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NEB: revamp output (#5382)
This commit is contained in:
HE Zilong
GitHub
parent
20ea36f044
commit
3d922ff5b6
4 changed files with 319 additions and 46 deletions
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@ -109,7 +109,13 @@ CONTAINS
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="NUMBER_OF_REPLICA", &
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description="Specify the number of Replica to use in the BAND", &
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description="Specify the number of Replica to use in the BAND. This may "// &
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"be equal to or larger than the number of defined &REPLICA sections. If "// &
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"larger, the rest of missing replica will automatically be interpolated "// &
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"in an iterative bisection procedure: on each step, the largest distance "// &
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"between adjacent replica is found and a new replica is inserted there by "// &
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"taking the average of adjacent replica; this is repeated until getting "// &
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"requested number of replica.", &
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default_i_val=10)
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CALL section_add_keyword(section, keyword)
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CALL keyword_release(keyword)
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@ -263,9 +269,9 @@ CONTAINS
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CALL section_release(subsection)
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! Print key section
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CALL cp_print_key_section_create(print_key, __LOCATION__, "program_run_info", &
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CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
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description="Controls the printing basic info about the BAND run", &
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print_level=medium_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
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print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
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CALL keyword_create(keyword, __LOCATION__, name="INITIAL_CONFIGURATION_INFO", &
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description="Print information for the setup of the initial configuration.", &
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@ -274,16 +280,26 @@ CONTAINS
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CALL section_add_keyword(print_key, keyword)
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="PLOT_REL_ENERGY", &
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description="If a simple plot of relative energy of each replica is shown "// &
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"alongside data vertically. This makes the output format less compact than "// &
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"default, but creates a visual aid for ease of monitoring with some special "// &
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"marks for the local maxima (X) or minima (x) in the plot.", &
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usage="PLOT_REL_ENERGY <LOGICAL>", &
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default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
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CALL section_add_keyword(print_key, keyword)
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CALL keyword_release(keyword)
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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CALL cp_print_key_section_create(print_key, __LOCATION__, "convergence_info", &
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CALL cp_print_key_section_create(print_key, __LOCATION__, "CONVERGENCE_INFO", &
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description="Controls the printing of the convergence criteria during a BAND run", &
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print_level=medium_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
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print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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CALL cp_print_key_section_create(print_key, __LOCATION__, "replica_info", &
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CALL cp_print_key_section_create(print_key, __LOCATION__, "REPLICA_INFO", &
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description="Controls the printing of each replica info during a BAND run", &
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print_level=medium_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
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CALL section_add_subsection(section, print_key)
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@ -296,6 +312,24 @@ CONTAINS
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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CALL cp_print_key_section_create(print_key, __LOCATION__, "FINAL_BAND", &
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description="Controls the printing of the final structures as an "// &
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"XYZ trajectory file after a BAND run, regardless of convergence "// &
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"status. The unit is angstrom for coordinates and cell vectors.", &
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print_level=low_print_level, common_iter_levels=1, &
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filename="FINAL")
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CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
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description="Write the atom kind given in the subsys section instead "// &
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"of the element symbol in the XYZ trajectory file.", &
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usage="PRINT_ATOM_KIND {LOGICAL}", &
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default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
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CALL section_add_keyword(print_key, keyword)
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CALL keyword_release(keyword)
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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CALL cp_print_key_section_create(print_key, __LOCATION__, "BANNER", &
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description="Controls the printing of the BAND banner", &
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print_level=low_print_level, common_iter_levels=1, &
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@ -28,6 +28,7 @@ MODULE neb_io
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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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cp_print_key_generate_filename,&
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cp_print_key_unit_nr
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USE cp_units, ONLY: cp_unit_from_cp2k
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USE f77_interface, ONLY: f_env_add_defaults,&
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@ -38,6 +39,7 @@ MODULE neb_io
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USE header, ONLY: cp2k_footer
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USE input_constants, ONLY: band_md_opt,&
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do_sm,&
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dump_extxyz,&
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dump_xmol,&
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pot_neb_fe,&
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pot_neb_full,&
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@ -75,6 +77,7 @@ MODULE neb_io
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CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'neb_io'
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PUBLIC :: read_neb_section, &
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dump_neb_final, &
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dump_neb_info, &
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dump_replica_coordinates, &
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handle_band_file_names, &
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@ -150,6 +153,124 @@ CONTAINS
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END IF
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END SUBROUTINE read_neb_section
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! **************************************************************************************************
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!> \brief dump final structures after a NEB run
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!> \param neb_env ...
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!> \param energies ...
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!> \param coords ...
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!> \param particle_set ...
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!> \param logger ...
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!> \param output_unit ...
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!> \param converged ...
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!> \par
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!> History
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!> 06.2026 - Created
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!> \author HE Zilong
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!> \version 1.0
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! **************************************************************************************************
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SUBROUTINE dump_neb_final(neb_env, energies, coords, particle_set, logger, output_unit, converged)
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TYPE(neb_type), POINTER :: neb_env
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REAL(KIND=dp), DIMENSION(:), INTENT(IN) :: energies
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TYPE(neb_var_type), POINTER :: coords
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TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
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TYPE(cp_logger_type), POINTER :: logger
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INTEGER, INTENT(IN) :: output_unit
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LOGICAL :: converged
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CHARACTER(len=*), PARAMETER :: routineN = 'dump_neb_final'
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CHARACTER(LEN=1024) :: cell_str, ener_str, lm_str, record, &
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replica_str, title
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CHARACTER(LEN=4) :: l_ener
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CHARACTER(LEN=5) :: pbc_str
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INTEGER :: irep, iw
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LOGICAL :: print_kind
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REAL(KIND=dp) :: unit_conv
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TYPE(cell_type), POINTER :: cell
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TYPE(section_vals_type), POINTER :: final_band_section
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NULLIFY (final_band_section)
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final_band_section => section_vals_get_subs_vals(neb_env%neb_section, "FINAL_BAND")
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CALL force_env_get(neb_env%force_env, cell=cell) ! For now NEB has constant cell
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pbc_str = "F F F"
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IF (cell%perd(1) == 1) pbc_str(1:1) = "T"
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IF (cell%perd(2) == 1) pbc_str(3:3) = "T"
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IF (cell%perd(3) == 1) pbc_str(5:5) = "T"
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WRITE (UNIT=cell_str, FMT="(9(1X,F19.10))") &
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cell%hmat(:, 1)*angstrom, cell%hmat(:, 2)*angstrom, cell%hmat(:, 3)*angstrom
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unit_conv = cp_unit_from_cp2k(1.0_dp, "angstrom")
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! Print a message to log
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record = cp_print_key_generate_filename(logger, final_band_section, &
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extension=".xyz", &
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my_local=.FALSE.)
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IF (output_unit > 0) THEN
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IF (converged) THEN
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Band task converged, writing XYZ trajectory gladly:"
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ELSE
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Band task not yet converged, writing XYZ trajectory anyway:"
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END IF
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WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
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END IF
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! Write actual trajectory file
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iw = cp_print_key_unit_nr(logger, neb_env%neb_section, "FINAL_BAND", &
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extension=".xyz", file_form="FORMATTED", file_status="REPLACE")
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CALL section_vals_val_get(neb_env%neb_section, "FINAL_BAND%PRINT_ATOM_KIND", &
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l_val=print_kind)
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DO irep = 1, neb_env%number_of_replica
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l_ener = "(**)"
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IF (irep > 1) THEN
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IF (energies(irep) - energies(irep - 1) > 0) THEN
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l_ener(2:2) = "+"
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ELSE
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l_ener(2:2) = "-"
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END IF
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END IF
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IF (irep < neb_env%number_of_replica) THEN
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IF (energies(irep + 1) - energies(irep) < 0) THEN
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l_ener(3:3) = "+"
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ELSE
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l_ener(3:3) = "-"
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END IF
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END IF
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SELECT CASE (l_ener)
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CASE ("(++)") ! local maximum
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WRITE (lm_str, '(A)') "Ener_loc_max=T Ener_loc_min=F"
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CASE ("(--)") ! local minimum
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WRITE (lm_str, '(A)') "Ener_loc_max=F Ener_loc_min=T"
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CASE DEFAULT
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WRITE (lm_str, '(A)') "Ener_loc_max=F Ener_loc_min=F"
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END SELECT
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WRITE (UNIT=replica_str, FMT="(I8)") irep
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WRITE (UNIT=ener_str, FMT="(F20.10)") energies(irep)
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WRITE (UNIT=title, FMT="(A)") &
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'Lattice="'//TRIM(ADJUSTL(cell_str))//'" '// &
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'Properties=species:S:1:pos:R:3 '// &
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'pbc="'//pbc_str//'" '// &
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'Replica='//TRIM(ADJUSTL(replica_str))//' '// &
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'Energy='//TRIM(ADJUSTL(ener_str))//' '// &
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TRIM(ADJUSTL(lm_str))
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IF (iw > 0) THEN
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! The iw condition does not hold for certain ranks/processes
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! that write to <proj>-BAND<n>.out where n > neb_env%number_of_replica
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CALL write_particle_coordinates(particle_set, iw, dump_extxyz, "POS", title, &
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cell=cell, array=coords%xyz(:, irep), unit_conv=unit_conv, &
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print_kind=print_kind)
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CALL m_flush(iw)
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END IF
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END DO
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IF (output_unit > 0) &
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WRITE (UNIT=output_unit, FMT='(/,T2,A)') &
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routineN//": Done!"
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CALL cp_print_key_finished_output(iw, logger, neb_env%neb_section, "FINAL_BAND")
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END SUBROUTINE dump_neb_final
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! **************************************************************************************************
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!> \brief dump print info of a NEB run
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!> \param neb_env ...
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@ -178,17 +299,20 @@ CONTAINS
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CHARACTER(len=*), PARAMETER :: routineN = 'dump_neb_info'
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CHARACTER(LEN=20) :: mytype
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CHARACTER(LEN=4) :: l_ener
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CHARACTER(LEN=default_string_length) :: line, title, unit_str
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INTEGER :: crd, ener, frc, handle, i, irep, ndig, &
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ndigl, ttst, vel
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LOGICAL :: explicit, lval, print_kind
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REAL(KIND=dp) :: f_ann, tmp_r1, unit_conv
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INTEGER :: crd, ener, frc, handle, i, irep, n_max, &
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n_min, ndig, ndigl, plt, ttst, vel
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LOGICAL :: explicit, lval, plot_rel_energy, &
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print_kind
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REAL(KIND=dp) :: ener_min, ener_range, f_ann, tmp_r1, &
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unit_conv
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REAL(KIND=dp), ALLOCATABLE, DIMENSION(:) :: ekin, temperatures
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TYPE(cell_type), POINTER :: cell
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TYPE(enumeration_type), POINTER :: enum
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TYPE(keyword_type), POINTER :: keyword
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TYPE(section_type), POINTER :: section
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TYPE(section_vals_type), POINTER :: tc_section, vc_section
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TYPE(section_vals_type), POINTER :: run_info_section, tc_section, vc_section
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CALL timeset(routineN, handle)
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ndig = CEILING(LOG10(REAL(neb_env%number_of_replica + 1, KIND=dp)))
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@ -264,6 +388,8 @@ CONTAINS
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IF (output_unit > 0) THEN
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tc_section => section_vals_get_subs_vals(neb_env%neb_section, "OPTIMIZE_BAND%MD%TEMP_CONTROL")
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vc_section => section_vals_get_subs_vals(neb_env%neb_section, "OPTIMIZE_BAND%MD%VEL_CONTROL")
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run_info_section => section_vals_get_subs_vals(neb_env%neb_section, "PROGRAM_RUN_INFO")
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CALL section_vals_val_get(run_info_section, "PLOT_REL_ENERGY", l_val=plot_rel_energy)
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ALLOCATE (temperatures(neb_env%number_of_replica))
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ALLOCATE (ekin(neb_env%number_of_replica))
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CALL get_temperatures(vels, particle_set, temperatures, ekin=ekin)
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@ -312,23 +438,81 @@ CONTAINS
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END IF
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WRITE (output_unit, '( A,T71,I10 )') &
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' NUMBER OF NEB REPLICA =', neb_env%number_of_replica
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WRITE (output_unit, '( A,T17,4F16.6)') &
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' DISTANCES REP =', distances(1:MIN(4, SIZE(distances)))
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IF (SIZE(distances) > 4) THEN
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WRITE (output_unit, '( T17,4F16.6)') distances(5:SIZE(distances))
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END IF
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WRITE (output_unit, '( A,T17,4F16.6)') &
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' ENERGIES [au] =', energies(1:MIN(4, SIZE(energies)))
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IF (SIZE(energies) > 4) THEN
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WRITE (output_unit, '( T17,4F16.6)') energies(5:SIZE(energies))
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END IF
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IF (neb_env%opt_type == band_md_opt) THEN
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WRITE (output_unit, '( A,T33,4(1X,F11.5))') &
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' REPLICA TEMPERATURES (K) =', temperatures(1:MIN(4, SIZE(temperatures)))
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DO i = 5, SIZE(temperatures), 4
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WRITE (output_unit, '( T33,4(1X,F11.5))') &
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temperatures(i:MIN(i + 3, SIZE(temperatures)))
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! switch between a longer visual format and a compact data-only print format
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IF (plot_rel_energy) THEN
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CPASSERT(SIZE(distances) == neb_env%number_of_replica - 1)
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CPASSERT(SIZE(energies) == neb_env%number_of_replica)
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CPASSERT(SIZE(temperatures) == neb_env%number_of_replica)
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ener_min = MINVAL(energies(:))
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ener_range = MAXVAL(energies(:)) - ener_min
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n_max = 0
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n_min = 0
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WRITE (output_unit, '(T2,A,T22,A,T35,A,T52,A)') &
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'REPLICA', 'ENERGY [au]', 'TEMPERATURE [K]', 'o-------------------------> E'
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DO i = 1, SIZE(distances)
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plt = FLOOR((energies(i) - ener_min)/ener_range*25)
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l_ener = "(**)"
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IF (i > 1) THEN
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IF (energies(i) - energies(i - 1) > 0) THEN
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l_ener(2:2) = "+"
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ELSE
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l_ener(2:2) = "-"
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END IF
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END IF
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IF (energies(i + 1) - energies(i) < 0) THEN
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l_ener(3:3) = "+"
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ELSE
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l_ener(3:3) = "-"
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END IF
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SELECT CASE (l_ener)
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CASE ("(++)") ! local maximum
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n_max = n_max + 1
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WRITE (line, '(A,A,A)') "|", REPEAT(" ", plt), "X"
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CASE ("(--)") ! local minimum
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n_min = n_min + 1
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WRITE (line, '(A,A,A)') "|", REPEAT(" ", plt), "x"
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CASE DEFAULT
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WRITE (line, '(A,A,A)') "|", REPEAT(" ", plt), "O"
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END SELECT
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WRITE (output_unit, '(T2,I7,T10,F18.8,1X,A,T34,F16.6,T52,A)') &
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i, energies(i), l_ener, temperatures(i), TRIM(line)
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WRITE (output_unit, '(T2,A,1X,F16.6,T52,A)') &
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"DISTANCE = ", distances(i), "|"
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END DO
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plt = FLOOR((energies(neb_env%number_of_replica) - ener_min)/ener_range*25)
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l_ener = "(**)"
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IF (energies(neb_env%number_of_replica) - energies(neb_env%number_of_replica - 1) > 0) THEN
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l_ener(2:2) = "+"
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ELSE
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l_ener(2:2) = "-"
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END IF
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! The last point would not be local maximum or minimum, as is the first
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WRITE (line, '(A,A,A)') "|", REPEAT(" ", plt), "O"
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WRITE (output_unit, '(T2,I7,T10,F18.8,1X,A,T34,F16.6,T52,A)') &
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neb_env%number_of_replica, energies(neb_env%number_of_replica), &
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l_ener, temperatures(neb_env%number_of_replica), TRIM(line)
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WRITE (output_unit, '(T52,A)') "v Nr."
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WRITE (output_unit, '(T2,A,T44,2(1X,I4))') &
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"NUMBER OF LOCAL MAXIMA (X) and MINIMA (x):", n_max, n_min
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ELSE
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WRITE (output_unit, '( A,T17,4F16.6)') &
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' DISTANCES REP =', distances(1:MIN(4, SIZE(distances)))
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IF (SIZE(distances) > 4) THEN
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WRITE (output_unit, '( T17,4F16.6)') distances(5:SIZE(distances))
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END IF
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WRITE (output_unit, '( A,T17,4F16.6)') &
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' ENERGIES [au] =', energies(1:MIN(4, SIZE(energies)))
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IF (SIZE(energies) > 4) THEN
|
||||
WRITE (output_unit, '( T17,4F16.6)') energies(5:SIZE(energies))
|
||||
END IF
|
||||
IF (neb_env%opt_type == band_md_opt) THEN
|
||||
WRITE (output_unit, '( A,T33,4(1X,F11.5))') &
|
||||
' REPLICA TEMPERATURES (K) =', temperatures(1:MIN(4, SIZE(temperatures)))
|
||||
DO i = 5, SIZE(temperatures), 4
|
||||
WRITE (output_unit, '( T33,4(1X,F11.5))') &
|
||||
temperatures(i:MIN(i + 3, SIZE(temperatures)))
|
||||
END DO
|
||||
END IF
|
||||
END IF
|
||||
WRITE (output_unit, '( A,T56,F25.14)') &
|
||||
' BAND TOTAL ENERGY [au] =', SUM(energies(:) + ekin(:)) + &
|
||||
|
|
|
|||
|
|
@ -48,7 +48,8 @@ MODULE neb_methods
|
|||
section_vals_val_get
|
||||
USE kinds, ONLY: dp
|
||||
USE message_passing, ONLY: mp_para_env_type
|
||||
USE neb_io, ONLY: dump_neb_info,&
|
||||
USE neb_io, ONLY: dump_neb_final,&
|
||||
dump_neb_info,&
|
||||
neb_rep_env_map_info,&
|
||||
read_neb_section
|
||||
USE neb_md_utils, ONLY: control_vels_a,&
|
||||
|
|
@ -334,10 +335,18 @@ CONTAINS
|
|||
energies=energies, &
|
||||
distances=distances, &
|
||||
output_unit=output_unit)
|
||||
converged = check_convergence(neb_env, Dcoords, forces)
|
||||
IF (converged) EXIT md_opt_loop
|
||||
converged = check_convergence(neb_env, Dcoords, forces, logger)
|
||||
IF (converged) THEN
|
||||
IF (output_unit > 0) THEN
|
||||
WRITE (UNIT=output_unit, FMT="(/,T2,A)") REPEAT("*", 79)
|
||||
WRITE (UNIT=output_unit, FMT="(T2,A,T32,A,T78,A)") &
|
||||
"***", "BAND TASK COMPLETED", "***"
|
||||
WRITE (UNIT=output_unit, FMT="(T2,A)") REPEAT("*", 79)
|
||||
END IF
|
||||
EXIT md_opt_loop
|
||||
END IF
|
||||
END DO md_opt_loop
|
||||
|
||||
CALL dump_neb_final(neb_env, energies, coords, particle_set, logger, output_unit, converged)
|
||||
DEALLOCATE (mass)
|
||||
DEALLOCATE (energies)
|
||||
DEALLOCATE (distances)
|
||||
|
|
@ -494,15 +503,26 @@ CONTAINS
|
|||
vels=vels, &
|
||||
output_unit=output_unit)
|
||||
|
||||
converged = check_convergence(neb_env, sline, forces)
|
||||
IF (converged) EXIT
|
||||
converged = check_convergence(neb_env, sline, forces, logger)
|
||||
IF (converged) THEN
|
||||
IF (output_unit > 0) THEN
|
||||
WRITE (UNIT=output_unit, FMT="(/,T2,A)") REPEAT("*", 79)
|
||||
WRITE (UNIT=output_unit, FMT="(T2,A,T32,A,T78,A)") &
|
||||
"***", "BAND TASK COMPLETED", "***"
|
||||
WRITE (UNIT=output_unit, FMT="(T2,A)") REPEAT("*", 79)
|
||||
END IF
|
||||
EXIT
|
||||
END IF
|
||||
END DO
|
||||
CALL dump_neb_final(neb_env, energies, coords, particle_set, logger, output_unit, converged)
|
||||
DEALLOCATE (energies)
|
||||
DEALLOCATE (distances)
|
||||
DEALLOCATE (err)
|
||||
DEALLOCATE (crr)
|
||||
DEALLOCATE (set_err)
|
||||
CALL neb_var_release(sline)
|
||||
CALL cp_print_key_finished_output(iw, logger, neb_env%neb_section, &
|
||||
"REPLICA_INFO")
|
||||
CALL timestop(handle)
|
||||
END SUBROUTINE neb_diis
|
||||
|
||||
|
|
|
|||
|
|
@ -148,8 +148,9 @@ CONTAINS
|
|||
CHARACTER(len=*), PARAMETER :: routineN = 'build_replica_coords'
|
||||
|
||||
CHARACTER(LEN=default_path_length) :: filename
|
||||
INTEGER :: handle, i_rep, iatom, ic, input_nr_replica, is, ivar, j, jtarg, n_rep, natom, &
|
||||
INTEGER :: handle, i_rep, iatom, ic, input_nr_replica, is, ivar, j, jtarg, k, n_rep, natom, &
|
||||
neb_nr_replica, nr_replica_to_interpolate, nval, nvar, shell_index
|
||||
INTEGER, ALLOCATABLE, DIMENSION(:) :: rep_map
|
||||
LOGICAL :: check, explicit, skip_vel_section
|
||||
REAL(KIND=dp), ALLOCATABLE, DIMENSION(:) :: distance
|
||||
REAL(KIND=dp), DIMENSION(3) :: r
|
||||
|
|
@ -181,10 +182,14 @@ CONTAINS
|
|||
END DO
|
||||
! Setup cartesian coordinates and COLVAR (if requested)
|
||||
coords%xyz(:, :) = 0.0_dp
|
||||
! Mapping between input replica and actual replica
|
||||
ALLOCATE (rep_map(neb_nr_replica))
|
||||
rep_map(:) = 0
|
||||
DO i_rep = 1, input_nr_replica
|
||||
coord_section => section_vals_get_subs_vals(replica_section, "COORD", &
|
||||
i_rep_section=i_rep)
|
||||
CALL section_vals_get(coord_section, explicit=explicit)
|
||||
rep_map(i_rep) = i_rep
|
||||
! Cartesian Coordinates
|
||||
IF (explicit) THEN
|
||||
CALL section_vals_val_get(coord_section, "_DEFAULT_KEYWORD_", &
|
||||
|
|
@ -293,12 +298,23 @@ CONTAINS
|
|||
END IF
|
||||
END DO ! i_rep
|
||||
ALLOCATE (distance(neb_nr_replica - 1))
|
||||
IF (iw > 0) THEN
|
||||
WRITE (iw, '(T2,A)') 'NEB| Mapping between input and requested replica so far'
|
||||
WRITE (iw, '(T2,A)') 'NEB| 1, 2, ... = input replica in sections order,'
|
||||
WRITE (iw, '(T2,A)') 'NEB| -1, -2, ... = added replica in insertion order (if any),'
|
||||
WRITE (iw, '(T2,A)') 'NEB| 0 = yet to be completed replica (if any)'
|
||||
DO j = 1, neb_nr_replica, 8
|
||||
WRITE (iw, '(T2,A,T9,8(1X,I8))') 'NEB|', rep_map(j:MIN(j + 7, neb_nr_replica))
|
||||
END DO
|
||||
END IF
|
||||
IF (input_nr_replica < neb_nr_replica) THEN
|
||||
! Interpolate missing replicas
|
||||
nr_replica_to_interpolate = neb_nr_replica - input_nr_replica
|
||||
k = 0
|
||||
distance = 0.0_dp
|
||||
IF (iw > 0) THEN
|
||||
WRITE (iw, '(T2,A,I0,A)') 'NEB| Interpolating ', nr_replica_to_interpolate, ' missing Replica.'
|
||||
WRITE (iw, '(T2,A,I0,A)') 'NEB| Interpolating ', nr_replica_to_interpolate, ' missing replica '// &
|
||||
'by stepwise bisection of distance.'
|
||||
END IF
|
||||
DO WHILE (nr_replica_to_interpolate > 0)
|
||||
! Compute distances between known images to find the interval
|
||||
|
|
@ -309,12 +325,15 @@ CONTAINS
|
|||
END DO
|
||||
jtarg = MAXLOC(distance(1:input_nr_replica), 1)
|
||||
IF (iw > 0) THEN
|
||||
WRITE (iw, '(T2,3(A,I0),A)') 'NEB| Interpolating Nr. ', &
|
||||
nr_replica_to_interpolate, ' missing Replica between Replica Nr. ', &
|
||||
WRITE (iw, '(/,T2,3(A,I0),A)') 'NEB| Interpolating Nr. ', &
|
||||
nr_replica_to_interpolate, ' missing Replica; next between Replica Nr. ', &
|
||||
jtarg, ' and ', jtarg + 1, '.'
|
||||
END IF
|
||||
input_nr_replica = input_nr_replica + 1
|
||||
nr_replica_to_interpolate = nr_replica_to_interpolate - 1
|
||||
k = k + 1
|
||||
rep_map(jtarg + 2:input_nr_replica) = rep_map(jtarg + 1:input_nr_replica - 1)
|
||||
IF (jtarg + 1 <= neb_nr_replica .AND. jtarg + 1 >= 1) rep_map(jtarg + 1) = -k
|
||||
! Interpolation is a simple bisection in XYZ
|
||||
coords%xyz(:, jtarg + 2:input_nr_replica) = coords%xyz(:, jtarg + 1:input_nr_replica - 1)
|
||||
coords%xyz(:, jtarg + 1) = (coords%xyz(:, jtarg) + coords%xyz(:, jtarg + 2))/2.0_dp
|
||||
|
|
@ -332,6 +351,12 @@ CONTAINS
|
|||
input_nr_replica, iw, neb_env%use_colvar)
|
||||
CALL neb_initialize_velocity(vels%wrk, neb_section, particle_set, &
|
||||
jtarg + 1, iw, globenv, neb_env)
|
||||
IF (iw > 0) THEN
|
||||
WRITE (iw, '(T2,A)') 'NEB| Mapping between input and requested replica so far'
|
||||
DO j = 1, neb_nr_replica, 8
|
||||
WRITE (iw, '(T2,A,T9,8(1X,I8))') 'NEB|', rep_map(j:MIN(j + 7, neb_nr_replica))
|
||||
END DO
|
||||
END IF
|
||||
END DO
|
||||
END IF
|
||||
vels%wrk(:, 1) = 0.0_dp
|
||||
|
|
@ -344,7 +369,17 @@ CONTAINS
|
|||
CALL neb_replica_distance(particle_set, coords, j, j + 1, distance(j), iw, &
|
||||
rotate=neb_env%align_frames)
|
||||
END DO
|
||||
! If there are still large distances, hint that more replica may be requested
|
||||
IF (MAXVAL(distance)/MINVAL(distance) > 1.5_dp) THEN
|
||||
IF (iw > 0) THEN
|
||||
WRITE (iw, '(/,T2,A)') 'NEB| After interpolating replica, the maximum distance between adjacent replica'
|
||||
WRITE (iw, '(T2,A)') 'NEB| is still larger than 1.5 times the minimum distance. In order to make the'
|
||||
WRITE (iw, '(T2,A)') 'NEB| distribution of replica more uniform, consider providing more structures'
|
||||
WRITE (iw, '(T2,A)') 'NEB| with &BAND/&REPLICA sections or increasing &BAND/NUMBER_OF_REPLICA value.'
|
||||
END IF
|
||||
END IF
|
||||
DEALLOCATE (distance)
|
||||
DEALLOCATE (rep_map)
|
||||
|
||||
CALL timestop(handle)
|
||||
|
||||
|
|
@ -987,12 +1022,14 @@ CONTAINS
|
|||
!> \param neb_env ...
|
||||
!> \param Dcoords ...
|
||||
!> \param forces ...
|
||||
!> \param logger ...
|
||||
!> \return ...
|
||||
!> \author Teodoro Laino 10.2006
|
||||
! **************************************************************************************************
|
||||
FUNCTION check_convergence(neb_env, Dcoords, forces) RESULT(converged)
|
||||
FUNCTION check_convergence(neb_env, Dcoords, forces, logger) RESULT(converged)
|
||||
TYPE(neb_type), POINTER :: neb_env
|
||||
TYPE(neb_var_type), POINTER :: Dcoords, forces
|
||||
TYPE(cp_logger_type), POINTER :: logger
|
||||
LOGICAL :: converged
|
||||
|
||||
CHARACTER(LEN=3), DIMENSION(4) :: labels
|
||||
|
|
@ -1000,11 +1037,9 @@ CONTAINS
|
|||
REAL(KIND=dp) :: max_dr, max_force, my_max_dr, &
|
||||
my_max_force, my_rms_dr, my_rms_force, &
|
||||
rms_dr, rms_force
|
||||
TYPE(cp_logger_type), POINTER :: logger
|
||||
TYPE(section_vals_type), POINTER :: cc_section
|
||||
|
||||
NULLIFY (logger, cc_section)
|
||||
logger => cp_get_default_logger()
|
||||
NULLIFY (cc_section)
|
||||
cc_section => section_vals_get_subs_vals(neb_env%neb_section, "CONVERGENCE_CONTROL")
|
||||
CALL section_vals_val_get(cc_section, "MAX_DR", r_val=max_dr)
|
||||
CALL section_vals_val_get(cc_section, "MAX_FORCE", r_val=max_force)
|
||||
|
|
@ -1028,11 +1063,11 @@ CONTAINS
|
|||
! Print convergence info
|
||||
WRITE (iw, FMT='(A,A)') ' **************************************', &
|
||||
'*****************************************'
|
||||
WRITE (iw, FMT='(1X,A,2X,F8.5,5X,"[",F8.5,"]",1X,T76,"(",A,")")') &
|
||||
'RMS DISPLACEMENT =', my_rms_dr, rms_dr, labels(3), &
|
||||
'MAX DISPLACEMENT =', my_max_dr, max_dr, labels(1), &
|
||||
'RMS FORCE =', my_rms_force, rms_force, labels(4), &
|
||||
'MAX FORCE =', my_max_force, max_force, labels(2)
|
||||
WRITE (iw, FMT='(1X,A,2X,F16.10,5X,"[",F16.10,1X,"]",T76,"(",A,")")') &
|
||||
'RMS DISPLACEMENT =', my_rms_dr, rms_dr, labels(3), &
|
||||
'MAX DISPLACEMENT =', my_max_dr, max_dr, labels(1), &
|
||||
'RMS FORCE =', my_rms_force, rms_force, labels(4), &
|
||||
'MAX FORCE =', my_max_force, max_force, labels(2)
|
||||
WRITE (iw, FMT='(A,A)') ' **************************************', &
|
||||
'*****************************************'
|
||||
END IF
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue