * pack all changes in tddft * solve conflicts * delete td_val * simplify matrix multiplication and update new propagator for tddft * add autotests for new propagator * fix bug of ekb in tddft * delete temp output * update ref of new propagator * update CASES --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> * delete td_htype and update ref of tddft autotests * delete td_htype * refactor tddft code * move read_paramter of electric field to input_conv.cpp for tddft * sve conflicts * move definition of tag * convert read_parameter * add namespace module_tddft * remove tmp file * move read_paramters of electric field in tddft to input_conv.cpp * add force of tddft efield * add annotations * move read_parameters from H_TDDFT_pw.cpp to input_conv.cpp * add ifdef __LCAO * remove input parameter of read_td_efield * remove input parameter of read_td_efield * fix bug for input UTs * change name of parameters of compute_force in H_TDDFT_pw.h * improve annotation * solve conflicts * solve conflicts * add UT for read_td_efield * add ifdef __LCAO * add ifdef __LCAO * mistake for TEST and TEST_F * fix ReadTdEfieldTest * fix ReadTdEfieldTest * add doublenear() for EXPECT_EQ in ReadEfieldTest * add nampspace for doublenear * add nampspace for doublenear * mistake * replace doublenear with EXPECT_NEAR * TEST_F * delete nband in propagator * add UT for module tddft * comment add_test * fix bug of prepare() in H_TDDFT_pw.cpp * split tddft_test * fix bug * fix bug of UT for tddft * add tddft prefix * add UT for cblacs_gridinit * fix bug of UT for tddft * fix bug of UT for tddft --------- Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]> * Test: add module_io/bessel_basis unit test (#2614) * Test: module_io/bessel_basis unit test still leave readin_C4 and allocate_C4 two functions untested, will complete soon. * Update bessel_basis_test.cpp add annotations to describe tested functions * Revert "Refactor: output efermi in pw basis (#2604)" (#2616) This reverts commit a23df80. * const qualifiers appended --------- Co-authored-by: dyzheng <[email protected]> Co-authored-by: dyzheng <[email protected]> Co-authored-by: lyb9812 <[email protected]> Co-authored-by: HeFuxiang94 <[email protected]> Co-authored-by: jiyuyang <[email protected]> Co-authored-by: jiyuang <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: Omega <[email protected]> Co-authored-by: Qianrui <[email protected]> Co-authored-by: Yike Huang <[email protected]>
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tweak the script to output data of absorption spectra