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Atomic polarization tensors via numerical differentiation
Co-authored-by: Leo Decking <ldecking@mail.uni-paderborn.de>
This commit is contained in:
Hossam Elgabarty
GitHub
parent
ae167406ec
commit
716159d91c
10 changed files with 450 additions and 7 deletions
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@ -13,6 +13,9 @@ AM1
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AMBER
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Assisted Model Building and Energy Refinement
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APT
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Atomic Polarization Tensor
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ASE
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Atomic Simulation Environment
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@ -511,6 +511,8 @@ list(
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qcschema.F
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hdf5_wrapper.F
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sockets_interface.F
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qs_apt_fdiff_methods.F
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qs_apt_fdiff_types.F
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qs_atomic_block.F
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qs_band_structure.F
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qs_basis_gradient.F
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@ -39,7 +39,9 @@ MODULE force_env_methods
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cp_logger_type,&
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cp_rm_default_logger,&
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cp_to_string
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USE cp_output_handling, ONLY: cp_print_key_finished_output,&
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USE cp_output_handling, ONLY: cp_p_file,&
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cp_print_key_finished_output,&
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cp_print_key_should_output,&
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cp_print_key_unit_nr,&
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low_print_level
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USE cp_result_methods, ONLY: cp_results_erase,&
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@ -143,6 +145,7 @@ MODULE force_env_methods
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USE qmmm_util, ONLY: apply_qmmm_translate
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USE qmmmx_force, ONLY: qmmmx_calc_energy_force
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USE qmmmx_types, ONLY: qmmmx_env_type
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USE qs_apt_fdiff_methods, ONLY: apt_fdiff
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USE qs_energy_types, ONLY: qs_energy_type
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USE qs_environment_types, ONLY: get_qs_env,&
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qs_environment_type,&
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@ -205,8 +208,8 @@ CONTAINS
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nfixed_atoms_total, nkind, &
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output_unit, print_forces, print_grrm, &
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print_scine
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LOGICAL :: calculate_forces, calculate_stress_tensor, energy_consistency, eval_ef, &
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linres_run, my_skip, print_components
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LOGICAL :: calculate_forces, calculate_stress_tensor, do_apt_fd, energy_consistency, &
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eval_ef, linres_run, my_skip, print_components
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REAL(KIND=dp) :: checksum, e_entropy, e_gap, e_pot, &
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fconv, sum_energy
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REAL(KIND=dp), DIMENSION(3) :: grand_total_force, total_force
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@ -219,6 +222,7 @@ CONTAINS
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TYPE(molecule_kind_type), POINTER :: molecule_kind
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TYPE(particle_list_type), POINTER :: core_particles, particles, &
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shell_particles
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TYPE(section_vals_type), POINTER :: print_key
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TYPE(virial_type), POINTER :: virial
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NULLIFY (logger, virial, subsys, atprop_env, cell)
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@ -310,6 +314,19 @@ CONTAINS
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END IF
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END IF
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! In case requested, compute the APT numerically
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do_apt_FD = .FALSE.
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IF (force_env%in_use == use_qs_force) THEN
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CALL section_vals_val_get(force_env%qs_env%input, "PROPERTIES%LINRES%DCDR%APT_FD", l_val=do_apt_FD)
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IF (do_apt_FD) THEN
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print_key => section_vals_get_subs_vals(force_env%qs_env%input, &
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subsection_name="PROPERTIES%LINRES%DCDR%PRINT%APT")
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IF (BTEST(cp_print_key_should_output(logger%iter_info, print_key), cp_p_file)) THEN
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CALL apt_fdiff(force_env)
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END IF
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END IF
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END IF
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!sample peak memory
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CALL m_memory()
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@ -414,6 +414,39 @@ CONTAINS
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CALL section_add_keyword(section, keyword)
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="APT_FD", &
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description="Use numerical differentiation to compute the APT, "// &
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"switches off the calculation of dcdr analytical derivatives. "// &
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"Requires RUN_TYPE = ENERGY_FORCE or MD.", &
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usage="APT_FD T", &
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default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
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CALL section_add_keyword(section, keyword)
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="APT_FD_DE", &
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description="Electric field strength (atomic units) to use for finite differences", &
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repeats=.FALSE., &
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n_var=1, &
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type_of_var=real_t, &
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default_r_val=0.0003_dp, &
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usage="APT_FD_DE 1.0E-4")
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CALL section_add_keyword(section, keyword)
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="APT_FD_METHOD", &
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description="Numerical differentiation method", &
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usage="APT_FD_METHOD FD", &
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default_i_val=1, &
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!enum_c_vals=s2a("FD", "2PNT"), &
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enum_c_vals=s2a("2PNT"), &
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!enum_desc=s2a("Forward differences.", &
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! "Symmetric two-point differences."), &
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enum_desc=s2a("Symmetric two-point differences."), &
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!enum_i_vals=(/0, 1/))
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enum_i_vals=(/1/))
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CALL section_add_keyword(section, keyword)
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CALL keyword_release(keyword)
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NULLIFY (subsection)
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CALL section_create(subsection, __LOCATION__, name="PRINT", &
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description="print results of the magnetic dipole moment calculation", &
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260
src/qs_apt_fdiff_methods.F
Normal file
260
src/qs_apt_fdiff_methods.F
Normal file
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@ -0,0 +1,260 @@
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!--------------------------------------------------------------------------------------------------!
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! CP2K: A general program to perform molecular dynamics simulations !
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! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
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! !
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! SPDX-License-Identifier: GPL-2.0-or-later !
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!--------------------------------------------------------------------------------------------------!
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! **************************************************************************************************
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!> \brief Atomic Polarization Tensor calculation by dF/d(E-field) finite differences
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!> \author Leo Decking, Hossam Elgabarty
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! **************************************************************************************************
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MODULE qs_apt_fdiff_methods
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USE cp_control_types, ONLY: dft_control_type
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USE cp_log_handling, ONLY: cp_add_default_logger,&
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cp_get_default_logger,&
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cp_logger_create,&
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cp_logger_get_default_io_unit,&
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cp_logger_release,&
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cp_logger_set,&
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cp_logger_type,&
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cp_rm_default_logger
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USE cp_output_handling, ONLY: cp_print_key_finished_output,&
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cp_print_key_unit_nr
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USE cp_subsys_types, ONLY: cp_subsys_get,&
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cp_subsys_type
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USE force_env_types, ONLY: force_env_get,&
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force_env_type
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USE input_section_types, ONLY: section_vals_get_subs_vals,&
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section_vals_type,&
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section_vals_val_get
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USE kinds, ONLY: dp
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USE message_passing, ONLY: mp_para_env_type
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USE particle_list_types, ONLY: particle_list_type
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USE qs_apt_fdiff_types, ONLY: apt_fdiff_point_type,&
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apt_fdiff_points_type
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USE qs_environment_types, ONLY: get_qs_env,&
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qs_environment_type
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USE qs_force, ONLY: qs_calc_energy_force
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USE qs_subsys_types, ONLY: qs_subsys_type
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#include "./base/base_uses.f90"
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IMPLICIT NONE
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PRIVATE
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CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'qs_apt_fdiff_methods'
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LOGICAL, PARAMETER, PRIVATE :: debug_this_module = .FALSE.
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PUBLIC :: apt_fdiff
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CONTAINS
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! **************************************************************************************************
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!> \brief Perform the 2PNT symmetric difference
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!> \param apt_fdiff_points ...
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!> \param ap_tensor ...
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!> \param natoms ...
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!> \author Leo Decking
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! **************************************************************************************************
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SUBROUTINE fdiff_2pnt(apt_fdiff_points, ap_tensor, natoms)
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TYPE(apt_fdiff_points_type) :: apt_fdiff_points
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REAL(kind=dp), DIMENSION(:, :, :) :: ap_tensor
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INTEGER, INTENT(IN) :: natoms
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INTEGER :: i, j, n
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DO j = 1, 3 ! axis force
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DO i = 1, 3 ! axis field
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DO n = 1, natoms
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ap_tensor(n, i, j) = (apt_fdiff_points%point_field(i, 1)%forces(n, j) - &
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apt_fdiff_points%point_field(i, 2)%forces(n, j)) &
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/(2*apt_fdiff_points%field_strength)
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END DO
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END DO
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END DO
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END SUBROUTINE fdiff_2pnt
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! **************************************************************************************************
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!> \brief ...
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!> \param apt_fdiff_point ...
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!> \param particles ...
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!> \author Leo Decking
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! **************************************************************************************************
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SUBROUTINE get_forces(apt_fdiff_point, particles)
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TYPE(apt_fdiff_point_type) :: apt_fdiff_point
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TYPE(particle_list_type), POINTER :: particles
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INTEGER :: i
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CPASSERT(ASSOCIATED(particles))
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DO i = 1, particles%n_els
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apt_fdiff_point%forces(i, 1:3) = particles%els(i)%f(1:3)
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END DO
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END SUBROUTINE get_forces
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! **************************************************************************************************
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!> \brief Calculate Atomic Polarization Tensors by dF/d(E-field) finite differences
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!> \param force_env ...
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!> \author Leo Decking, Hossam Elgabarty
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! **************************************************************************************************
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SUBROUTINE apt_fdiff(force_env)
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TYPE(force_env_type), POINTER :: force_env
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CHARACTER(LEN=*), PARAMETER :: routineN = 'apt_fdiff'
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INTEGER :: apt_log, fd_method, handle, i, j, &
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log_unit, n, natoms, output_fdiff_scf
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REAL(kind=dp) :: born_sum
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REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :, :) :: ap_tensor
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TYPE(apt_fdiff_points_type) :: apt_fdiff_points
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TYPE(cp_logger_type), POINTER :: logger, logger_apt
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TYPE(cp_subsys_type), POINTER :: cp_subsys
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TYPE(dft_control_type), POINTER :: dft_control
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TYPE(mp_para_env_type), POINTER :: para_env
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TYPE(particle_list_type), POINTER :: particles
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TYPE(qs_environment_type), POINTER :: qs_env
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TYPE(qs_subsys_type), POINTER :: subsys
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TYPE(section_vals_type), POINTER :: dcdr_section
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CALL timeset(routineN, handle)
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NULLIFY (qs_env, logger, dcdr_section, logger_apt, para_env, dft_control, subsys)
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NULLIFY (particles)
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CPASSERT(ASSOCIATED(force_env))
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CALL force_env_get(force_env, subsys=cp_subsys, qs_env=qs_env, para_env=para_env)
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CALL cp_subsys_get(cp_subsys, particles=particles)
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CPASSERT(ASSOCIATED(particles))
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CALL get_qs_env(qs_env=qs_env, dft_control=dft_control)!, para_env=para_env)
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natoms = particles%n_els
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IF (dft_control%apply_period_efield .OR. dft_control%apply_efield) THEN
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CPABORT("APT calculation not available in the presence of an external electric field")
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END IF
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logger => cp_get_default_logger()
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log_unit = cp_logger_get_default_io_unit(logger)
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dcdr_section => section_vals_get_subs_vals(qs_env%input, "PROPERTIES%LINRES%DCDR")
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apt_log = cp_print_key_unit_nr(logger, dcdr_section, "PRINT%APT", &
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extension=".data", middle_name="apt", log_filename=.FALSE., &
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file_position="APPEND", file_status="UNKNOWN")
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output_fdiff_scf = cp_print_key_unit_nr(logger, dcdr_section, "PRINT%APT", &
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extension=".scfLog", middle_name="apt", log_filename=.FALSE., &
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file_position="APPEND", file_status="UNKNOWN")
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CALL cp_logger_create(logger_apt, para_env=para_env, print_level=0, &
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default_global_unit_nr=output_fdiff_scf, &
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close_global_unit_on_dealloc=.TRUE.)
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CALL cp_logger_set(logger_apt, global_filename="APT_localLog")
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CALL cp_add_default_logger(logger_apt)
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IF (output_fdiff_scf > 0) THEN
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WRITE (output_fdiff_scf, '(T2,A)') &
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'!----------------------------------------------------------------------------!'
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WRITE (output_fdiff_scf, '(/,T2,A)') "SCF log for finite difference steps"
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WRITE (output_fdiff_scf, '(/,T2,A)') &
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'!----------------------------------------------------------------------------!'
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END IF
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IF (log_unit > 0) THEN
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WRITE (log_unit, '(/,T2,A)') &
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'!----------------------------------------------------------------------------!'
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WRITE (log_unit, '(/,T10,A)') "Computing Atomic polarization tensors using finite differences"
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WRITE (log_unit, '(T2,A)') " "
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END IF
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CALL section_vals_val_get(dcdr_section, "APT_FD_DE", r_val=apt_fdiff_points%field_strength)
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CALL section_vals_val_get(dcdr_section, "APT_FD_METHOD", i_val=fd_method)
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dft_control%apply_period_efield = .TRUE.
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ALLOCATE (dft_control%period_efield)
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dft_control%period_efield%displacement_field = .FALSE.
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DO i = 1, 3
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dft_control%period_efield%polarisation(1:3) = (/0.0_dp, 0.0_dp, 0.0_dp/)
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dft_control%period_efield%polarisation(i) = 1.0_dp
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IF (log_unit > 0) THEN
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WRITE (log_unit, '(T2,A)') " "
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WRITE (log_unit, "(T2,A)") "Computing forces under efield in direction +/-"//ACHAR(i + 119)
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END IF
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DO j = 1, 2 ! 1 -> positive, 2 -> negative
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IF (j == 1) THEN
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dft_control%period_efield%strength = apt_fdiff_points%field_strength
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ELSE
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dft_control%period_efield%strength = -1.0*apt_fdiff_points%field_strength
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END IF
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CALL qs_calc_energy_force(qs_env, calc_force=.TRUE., consistent_energies=.TRUE., linres=.FALSE.)
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ALLOCATE (apt_fdiff_points%point_field(i, j)%forces(natoms, 1:3))
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CALL get_forces(apt_fdiff_points%point_field(i, j), particles)
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END DO
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END DO
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IF (output_fdiff_scf > 0) THEN
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WRITE (output_fdiff_scf, '(/,T2,A)') &
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'!----------------------------------------------------------------------------!'
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WRITE (output_fdiff_scf, '(/,T2,A)') "Finite differences done!"
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WRITE (output_fdiff_scf, '(/,T2,A)') &
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'!----------------------------------------------------------------------------!'
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END IF
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CALL cp_print_key_finished_output(output_fdiff_scf, logger_apt, dcdr_section, "PRINT%APT")
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CALL cp_logger_release(logger_apt)
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CALL cp_rm_default_logger()
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ALLOCATE (ap_tensor(natoms, 3, 3))
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CALL fdiff_2pnt(apt_fdiff_points, ap_tensor, natoms)
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!Print
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born_sum = 0.0_dp
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IF (apt_log > 0) THEN
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DO n = 1, natoms
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born_sum = born_sum + (ap_tensor(n, 1, 1) + ap_tensor(n, 1, 1) + ap_tensor(n, 1, 1))/3.0
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WRITE (apt_log, "(I6, A6, F20.10)") n, particles%els(n)%atomic_kind%element_symbol, &
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(ap_tensor(n, 1, 1) + ap_tensor(n, 2, 2) + ap_tensor(n, 3, 3))/3.0
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WRITE (apt_log, '(F20.10,F20.10,F20.10)') &
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ap_tensor(n, 1, 1), ap_tensor(n, 1, 2), ap_tensor(n, 1, 3)
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WRITE (apt_log, '(F20.10,F20.10,F20.10)') &
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ap_tensor(n, 2, 1), ap_tensor(n, 2, 2), ap_tensor(n, 2, 3)
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WRITE (apt_log, '(F20.10,F20.10,F20.10)') &
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ap_tensor(n, 3, 1), ap_tensor(n, 3, 2), ap_tensor(n, 3, 3)
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END DO
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WRITE (apt_log, '(/,A20, F20.10)') "Sum of Born charges:", born_sum
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WRITE (log_unit, '(/,A30, F20.10)') "Checksum (Acoustic Sum Rule):", born_sum
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END IF
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DEALLOCATE (ap_tensor)
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DEALLOCATE (dft_control%period_efield)
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CALL cp_print_key_finished_output(apt_log, logger, dcdr_section, "PRINT%APT")
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dft_control%apply_period_efield = .FALSE.
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qs_env%linres_run = .FALSE.
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IF (log_unit > 0) THEN
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WRITE (log_unit, '(T2,A)') " "
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WRITE (log_unit, '(T2,A)') " "
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WRITE (log_unit, '(T22,A)') "APT calculation Done!"
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WRITE (log_unit, '(/,T2,A)') &
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'!----------------------------------------------------------------------------!'
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END IF
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CALL timestop(handle)
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END SUBROUTINE apt_fdiff
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END MODULE qs_apt_fdiff_methods
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35
src/qs_apt_fdiff_types.F
Normal file
35
src/qs_apt_fdiff_types.F
Normal file
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@ -0,0 +1,35 @@
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!--------------------------------------------------------------------------------------------------!
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! CP2K: A general program to perform molecular dynamics simulations !
|
||||
! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
|
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! !
|
||||
! SPDX-License-Identifier: GPL-2.0-or-later !
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!--------------------------------------------------------------------------------------------------!
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! **************************************************************************************************
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!> \brief Atomic Polarization Tensor calculation by dF/d(E-field) finite differences
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!> \author Leo Decking, Hossam Elgabarty
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! **************************************************************************************************
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MODULE qs_apt_fdiff_types
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USE kinds, ONLY: dp
|
||||
!USE physcon, ONLY: debye
|
||||
#include "./base/base_uses.f90"
|
||||
|
||||
IMPLICIT NONE
|
||||
PRIVATE
|
||||
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'qs_apt_fdiff_types'
|
||||
LOGICAL, PARAMETER, PRIVATE :: debug_this_module = .FALSE.
|
||||
PUBLIC :: apt_fdiff_point_type, apt_fdiff_points_type
|
||||
|
||||
TYPE apt_fdiff_point_type
|
||||
REAL(kind=dp), DIMENSION(:, :), ALLOCATABLE :: forces
|
||||
END TYPE apt_fdiff_point_type
|
||||
|
||||
TYPE apt_fdiff_points_type
|
||||
!TYPE(apt_fdiff_point_type) :: point_no_field ! Only for forward differences
|
||||
TYPE(apt_fdiff_point_type), DIMENSION(1:3, 1:2) :: point_field
|
||||
REAL(kind=dp) :: field_strength
|
||||
END TYPE apt_fdiff_points_type
|
||||
|
||||
END MODULE qs_apt_fdiff_types
|
||||
|
|
@ -357,9 +357,9 @@ CONTAINS
|
|||
CHARACTER(LEN=*), PARAMETER :: routineN = 'linres_calculation_low'
|
||||
|
||||
INTEGER :: every_n_step, handle, iounit
|
||||
LOGICAL :: dcdr_present, epr_present, issc_present, &
|
||||
lr_calculation, nmr_present, &
|
||||
polar_present, vcd_present
|
||||
LOGICAL :: dcdr_present, do_apt_fd, epr_present, &
|
||||
issc_present, lr_calculation, &
|
||||
nmr_present, polar_present, vcd_present
|
||||
TYPE(cp_logger_type), POINTER :: logger
|
||||
TYPE(dft_control_type), POINTER :: dft_control
|
||||
TYPE(linres_control_type), POINTER :: linres_control
|
||||
|
|
@ -374,13 +374,21 @@ CONTAINS
|
|||
issc_present = .FALSE.
|
||||
polar_present = .FALSE.
|
||||
dcdr_present = .FALSE.
|
||||
do_apt_fd = .FALSE.
|
||||
|
||||
NULLIFY (dft_control, linres_control, logger, prop_section, lr_section)
|
||||
logger => cp_get_default_logger()
|
||||
|
||||
lr_section => section_vals_get_subs_vals(qs_env%input, "PROPERTIES%LINRES")
|
||||
CALL section_vals_get(lr_section, explicit=lr_calculation)
|
||||
|
||||
CALL section_vals_val_get(lr_section, "DCDR%APT_FD", explicit=do_apt_fd)
|
||||
IF (do_apt_fd) THEN
|
||||
CALL timestop(handle)
|
||||
RETURN
|
||||
END IF
|
||||
|
||||
logger => cp_get_default_logger()
|
||||
|
||||
CALL section_vals_val_get(lr_section, "EVERY_N_STEP", i_val=every_n_step)
|
||||
|
||||
IF (lr_calculation .AND. MODULO(qs_env%sim_step, every_n_step) == 0) THEN
|
||||
|
|
|
|||
|
|
@ -12,4 +12,5 @@
|
|||
"h2o_apt_pbc.inp" = [{matcher="M096", tol=1e-06, ref=-0.938707}]
|
||||
"h2o_apt_pbc_loc.inp" = [{matcher="M096", tol=1e-06, ref=-0.938770}]
|
||||
"h2o_aat.inp" = [{matcher="M100", tol=1e-06, ref=-0.857427}]
|
||||
"h2o_apt_fdiff.inp" = [{matcher="M127", tol=1e-04, ref=0.0034319}]
|
||||
#EOF
|
||||
|
|
|
|||
82
tests/QS/regtest-dcdr/h2o_apt_fdiff.inp
Normal file
82
tests/QS/regtest-dcdr/h2o_apt_fdiff.inp
Normal file
|
|
@ -0,0 +1,82 @@
|
|||
&GLOBAL
|
||||
PRINT_LEVEL LOW
|
||||
PROJECT wat-dim-apt-fdiff
|
||||
RUN_TYPE ENERGY
|
||||
#RUN_TYPE MD
|
||||
&END GLOBAL
|
||||
|
||||
&FORCE_EVAL
|
||||
METHOD Quickstep
|
||||
&DFT
|
||||
BASIS_SET_FILE_NAME GTH_BASIS_SETS
|
||||
CHARGE 0
|
||||
POTENTIAL_FILE_NAME POTENTIAL
|
||||
&MGRID
|
||||
CUTOFF 200
|
||||
NGRIDS 2
|
||||
&END MGRID
|
||||
&POISSON
|
||||
PERIODIC XYZ
|
||||
POISSON_SOLVER PERIODIC
|
||||
&END POISSON
|
||||
&QS
|
||||
METHOD GPW
|
||||
&END QS
|
||||
&SCF
|
||||
EPS_SCF 1.0E-3
|
||||
MAX_SCF 50
|
||||
SCF_GUESS ATOMIC
|
||||
&OT
|
||||
PRECONDITIONER FULL_SINGLE_INVERSE
|
||||
&END OT
|
||||
&END SCF
|
||||
&XC
|
||||
&XC_FUNCTIONAL LDA
|
||||
&END XC_FUNCTIONAL
|
||||
&END XC
|
||||
&END DFT
|
||||
&PROPERTIES
|
||||
&LINRES
|
||||
&DCDR
|
||||
APT_FD
|
||||
# &PRINT
|
||||
# &APT
|
||||
# &EACH
|
||||
# MD 5
|
||||
# &END EACH
|
||||
# &END APT
|
||||
# &END PRINT
|
||||
&END DCDR
|
||||
&END LINRES
|
||||
&END PROPERTIES
|
||||
&SUBSYS
|
||||
&CELL
|
||||
ABC [angstrom] 8.0 5.0 5.0
|
||||
PERIODIC XYZ
|
||||
&END CELL
|
||||
&COORD
|
||||
O 7.0414782577 8.1944693132 4.7203167161
|
||||
O 6.4136423281 6.9680225843 7.2942345321
|
||||
H 7.0024272528 9.1522284981 4.7945554450
|
||||
H 6.3623068415 7.9578974691 4.0821913660
|
||||
H 7.1357809996 6.4074215266 7.5863285535
|
||||
H 6.7003933205 7.3362896088 6.4455943873
|
||||
&END COORD
|
||||
&KIND DEFAULT
|
||||
BASIS_SET SZV-GTH
|
||||
POTENTIAL GTH-LDA
|
||||
&END KIND
|
||||
&END SUBSYS
|
||||
&END FORCE_EVAL
|
||||
|
||||
# &MOTION
|
||||
# &MD
|
||||
# STEPS 20
|
||||
# TIMESTEP 0.5
|
||||
# &THERMOSTAT
|
||||
# &CSVR
|
||||
# TIMECON 5
|
||||
# &END CSVR
|
||||
# &END
|
||||
# &END MD
|
||||
# &END MOTION
|
||||
|
|
@ -257,4 +257,6 @@ registry["RTBSE_GXAC_H2_pol"] = GenericMatcher(
|
|||
)
|
||||
|
||||
registry["M126"] = GenericMatcher(r" # Total charge ", col=5)
|
||||
|
||||
registry["M127"] = GenericMatcher(r"Checksum (Acoustic Sum Rule):", col=5)
|
||||
# EOF
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue