| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | module raffle__distribs_container | ||
| 2 | !! Module for handling the distribution function container. | ||
| 3 | !! | ||
| 4 | !! This module defines the distribution function container and associated | ||
| 5 | !! procedures. | ||
| 6 | !! The container holds the distribution functions for a set of atomic | ||
| 7 | !! structures, alongside parameters for initialising the distributions. | ||
| 8 | !! The container also holds the generalised distribution functions, built | ||
| 9 | !! from the distribution functions of the individual systems. | ||
| 10 | !! The generalised distribution functions are used to evaluate the viability | ||
| 11 | !! of a new structure. | ||
| 12 | use raffle__constants, only: real32, pi | ||
| 13 | use raffle__io_utils, only: stop_program, print_warning, suppress_warnings | ||
| 14 | use raffle__misc, only: set, icount, strip_null, sort_str | ||
| 15 | use raffle__misc_maths, only: triangular_number, set_difference | ||
| 16 | use raffle__geom_rw, only: basis_type, get_element_properties | ||
| 17 | use raffle__element_utils, only: & | ||
| 18 | element_type, element_bond_type, & | ||
| 19 | element_database, element_bond_database | ||
| 20 | use raffle__distribs, only: distribs_base_type, distribs_type, get_distrib | ||
| 21 | use raffle__distribs_host, only: distribs_host_type | ||
| 22 | implicit none | ||
| 23 | |||
| 24 | |||
| 25 | private | ||
| 26 | |||
| 27 | public :: distribs_container_type | ||
| 28 | |||
| 29 | |||
| 30 | type :: distribs_container_type | ||
| 31 | !! Container for distribution functions. | ||
| 32 | !! | ||
| 33 | !! This type contains the distribution functions for a set of atomic | ||
| 34 | !! structures, alongside parameters for initialising the distributions. | ||
| 35 | integer :: num_evaluated = 0 | ||
| 36 | !! Number of evaluated systems. | ||
| 37 | integer :: num_evaluated_allocated = 0 | ||
| 38 | !! Number of evaluated systems still allocated. | ||
| 39 | real(real32) :: kBT = 0.2_real32 | ||
| 40 | !! Boltzmann constant times temperature. | ||
| 41 | logical :: weight_by_hull = .false. | ||
| 42 | !! Boolean whether to weight the distribution functions by the energy | ||
| 43 | !! above the hull. If false, the formation energy from the element | ||
| 44 | !! reference energies is used. | ||
| 45 | real(real32) :: & | ||
| 46 | viability_3body_default = 0.1_real32, & | ||
| 47 | viability_4body_default = 0.1_real32 | ||
| 48 | !! Default viability for the 3- and 4-body distribution functions. | ||
| 49 | logical, dimension(:), allocatable :: & | ||
| 50 | in_dataset_2body, in_dataset_3body, in_dataset_4body | ||
| 51 | !! Whether the 2-, 3-, and 4-body distribution functions are in | ||
| 52 | !! the dataset. | ||
| 53 | real(real32), dimension(:), allocatable :: & | ||
| 54 | best_energy_pair, & | ||
| 55 | best_energy_per_species | ||
| 56 | !! Best energy for the 2-body and species distribution functions. | ||
| 57 | integer, dimension(3) :: nbins = -1 | ||
| 58 | !! Number of bins for the 2-, 3-, and 4-body distribution functions. | ||
| 59 | real(real32), dimension(3) :: & | ||
| 60 | sigma = [ 0.1_real32, 0.1_real32, 0.1_real32 ] | ||
| 61 | !! Sigma of the gaussians used in the 2-, 3-, and 4-body | ||
| 62 | !! distribution functions. | ||
| 63 | real(real32), dimension(3) :: & | ||
| 64 | width = [ 0.025_real32, pi/64._real32, pi/64._real32 ] | ||
| 65 | !! Width of the bins used in the 2-, 3-, and 4-body distribution functions. | ||
| 66 | real(real32), dimension(3) :: & | ||
| 67 | cutoff_min = [ 0.5_real32, 0._real32, 0._real32 ] | ||
| 68 | !! Minimum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 69 | real(real32), dimension(3) :: & | ||
| 70 | cutoff_max = [ 6._real32, pi, pi ] | ||
| 71 | !! Maximum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 72 | real(real32), dimension(4) :: & | ||
| 73 | radius_distance_tol = [ 1.5_real32, 2.5_real32, 3._real32, 6._real32 ] | ||
| 74 | !! Tolerance for the distance between atoms for 3- and 4-body. | ||
| 75 | !! index 1 = lower bound for 3-body | ||
| 76 | !! index 2 = upper bound for 3-body | ||
| 77 | !! index 3 = lower bound for 4-body | ||
| 78 | !! index 4 = upper bound for 4-body | ||
| 79 | real(real32), dimension(:), allocatable :: & | ||
| 80 | norm_2body, norm_3body, norm_4body | ||
| 81 | !! Normalisation factors for the 2-, 3-, and 4-body distribution functions. | ||
| 82 | type(distribs_base_type) :: gdf | ||
| 83 | !! Generalised distribution functions for all systems. | ||
| 84 | !! Generated from combining the energy-weighted distribution functions | ||
| 85 | !! of all systems | ||
| 86 | integer, dimension(:), allocatable :: element_map | ||
| 87 | !! Mapping of host elements to distribution function elements. | ||
| 88 | type(distribs_host_type) :: host_system | ||
| 89 | !! Host structure for the distribution functions. | ||
| 90 | type(distribs_type), dimension(:), allocatable :: system | ||
| 91 | !! Distribution functions for each system. | ||
| 92 | type(element_type), dimension(:), allocatable :: element_info | ||
| 93 | !! Information about the elements in the container. | ||
| 94 | type(element_bond_type), dimension(:), allocatable :: bond_info | ||
| 95 | !! Information about the 2-body bonds in the container. | ||
| 96 | contains | ||
| 97 | procedure, pass(this) :: set_width | ||
| 98 | !! Set the width of the bins used in the 2-, 3-, and 4-body. | ||
| 99 | procedure, pass(this) :: set_sigma | ||
| 100 | !! Set the sigma of the gaussians used in the 2-, 3-, and 4-body. | ||
| 101 | procedure, pass(this) :: set_cutoff_min | ||
| 102 | !! Set the minimum cutoff for the 2-, 3-, and 4-body. | ||
| 103 | procedure, pass(this) :: set_cutoff_max | ||
| 104 | !! Set the maximum cutoff for the 2-, 3-, and 4-body. | ||
| 105 | procedure, pass(this) :: set_radius_distance_tol | ||
| 106 | !! Set the tolerance for the distance between atoms for 3- and 4-body. | ||
| 107 | |||
| 108 | procedure, pass(this) :: create | ||
| 109 | !! Create the distribution functions for all systems, and the learned one. | ||
| 110 | procedure, pass(this) :: update | ||
| 111 | !! Update the distribution functions for all systems, and the learned one. | ||
| 112 | |||
| 113 | procedure, pass(this) :: deallocate_systems | ||
| 114 | !! Deallocate the systems in the container. | ||
| 115 | |||
| 116 | procedure, pass(this) :: add, add_basis | ||
| 117 | !! Add a system to the container. | ||
| 118 | |||
| 119 | procedure, pass(this), private :: set_element_info | ||
| 120 | !! Set the list of elements for the container. | ||
| 121 | procedure, pass(this), private :: update_element_info | ||
| 122 | !! Update the element information in the container. | ||
| 123 | procedure, pass(this) :: set_element_energy | ||
| 124 | !! Set the energy of an element in the container. | ||
| 125 | procedure, pass(this) :: set_element_energies | ||
| 126 | !! Set the energies of elements in the container. | ||
| 127 | procedure, pass(this) :: get_element_energies | ||
| 128 | !! Return the energies of elements in the container. | ||
| 129 | procedure, pass(this) :: get_element_energies_staticmem | ||
| 130 | !! Return the energies of elements in the container. | ||
| 131 | !! Used in Python interface. | ||
| 132 | |||
| 133 | |||
| 134 | procedure, pass(this) :: set_element_map | ||
| 135 | !! Set the mapping of elements to distribution function elements. | ||
| 136 | procedure, pass(this), private :: set_bond_info | ||
| 137 | !! Set the 2-body bond information for the container. | ||
| 138 | procedure, pass(this), private :: update_bond_info | ||
| 139 | !! Update the bond information in the container. | ||
| 140 | procedure, pass(this) :: set_bond_radius | ||
| 141 | !! Set the radius of a bond in the container. | ||
| 142 | procedure, pass(this) :: set_bond_radii | ||
| 143 | !! Set the radii of multiple bonds in the container. | ||
| 144 | procedure, pass(this) :: get_bond_radii | ||
| 145 | !! Return the radii of all bonds in the container. | ||
| 146 | procedure, pass(this) :: get_bond_radii_staticmem | ||
| 147 | !! Return the radii of all bonds in the container. | ||
| 148 | !! Used in Python interface. | ||
| 149 | |||
| 150 | |||
| 151 | procedure, pass(this) :: set_best_energy | ||
| 152 | !! Set the best energy and system in the container. | ||
| 153 | procedure, pass(this) :: initialise_gdfs | ||
| 154 | !! Initialise the distribution functions in the container. | ||
| 155 | procedure, pass(this) :: set_gdfs_to_default | ||
| 156 | !! Set the generalised distribution function to the default value. | ||
| 157 | procedure, pass(this) :: evolve | ||
| 158 | !! Evolve the learned distribution function. | ||
| 159 | |||
| 160 | |||
| 161 | procedure, pass(this) :: write_gdfs | ||
| 162 | !! Write the generalised distribution functions to a file. | ||
| 163 | procedure, pass(this) :: read_gdfs | ||
| 164 | !! Read the generalised distribution functions from a file. | ||
| 165 | procedure, pass(this) :: write_dfs | ||
| 166 | !! Write all distribution functions to a file. | ||
| 167 | procedure, pass(this) :: read_dfs | ||
| 168 | !! Read all distribution functions from a file. | ||
| 169 | procedure, pass(this) :: write_2body | ||
| 170 | !! Write the learned 2-body distribution function to a file. | ||
| 171 | procedure, pass(this) :: write_3body | ||
| 172 | !! Write the learned 3-body distribution function to a file. | ||
| 173 | procedure, pass(this) :: write_4body | ||
| 174 | !! Write the learned 4-body distribution function to a file. | ||
| 175 | procedure, pass(this) :: get_pair_index | ||
| 176 | !! Return the index for bond_info given two elements. | ||
| 177 | procedure, pass(this) :: get_element_index | ||
| 178 | !! Return the index for element_info given one element. | ||
| 179 | procedure, pass(this) :: get_bin | ||
| 180 | !! Return the bin index for a given distance. | ||
| 181 | end type distribs_container_type | ||
| 182 | |||
| 183 | interface distribs_container_type | ||
| 184 | !! Interface for the distribution functions container. | ||
| 185 | module function init_distribs_container( & | ||
| 186 | nbins, width, sigma, cutoff_min, cutoff_max & | ||
| 187 | ) result(distribs_container) | ||
| 188 | !! Initialise the distribution functions container. | ||
| 189 | integer, dimension(3), intent(in), optional :: nbins | ||
| 190 | !! Optional. Number of bins for the 2-, 3-, and 4-body distribution | ||
| 191 | !! functions. | ||
| 192 | real(real32), dimension(3), intent(in), optional :: width, sigma | ||
| 193 | !! Optional. Width and sigma of the gaussians used in the 2-, 3-, and | ||
| 194 | !! 4-body. | ||
| 195 | real(real32), dimension(3), intent(in), optional :: & | ||
| 196 | cutoff_min, cutoff_max | ||
| 197 | !! Optional. Minimum and maximum cutoff for the 2-, 3-, and 4-body. | ||
| 198 | type(distribs_container_type) :: distribs_container | ||
| 199 | !! Instance of the distribution functions container. | ||
| 200 | end function init_distribs_container | ||
| 201 | end interface distribs_container_type | ||
| 202 | |||
| 203 | |||
| 204 | contains | ||
| 205 | |||
| 206 | !############################################################################### | ||
| 207 | 3 | module function init_distribs_container( & | |
| 208 | nbins, width, sigma, & | ||
| 209 | cutoff_min, cutoff_max & | ||
| 210 | ) result(distribs_container) | ||
| 211 | !! Initialise the distribution functions container. | ||
| 212 | implicit none | ||
| 213 | |||
| 214 | ! Arguments | ||
| 215 | integer, dimension(3), intent(in), optional :: nbins | ||
| 216 | !! Optional. Number of bins for the 2-, 3-, and 4-body distribution | ||
| 217 | !! functions. | ||
| 218 | real(real32), dimension(3), intent(in), optional :: width, sigma | ||
| 219 | !! Optional. Width and sigma of the gaussians used in the 2-, 3-, and | ||
| 220 | !! 4-body. | ||
| 221 | real(real32), dimension(3), intent(in), optional :: cutoff_min, cutoff_max | ||
| 222 | !! Optional. Minimum and maximum cutoff for the 2-, 3-, and 4-body. | ||
| 223 | type(distribs_container_type) :: distribs_container | ||
| 224 | !! Instance of the distribution functions container. | ||
| 225 | |||
| 226 | ! Local variables | ||
| 227 | character(256) :: stop_msg | ||
| 228 | !! Error message. | ||
| 229 | |||
| 230 | |||
| 231 | 3 | if(present(nbins))then | |
| 232 |
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7 | if(all(nbins .gt. 0)) distribs_container%nbins = nbins |
| 233 | end if | ||
| 234 | |||
| 235 |
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3 | if(present(width))then |
| 236 |
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7 | if(all(width.ge.0._real32)) distribs_container%width = width |
| 237 | end if | ||
| 238 | |||
| 239 |
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3 | if(present(sigma))then |
| 240 |
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7 | if(all(sigma.ge.0._real32)) distribs_container%sigma = sigma |
| 241 | end if | ||
| 242 | |||
| 243 |
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3 | if(present(cutoff_min))then |
| 244 |
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2 | if(any(cutoff_min.ge.0._real32)) & |
| 245 |
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8 | distribs_container%cutoff_min = cutoff_min |
| 246 | end if | ||
| 247 |
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3 | if(present(cutoff_max))then |
| 248 |
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8 | if(all(cutoff_max.ge.0._real32)) & |
| 249 |
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8 | distribs_container%cutoff_max = cutoff_max |
| 250 | end if | ||
| 251 |
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9 | if( & |
| 252 | any(distribs_container%cutoff_max .le. distribs_container%cutoff_min) & | ||
| 253 | )then | ||
| 254 | write(stop_msg,*) & | ||
| 255 | "cutoff_max <= cutoff_min" // & | ||
| 256 | achar(13) // achar(10) // & | ||
| 257 | 1 | "cutoff min: ", distribs_container%cutoff_min, & | |
| 258 | achar(13) // achar(10) // & | ||
| 259 | 2 | "cutoff max: ", distribs_container%cutoff_max | |
| 260 | 1 | call stop_program( stop_msg ) | |
| 261 | 1 | return | |
| 262 | end if | ||
| 263 | |||
| 264 |
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107 | end function init_distribs_container |
| 265 | !############################################################################### | ||
| 266 | |||
| 267 | |||
| 268 | !############################################################################### | ||
| 269 | 4 | subroutine set_width(this, width) | |
| 270 | !! Set the width of the gaussians used in the 2-, 3-, and 4-body | ||
| 271 | !! distribution functions. | ||
| 272 | implicit none | ||
| 273 | |||
| 274 | ! Arguments | ||
| 275 | class(distribs_container_type), intent(inout) :: this | ||
| 276 | !! Parent. Instance of distribution functions container. | ||
| 277 | real(real32), dimension(3), intent(in) :: width | ||
| 278 | !! Width of the gaussians used in the 2-, 3-, and 4-body | ||
| 279 | !! distribution functions. | ||
| 280 | |||
| 281 |
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16 | this%width = width |
| 282 | |||
| 283 | 4 | end subroutine set_width | |
| 284 | !############################################################################### | ||
| 285 | |||
| 286 | |||
| 287 | !############################################################################### | ||
| 288 | 2 | subroutine set_sigma(this, sigma) | |
| 289 | !! Set the sigma of the gaussians used in the 2-, 3-, and 4-body | ||
| 290 | !! distribution functions. | ||
| 291 | implicit none | ||
| 292 | |||
| 293 | ! Arguments | ||
| 294 | class(distribs_container_type), intent(inout) :: this | ||
| 295 | !! Parent. Instance of distribution functions container. | ||
| 296 | real(real32), dimension(3), intent(in) :: sigma | ||
| 297 | !! Sigma of the gaussians used in the 2-, 3-, and 4-body distribution | ||
| 298 | !! functions. | ||
| 299 | |||
| 300 |
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8 | this%sigma = sigma |
| 301 | |||
| 302 | 2 | end subroutine set_sigma | |
| 303 | !############################################################################### | ||
| 304 | |||
| 305 | |||
| 306 | !############################################################################### | ||
| 307 | 2 | subroutine set_cutoff_min(this, cutoff_min) | |
| 308 | !! Set the minimum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 309 | implicit none | ||
| 310 | |||
| 311 | ! Arguments | ||
| 312 | class(distribs_container_type), intent(inout) :: this | ||
| 313 | !! Parent. Instance of distribution functions container. | ||
| 314 | real(real32), dimension(3), intent(in) :: cutoff_min | ||
| 315 | !! Minimum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 316 | |||
| 317 |
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8 | this%cutoff_min = cutoff_min |
| 318 | |||
| 319 | 2 | end subroutine set_cutoff_min | |
| 320 | !############################################################################### | ||
| 321 | |||
| 322 | |||
| 323 | !############################################################################### | ||
| 324 | 2 | subroutine set_cutoff_max(this, cutoff_max) | |
| 325 | !! Set the maximum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 326 | implicit none | ||
| 327 | |||
| 328 | ! Arguments | ||
| 329 | class(distribs_container_type), intent(inout) :: this | ||
| 330 | !! Parent. Instance of distribution functions container. | ||
| 331 | real(real32), dimension(3), intent(in) :: cutoff_max | ||
| 332 | !! Maximum cutoff for the 2-, 3-, and 4-body distribution functions. | ||
| 333 | |||
| 334 |
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8 | this%cutoff_max = cutoff_max |
| 335 | |||
| 336 | 2 | end subroutine set_cutoff_max | |
| 337 | !############################################################################### | ||
| 338 | |||
| 339 | |||
| 340 | !############################################################################### | ||
| 341 | 1 | subroutine set_radius_distance_tol(this, radius_distance_tol) | |
| 342 | !! Set the tolerance for the distance between atoms for 3- and 4-body. | ||
| 343 | implicit none | ||
| 344 | |||
| 345 | ! Arguments | ||
| 346 | class(distribs_container_type), intent(inout) :: this | ||
| 347 | !! Parent. Instance of distribution functions container. | ||
| 348 | real(real32), dimension(4), intent(in) :: radius_distance_tol | ||
| 349 | !! Tolerance for the distance between atoms for 3- and 4-body. | ||
| 350 | |||
| 351 |
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5 | this%radius_distance_tol = radius_distance_tol |
| 352 | |||
| 353 | 1 | end subroutine set_radius_distance_tol | |
| 354 | !############################################################################### | ||
| 355 | |||
| 356 | |||
| 357 | !############################################################################### | ||
| 358 | 14 | subroutine create( & | |
| 359 |
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14 | this, basis_list, energy_above_hull_list, deallocate_systems, & |
| 360 | verbose & | ||
| 361 | ) | ||
| 362 | !! create the distribution functions from the input file | ||
| 363 | implicit none | ||
| 364 | ! Arguments | ||
| 365 | class(distribs_container_type), intent(inout) :: this | ||
| 366 | !! Parent. Instance of distribution functions container. | ||
| 367 | type(basis_type), dimension(:), intent(in) :: basis_list | ||
| 368 | !! List of basis structures. | ||
| 369 | real(real32), dimension(:), intent(in), optional :: energy_above_hull_list | ||
| 370 | !! List of energies above the hull for the structures. | ||
| 371 | logical, intent(in), optional :: deallocate_systems | ||
| 372 | !! Boolean whether to deallocate the systems after the | ||
| 373 | !! distribution functions are created. | ||
| 374 | integer, intent(in), optional :: verbose | ||
| 375 | !! Verbosity level. | ||
| 376 | |||
| 377 | ! Local variables | ||
| 378 | logical :: deallocate_systems_ | ||
| 379 | !! Boolean whether to deallocate the systems after the distribution | ||
| 380 | character(256) :: stop_msg | ||
| 381 | !! Error message. | ||
| 382 | integer :: verbose_ | ||
| 383 | !! Verbosity level. | ||
| 384 | logical :: suppress_warnings_store | ||
| 385 | !! Boolean to store the suppress_warnings value. | ||
| 386 | |||
| 387 | |||
| 388 | ! Set the verbosity level | ||
| 389 | 14 | verbose_ = 0 | |
| 390 |
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14 | if(present(verbose)) verbose_ = verbose |
| 391 |
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14 | if(verbose_ .eq. 0)then |
| 392 | 14 | suppress_warnings_store = suppress_warnings | |
| 393 | 14 | suppress_warnings = .true. | |
| 394 | end if | ||
| 395 | |||
| 396 | ! Check if element_database is allocated | ||
| 397 |
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14 | if(.not.allocated(element_database))then |
| 398 | write(stop_msg,*) "element_database not allocated" // & | ||
| 399 | achar(13) // achar(10) // & | ||
| 400 | "Run the set_element_energies() procedure of " // & | ||
| 401 | 1 | "distribs_container_type before calling create()" | |
| 402 | 1 | call stop_program( stop_msg ) | |
| 403 | 1 | return | |
| 404 | end if | ||
| 405 | |||
| 406 | ! Check if energy_above_hull_list and basis_list are the same size | ||
| 407 |
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13 | if(present(energy_above_hull_list))then |
| 408 | ✗ | if(size(energy_above_hull_list).eq.0)then | |
| 409 | ✗ | this%weight_by_hull = .false. | |
| 410 | ✗ | elseif(size(energy_above_hull_list) .ne. size(basis_list))then | |
| 411 | ✗ | this%weight_by_hull = .true. | |
| 412 | write(stop_msg,*) "energy_above_hull_list and basis_list " // & | ||
| 413 | "not the same size" // & | ||
| 414 | achar(13) // achar(10) // & | ||
| 415 | ✗ | "energy_above_hull_list: ", size(energy_above_hull_list), & | |
| 416 | achar(13) // achar(10) // & | ||
| 417 | ✗ | "basis_list: ", size(basis_list) | |
| 418 | ✗ | call stop_program( stop_msg ) | |
| 419 | ✗ | return | |
| 420 | end if | ||
| 421 | end if | ||
| 422 |
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13 | if(this%weight_by_hull.and..not.present(energy_above_hull_list))then |
| 423 | write(stop_msg,*) "energy_above_hull_list not present" // & | ||
| 424 | achar(13) // achar(10) // & | ||
| 425 | ✗ | "energy_above_hull_list must be present when using hull weighting" | |
| 426 | ✗ | call stop_program( stop_msg ) | |
| 427 | ✗ | return | |
| 428 | end if | ||
| 429 | |||
| 430 | |||
| 431 | ! Check if deallocate_systems is present | ||
| 432 | 13 | deallocate_systems_ = .true. | |
| 433 |
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13 | if(present(deallocate_systems)) deallocate_systems_ = deallocate_systems |
| 434 | |||
| 435 | 13 | this%num_evaluated = 0 | |
| 436 | 13 | this%num_evaluated_allocated = 0 | |
| 437 |
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13 | if(allocated(this%gdf%df_2body)) deallocate(this%gdf%df_2body) |
| 438 |
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13 | if(allocated(this%gdf%df_3body)) deallocate(this%gdf%df_3body) |
| 439 |
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13 | if(allocated(this%gdf%df_4body)) deallocate(this%gdf%df_4body) |
| 440 |
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13 | if(allocated(this%norm_2body)) deallocate(this%norm_2body) |
| 441 |
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13 | if(allocated(this%norm_3body)) deallocate(this%norm_3body) |
| 442 |
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13 | if(allocated(this%norm_4body)) deallocate(this%norm_4body) |
| 443 |
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21 | if(allocated(this%system)) deallocate(this%system) |
| 444 |
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13 | if(allocated(this%in_dataset_2body)) deallocate(this%in_dataset_2body) |
| 445 |
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13 | if(allocated(this%in_dataset_3body)) deallocate(this%in_dataset_3body) |
| 446 |
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13 | if(allocated(this%in_dataset_4body)) deallocate(this%in_dataset_4body) |
| 447 |
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13 | if(allocated(this%best_energy_pair)) deallocate(this%best_energy_pair) |
| 448 |
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13 | if(allocated(this%best_energy_per_species)) & |
| 449 |
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3 | deallocate(this%best_energy_per_species) |
| 450 |
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13 | allocate(this%system(0)) |
| 451 | 13 | call this%add(basis_list) | |
| 452 |
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13 | if(present(energy_above_hull_list).and.this%weight_by_hull)then |
| 453 | ✗ | this%system(:)%energy_above_hull = energy_above_hull_list(:) | |
| 454 | end if | ||
| 455 | 13 | call this%set_bond_info() | |
| 456 | 13 | call this%evolve() | |
| 457 |
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13 | if(deallocate_systems_) call this%deallocate_systems() |
| 458 |
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13 | if(this%host_system%defined) & |
| 459 | 6 | call this%host_system%set_element_map(this%element_info) | |
| 460 | |||
| 461 |
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13 | if(verbose_ .eq. 0)then |
| 462 | 13 | suppress_warnings = suppress_warnings_store | |
| 463 | end if | ||
| 464 | |||
| 465 | end subroutine create | ||
| 466 | !############################################################################### | ||
| 467 | |||
| 468 | |||
| 469 | !############################################################################### | ||
| 470 | 4 | subroutine update( & | |
| 471 |
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4 | this, basis_list, energy_above_hull_list, from_host, & |
| 472 | deallocate_systems, & | ||
| 473 | verbose & | ||
| 474 | ) | ||
| 475 | !! update the distribution functions from the input file | ||
| 476 | implicit none | ||
| 477 | ! Arguments | ||
| 478 | class(distribs_container_type), intent(inout) :: this | ||
| 479 | !! Parent. Instance of distribution functions container. | ||
| 480 | type(basis_type), dimension(:), intent(in) :: basis_list | ||
| 481 | !! List of basis structures. | ||
| 482 | real(real32), dimension(:), intent(in), optional :: energy_above_hull_list | ||
| 483 | !! List of energies above the hull for the structures. | ||
| 484 | logical, intent(in), optional :: from_host | ||
| 485 | !! Optional. Boolean whether structures are derived from the host. | ||
| 486 | logical, intent(in), optional :: deallocate_systems | ||
| 487 | !! Boolean whether to deallocate the systems after the | ||
| 488 | !! distribution functions are created. | ||
| 489 | integer, intent(in), optional :: verbose | ||
| 490 | !! Verbosity level. | ||
| 491 | |||
| 492 | ! Local variables | ||
| 493 | integer :: i | ||
| 494 | !! Loop index. | ||
| 495 | logical :: deallocate_systems_ | ||
| 496 | !! Boolean whether to deallocate the systems after the distribution | ||
| 497 | logical :: from_host_ | ||
| 498 | !! Boolean whether structures are derived from the host. | ||
| 499 | character(256) :: stop_msg | ||
| 500 | !! Error message. | ||
| 501 | integer :: verbose_ | ||
| 502 | !! Verbosity level. | ||
| 503 | logical :: suppress_warnings_store | ||
| 504 | !! Boolean to store the suppress_warnings value. | ||
| 505 | |||
| 506 | |||
| 507 | ! Set the verbosity level | ||
| 508 | 4 | verbose_ = 0 | |
| 509 |
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4 | if(present(verbose)) verbose_ = verbose |
| 510 |
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4 | if(verbose_ .eq. 0)then |
| 511 | 4 | suppress_warnings_store = suppress_warnings | |
| 512 | 4 | suppress_warnings = .true. | |
| 513 | end if | ||
| 514 | |||
| 515 | ! Check if energy_above_hull_list and basis_list are the same size | ||
| 516 |
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4 | if(present(energy_above_hull_list))then |
| 517 | ✗ | if(size(energy_above_hull_list).eq.0 .and. .not. this%weight_by_hull)then | |
| 518 | ✗ | elseif(size(energy_above_hull_list) .ne. size(basis_list) .and. & | |
| 519 | this%weight_by_hull & | ||
| 520 | )then | ||
| 521 | write(stop_msg,*) "energy_above_hull_list and basis_list " // & | ||
| 522 | "not the same size whilst using hull weighting" // & | ||
| 523 | achar(13) // achar(10) // & | ||
| 524 | ✗ | "energy_above_hull_list: ", size(energy_above_hull_list), & | |
| 525 | achar(13) // achar(10) // & | ||
| 526 | ✗ | "basis_list: ", size(basis_list) | |
| 527 | ✗ | call stop_program( stop_msg ) | |
| 528 | ✗ | return | |
| 529 | end if | ||
| 530 | end if | ||
| 531 |
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4 | if(this%weight_by_hull.and..not.present(energy_above_hull_list))then |
| 532 | write(stop_msg,*) "energy_above_hull_list not present" // & | ||
| 533 | achar(13) // achar(10) // & | ||
| 534 | ✗ | "energy_above_hull_list must be present when using hull weighting" | |
| 535 | ✗ | call stop_program( stop_msg ) | |
| 536 | ✗ | return | |
| 537 | end if | ||
| 538 | |||
| 539 | ! Check if from_host is present | ||
| 540 |
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4 | if(present(from_host))then |
| 541 | ✗ | from_host_ = from_host | |
| 542 | ✗ | if(this%weight_by_hull.and.from_host_)then | |
| 543 | write(stop_msg,*) "Hull weighting and from_host are incompatible" // & | ||
| 544 | achar(13) // achar(10) // & | ||
| 545 | ✗ | "Set from_host = .false. to use hull weighting" | |
| 546 | ✗ | call stop_program( stop_msg ) | |
| 547 | ✗ | return | |
| 548 | end if | ||
| 549 | else | ||
| 550 |
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4 | if(this%weight_by_hull)then |
| 551 | ✗ | from_host_ = .false. | |
| 552 | else | ||
| 553 | 4 | from_host_ = .true. | |
| 554 | end if | ||
| 555 | end if | ||
| 556 | |||
| 557 | ! Check if deallocate_systems is present | ||
| 558 | 4 | deallocate_systems_ = .true. | |
| 559 |
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4 | if(present(deallocate_systems)) deallocate_systems_ = deallocate_systems |
| 560 | |||
| 561 | ! Add the new basis structures | ||
| 562 | 4 | call this%add(basis_list) | |
| 563 | 4 | call this%update_bond_info() | |
| 564 |
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4 | if(present(energy_above_hull_list).and.this%weight_by_hull)then |
| 565 | this%system(this%num_evaluated_allocated + 1:)%energy_above_hull = & | ||
| 566 | ✗ | energy_above_hull_list(:) | |
| 567 | end if | ||
| 568 | |||
| 569 | ! If the structures are derived from the host, subtract the interface energy | ||
| 570 |
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4 | if(from_host_)then |
| 571 |
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4 | if(.not.this%host_system%defined)then |
| 572 | write(stop_msg,*) "host not set" // & | ||
| 573 | achar(13) // achar(10) // & | ||
| 574 | "Run the set_host() procedure of parent of" // & | ||
| 575 | ✗ | "distribs_container_type before calling create()" | |
| 576 | ✗ | call stop_program( stop_msg ) | |
| 577 | ✗ | return | |
| 578 | else | ||
| 579 |
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4 | if(.not.allocated(this%host_system%df_2body))then |
| 580 | call this%host_system%calculate( & | ||
| 581 | this%host_system%basis, & | ||
| 582 | width = this%width, & | ||
| 583 | sigma = this%sigma, & | ||
| 584 | cutoff_min = this%cutoff_min, & | ||
| 585 | cutoff_max = this%cutoff_max, & | ||
| 586 | radius_distance_tol = this%radius_distance_tol & | ||
| 587 | 2 | ) | |
| 588 | end if | ||
| 589 | 4 | call this%host_system%calculate_interface_energy(this%element_info) | |
| 590 |
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8 | do i = this%num_evaluated_allocated + 1, size(this%system), 1 |
| 591 | 4 | this%system(i)%from_host = .true. | |
| 592 | this%system(i)%energy = this%system(i)%energy - & | ||
| 593 | 4 | this%host_system%interface_energy | |
| 594 | this%system(i)%num_atoms = this%system(i)%num_atoms - & | ||
| 595 | 8 | this%host_system%num_atoms | |
| 596 | end do | ||
| 597 | end if | ||
| 598 | end if | ||
| 599 | |||
| 600 | 4 | call this%evolve() | |
| 601 |
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4 | if(deallocate_systems_) call this%deallocate_systems() |
| 602 |
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4 | if(this%host_system%defined) & |
| 603 | 4 | call this%host_system%set_element_map(this%element_info) | |
| 604 | |||
| 605 |
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4 | if(verbose_ .eq. 0)then |
| 606 | 4 | suppress_warnings = suppress_warnings_store | |
| 607 | end if | ||
| 608 | |||
| 609 | end subroutine update | ||
| 610 | !############################################################################### | ||
| 611 | |||
| 612 | |||
| 613 | !############################################################################### | ||
| 614 | 10 | subroutine deallocate_systems(this) | |
| 615 | !! Deallocate the systems in the container. | ||
| 616 | implicit none | ||
| 617 | |||
| 618 | ! Arguments | ||
| 619 | class(distribs_container_type), intent(inout) :: this | ||
| 620 | !! Parent. Instance of distribution functions container. | ||
| 621 | |||
| 622 |
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35 | deallocate(this%system) |
| 623 | 10 | this%num_evaluated_allocated = 0 | |
| 624 | |||
| 625 | 10 | end subroutine deallocate_systems | |
| 626 | !############################################################################### | ||
| 627 | |||
| 628 | |||
| 629 | !############################################################################### | ||
| 630 | ✗ | subroutine write_gdfs(this, file) | |
| 631 | !! Write the generalised distribution functions to a file. | ||
| 632 | implicit none | ||
| 633 | |||
| 634 | ! Arguments | ||
| 635 | class(distribs_container_type), intent(in) :: this | ||
| 636 | !! Parent. Instance of distribution functions container. | ||
| 637 | character(*), intent(in) :: file | ||
| 638 | !! Filename to write the generalised distribution functions to. | ||
| 639 | |||
| 640 | ! Local variables | ||
| 641 | integer :: unit | ||
| 642 | !! File unit. | ||
| 643 | integer :: i | ||
| 644 | !! Loop index. | ||
| 645 | character(256) :: fmt | ||
| 646 | !! Format string. | ||
| 647 | character(256) :: stop_msg | ||
| 648 | !! Error message. | ||
| 649 | |||
| 650 | ✗ | if(.not.allocated(this%gdf%df_2body))then | |
| 651 | write(stop_msg,*) & | ||
| 652 | "Generalised distribution functions are not allocated." // & | ||
| 653 | achar(13) // achar(10) // & | ||
| 654 | "create() or read() must be called before writing the " // & | ||
| 655 | ✗ | "generalised distribution functions." | |
| 656 | ✗ | call stop_program( stop_msg ) | |
| 657 | ✗ | return | |
| 658 | end if | ||
| 659 | ✗ | open(newunit=unit, file=file) | |
| 660 | ✗ | write(unit, '("# nbins",3(1X,I0))') this%nbins | |
| 661 | ✗ | write(unit, '("# width",3(1X,ES0.4))') this%width | |
| 662 | ✗ | write(unit, '("# sigma",3(1X,ES0.4))') this%sigma | |
| 663 | ✗ | write(unit, '("# cutoff_min",3(1X,ES0.4))') this%cutoff_min | |
| 664 | ✗ | write(unit, '("# cutoff_max",3(1X,ES0.4))') this%cutoff_max | |
| 665 | write(unit, '("# radius_distance_tol",4(1X,ES0.4))') & | ||
| 666 | ✗ | this%radius_distance_tol | |
| 667 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,A))")') size(this%element_info) | |
| 668 | ✗ | write(unit, fmt) "elements", this%element_info(:)%name | |
| 669 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,ES0.4))")') size(this%element_info) | |
| 670 | ✗ | write(unit, fmt) "energies", this%element_info(:)%energy | |
| 671 | ✗ | write(unit, fmt) "best_energy_per_element", this%best_energy_per_species | |
| 672 | ✗ | write(unit, fmt) "3-body_norm", this%norm_3body | |
| 673 | ✗ | write(unit, fmt) "4-body_norm", this%norm_4body | |
| 674 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,L1))")') size(this%element_info) | |
| 675 | ✗ | write(unit, fmt) "in_dataset_3body", this%in_dataset_3body | |
| 676 | ✗ | write(unit, fmt) "in_dataset_4body", this%in_dataset_4body | |
| 677 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,A))")') size(this%bond_info) | |
| 678 | ✗ | write(unit, fmt) "element_pairs", & | |
| 679 | ( & | ||
| 680 | trim(this%bond_info(i)%element(1)) // "-" // & | ||
| 681 | ✗ | trim(this%bond_info(i)%element(2)), & | |
| 682 | ✗ | i = 1, size(this%bond_info) & | |
| 683 | ✗ | ) | |
| 684 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,ES0.4))")') size(this%bond_info) | |
| 685 | ✗ | write(unit, fmt) "radii", this%bond_info(:)%radius_covalent | |
| 686 | ✗ | write(unit, fmt) "best_energy_per_pair", this%best_energy_pair | |
| 687 | ✗ | write(unit, fmt) "2-body_norm", this%norm_2body | |
| 688 | ✗ | write(fmt, '("(""# "",A,",I0,"(1X,L1))")') size(this%bond_info) | |
| 689 | ✗ | write(unit, fmt) "in_dataset_2body", this%in_dataset_2body | |
| 690 | ✗ | write(unit, *) | |
| 691 | ✗ | write(unit, '("# 2-body")') | |
| 692 | ✗ | write(fmt,'("(""# bond-length "",",I0,"(1X,A))")') size(this%bond_info) | |
| 693 | write(unit, fmt) & | ||
| 694 | ( & | ||
| 695 | trim(this%bond_info(i)%element(1)) // "-" // & | ||
| 696 | ✗ | trim(this%bond_info(i)%element(2)), & | |
| 697 | ✗ | i = 1, size(this%bond_info) & | |
| 698 | ✗ | ) | |
| 699 | ✗ | do i = 1, this%nbins(1) | |
| 700 | write(unit, *) & | ||
| 701 | ✗ | this%cutoff_min(1) + this%width(1) * ( i - 1 ), & | |
| 702 | ✗ | this%gdf%df_2body(i,:) | |
| 703 | end do | ||
| 704 | ✗ | write(unit, *) | |
| 705 | ✗ | write(unit, '("# 3-body")') | |
| 706 | ✗ | write(fmt,'("(""# bond-angle "",",I0,"(1X,A))")') size(this%bond_info) | |
| 707 | ✗ | write(unit, fmt) this%element_info(:)%name | |
| 708 | ✗ | do i = 1, this%nbins(2) | |
| 709 | write(unit, *) & | ||
| 710 | ✗ | this%cutoff_min(2) + this%width(2) * ( i - 1 ), & | |
| 711 | ✗ | this%gdf%df_3body(i,:) | |
| 712 | end do | ||
| 713 | ✗ | write(unit, *) | |
| 714 | ✗ | write(unit, '("# 4-body")') | |
| 715 | ✗ | write(fmt,'("(""# dihedral-angle "",",I0,"(1X,A))")') size(this%bond_info) | |
| 716 | ✗ | write(unit, fmt) this%element_info(:)%name | |
| 717 | ✗ | do i = 1, this%nbins(3) | |
| 718 | write(unit, *) & | ||
| 719 | ✗ | this%cutoff_min(2) + this%width(2) * ( i - 1 ), & | |
| 720 | ✗ | this%gdf%df_4body(i,:) | |
| 721 | end do | ||
| 722 | ✗ | close(unit) | |
| 723 | |||
| 724 | ✗ | end subroutine write_gdfs | |
| 725 | !############################################################################### | ||
| 726 | |||
| 727 | |||
| 728 | !############################################################################### | ||
| 729 | ✗ | subroutine read_gdfs(this, file) | |
| 730 | !! Read the generalised distribution functions from a file. | ||
| 731 | implicit none | ||
| 732 | |||
| 733 | ! Arguments | ||
| 734 | class(distribs_container_type), intent(inout) :: this | ||
| 735 | !! Parent. Instance of distribution functions container. | ||
| 736 | character(*), intent(in) :: file | ||
| 737 | !! Filename to read the generalised distribution functions from. | ||
| 738 | |||
| 739 | ! Local variables | ||
| 740 | integer :: unit | ||
| 741 | !! File unit. | ||
| 742 | |||
| 743 | integer :: i | ||
| 744 | !! Loop index. | ||
| 745 | integer :: nspec | ||
| 746 | !! Number of species. | ||
| 747 | logical :: exist | ||
| 748 | !! Boolean whether the file exists. | ||
| 749 | character(256) :: buffer, buffer1, buffer2 | ||
| 750 | !! Buffer for reading lines. | ||
| 751 | |||
| 752 | ! check if file exists | ||
| 753 | ✗ | inquire(file=file, exist=exist) | |
| 754 | ✗ | if(.not.exist)then | |
| 755 | ✗ | call stop_program( "File does not exist" ) | |
| 756 | ✗ | return | |
| 757 | end if | ||
| 758 | |||
| 759 | ! read the file | ||
| 760 | ✗ | open(newunit=unit, file=file) | |
| 761 | ✗ | read(unit, *) buffer1, buffer2, this%nbins | |
| 762 | ✗ | read(unit, *) buffer1, buffer2, this%width | |
| 763 | ✗ | read(unit, *) buffer1, buffer2, this%sigma | |
| 764 | ✗ | read(unit, *) buffer1, buffer2, this%cutoff_min | |
| 765 | ✗ | read(unit, *) buffer1, buffer2, this%cutoff_max | |
| 766 | ✗ | read(unit, *) buffer1, buffer2, this%radius_distance_tol | |
| 767 | ✗ | read(unit, '(A)') buffer | |
| 768 | ✗ | nspec = icount(buffer(index(buffer,"elements")+8:)) | |
| 769 | ✗ | allocate(this%element_info(nspec)) | |
| 770 | ✗ | read(buffer, *) buffer1, buffer2, this%element_info(:)%name | |
| 771 | ✗ | read(unit, *) buffer1, buffer2, this%element_info(:)%energy | |
| 772 | ✗ | do i = 1, nspec | |
| 773 | call this%set_element_energy( & | ||
| 774 | this%element_info(i)%name, & | ||
| 775 | this%element_info(i)%energy & | ||
| 776 | ✗ | ) | |
| 777 | ✗ | call this%element_info(i)%set(this%element_info(i)%name) | |
| 778 | end do | ||
| 779 | ✗ | call this%update_bond_info() | |
| 780 | ✗ | allocate(this%best_energy_per_species(nspec)) | |
| 781 | ✗ | allocate(this%norm_3body(nspec)) | |
| 782 | ✗ | allocate(this%norm_4body(nspec)) | |
| 783 | ✗ | allocate(this%in_dataset_3body(nspec)) | |
| 784 | ✗ | allocate(this%in_dataset_4body(nspec)) | |
| 785 | ✗ | read(unit, *) buffer1, buffer2, this%best_energy_per_species | |
| 786 | ✗ | read(unit, *) buffer1, buffer2, this%norm_3body | |
| 787 | ✗ | read(unit, *) buffer1, buffer2, this%norm_4body | |
| 788 | ✗ | read(unit, *) buffer1, buffer2, this%in_dataset_3body | |
| 789 | ✗ | read(unit, *) buffer1, buffer2, this%in_dataset_4body | |
| 790 | ✗ | read(unit, *) | |
| 791 | ✗ | allocate(this%best_energy_pair(size(this%bond_info))) | |
| 792 | ✗ | allocate(this%norm_2body(size(this%bond_info))) | |
| 793 | ✗ | allocate(this%in_dataset_2body(size(this%bond_info))) | |
| 794 | ✗ | read(unit, *) buffer1, buffer2, this%bond_info(:)%radius_covalent | |
| 795 | ✗ | read(unit, *) buffer1, buffer2, this%best_energy_pair | |
| 796 | ✗ | read(unit, *) buffer1, buffer2, this%norm_2body | |
| 797 | ✗ | read(unit, *) buffer1, buffer2, this%in_dataset_2body | |
| 798 | ✗ | read(unit, *) | |
| 799 | ✗ | read(unit, *) | |
| 800 | ✗ | read(unit, *) | |
| 801 | ✗ | allocate(this%gdf%df_2body(this%nbins(1),size(this%bond_info))) | |
| 802 | ✗ | do i = 1, this%nbins(1) | |
| 803 | ✗ | read(unit, *) buffer, this%gdf%df_2body(i,:) | |
| 804 | end do | ||
| 805 | ✗ | read(unit, *) | |
| 806 | ✗ | read(unit, *) | |
| 807 | ✗ | read(unit, *) | |
| 808 | ✗ | allocate(this%gdf%df_3body(this%nbins(2),nspec)) | |
| 809 | ✗ | do i = 1, this%nbins(2) | |
| 810 | ✗ | read(unit, *) buffer, this%gdf%df_3body(i,:) | |
| 811 | end do | ||
| 812 | ✗ | read(unit, *) | |
| 813 | ✗ | read(unit, *) | |
| 814 | ✗ | read(unit, *) | |
| 815 | ✗ | allocate(this%gdf%df_4body(this%nbins(3),nspec)) | |
| 816 | ✗ | do i = 1, this%nbins(3) | |
| 817 | ✗ | read(unit, *) buffer, this%gdf%df_4body(i,:) | |
| 818 | end do | ||
| 819 | ✗ | close(unit) | |
| 820 | |||
| 821 | ✗ | end subroutine read_gdfs | |
| 822 | !############################################################################### | ||
| 823 | |||
| 824 | |||
| 825 | !############################################################################### | ||
| 826 | ✗ | subroutine write_dfs(this, file) | |
| 827 | !! Write all distribution functions for each system to a file. | ||
| 828 | implicit none | ||
| 829 | |||
| 830 | ! Arguments | ||
| 831 | class(distribs_container_type), intent(in) :: this | ||
| 832 | !! Parent. Instance of distribution functions container. | ||
| 833 | character(*), intent(in) :: file | ||
| 834 | !! Filename to write the distribution functions to. | ||
| 835 | |||
| 836 | ! Local variables | ||
| 837 | integer :: unit | ||
| 838 | !! File unit. | ||
| 839 | integer :: i, j | ||
| 840 | !! Loop indices. | ||
| 841 | character(256) :: stop_msg | ||
| 842 | !! Error message. | ||
| 843 | |||
| 844 | ✗ | if(.not.allocated(this%system))then | |
| 845 | write(stop_msg,*) "No systems to write" // & | ||
| 846 | achar(13) // achar(10) // & | ||
| 847 | "Systems either not created or deallocated after evolve" // & | ||
| 848 | achar(13) // achar(10) // & | ||
| 849 | "To stop automatic deallocation, " // & | ||
| 850 | "use the following flag in create()" // & | ||
| 851 | achar(13) // achar(10) // & | ||
| 852 | ✗ | " deallocate_systems = .false." | |
| 853 | ✗ | call stop_program( stop_msg ) | |
| 854 | ✗ | return | |
| 855 | end if | ||
| 856 | ✗ | open(newunit=unit, file=file) | |
| 857 | ✗ | write(unit, *) "nbins", this%nbins | |
| 858 | ✗ | write(unit, *) "width", this%width | |
| 859 | ✗ | write(unit, *) "sigma", this%sigma | |
| 860 | ✗ | write(unit, *) "cutoff_min", this%cutoff_min | |
| 861 | ✗ | write(unit, *) "cutoff_max", this%cutoff_max | |
| 862 | ✗ | write(unit, *) | |
| 863 | ✗ | do i = 1, size(this%system,1) | |
| 864 | ✗ | write(unit, *) this%system(i)%energy | |
| 865 | ✗ | write(unit, *) this%system(i)%element_symbols | |
| 866 | ✗ | write(unit, *) this%system(i)%stoichiometry | |
| 867 | ✗ | do j = 1, this%nbins(1) | |
| 868 | ✗ | write(unit, *) this%system(i)%df_2body(j,:) | |
| 869 | end do | ||
| 870 | ✗ | do j = 1, this%nbins(2) | |
| 871 | ✗ | write(unit, *) this%system(i)%df_3body(j,:) | |
| 872 | end do | ||
| 873 | ✗ | do j = 1, this%nbins(3) | |
| 874 | ✗ | write(unit, *) this%system(i)%df_4body(j,:) | |
| 875 | end do | ||
| 876 | ✗ | write(unit, *) | |
| 877 | end do | ||
| 878 | ✗ | close(unit) | |
| 879 | |||
| 880 | ✗ | end subroutine write_dfs | |
| 881 | !############################################################################### | ||
| 882 | |||
| 883 | |||
| 884 | !############################################################################### | ||
| 885 | ✗ | subroutine read_dfs(this, file) | |
| 886 | !! Read all distribution functions for each system from a file. | ||
| 887 | implicit none | ||
| 888 | |||
| 889 | ! Arguments | ||
| 890 | class(distribs_container_type), intent(inout) :: this | ||
| 891 | !! Parent. Instance of distribution functions container. | ||
| 892 | character(*), intent(in) :: file | ||
| 893 | !! Filename to read the distribution functions from. | ||
| 894 | |||
| 895 | ! Local variables | ||
| 896 | integer :: unit | ||
| 897 | !! File unit. | ||
| 898 | integer :: j | ||
| 899 | !! Loop indices. | ||
| 900 | integer :: iostat | ||
| 901 | !! I/O status. | ||
| 902 | integer :: num_species, num_pairs | ||
| 903 | !! Number of species and pairs. | ||
| 904 | character(256) :: buffer | ||
| 905 | !! Buffer for reading lines. | ||
| 906 | ✗ | type(distribs_type) :: system | |
| 907 | !! System to read distribution functions into. | ||
| 908 | |||
| 909 | |||
| 910 | ✗ | open(newunit=unit, file=file) | |
| 911 | ✗ | read(unit, *) buffer, this%nbins | |
| 912 | ✗ | read(unit, *) buffer, this%width | |
| 913 | ✗ | read(unit, *) buffer, this%sigma | |
| 914 | ✗ | read(unit, *) buffer, this%cutoff_min | |
| 915 | ✗ | read(unit, *) buffer, this%cutoff_max | |
| 916 | ✗ | do | |
| 917 | ✗ | read(unit, '(A)', iostat=iostat) buffer | |
| 918 | ✗ | if(iostat.ne.0) exit | |
| 919 | ✗ | if(trim(buffer).eq.''.or.trim(buffer).eq.'#') cycle | |
| 920 | ✗ | read(buffer, *) system%energy | |
| 921 | ✗ | read(unit, '(A)') buffer | |
| 922 | ✗ | num_species = icount(buffer) | |
| 923 | ✗ | allocate(system%element_symbols(num_species)) | |
| 924 | ✗ | allocate(system%stoichiometry(num_species)) | |
| 925 | ✗ | read(buffer, *) system%element_symbols | |
| 926 | ✗ | read(unit, *) system%stoichiometry | |
| 927 | ✗ | system%num_atoms = sum(system%stoichiometry) | |
| 928 | num_pairs = nint( & | ||
| 929 | gamma(real(num_species + 2, real32)) / & | ||
| 930 | ( gamma(real(num_species, real32)) * gamma( 3._real32 ) ) & | ||
| 931 | ✗ | ) | |
| 932 | ✗ | allocate(system%df_2body(this%nbins(1),num_pairs)) | |
| 933 | ✗ | do j = 1, this%nbins(1) | |
| 934 | ✗ | read(unit, *) system%df_2body(j,:) | |
| 935 | end do | ||
| 936 | ✗ | allocate(system%df_3body(this%nbins(2),num_species)) | |
| 937 | ✗ | do j = 1, this%nbins(2) | |
| 938 | ✗ | read(unit, *) system%df_3body(j,:) | |
| 939 | end do | ||
| 940 | ✗ | allocate(system%df_4body(this%nbins(3),num_species)) | |
| 941 | ✗ | do j = 1, this%nbins(3) | |
| 942 | ✗ | read(unit, *) system%df_4body(j,:) | |
| 943 | end do | ||
| 944 | |||
| 945 | ✗ | this%system = [ this%system, system ] | |
| 946 | ✗ | deallocate(& | |
| 947 | ✗ | system%element_symbols, system%stoichiometry, & | |
| 948 | ✗ | system%df_2body, system%df_3body, system%df_4body & | |
| 949 | ✗ | ) | |
| 950 | end do | ||
| 951 | ✗ | close(unit) | |
| 952 | |||
| 953 | ✗ | end subroutine read_dfs | |
| 954 | !############################################################################### | ||
| 955 | |||
| 956 | |||
| 957 | !############################################################################### | ||
| 958 | ✗ | subroutine write_2body(this, file) | |
| 959 | !! Write the learned 2-body distribution functions to a file. | ||
| 960 | implicit none | ||
| 961 | |||
| 962 | ! Arguments | ||
| 963 | class(distribs_container_type), intent(in) :: this | ||
| 964 | !! Parent. Instance of distribution functions container. | ||
| 965 | character(*), intent(in) :: file | ||
| 966 | !! Filename to write the 2-body distribution functions to. | ||
| 967 | |||
| 968 | ! Local variables | ||
| 969 | integer :: unit | ||
| 970 | !! File unit. | ||
| 971 | integer :: i, j, is, js | ||
| 972 | !! Loop indices. | ||
| 973 | integer :: num_pairs | ||
| 974 | !! Number of pairs. | ||
| 975 | ✗ | integer, allocatable, dimension(:,:) :: idx | |
| 976 | !! Pair indices. | ||
| 977 | |||
| 978 | |||
| 979 | num_pairs = nint( & | ||
| 980 | gamma(real(size(this%element_info) + 2, real32)) / & | ||
| 981 | ( gamma(real(size(this%element_info), real32)) * gamma( 3._real32 ) ) & | ||
| 982 | ✗ | ) | |
| 983 | ✗ | allocate(idx(2,num_pairs)) | |
| 984 | ✗ | i = 0 | |
| 985 | ✗ | do is = 1, size(this%element_info) | |
| 986 | ✗ | do js = is, size(this%element_info), 1 | |
| 987 | ✗ | i = i + 1 | |
| 988 | ✗ | idx(:,i) = [is, js] | |
| 989 | end do | ||
| 990 | end do | ||
| 991 | |||
| 992 | ✗ | open(newunit=unit, file=file) | |
| 993 | ✗ | do i = 1, size(this%gdf%df_2body, dim=2) | |
| 994 | write(unit,'("# ",A,2X,A)') & | ||
| 995 | ✗ | this%element_info(idx(1,i))%name, & | |
| 996 | ✗ | this%element_info(idx(2,i))%name | |
| 997 | ✗ | do j = 1, size(this%gdf%df_2body, dim=1) | |
| 998 | write(unit,*) & | ||
| 999 | ✗ | this%cutoff_min(1) + this%width(1) * ( j - 1 ), & | |
| 1000 | ✗ | this%gdf%df_2body(j,i) | |
| 1001 | end do | ||
| 1002 | ✗ | write(unit,*) | |
| 1003 | end do | ||
| 1004 | ✗ | close(unit) | |
| 1005 | |||
| 1006 | ✗ | end subroutine write_2body | |
| 1007 | !############################################################################### | ||
| 1008 | |||
| 1009 | |||
| 1010 | !############################################################################### | ||
| 1011 | ✗ | subroutine write_3body(this, file) | |
| 1012 | !! Write the learned 3-body distribution functions to a file. | ||
| 1013 | implicit none | ||
| 1014 | |||
| 1015 | ! Arguments | ||
| 1016 | class(distribs_container_type), intent(in) :: this | ||
| 1017 | !! Parent. Instance of distribution functions container. | ||
| 1018 | character(*), intent(in) :: file | ||
| 1019 | !! Filename to write the 3-body distribution functions to. | ||
| 1020 | |||
| 1021 | ! Local variables | ||
| 1022 | integer :: unit | ||
| 1023 | !! File unit. | ||
| 1024 | integer :: i, j | ||
| 1025 | !! Loop indices. | ||
| 1026 | |||
| 1027 | |||
| 1028 | ✗ | open(newunit=unit, file=file) | |
| 1029 | ✗ | do i = 1, size(this%gdf%df_3body, dim=2) | |
| 1030 | ✗ | write(unit,'("# ",A)') this%element_info(i)%name | |
| 1031 | ✗ | do j = 1, size(this%gdf%df_3body, dim=1) | |
| 1032 | write(unit,*) & | ||
| 1033 | ✗ | this%cutoff_min(2) + this%width(2) * ( j - 1 ), & | |
| 1034 | ✗ | this%gdf%df_3body(j,i) | |
| 1035 | end do | ||
| 1036 | ✗ | write(unit,*) | |
| 1037 | end do | ||
| 1038 | ✗ | close(unit) | |
| 1039 | |||
| 1040 | ✗ | end subroutine write_3body | |
| 1041 | !############################################################################### | ||
| 1042 | |||
| 1043 | |||
| 1044 | !############################################################################### | ||
| 1045 | ✗ | subroutine write_4body(this, file) | |
| 1046 | !! Write the learned 4-body distribution functions to a file. | ||
| 1047 | implicit none | ||
| 1048 | |||
| 1049 | ! Arguments | ||
| 1050 | class(distribs_container_type), intent(in) :: this | ||
| 1051 | !! Parent. Instance of distribution functions container. | ||
| 1052 | character(*), intent(in) :: file | ||
| 1053 | !! Filename to write the 4-body distribution functions to. | ||
| 1054 | |||
| 1055 | ! Local variables | ||
| 1056 | integer :: unit | ||
| 1057 | !! File unit. | ||
| 1058 | integer :: i, j | ||
| 1059 | !! Loop indices. | ||
| 1060 | |||
| 1061 | |||
| 1062 | ✗ | open(newunit=unit, file=file) | |
| 1063 | ✗ | do i = 1, size(this%gdf%df_4body, dim=2) | |
| 1064 | ✗ | write(unit,'("# ",A)') this%element_info(i)%name | |
| 1065 | ✗ | do j = 1, size(this%gdf%df_4body, dim=1) | |
| 1066 | write(unit,*) & | ||
| 1067 | ✗ | this%cutoff_min(3) + this%width(3) * ( j - 1 ), & | |
| 1068 | ✗ | this%gdf%df_4body(j,i) | |
| 1069 | end do | ||
| 1070 | ✗ | write(unit,*) | |
| 1071 | end do | ||
| 1072 | ✗ | close(unit) | |
| 1073 | |||
| 1074 | ✗ | end subroutine write_4body | |
| 1075 | !############################################################################### | ||
| 1076 | |||
| 1077 | |||
| 1078 | !############################################################################### | ||
| 1079 | 27 | subroutine add(this, system) | |
| 1080 | !! Add a system to the container. | ||
| 1081 | implicit none | ||
| 1082 | |||
| 1083 | ! Arguments | ||
| 1084 | class(distribs_container_type), intent(inout) :: this | ||
| 1085 | !! Parent. Instance of distribution functions container. | ||
| 1086 | class(*), dimension(..), intent(in) :: system | ||
| 1087 | !! System to add to the container. | ||
| 1088 | |||
| 1089 | ! Local variables | ||
| 1090 | integer :: i | ||
| 1091 | !! Loop index. | ||
| 1092 | integer :: num_structures_previous | ||
| 1093 | !! Number of structures in the container before adding the system. | ||
| 1094 | character(256) :: stop_msg | ||
| 1095 | !! Error message. | ||
| 1096 | |||
| 1097 | select rank(rank_ptr => system) | ||
| 1098 | rank(0) | ||
| 1099 |
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|
6 | select type(type_ptr => rank_ptr) |
| 1100 | type is (distribs_type) | ||
| 1101 |
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|
16 | this%system = [ this%system, type_ptr ] |
| 1102 | class is (basis_type) | ||
| 1103 | #if defined(GFORTRAN) | ||
| 1104 | call this%add_basis(type_ptr) | ||
| 1105 | #else | ||
| 1106 | 24 | block | |
| 1107 |
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|
96 | type(basis_type), dimension(1) :: basis |
| 1108 | |||
| 1109 |
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|
12 | basis = type_ptr |
| 1110 | 4 | call this%add_basis(basis(1)) | |
| 1111 | end block | ||
| 1112 | #endif | ||
| 1113 | class default | ||
| 1114 | write(stop_msg,*) "Invalid type for system" // & | ||
| 1115 | achar(13) // achar(10) // & | ||
| 1116 | 1 | "Expected type distribs_type or basis_type" | |
| 1117 | 1 | call stop_program( stop_msg ) | |
| 1118 | 1 | return | |
| 1119 | end select | ||
| 1120 | rank(1) | ||
| 1121 | 20 | num_structures_previous = size(this%system) | |
| 1122 | 20 | if(.not.allocated(this%system))then | |
| 1123 | ✗ | allocate(this%system(0)) | |
| 1124 | end if | ||
| 1125 |
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|
40 | select type(type_ptr => rank_ptr) |
| 1126 | type is (distribs_type) | ||
| 1127 |
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|
30 | this%system = [ this%system, type_ptr ] |
| 1128 | class is (basis_type) | ||
| 1129 |
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|
57 | do i = 1, size(type_ptr) |
| 1130 | 39 | call this%add_basis(type_ptr(i)) | |
| 1131 | end do | ||
| 1132 | class default | ||
| 1133 | write(stop_msg,*) "Invalid type for system" // & | ||
| 1134 | achar(13) // achar(10) // & | ||
| 1135 | 1 | "Expected type distribs_type or basis_type" | |
| 1136 | 1 | call stop_program( stop_msg ) | |
| 1137 | 1 | return | |
| 1138 | end select | ||
| 1139 | rank default | ||
| 1140 | write(stop_msg,*) "Invalid rank for system" // & | ||
| 1141 | achar(13) // achar(10) // & | ||
| 1142 | 1 | "Expected rank 0 or 1, got ", rank(rank_ptr) | |
| 1143 | 1 | call stop_program( stop_msg ) | |
| 1144 | 1 | return | |
| 1145 | end select | ||
| 1146 | 24 | call this%update_element_info() | |
| 1147 | 24 | call this%update_bond_info() | |
| 1148 | |||
| 1149 | end subroutine add | ||
| 1150 | !############################################################################### | ||
| 1151 | |||
| 1152 | |||
| 1153 | !############################################################################### | ||
| 1154 | 25 | subroutine add_basis(this, basis) | |
| 1155 | !! Add a basis to the container. | ||
| 1156 | implicit none | ||
| 1157 | |||
| 1158 | ! Arguments | ||
| 1159 | class(distribs_container_type), intent(inout) :: this | ||
| 1160 | !! Parent. Instance of distribution functions container. | ||
| 1161 | type(basis_type), intent(in) :: basis | ||
| 1162 | !! Basis to add to the container. | ||
| 1163 | |||
| 1164 | ! Local variables | ||
| 1165 | 25 | type(distribs_type) :: system | |
| 1166 | !! System to add to the container. | ||
| 1167 | |||
| 1168 | call system%calculate( & | ||
| 1169 | basis, & | ||
| 1170 | width = this%width, & | ||
| 1171 | sigma = this%sigma, & | ||
| 1172 | cutoff_min = this%cutoff_min, & | ||
| 1173 | cutoff_max = this%cutoff_max, & | ||
| 1174 | radius_distance_tol = this%radius_distance_tol & | ||
| 1175 | 25 | ) | |
| 1176 | |||
| 1177 |
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25 | if(.not.allocated(this%system))then |
| 1178 |
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|
16 | this%system = [ system ] |
| 1179 | else | ||
| 1180 |
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|
176 | this%system = [ this%system, system ] |
| 1181 | end if | ||
| 1182 |
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|
25 | end subroutine add_basis |
| 1183 | !############################################################################### | ||
| 1184 | |||
| 1185 | |||
| 1186 | !############################################################################### | ||
| 1187 |
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|
9 | subroutine set_element_map(this, element_list) |
| 1188 | !! Set the element map for the container. | ||
| 1189 | implicit none | ||
| 1190 | |||
| 1191 | ! Arguments | ||
| 1192 | class(distribs_container_type), intent(inout) :: this | ||
| 1193 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1194 | character(3), dimension(:), intent(in) :: element_list | ||
| 1195 | !! Element information. | ||
| 1196 | |||
| 1197 | ! Local variables | ||
| 1198 | integer :: is | ||
| 1199 | !! Loop index. | ||
| 1200 | integer :: idx | ||
| 1201 | !! Index of the element in the element_info array. | ||
| 1202 | character(256) :: stop_msg | ||
| 1203 | !! Error message. | ||
| 1204 | |||
| 1205 |
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|
9 | if(allocated(this%element_map)) deallocate(this%element_map) |
| 1206 |
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|
9 | allocate(this%element_map(size(element_list))) |
| 1207 |
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|
20 | do is = 1, size(element_list) |
| 1208 | idx = findloc( & | ||
| 1209 | [ this%element_info(:)%name ], element_list(is), dim=1 & | ||
| 1210 |
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|
45 | ) |
| 1211 |
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|
11 | if(idx.eq.0)then |
| 1212 | write(stop_msg,*) "Element not found in element_info array" // & | ||
| 1213 | achar(13) // achar(10) // & | ||
| 1214 | ✗ | "Element: ", element_list(is) | |
| 1215 | ✗ | call stop_program( stop_msg ) | |
| 1216 | ✗ | return | |
| 1217 | end if | ||
| 1218 | 20 | this%element_map(is) = idx | |
| 1219 | end do | ||
| 1220 | |||
| 1221 | end subroutine set_element_map | ||
| 1222 | !############################################################################### | ||
| 1223 | |||
| 1224 | |||
| 1225 | !############################################################################### | ||
| 1226 | 14 | subroutine set_element_info(this) | |
| 1227 | !! Set the list of elements for the container. | ||
| 1228 | implicit none | ||
| 1229 | |||
| 1230 | ! Arguments | ||
| 1231 | class(distribs_container_type), intent(inout) :: this | ||
| 1232 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1233 | |||
| 1234 | ! Local variables | ||
| 1235 | integer :: i | ||
| 1236 | !! Loop index. | ||
| 1237 | real(real32) :: radius | ||
| 1238 | !! Element radii. | ||
| 1239 | 14 | character(len=3), dimension(:), allocatable :: element_list | |
| 1240 | !! List of elements in the container. | ||
| 1241 | |||
| 1242 | |||
| 1243 | !--------------------------------------------------------------------------- | ||
| 1244 | ! get list of species in dataset | ||
| 1245 | !--------------------------------------------------------------------------- | ||
| 1246 |
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|
14 | allocate(element_list(0)) |
| 1247 |
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|
46 | element_list = [ this%system(1)%element_symbols ] |
| 1248 |
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15 | do i = 2, size(this%system),1 |
| 1249 |
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|
24 | element_list = [ element_list, this%system(i)%element_symbols ] |
| 1250 | end do | ||
| 1251 | 14 | call set(element_list) | |
| 1252 |
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14 | if(allocated(this%element_info)) deallocate(this%element_info) |
| 1253 |
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14 | if(.not.allocated(element_database)) allocate(element_database(0)) |
| 1254 |
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|
32 | allocate(this%element_info(size(element_list))) |
| 1255 |
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32 | do i = 1, size(element_list) |
| 1256 |
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|
98 | if( findloc( & |
| 1257 | [ element_database(:)%name ], element_list(i), dim=1 ) .lt. 1 )then | ||
| 1258 | ✗ | call get_element_properties(element_list(i), radius=radius) | |
| 1259 | element_database = [ & | ||
| 1260 | element_database(:), & | ||
| 1261 | element_type(name = element_list(i), radius = radius) & | ||
| 1262 | ✗ | ] | |
| 1263 | end if | ||
| 1264 | 32 | call this%element_info(i)%set(element_list(i)) | |
| 1265 | end do | ||
| 1266 | |||
| 1267 |
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|
14 | end subroutine set_element_info |
| 1268 | !############################################################################### | ||
| 1269 | |||
| 1270 | |||
| 1271 | !############################################################################### | ||
| 1272 | 24 | subroutine update_element_info(this) | |
| 1273 | !! Update the element information in the container. | ||
| 1274 | implicit none | ||
| 1275 | |||
| 1276 | ! Arguments | ||
| 1277 | class(distribs_container_type), intent(inout) :: this | ||
| 1278 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1279 | |||
| 1280 | ! Local variables | ||
| 1281 | integer :: i | ||
| 1282 | !! Loop index. | ||
| 1283 | real(real32) :: radius | ||
| 1284 | !! Element radii. | ||
| 1285 | 24 | character(len=3), dimension(:), allocatable :: element_list | |
| 1286 | !! List of elements in the container. | ||
| 1287 | |||
| 1288 | |||
| 1289 | !--------------------------------------------------------------------------- | ||
| 1290 | ! check if element_info is allocated, if not, set it and return | ||
| 1291 | !--------------------------------------------------------------------------- | ||
| 1292 |
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24 | if(.not.allocated(this%element_info))then |
| 1293 | 14 | call this%set_element_info() | |
| 1294 | 14 | return | |
| 1295 |
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|
10 | elseif(size(this%element_info).eq.0)then |
| 1296 | ✗ | call this%set_element_info() | |
| 1297 | ✗ | return | |
| 1298 | end if | ||
| 1299 | |||
| 1300 | |||
| 1301 | !--------------------------------------------------------------------------- | ||
| 1302 | ! get list of species in dataset | ||
| 1303 | !--------------------------------------------------------------------------- | ||
| 1304 |
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10 | allocate(element_list(0)) |
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30 | element_list = [ this%system(1)%element_symbols ] |
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26 | do i = 2, size(this%system),1 |
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|
179 | element_list = [ element_list, this%system(i)%element_symbols ] |
| 1308 | end do | ||
| 1309 | 10 | call set(element_list) | |
| 1310 | |||
| 1311 | |||
| 1312 | !--------------------------------------------------------------------------- | ||
| 1313 | ! check if all elements are in the element_info array | ||
| 1314 | !--------------------------------------------------------------------------- | ||
| 1315 |
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10 | if(.not.allocated(element_database)) allocate(element_database(0)) |
| 1316 |
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28 | do i = 1, size(element_list) |
| 1317 |
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|
114 | if(findloc( & |
| 1318 | [ element_database(:)%name ], & | ||
| 1319 | element_list(i), dim=1 ) .lt. 1 )then | ||
| 1320 | ✗ | call get_element_properties(element_list(i), radius=radius) | |
| 1321 | element_database = [ & | ||
| 1322 | element_database(:), & | ||
| 1323 | element_type(name = element_list(i), radius = radius) & | ||
| 1324 | ✗ | ] | |
| 1325 | end if | ||
| 1326 |
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|
92 | if( findloc( & |
| 1327 | [ this%element_info(:)%name ], & | ||
| 1328 | 10 | element_list(i), dim=1 ) .lt. 1 )then | |
| 1329 | this%element_info = [ & | ||
| 1330 | this%element_info(:), & | ||
| 1331 | element_type(element_list(i)) & | ||
| 1332 |
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|
15 | ] |
| 1333 | 2 | call this%element_info(size(this%element_info))%set(element_list(i)) | |
| 1334 | end if | ||
| 1335 | end do | ||
| 1336 | |||
| 1337 |
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|
24 | end subroutine update_element_info |
| 1338 | !############################################################################### | ||
| 1339 | |||
| 1340 | |||
| 1341 | !############################################################################### | ||
| 1342 | 20 | subroutine set_element_energy(this, element, energy) | |
| 1343 | !! Set the energy of an element in the container. | ||
| 1344 | implicit none | ||
| 1345 | |||
| 1346 | ! Arguments | ||
| 1347 | class(distribs_container_type), intent(inout) :: this | ||
| 1348 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1349 | character(len=3), intent(in) :: element | ||
| 1350 | !! Element name. | ||
| 1351 | real(real32), intent(in) :: energy | ||
| 1352 | !! Energy of the element. | ||
| 1353 | |||
| 1354 | ! Local variables | ||
| 1355 | integer :: idx, idx_db | ||
| 1356 | !! Index of the element in the element_info array. | ||
| 1357 | real(real32) :: radius | ||
| 1358 | !! Element radius. | ||
| 1359 | character(len=3) :: element_ | ||
| 1360 | !! Element name without null characters. | ||
| 1361 | |||
| 1362 | |||
| 1363 | !--------------------------------------------------------------------------- | ||
| 1364 | ! remove python formatting | ||
| 1365 | !--------------------------------------------------------------------------- | ||
| 1366 | 20 | element_ = strip_null(element) | |
| 1367 | |||
| 1368 | |||
| 1369 | !--------------------------------------------------------------------------- | ||
| 1370 | ! if element_info is allocated, update energy of associated index | ||
| 1371 | !--------------------------------------------------------------------------- | ||
| 1372 |
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20 | if(allocated(this%element_info))then |
| 1373 |
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21 | idx = findloc( [ this%element_info(:)%name ], element_, dim=1 ) |
| 1374 |
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3 | if(idx.ge.1) this%element_info(idx)%energy = energy |
| 1375 | end if | ||
| 1376 | |||
| 1377 | |||
| 1378 | !--------------------------------------------------------------------------- | ||
| 1379 | ! if element_database is allocated, update energy of associated index | ||
| 1380 | !--------------------------------------------------------------------------- | ||
| 1381 |
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20 | if(.not.allocated(element_database)) allocate(element_database(0)) |
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|
82 | idx_db = findloc( [ element_database(:)%name ], element_, dim=1 ) |
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20 | if(idx_db.lt.1)then |
| 1384 | 8 | call get_element_properties( element_, radius = radius ) | |
| 1385 | element_database = [ & | ||
| 1386 | element_database(:), & | ||
| 1387 | element_type(name = element_, energy = energy, radius = radius) & | ||
| 1388 |
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|
33 | ] |
| 1389 | else | ||
| 1390 | 12 | element_database(idx_db)%energy = energy | |
| 1391 | end if | ||
| 1392 | |||
| 1393 | 20 | end subroutine set_element_energy | |
| 1394 | !############################################################################### | ||
| 1395 | |||
| 1396 | |||
| 1397 | !############################################################################### | ||
| 1398 |
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|
17 | subroutine set_element_energies(this, elements, energies) |
| 1399 | !! Set the energies of elements in the container. | ||
| 1400 | implicit none | ||
| 1401 | |||
| 1402 | ! Arguments | ||
| 1403 | class(distribs_container_type), intent(inout) :: this | ||
| 1404 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1405 | character(len=3), dimension(:), intent(in) :: elements | ||
| 1406 | !! Element names. | ||
| 1407 | real(real32), dimension(:), intent(in) :: energies | ||
| 1408 | !! Energies of the elements. | ||
| 1409 | |||
| 1410 | ! Local variables | ||
| 1411 | integer :: i | ||
| 1412 | |||
| 1413 |
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|
36 | do i = 1, size(elements) |
| 1414 | 36 | call this%set_element_energy(elements(i), energies(i)) | |
| 1415 | end do | ||
| 1416 | |||
| 1417 | 17 | end subroutine set_element_energies | |
| 1418 | !############################################################################### | ||
| 1419 | |||
| 1420 | |||
| 1421 | !############################################################################### | ||
| 1422 | 1 | subroutine get_element_energies(this, elements, energies) | |
| 1423 | !! Return the energies of elements in the container. | ||
| 1424 | implicit none | ||
| 1425 | |||
| 1426 | ! Arguments | ||
| 1427 | class(distribs_container_type), intent(in) :: this | ||
| 1428 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1429 | character(len=3), dimension(:), allocatable, intent(out) :: elements | ||
| 1430 | !! Element names. | ||
| 1431 | real(real32), dimension(:), allocatable, intent(out) :: energies | ||
| 1432 | !! Energies of the elements. | ||
| 1433 | |||
| 1434 | ! Local variables | ||
| 1435 | integer :: i | ||
| 1436 | !! Loop index. | ||
| 1437 | |||
| 1438 | |||
| 1439 |
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|
1 | allocate(elements(size(this%element_info))) |
| 1440 |
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|
1 | allocate(energies(size(this%element_info))) |
| 1441 |
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|
2 | do i = 1, size(this%element_info) |
| 1442 | 1 | elements(i) = this%element_info(i)%name | |
| 1443 | 2 | energies(i) = this%element_info(i)%energy | |
| 1444 | end do | ||
| 1445 | |||
| 1446 | 1 | end subroutine get_element_energies | |
| 1447 | !############################################################################### | ||
| 1448 | |||
| 1449 | |||
| 1450 | !############################################################################### | ||
| 1451 | 1 | subroutine get_element_energies_staticmem(this, elements, energies) | |
| 1452 | !! Return the energies of elements in the container. | ||
| 1453 | !! | ||
| 1454 | !! This subroutine is used when the memory for the output arrays is | ||
| 1455 | !! allocated outside of the subroutine. Used in Python interface. | ||
| 1456 | implicit none | ||
| 1457 | |||
| 1458 | ! Arguments | ||
| 1459 | class(distribs_container_type), intent(in) :: this | ||
| 1460 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1461 | character(len=3), dimension(size(this%element_info,1)), intent(out) :: & | ||
| 1462 | elements | ||
| 1463 | !! Element names. | ||
| 1464 | real(real32), dimension(size(this%element_info,1)), intent(out) :: energies | ||
| 1465 | !! Energies of the elements. | ||
| 1466 | |||
| 1467 | ! Local variables | ||
| 1468 | integer :: i | ||
| 1469 | !! Loop index. | ||
| 1470 | |||
| 1471 | |||
| 1472 |
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|
2 | do i = 1, size(this%element_info,1) |
| 1473 | 1 | elements(i) = this%element_info(i)%name | |
| 1474 | 2 | energies(i) = this%element_info(i)%energy | |
| 1475 | end do | ||
| 1476 | |||
| 1477 | 1 | end subroutine get_element_energies_staticmem | |
| 1478 | !############################################################################### | ||
| 1479 | |||
| 1480 | |||
| 1481 | !############################################################################### | ||
| 1482 | 27 | subroutine set_bond_info(this) | |
| 1483 | !! Set the 2-body bond information for the container. | ||
| 1484 | implicit none | ||
| 1485 | |||
| 1486 | ! Arguments | ||
| 1487 | class(distribs_container_type), intent(inout) :: this | ||
| 1488 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1489 | |||
| 1490 | ! Local variables | ||
| 1491 | integer :: i, j | ||
| 1492 | !! Loop index. | ||
| 1493 | integer :: num_elements, num_pairs | ||
| 1494 | !! Number of elements and pairs. | ||
| 1495 | logical :: success | ||
| 1496 | !! Success flag. | ||
| 1497 | |||
| 1498 | |||
| 1499 | !--------------------------------------------------------------------------- | ||
| 1500 | ! allocate the bond information array | ||
| 1501 | !--------------------------------------------------------------------------- | ||
| 1502 | 27 | num_elements = size(this%element_info) | |
| 1503 | num_pairs = nint(gamma(real(num_elements + 2, real32)) / & | ||
| 1504 | 27 | ( gamma(real(num_elements, real32)) * gamma( 3._real32 ) ) ) | |
| 1505 |
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27 | if(allocated(this%bond_info)) deallocate(this%bond_info) |
| 1506 |
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|
84 | allocate(this%bond_info(num_pairs)) |
| 1507 | |||
| 1508 | |||
| 1509 | !--------------------------------------------------------------------------- | ||
| 1510 | ! loop over all pairs of elements to set the bond information | ||
| 1511 | !--------------------------------------------------------------------------- | ||
| 1512 | 27 | num_pairs = 0 | |
| 1513 |
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66 | pair_loop1: do i = 1, num_elements |
| 1514 |
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|
123 | pair_loop2: do j = i, num_elements |
| 1515 | 57 | num_pairs = num_pairs + 1 | |
| 1516 | call this%bond_info(num_pairs)%set( & | ||
| 1517 | this%element_info(i)%name, & | ||
| 1518 | this%element_info(j)%name, & | ||
| 1519 | success & | ||
| 1520 | 57 | ) | |
| 1521 |
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|
57 | if(success) cycle pair_loop2 |
| 1522 | call set_bond_radius_to_default( [ & | ||
| 1523 | this%element_info(i)%name, & | ||
| 1524 | this%element_info(j)%name & | ||
| 1525 |
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|
6 | ] ) |
| 1526 | call this%bond_info(num_pairs)%set( & | ||
| 1527 | this%element_info(i)%name, & | ||
| 1528 | this%element_info(j)%name, & | ||
| 1529 | success & | ||
| 1530 | 41 | ) | |
| 1531 | end do pair_loop2 | ||
| 1532 | end do pair_loop1 | ||
| 1533 | |||
| 1534 | 27 | end subroutine set_bond_info | |
| 1535 | !############################################################################### | ||
| 1536 | |||
| 1537 | |||
| 1538 | !############################################################################### | ||
| 1539 | 2 | subroutine set_bond_radius_to_default(elements) | |
| 1540 | !! Set the bond radius to the default value. | ||
| 1541 | !! | ||
| 1542 | !! The default value is the average of the covalent radii of the elements. | ||
| 1543 | implicit none | ||
| 1544 | |||
| 1545 | ! Arguments | ||
| 1546 | character(len=3), dimension(2), intent(in) :: elements | ||
| 1547 | !! Element symbols. | ||
| 1548 | |||
| 1549 | ! Local variables | ||
| 1550 | integer :: idx1, idx2 | ||
| 1551 | !! Index of the elements in the element database. | ||
| 1552 | real(real32) :: radius, radius1, radius2 | ||
| 1553 | !! Average of covalent radii. | ||
| 1554 | character(256) :: warn_msg | ||
| 1555 | |||
| 1556 | |||
| 1557 | write(warn_msg,'("No bond data for element pair ",A," and ",A)') & | ||
| 1558 | 2 | elements(1), elements(2) | |
| 1559 | warn_msg = trim(warn_msg) // & | ||
| 1560 | achar(13) // achar(10) // & | ||
| 1561 |
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2 | "Setting bond to average of covalent radii" |
| 1562 | 2 | call print_warning(warn_msg) | |
| 1563 |
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2 | if(.not.allocated(element_database)) allocate(element_database(0)) |
| 1564 | idx1 = findloc([ element_database(:)%name ], & | ||
| 1565 |
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|
14 | elements(1), dim=1) |
| 1566 |
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2 | if(idx1.lt.1)then |
| 1567 | ✗ | call get_element_properties(elements(1), radius=radius1) | |
| 1568 | element_database = [ element_database, & | ||
| 1569 | ✗ | element_type(name=elements(1), radius=radius1) ] | |
| 1570 | ✗ | idx1 = size(element_database) | |
| 1571 | end if | ||
| 1572 | idx2 = findloc([ element_database(:)%name ], & | ||
| 1573 |
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|
14 | elements(2), dim=1) |
| 1574 |
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2 | if(idx2.lt.1)then |
| 1575 | ✗ | call get_element_properties(elements(2), radius=radius2) | |
| 1576 | element_database = [ element_database, & | ||
| 1577 | ✗ | element_type(name=elements(2), radius=radius2) ] | |
| 1578 | ✗ | idx2 = size(element_database) | |
| 1579 | end if | ||
| 1580 | radius = ( element_database(idx1)%radius + & | ||
| 1581 | 2 | element_database(idx2)%radius ) / 2._real32 | |
| 1582 |
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2 | if(.not.allocated(element_bond_database)) & |
| 1583 | ✗ | allocate(element_bond_database(0)) | |
| 1584 | element_bond_database = [ element_bond_database, & | ||
| 1585 | element_bond_type(elements=[ & | ||
| 1586 | elements(1), & | ||
| 1587 | elements(2) & | ||
| 1588 | ], radius=radius) & | ||
| 1589 |
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|
37 | ] |
| 1590 | call sort_str( & | ||
| 1591 | element_bond_database(size(element_bond_database))%element & | ||
| 1592 | 2 | ) | |
| 1593 | |||
| 1594 | 2 | end subroutine set_bond_radius_to_default | |
| 1595 | !############################################################################### | ||
| 1596 | |||
| 1597 | |||
| 1598 | !############################################################################### | ||
| 1599 | 28 | subroutine update_bond_info(this) | |
| 1600 | !! Update the element information in the container. | ||
| 1601 | implicit none | ||
| 1602 | |||
| 1603 | ! Arguments | ||
| 1604 | class(distribs_container_type), intent(inout) :: this | ||
| 1605 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1606 | |||
| 1607 | ! Local variables | ||
| 1608 | integer :: i, j, k, is, js | ||
| 1609 | !! Loop index. | ||
| 1610 | real(real32) :: radius, radius1, radius2 | ||
| 1611 | !! Average of covalent radii. | ||
| 1612 | 28 | character(len=3), dimension(:), allocatable :: element_list | |
| 1613 | !! List of elements in the container. | ||
| 1614 | 28 | character(len=3), dimension(:,:), allocatable :: pair_list | |
| 1615 | !! List of element pairs in the container. | ||
| 1616 | |||
| 1617 | |||
| 1618 | !--------------------------------------------------------------------------- | ||
| 1619 | ! check if bond_info is allocated, if not, set it and return | ||
| 1620 | !--------------------------------------------------------------------------- | ||
| 1621 |
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28 | if(.not.allocated(this%bond_info))then |
| 1622 | 14 | call this%set_bond_info() | |
| 1623 | 14 | return | |
| 1624 |
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14 | elseif(size(this%bond_info).eq.0)then |
| 1625 | ✗ | call this%set_bond_info() | |
| 1626 | ✗ | return | |
| 1627 | end if | ||
| 1628 | |||
| 1629 | |||
| 1630 | !--------------------------------------------------------------------------- | ||
| 1631 | ! get list of element pairs in dataset | ||
| 1632 | !--------------------------------------------------------------------------- | ||
| 1633 |
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|
14 | allocate(element_list(0)) |
| 1634 |
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|
42 | element_list = [ this%system(1)%element_symbols ] |
| 1635 |
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36 | do i = 2, size(this%system),1 |
| 1636 |
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|
243 | element_list = [ element_list, this%system(i)%element_symbols ] |
| 1637 | end do | ||
| 1638 | 14 | call set(element_list) | |
| 1639 |
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|
14 | allocate(pair_list(triangular_number(size(element_list)),2)) |
| 1640 | 14 | k = 0 | |
| 1641 |
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40 | do i = 1, size(element_list) |
| 1642 |
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84 | do j = i, size(element_list) |
| 1643 | 44 | k = k + 1 | |
| 1644 |
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|
132 | pair_list(k,:) = [ element_list(i), element_list(j) ] |
| 1645 | 70 | call sort_str(pair_list(k,:)) | |
| 1646 | end do | ||
| 1647 | end do | ||
| 1648 | |||
| 1649 | !--------------------------------------------------------------------------- | ||
| 1650 | ! check if all element pairs are in the database | ||
| 1651 | !--------------------------------------------------------------------------- | ||
| 1652 |
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14 | if(.not.allocated(element_bond_database)) allocate(element_bond_database(0)) |
| 1653 |
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|
58 | pair_loop1: do i = 1, size(pair_list,1) |
| 1654 |
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134 | do j = 1, size(element_bond_database) |
| 1655 | if( ( & | ||
| 1656 | element_bond_database(j)%element(1) .eq. pair_list(i,1) .and. & | ||
| 1657 | element_bond_database(j)%element(2) .eq. pair_list(i,2) & | ||
| 1658 |
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|
134 | ) .or. ( & |
| 1659 | element_bond_database(j)%element(1) .eq. pair_list(i,2) .and. & | ||
| 1660 | element_bond_database(j)%element(2) .eq. pair_list(i,1) & | ||
| 1661 | 44 | ) ) cycle pair_loop1 | |
| 1662 | end do | ||
| 1663 | ! if not found, add to the database | ||
| 1664 | ✗ | is = findloc([ this%element_info(:)%name ], pair_list(i,1), dim=1) | |
| 1665 | ✗ | js = findloc([ this%element_info(:)%name ], pair_list(i,2), dim=1) | |
| 1666 | ✗ | radius1 = this%element_info(is)%radius | |
| 1667 | ✗ | if(radius1.le.1.E-6) & | |
| 1668 | ✗ | call get_element_properties(pair_list(i,1), radius = radius1) | |
| 1669 | ✗ | radius2 = this%element_info(js)%radius | |
| 1670 | ✗ | if(radius2.le.1.E-6) & | |
| 1671 | ✗ | call get_element_properties(pair_list(i,2), radius = radius2) | |
| 1672 | ✗ | radius = ( radius1 + radius2 ) / 2._real32 | |
| 1673 | element_bond_database = [ element_bond_database, & | ||
| 1674 | ✗ | element_bond_type(elements=[pair_list(i,:)], radius=radius) ] | |
| 1675 | 14 | call sort_str(element_bond_database(size(element_bond_database))%element) | |
| 1676 | end do pair_loop1 | ||
| 1677 | |||
| 1678 | |||
| 1679 | ! -------------------------------------------------------------------------- | ||
| 1680 | ! check if all element pairs are in the bond_info array | ||
| 1681 | ! -------------------------------------------------------------------------- | ||
| 1682 |
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|
58 | pair_loop2: do i = 1, size(pair_list,1) |
| 1683 |
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|
134 | info_loop: do j = 1, size(this%bond_info) |
| 1684 | if( ( & | ||
| 1685 | this%bond_info(j)%element(1) .eq. pair_list(i,1) .and. & | ||
| 1686 | this%bond_info(j)%element(2) .eq. pair_list(i,2) & | ||
| 1687 |
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|
129 | ) .or. ( & |
| 1688 | this%bond_info(j)%element(1) .eq. pair_list(i,2) .and. & | ||
| 1689 | this%bond_info(j)%element(2) .eq. pair_list(i,1) & | ||
| 1690 | 44 | ) ) cycle pair_loop2 | |
| 1691 | end do info_loop | ||
| 1692 | this%bond_info = [ & | ||
| 1693 | this%bond_info(:), & | ||
| 1694 | element_bond_type( [ pair_list(i,1:2) ] ) & | ||
| 1695 |
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|
80 | ] |
| 1696 | call this%bond_info(size(this%bond_info))%set( & | ||
| 1697 | pair_list(i,1), & | ||
| 1698 | 19 | pair_list(i,2) ) | |
| 1699 | end do pair_loop2 | ||
| 1700 | |||
| 1701 |
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|
28 | end subroutine update_bond_info |
| 1702 | !############################################################################### | ||
| 1703 | |||
| 1704 | |||
| 1705 | !############################################################################### | ||
| 1706 | 3 | subroutine set_bond_radius(this, elements, radius) | |
| 1707 | !! Set the bond radius for a pair of elements in the container. | ||
| 1708 | implicit none | ||
| 1709 | |||
| 1710 | ! Arguments | ||
| 1711 | class(distribs_container_type), intent(inout) :: this | ||
| 1712 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1713 | character(len=3), dimension(2), intent(in) :: elements | ||
| 1714 | !! Element name. | ||
| 1715 | real(real32), intent(in) :: radius | ||
| 1716 | !! Bond radius. | ||
| 1717 | |||
| 1718 | ! Local variables | ||
| 1719 | integer :: idx, i | ||
| 1720 | !! Index of the bond in the bond_info array. | ||
| 1721 | character(len=3) :: element_1, element_2 | ||
| 1722 | !! Element names. | ||
| 1723 | |||
| 1724 | |||
| 1725 | !--------------------------------------------------------------------------- | ||
| 1726 | ! remove python formatting | ||
| 1727 | !--------------------------------------------------------------------------- | ||
| 1728 | 3 | element_1 = strip_null(elements(1)) | |
| 1729 | 3 | element_2 = strip_null(elements(2)) | |
| 1730 | |||
| 1731 | |||
| 1732 | !--------------------------------------------------------------------------- | ||
| 1733 | ! if bond_info is allocated, update radius of associated index | ||
| 1734 | !--------------------------------------------------------------------------- | ||
| 1735 |
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|
3 | if(allocated(this%bond_info))then |
| 1736 | 1 | idx = this%get_pair_index(element_1, element_2) | |
| 1737 |
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1 | if(idx.ge.1) this%bond_info(idx)%radius_covalent = radius |
| 1738 | end if | ||
| 1739 | |||
| 1740 | |||
| 1741 | !--------------------------------------------------------------------------- | ||
| 1742 | ! if element_bond_database is allocated, update radius of associated index | ||
| 1743 | !--------------------------------------------------------------------------- | ||
| 1744 |
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|
3 | if(.not.allocated(element_bond_database))then |
| 1745 | ✗ | allocate(element_bond_database(1)) | |
| 1746 | ✗ | element_bond_database(1)%element = [ element_1, element_2 ] | |
| 1747 | ✗ | call sort_str(element_bond_database(1)%element) | |
| 1748 | ✗ | element_bond_database(1)%radius_covalent = radius | |
| 1749 | 3 | return | |
| 1750 | end if | ||
| 1751 |
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3 | do i = 1, size(element_bond_database) |
| 1752 | if( ( & | ||
| 1753 | element_bond_database(i)%element(1) .eq. element_1 .and. & | ||
| 1754 | element_bond_database(i)%element(2) .eq. element_2 & | ||
| 1755 |
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3 | ) .or. ( & |
| 1756 | element_bond_database(i)%element(1) .eq. element_2 .and. & | ||
| 1757 | element_bond_database(i)%element(2) .eq. element_1 & | ||
| 1758 | ✗ | ) )then | |
| 1759 | 3 | element_bond_database(i)%radius_covalent = radius | |
| 1760 | 3 | return | |
| 1761 | end if | ||
| 1762 | end do | ||
| 1763 | ! if allocated and not found, add to the database | ||
| 1764 | element_bond_database = [ element_bond_database, & | ||
| 1765 | ✗ | element_bond_type([ element_1, element_2 ], radius) ] | |
| 1766 | ✗ | call sort_str(element_bond_database(size(element_bond_database))%element) | |
| 1767 | |||
| 1768 | end subroutine set_bond_radius | ||
| 1769 | !############################################################################### | ||
| 1770 | |||
| 1771 | |||
| 1772 | !############################################################################### | ||
| 1773 |
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|
2 | subroutine set_bond_radii(this, elements, radii) |
| 1774 | !! Set the bond radii for a pair of elements in the container. | ||
| 1775 | implicit none | ||
| 1776 | |||
| 1777 | ! Arguments | ||
| 1778 | class(distribs_container_type), intent(inout) :: this | ||
| 1779 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1780 | character(len=3), dimension(:,:), intent(in) :: elements | ||
| 1781 | !! Element names. | ||
| 1782 | real(real32), dimension(:), intent(in) :: radii | ||
| 1783 | !! Bond radii. | ||
| 1784 | |||
| 1785 | ! Local variables | ||
| 1786 | integer :: i | ||
| 1787 | !! Loop index. | ||
| 1788 | |||
| 1789 | |||
| 1790 |
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4 | do i = 1, size(elements,1) |
| 1791 |
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4 | call this%set_bond_radius(elements(i,:), radii(i)) |
| 1792 | end do | ||
| 1793 | |||
| 1794 | 2 | end subroutine set_bond_radii | |
| 1795 | !############################################################################### | ||
| 1796 | |||
| 1797 | |||
| 1798 | !############################################################################### | ||
| 1799 | 2 | subroutine get_bond_radii(this, elements, radii) | |
| 1800 | !! Return the bond radii of elements in the container. | ||
| 1801 | implicit none | ||
| 1802 | |||
| 1803 | ! Arguments | ||
| 1804 | class(distribs_container_type), intent(in) :: this | ||
| 1805 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1806 | character(len=3), dimension(:,:), allocatable, intent(out) :: elements | ||
| 1807 | !! Element pair names. | ||
| 1808 | real(real32), dimension(:), allocatable, intent(out) :: radii | ||
| 1809 | !! Radii of the bond pairs. | ||
| 1810 | |||
| 1811 | ! Local variables | ||
| 1812 | integer :: i | ||
| 1813 | !! Loop index. | ||
| 1814 | |||
| 1815 | |||
| 1816 |
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2 | allocate(elements(size(this%bond_info),2)) |
| 1817 |
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2 | allocate(radii(size(this%bond_info))) |
| 1818 |
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4 | do i = 1, size(this%bond_info) |
| 1819 |
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6 | elements(i,:) = this%bond_info(i)%element |
| 1820 | 4 | radii(i) = this%bond_info(i)%radius_covalent | |
| 1821 | end do | ||
| 1822 | |||
| 1823 | 2 | end subroutine get_bond_radii | |
| 1824 | !############################################################################### | ||
| 1825 | |||
| 1826 | |||
| 1827 | !############################################################################### | ||
| 1828 | 2 | subroutine get_bond_radii_staticmem(this, elements, radii) | |
| 1829 | !! Return the energies of elements in the container. | ||
| 1830 | !! | ||
| 1831 | !! This subroutine is used when the memory for the output arrays is | ||
| 1832 | !! allocated outside of the subroutine. Used in Python interface. | ||
| 1833 | implicit none | ||
| 1834 | |||
| 1835 | ! Arguments | ||
| 1836 | class(distribs_container_type), intent(in) :: this | ||
| 1837 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1838 | character(len=3), dimension(size(this%bond_info,1),2), intent(out) :: & | ||
| 1839 | elements | ||
| 1840 | !! Element pair names. | ||
| 1841 | real(real32), dimension(size(this%bond_info,1)), intent(out) :: radii | ||
| 1842 | !! Radii of the bond pairs. | ||
| 1843 | |||
| 1844 | ! Local variables | ||
| 1845 | integer :: i | ||
| 1846 | !! Loop index. | ||
| 1847 | |||
| 1848 | |||
| 1849 |
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4 | do i = 1, size(this%bond_info) |
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6 | elements(i,:) = this%bond_info(i)%element |
| 1851 | 4 | radii(i) = this%bond_info(i)%radius_covalent | |
| 1852 | end do | ||
| 1853 | |||
| 1854 | 2 | end subroutine get_bond_radii_staticmem | |
| 1855 | !############################################################################### | ||
| 1856 | |||
| 1857 | |||
| 1858 | !############################################################################### | ||
| 1859 | 17 | subroutine set_best_energy(this) | |
| 1860 | !! Set the best energy in the container. | ||
| 1861 | implicit none | ||
| 1862 | |||
| 1863 | ! Arguments | ||
| 1864 | class(distribs_container_type), intent(inout) :: this | ||
| 1865 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 1866 | |||
| 1867 | ! Local variables | ||
| 1868 | integer :: i, j, is, js, idx1, idx2 | ||
| 1869 | !! Loop index. | ||
| 1870 | real(real32) :: energy, energy_per_species, energy_pair | ||
| 1871 | !! Energy of the system. | ||
| 1872 | 17 | integer, dimension(:,:), allocatable :: idx_list | |
| 1873 | !! Index list for pairs of elements. | ||
| 1874 | character(len=256) :: warn_msg | ||
| 1875 | !! Warning message. | ||
| 1876 | |||
| 1877 |
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17 | if(.not.allocated(this%best_energy_pair))then |
| 1878 | allocate( & | ||
| 1879 | ✗ | this%best_energy_pair(size(this%bond_info,1)), & | |
| 1880 | source = 0._real32 & | ||
| 1881 |
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46 | ) |
| 1882 |
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4 | elseif(size(this%best_energy_pair).ne.size(this%bond_info))then |
| 1883 |
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1 | deallocate(this%best_energy_pair) |
| 1884 | allocate( & | ||
| 1885 | ✗ | this%best_energy_pair(size(this%bond_info,1)), & | |
| 1886 | source = 0._real32 & | ||
| 1887 |
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7 | ) |
| 1888 | end if | ||
| 1889 | |||
| 1890 |
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17 | if(.not.allocated(this%best_energy_per_species))then |
| 1891 | allocate( & | ||
| 1892 | ✗ | this%best_energy_per_species(size(this%element_info,1)), & | |
| 1893 | source = 0._real32 & | ||
| 1894 |
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34 | ) |
| 1895 |
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4 | elseif(size(this%best_energy_per_species).ne.size(this%element_info))then |
| 1896 |
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1 | deallocate(this%best_energy_per_species) |
| 1897 | allocate( & | ||
| 1898 | ✗ | this%best_energy_per_species(size(this%element_info,1)), & | |
| 1899 | source = 0._real32 & | ||
| 1900 |
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4 | ) |
| 1901 | end if | ||
| 1902 | |||
| 1903 |
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|
43 | do i = 1, size(this%system) |
| 1904 | 26 | j = 0 | |
| 1905 | ✗ | allocate( idx_list( & | |
| 1906 | size(this%system(i)%element_symbols), & | ||
| 1907 | size(this%system(i)%element_symbols) & | ||
| 1908 |
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26 | ) ) |
| 1909 |
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60 | do is = 1, size(this%system(i)%element_symbols) |
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103 | do js = is, size(this%system(i)%element_symbols), 1 |
| 1911 | 43 | j = j + 1 | |
| 1912 | 43 | idx_list(is,js) = j | |
| 1913 | 77 | idx_list(js,is) = j | |
| 1914 | end do | ||
| 1915 | end do | ||
| 1916 | |||
| 1917 | 26 | energy = this%system(i)%energy | |
| 1918 |
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|
60 | do is = 1, size(this%system(i)%element_symbols) |
| 1919 | idx1 = findloc( & | ||
| 1920 | [ this%element_info(:)%name ], & | ||
| 1921 | this%system(i)%element_symbols(is), & | ||
| 1922 | dim = 1 & | ||
| 1923 |
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|
182 | ) |
| 1924 |
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34 | if(idx1.lt.1)then |
| 1925 | ✗ | call stop_program( "Species not found in element_info" ) | |
| 1926 | ✗ | return | |
| 1927 | end if | ||
| 1928 | energy = energy - & | ||
| 1929 | 60 | this%system(i)%stoichiometry(is) * this%element_info(idx1)%energy | |
| 1930 | end do | ||
| 1931 | 26 | energy = energy / this%system(i)%num_atoms | |
| 1932 | |||
| 1933 |
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60 | do is = 1, size(this%system(i)%element_symbols) |
| 1934 |
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34 | if(this%system(i)%num_per_species(is).eq.0)then |
| 1935 | write(warn_msg, & | ||
| 1936 | '("No neighbours found for species ",A," (",I0,") & | ||
| 1937 | &in system ",I0)' & | ||
| 1938 | ✗ | ) trim(this%system(i)%element_symbols(is)), is, i | |
| 1939 | ✗ | call print_warning(warn_msg) | |
| 1940 | ✗ | cycle | |
| 1941 | end if | ||
| 1942 | idx1 = findloc( & | ||
| 1943 | [ this%element_info(:)%name ], & | ||
| 1944 | this%system(i)%element_symbols(is), & | ||
| 1945 | dim = 1 & | ||
| 1946 |
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182 | ) |
| 1947 | energy_per_species = & | ||
| 1948 | energy * this%system(i)%weight_per_species(is) / & | ||
| 1949 |
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|
86 | real( sum( this%system(i)%num_per_species(:) ), real32 ) |
| 1950 | |||
| 1951 |
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34 | if( energy_per_species .lt. this%best_energy_per_species(idx1) )then |
| 1952 | 8 | this%best_energy_per_species(idx1) = energy_per_species | |
| 1953 | end if | ||
| 1954 |
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|
112 | do js = 1, size(this%system(i)%element_symbols) |
| 1955 | idx2 = findloc( & | ||
| 1956 | [ this%element_info(:)%name ], & | ||
| 1957 | this%system(i)%element_symbols(js), & | ||
| 1958 | dim = 1 & | ||
| 1959 |
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|
308 | ) |
| 1960 | j = nint( & | ||
| 1961 | ( & | ||
| 1962 | size(this%element_info) - & | ||
| 1963 | min( idx1, idx2 ) / 2._real32 & | ||
| 1964 | ) * ( min( idx1, idx2 ) - 1._real32 ) + max( idx1, idx2 ) & | ||
| 1965 | 52 | ) | |
| 1966 | |||
| 1967 | energy_pair = & | ||
| 1968 | energy * this%system(i)%weight_pair(idx_list(is,js)) / & | ||
| 1969 |
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|
146 | real( sum( this%system(i)%num_per_species(:) ), real32 ) |
| 1970 | |||
| 1971 |
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|
86 | if( energy_pair .lt. this%best_energy_pair(j) )then |
| 1972 | 12 | this%best_energy_pair(j) = energy_pair | |
| 1973 | end if | ||
| 1974 | |||
| 1975 | end do | ||
| 1976 | end do | ||
| 1977 |
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|
26 | deallocate(idx_list) |
| 1978 |
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|
43 | if( this%best_energy_pair(j) .lt. -1.E1 )then |
| 1979 | write(warn_msg, & | ||
| 1980 | '("Best energy pair is less than -10 eV, & | ||
| 1981 | &this is likely to be unphysical. Check the energy values.")' & | ||
| 1982 | ✗ | ) | |
| 1983 | ✗ | call print_warning(warn_msg) | |
| 1984 | end if | ||
| 1985 | |||
| 1986 | end do | ||
| 1987 | |||
| 1988 |
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|
17 | end subroutine set_best_energy |
| 1989 | !############################################################################### | ||
| 1990 | |||
| 1991 | |||
| 1992 | !############################################################################### | ||
| 1993 | 17707306 | pure function get_pair_index(this, species1, species2) result(idx) | |
| 1994 | !! Get the index of a pair of elements in the container. | ||
| 1995 | implicit none | ||
| 1996 | |||
| 1997 | ! Arguments | ||
| 1998 | class(distribs_container_type), intent(in) :: this | ||
| 1999 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2000 | character(len=3), intent(in) :: species1, species2 | ||
| 2001 | !! Element names. | ||
| 2002 | integer :: idx | ||
| 2003 | !! Index of the pair in the bond_info array. | ||
| 2004 | |||
| 2005 | ! Local variables | ||
| 2006 | integer :: is, js | ||
| 2007 | !! Index of the elements in the element_info array. | ||
| 2008 | |||
| 2009 |
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|
123238758 | is = findloc([ this%element_info(:)%name ], species1, dim=1) |
| 2010 |
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|
123238758 | js = findloc([ this%element_info(:)%name ], species2, dim=1) |
| 2011 | !! This comes from subtraction of nth triangular numbers | ||
| 2012 | !! nth triangular number: N_n = n(n+1)/2 = ( n^2 + n ) / 2 | ||
| 2013 | !! idx = N_n - N_{n-is+1} + ( js - is + 1) | ||
| 2014 | !! idx = ( n - is/2 ) * ( is - 1 ) + js | ||
| 2015 | !idx = nint( ( size(this%element_info) - min( is, js ) / 2._real32 ) * & | ||
| 2016 | ! ( is - 1._real32 ) + js ) | ||
| 2017 | idx = nint( ( size(this%element_info) - min( is, js ) / 2._real32 ) * & | ||
| 2018 | 17707306 | ( min( is, js ) - 1._real32 ) + max( is, js ) ) | |
| 2019 | |||
| 2020 | 17707306 | end function get_pair_index | |
| 2021 | !############################################################################### | ||
| 2022 | |||
| 2023 | |||
| 2024 | !############################################################################### | ||
| 2025 | 1 | pure function get_element_index(this, species) result(idx) | |
| 2026 | !! Get the index of an element in the container. | ||
| 2027 | implicit none | ||
| 2028 | |||
| 2029 | ! Arguments | ||
| 2030 | class(distribs_container_type), intent(in) :: this | ||
| 2031 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2032 | character(len=3), intent(in) :: species | ||
| 2033 | !! Element name. | ||
| 2034 | integer :: idx | ||
| 2035 | !! Index of the element in the element_info array. | ||
| 2036 | |||
| 2037 | ! Local variables | ||
| 2038 | |||
| 2039 |
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|
3 | idx = findloc([ this%element_info(:)%name ], species, dim=1) |
| 2040 | |||
| 2041 | 1 | end function get_element_index | |
| 2042 | !############################################################################### | ||
| 2043 | |||
| 2044 | |||
| 2045 | !############################################################################### | ||
| 2046 | 168160301 | pure function get_bin(this, value, dim) result(bin) | |
| 2047 | !! Get the bin index for a value in a dimension. | ||
| 2048 | implicit none | ||
| 2049 | |||
| 2050 | ! Arguments | ||
| 2051 | class(distribs_container_type), intent(in) :: this | ||
| 2052 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2053 | real(real32), intent(in) :: value | ||
| 2054 | !! Value to get the bin index for. | ||
| 2055 | integer, intent(in) :: dim | ||
| 2056 | !! Dimension to get the bin index for. | ||
| 2057 | integer :: bin | ||
| 2058 | !! Bin index for the value. | ||
| 2059 | |||
| 2060 |
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|
168160301 | if(value .lt. this%cutoff_min(dim) - this%width(dim) .or. & |
| 2061 | value .gt. this%cutoff_max(dim) + this%width(dim))then | ||
| 2062 | 2 | bin = 0 | |
| 2063 | else | ||
| 2064 | bin = nint( & | ||
| 2065 | ( this%nbins(dim) - 1 ) * & | ||
| 2066 | ( value - this%cutoff_min(dim) ) / & | ||
| 2067 | ( this%cutoff_max(dim) - this%cutoff_min(dim) ) & | ||
| 2068 | 168160299 | ) + 1 | |
| 2069 | end if | ||
| 2070 | |||
| 2071 | 168160301 | end function get_bin | |
| 2072 | !############################################################################### | ||
| 2073 | |||
| 2074 | |||
| 2075 | !############################################################################### | ||
| 2076 | 13 | subroutine initialise_gdfs(this) | |
| 2077 | !! Initialise the distribution functions for the container. | ||
| 2078 | implicit none | ||
| 2079 | |||
| 2080 | ! Arguments | ||
| 2081 | class(distribs_container_type), intent(inout) :: this | ||
| 2082 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2083 | |||
| 2084 | ! Local variables | ||
| 2085 | integer :: num_pairs | ||
| 2086 | !! Number of pairs. | ||
| 2087 | |||
| 2088 | |||
| 2089 | num_pairs = nint( gamma(real(size(this%element_info) + 2, real32)) / & | ||
| 2090 | 13 | ( gamma(real(size(this%element_info), real32)) * gamma( 3._real32 ) ) ) | |
| 2091 | ✗ | allocate(this%gdf%df_2body(this%nbins(1),num_pairs), & | |
| 2092 |
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|
7339 | source = 0._real32 ) |
| 2093 | ✗ | allocate(this%gdf%df_3body(this%nbins(2),size(this%element_info)), & | |
| 2094 |
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|
1943 | source = 0._real32 ) |
| 2095 | ✗ | allocate(this%gdf%df_4body(this%nbins(3),size(this%element_info)), & | |
| 2096 |
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|
1943 | source = 0._real32 ) |
| 2097 |
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|
46 | allocate(this%in_dataset_2body(num_pairs), source = .false. ) |
| 2098 |
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|
34 | allocate(this%in_dataset_3body(size(this%element_info)), source = .false. ) |
| 2099 |
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|
34 | allocate(this%in_dataset_4body(size(this%element_info)), source = .false. ) |
| 2100 | |||
| 2101 | 13 | end subroutine initialise_gdfs | |
| 2102 | !############################################################################### | ||
| 2103 | |||
| 2104 | |||
| 2105 | !############################################################################### | ||
| 2106 | 30 | subroutine set_gdfs_to_default(this, body, index) | |
| 2107 | !! Initialise the gdfs for index of body distribution function. | ||
| 2108 | implicit none | ||
| 2109 | |||
| 2110 | ! Arguments | ||
| 2111 | class(distribs_container_type), intent(inout) :: this | ||
| 2112 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2113 | integer, intent(in) :: body | ||
| 2114 | !! Body distribution function to initialise. | ||
| 2115 | integer, intent(in) :: index | ||
| 2116 | !! Index of the pair in the bond_info array. | ||
| 2117 | |||
| 2118 | ! Local variables | ||
| 2119 | real(real32) :: eta, weight, height | ||
| 2120 | !! Parameters for the distribution functions. | ||
| 2121 | real(real32), dimension(1) :: bonds | ||
| 2122 | |||
| 2123 | |||
| 2124 |
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|
30 | if( body .eq. 2 )then |
| 2125 | 18 | weight = exp( -4._real32 ) | |
| 2126 | 18 | height = 1._real32 / this%nbins(1) | |
| 2127 | 18 | eta = 1._real32 / ( 2._real32 * ( this%sigma(1) )**2._real32 ) | |
| 2128 |
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|
18 | if(size(this%bond_info).eq.0)then |
| 2129 | call set_bond_radius_to_default( [ & | ||
| 2130 | this%bond_info(index)%element(1), & | ||
| 2131 | this%bond_info(index)%element(2) & | ||
| 2132 | ✗ | ] ) | |
| 2133 | end if | ||
| 2134 |
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|
36 | bonds = [ 2._real32 * this%bond_info(index)%radius_covalent ] |
| 2135 |
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|
18 | if(abs(bonds(1)).lt.1.E-6)then |
| 2136 | ✗ | call stop_program( "Bond radius is zero" ) | |
| 2137 | end if | ||
| 2138 | this%gdf%df_2body(:,index) = weight * height * get_distrib( & | ||
| 2139 | bonds , & | ||
| 2140 | this%nbins(1), eta, this%width(1), & | ||
| 2141 | this%cutoff_min(1), & | ||
| 2142 | scale_list = [ 1._real32 ] & | ||
| 2143 |
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|
3996 | ) |
| 2144 |
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|
12 | elseif( body .eq. 3 )then |
| 2145 |
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|
396 | this%gdf%df_3body(:,index) = 1._real32/this%nbins(2) |
| 2146 |
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6 | elseif( body .eq. 4 )then |
| 2147 |
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|
396 | this%gdf%df_4body(:,index) = 1._real32/this%nbins(3) |
| 2148 | end if | ||
| 2149 | |||
| 2150 | 30 | end subroutine set_gdfs_to_default | |
| 2151 | !############################################################################### | ||
| 2152 | |||
| 2153 | |||
| 2154 | !############################################################################### | ||
| 2155 | 17 | subroutine evolve(this, system) | |
| 2156 | !! Evolve the generalised distribution functions for the container. | ||
| 2157 | implicit none | ||
| 2158 | |||
| 2159 | ! Arguments | ||
| 2160 | class(distribs_container_type), intent(inout) :: this | ||
| 2161 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 2162 | type(distribs_type), dimension(..), intent(in), optional :: system | ||
| 2163 | !! Optional. System to add to the container. | ||
| 2164 | |||
| 2165 | ! Local variables | ||
| 2166 | integer :: i, j, is, js | ||
| 2167 | !! Loop index. | ||
| 2168 | integer :: idx1, idx2 | ||
| 2169 | !! Index of the element in the element_info array. | ||
| 2170 | integer :: num_evaluated | ||
| 2171 | !! Number of systems evaluated this iteration. | ||
| 2172 | real(real32) :: weight, energy | ||
| 2173 | !! Energy and weight variables for a system. | ||
| 2174 | real(real32), dimension(:), allocatable :: & | ||
| 2175 | 17 | best_energy_pair_old, & | |
| 2176 | 17 | best_energy_per_species_old | |
| 2177 | !! Old best energies. | ||
| 2178 | 17 | integer, dimension(:,:), allocatable :: idx_list | |
| 2179 | !! Index list for the element pairs in a system. | ||
| 2180 | 17 | real(real32), dimension(:,:), allocatable :: tmp_df | |
| 2181 | !! Temporary array for the distribution functions. | ||
| 2182 | 17 | logical, dimension(:), allocatable :: tmp_in_dataset | |
| 2183 | |||
| 2184 | character(256) :: err_msg | ||
| 2185 | 17 | integer, dimension(:), allocatable :: host_idx_list | |
| 2186 | |||
| 2187 | |||
| 2188 | 17 | weight = 1._real32 | |
| 2189 | |||
| 2190 | !--------------------------------------------------------------------------- | ||
| 2191 | ! if present, add the system to the container | ||
| 2192 | !--------------------------------------------------------------------------- | ||
| 2193 |
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17 | if(present(system)) call this%add(system) |
| 2194 |
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|
68 | do i = 1, 3 |
| 2195 |
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|
68 | if(this%nbins(i).eq.-1)then |
| 2196 | this%nbins(i) = 1 + & | ||
| 2197 | nint( & | ||
| 2198 | ( this%cutoff_max(i) - this%cutoff_min(i) ) / & | ||
| 2199 | this%width(i) & | ||
| 2200 | 30 | ) | |
| 2201 | end if | ||
| 2202 | end do | ||
| 2203 | |||
| 2204 | |||
| 2205 | !--------------------------------------------------------------------------- | ||
| 2206 | ! initialise the generalised distribution functions and get | ||
| 2207 | ! best energies from lowest formation energy system | ||
| 2208 | !--------------------------------------------------------------------------- | ||
| 2209 |
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|
17 | if(.not.allocated(this%gdf%df_2body))then |
| 2210 | 13 | call this%set_best_energy() | |
| 2211 | 13 | call this%initialise_gdfs() | |
| 2212 | else | ||
| 2213 |
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|
13 | best_energy_pair_old = this%best_energy_pair |
| 2214 |
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|
10 | best_energy_per_species_old = this%best_energy_per_species |
| 2215 | 4 | call this%set_best_energy() | |
| 2216 |
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|
13 | do i = 1, size(this%gdf%df_2body,2) |
| 2217 | this%gdf%df_2body(:,i) = this%gdf%df_2body(:,i) * & | ||
| 2218 | exp( this%best_energy_pair(i) / this%kBT ) / & | ||
| 2219 |
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|
2002 | exp( best_energy_pair_old(i) / this%kBT ) |
| 2220 | end do | ||
| 2221 |
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|
10 | do i = 1, size(this%gdf%df_3body,2) |
| 2222 | this%gdf%df_3body(:,i) = & | ||
| 2223 | this%gdf%df_3body(:,i) * exp( & | ||
| 2224 | this%best_energy_per_species(i) / this%kBT & | ||
| 2225 |
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|
400 | ) / exp( best_energy_per_species_old(i) / this%kBT ) |
| 2226 | end do | ||
| 2227 |
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|
10 | do i = 1, size(this%gdf%df_4body,2) |
| 2228 | this%gdf%df_4body(:,i) = & | ||
| 2229 | this%gdf%df_4body(:,i) * exp( & | ||
| 2230 | this%best_energy_per_species(i) / this%kBT & | ||
| 2231 |
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|
400 | ) / exp( best_energy_per_species_old(i) / this%kBT ) |
| 2232 | end do | ||
| 2233 |
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|
4 | if(size(this%gdf%df_2body,2).ne.size(this%bond_info))then |
| 2234 | ✗ | allocate(tmp_df(this%nbins(1),size(this%bond_info)), & | |
| 2235 |
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|
1333 | source = 0._real32 ) |
| 2236 |
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|
223 | tmp_df(:,1:size(this%gdf%df_2body,2)) = this%gdf%df_2body |
| 2237 |
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|
1 | deallocate(this%gdf%df_2body) |
| 2238 |
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|
1 | call move_alloc( tmp_df, this%gdf%df_2body ) |
| 2239 |
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|
7 | allocate(tmp_in_dataset(size(this%bond_info)), source = .false. ) |
| 2240 |
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|
2 | tmp_in_dataset(1:size(this%in_dataset_2body)) = this%in_dataset_2body |
| 2241 |
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|
1 | deallocate(this%in_dataset_2body) |
| 2242 |
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|
1 | call move_alloc( tmp_in_dataset, this%in_dataset_2body ) |
| 2243 | end if | ||
| 2244 |
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|
4 | if(size(this%gdf%df_3body,2).ne.size(this%element_info))then |
| 2245 | ✗ | allocate(tmp_df(this%nbins(2),size(this%element_info)), & | |
| 2246 |
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|
199 | source = 0._real32 ) |
| 2247 |
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|
67 | tmp_df(:,1:size(this%gdf%df_3body,2)) = this%gdf%df_3body |
| 2248 |
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|
1 | deallocate(this%gdf%df_3body) |
| 2249 |
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|
1 | call move_alloc( tmp_df, this%gdf%df_3body ) |
| 2250 |
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|
4 | allocate(tmp_in_dataset(size(this%element_info)), source = .false. ) |
| 2251 |
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|
2 | tmp_in_dataset(1:size(this%in_dataset_3body)) = this%in_dataset_3body |
| 2252 |
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|
1 | deallocate(this%in_dataset_3body) |
| 2253 |
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|
1 | call move_alloc( tmp_in_dataset, this%in_dataset_3body ) |
| 2254 | end if | ||
| 2255 |
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|
4 | if(size(this%gdf%df_4body,2).ne.size(this%element_info))then |
| 2256 | ✗ | allocate(tmp_df(this%nbins(3),size(this%element_info)), & | |
| 2257 |
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|
199 | source = 0._real32 ) |
| 2258 |
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|
67 | tmp_df(:,1:size(this%gdf%df_4body,2)) = this%gdf%df_4body |
| 2259 |
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|
1 | deallocate(this%gdf%df_4body) |
| 2260 |
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|
1 | call move_alloc( tmp_df, this%gdf%df_4body ) |
| 2261 |
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|
4 | allocate(tmp_in_dataset(size(this%element_info)), source = .false. ) |
| 2262 |
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|
2 | tmp_in_dataset(1:size(this%in_dataset_4body)) = this%in_dataset_4body |
| 2263 |
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|
1 | deallocate(this%in_dataset_4body) |
| 2264 |
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|
1 | call move_alloc( tmp_in_dataset, this%in_dataset_4body ) |
| 2265 | end if | ||
| 2266 |
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|
18 | do j = 1, size(this%gdf%df_2body,2) |
| 2267 |
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|
18 | if(.not.this%in_dataset_2body(j))then |
| 2268 |
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|
2220 | this%gdf%df_2body(:,j) = 0._real32 |
| 2269 | else | ||
| 2270 | this%gdf%df_2body(:,j) = & | ||
| 2271 |
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|
888 | this%gdf%df_2body(:,j) * this%norm_2body(j) |
| 2272 | end if | ||
| 2273 | end do | ||
| 2274 |
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|
12 | do is = 1, size(this%element_info) |
| 2275 |
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|
8 | if(.not.this%in_dataset_3body(is))then |
| 2276 |
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|
264 | this%gdf%df_3body(:,is) = 0._real32 |
| 2277 | else | ||
| 2278 | this%gdf%df_3body(:,is) = & | ||
| 2279 |
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|
264 | this%gdf%df_3body(:,is) * this%norm_3body(is) |
| 2280 | end if | ||
| 2281 |
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|
12 | if(.not.this%in_dataset_4body(is))then |
| 2282 |
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|
264 | this%gdf%df_4body(:,is) = 0._real32 |
| 2283 | else | ||
| 2284 | this%gdf%df_4body(:,is) = & | ||
| 2285 |
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|
264 | this%gdf%df_4body(:,is) * this%norm_4body(is) |
| 2286 | end if | ||
| 2287 | end do | ||
| 2288 |
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|
4 | deallocate(this%norm_2body) |
| 2289 |
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|
4 | deallocate(this%norm_3body) |
| 2290 |
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|
4 | deallocate(this%norm_4body) |
| 2291 | end if | ||
| 2292 | |||
| 2293 | if( & | ||
| 2294 |
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|
33 | any(this%system(this%num_evaluated_allocated+1:)%from_host) .and. & |
| 2295 | this%host_system%defined & | ||
| 2296 | )then | ||
| 2297 | ! set host_idx_list | ||
| 2298 |
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|
4 | allocate(host_idx_list(size(this%element_info))) |
| 2299 |
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|
12 | host_idx_list = 0 |
| 2300 |
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|
8 | do is = 1, size(this%host_system%element_symbols) |
| 2301 | idx1 = findloc( & | ||
| 2302 | [ this%element_info(:)%name ], & | ||
| 2303 | this%host_system%element_symbols(is), & | ||
| 2304 | dim = 1 & | ||
| 2305 |
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|
20 | ) |
| 2306 |
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|
4 | if(idx1.lt.1)then |
| 2307 | ✗ | call stop_program( "Host species not found in species list" ) | |
| 2308 | ✗ | return | |
| 2309 | end if | ||
| 2310 | 8 | host_idx_list(idx1) = is | |
| 2311 | end do | ||
| 2312 | end if | ||
| 2313 | |||
| 2314 | !--------------------------------------------------------------------------- | ||
| 2315 | ! loop over all systems to calculate the generalised distribution functions | ||
| 2316 | !--------------------------------------------------------------------------- | ||
| 2317 | 17 | num_evaluated = 0 | |
| 2318 |
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|
37 | do i = this%num_evaluated_allocated + 1, size(this%system), 1 |
| 2319 | 20 | num_evaluated = num_evaluated + 1 | |
| 2320 |
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|
20 | if(this%weight_by_hull)then |
| 2321 | ✗ | weight = exp( this%system(i)%energy_above_hull / this%kBT ) | |
| 2322 | ✗ | if(weight.lt.1.E-6) cycle | |
| 2323 | end if | ||
| 2324 | !------------------------------------------------------------------------ | ||
| 2325 | ! get the list of 2-body species pairs the system | ||
| 2326 | !------------------------------------------------------------------------ | ||
| 2327 | 20 | j = 0 | |
| 2328 | ✗ | allocate( idx_list( & | |
| 2329 | size(this%system(i)%element_symbols), & | ||
| 2330 | size(this%system(i)%element_symbols) & | ||
| 2331 |
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|
20 | ) ) |
| 2332 |
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|
47 | do is = 1, size(this%system(i)%element_symbols) |
| 2333 |
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|
82 | do js = is, size(this%system(i)%element_symbols), 1 |
| 2334 | 35 | j = j + 1 | |
| 2335 | 35 | idx_list(is,js) = j | |
| 2336 | 62 | idx_list(js,is) = j | |
| 2337 | end do | ||
| 2338 | end do | ||
| 2339 | |||
| 2340 | |||
| 2341 | !------------------------------------------------------------------------ | ||
| 2342 | ! calculate the weight for the system | ||
| 2343 | !------------------------------------------------------------------------ | ||
| 2344 | 20 | energy = this%system(i)%energy | |
| 2345 |
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|
47 | do is = 1, size(this%system(i)%element_symbols) |
| 2346 | idx1 = findloc( & | ||
| 2347 | [ this%element_info(:)%name ], & | ||
| 2348 | this%system(i)%element_symbols(is), & | ||
| 2349 | dim = 1 & | ||
| 2350 |
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|
145 | ) |
| 2351 |
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|
27 | if(idx1.lt.1)then |
| 2352 | ✗ | call stop_program( "Species not found in species list" ) | |
| 2353 | ✗ | return | |
| 2354 | end if | ||
| 2355 | energy = energy - this%system(i)%stoichiometry(is) * & | ||
| 2356 | 47 | this%element_info(idx1)%energy | |
| 2357 | end do | ||
| 2358 | 20 | energy = energy / this%system(i)%num_atoms | |
| 2359 | 20 | j = 0 | |
| 2360 | !------------------------------------------------------------------------ | ||
| 2361 | ! loop over all species in the system to add the distributions | ||
| 2362 | !------------------------------------------------------------------------ | ||
| 2363 |
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|
47 | do is = 1, size(this%system(i)%element_symbols) |
| 2364 | |||
| 2365 |
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|
27 | if( this%system(i)%num_per_species(is).eq.0 )cycle |
| 2366 | |||
| 2367 | idx1 = findloc( & | ||
| 2368 | [ this%element_info(:)%name ], & | ||
| 2369 | this%system(i)%element_symbols(is), & | ||
| 2370 | dim = 1 & | ||
| 2371 |
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|
145 | ) |
| 2372 | |||
| 2373 |
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|
27 | if(.not.this%weight_by_hull)then |
| 2374 | weight = exp( & | ||
| 2375 | ( & | ||
| 2376 | this%best_energy_per_species(is) - & | ||
| 2377 | energy * ( & | ||
| 2378 | this%system(i)%weight_per_species(is) / & | ||
| 2379 | real( & | ||
| 2380 | sum( this%system(i)%num_per_species(:) ), & | ||
| 2381 | real32 & | ||
| 2382 | ) & | ||
| 2383 | ) & | ||
| 2384 | ) / this%kBT & | ||
| 2385 |
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|
70 | ) |
| 2386 |
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|
27 | if(weight.lt.1.E-6) cycle |
| 2387 | end if | ||
| 2388 | |||
| 2389 | this%gdf%df_3body(:,idx1) = this%gdf%df_3body(:,idx1) + & | ||
| 2390 | set_difference( & | ||
| 2391 | weight * this%system(i)%df_3body(:,is), & | ||
| 2392 | this%gdf%df_3body(:,idx1), & | ||
| 2393 | set_min_zero = .true. & | ||
| 2394 |
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|
4101 | ) |
| 2395 | |||
| 2396 | this%gdf%df_4body(:,idx1) = this%gdf%df_4body(:,idx1) + & | ||
| 2397 | set_difference( & | ||
| 2398 | weight * this%system(i)%df_4body(:,is), & | ||
| 2399 | this%gdf%df_4body(:,idx1), & | ||
| 2400 | set_min_zero = .true. & | ||
| 2401 |
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|
4101 | ) |
| 2402 | |||
| 2403 |
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|
72 | do js = is, size(this%system(i)%element_symbols), 1 |
| 2404 | idx2 = findloc( & | ||
| 2405 | [ this%element_info(:)%name ], & | ||
| 2406 | this%system(i)%element_symbols(js), & | ||
| 2407 | dim = 1 & | ||
| 2408 |
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|
159 | ) |
| 2409 | j = nint( ( & | ||
| 2410 | size(this%element_info) - min( idx1, idx2 ) / 2._real32 & | ||
| 2411 | 29 | ) * ( min( idx1, idx2 ) - 1._real32 ) + max( idx1, idx2 ) ) | |
| 2412 | |||
| 2413 |
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|
29 | if(.not.this%weight_by_hull)then |
| 2414 | weight = exp( & | ||
| 2415 | ( & | ||
| 2416 | this%best_energy_pair(j) - & | ||
| 2417 | energy * ( & | ||
| 2418 | this%system(i)%weight_pair(idx_list(is,js)) / & | ||
| 2419 | real( & | ||
| 2420 | sum( this%system(i)%num_per_species(:) ), & | ||
| 2421 | real32 & | ||
| 2422 | ) & | ||
| 2423 | ) & | ||
| 2424 | ) / this%kBT & | ||
| 2425 |
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|
79 | ) |
| 2426 |
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|
29 | if(weight.lt.1.E-6) cycle |
| 2427 | end if | ||
| 2428 | |||
| 2429 | this%gdf%df_2body(:,j) = this%gdf%df_2body(:,j) + & | ||
| 2430 | set_difference( & | ||
| 2431 | weight * this%system(i)%df_2body(:,idx_list(is,js)), & | ||
| 2432 | this%gdf%df_2body(:,j), & | ||
| 2433 | set_min_zero = .true. & | ||
| 2434 |
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|
12870 | ) |
| 2435 | |||
| 2436 | end do | ||
| 2437 | end do | ||
| 2438 |
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|
37 | deallocate(idx_list) |
| 2439 | end do | ||
| 2440 | |||
| 2441 | !--------------------------------------------------------------------------- | ||
| 2442 | ! if not in the dataset, set distribution functions to default | ||
| 2443 | !--------------------------------------------------------------------------- | ||
| 2444 |
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|
64 | do j = 1, size(this%gdf%df_2body,2) |
| 2445 |
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|
5509 | if(all(abs(this%gdf%df_2body(:,j)).lt.1.E-6))then |
| 2446 | 18 | call this%set_gdfs_to_default(2, j) | |
| 2447 | else | ||
| 2448 | 29 | this%in_dataset_2body(j) = .true. | |
| 2449 | end if | ||
| 2450 | end do | ||
| 2451 |
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|
46 | do is = 1, size(this%element_info) |
| 2452 |
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|
1109 | if(all(abs(this%gdf%df_3body(:,is)).lt.1.E-6))then |
| 2453 | 6 | call this%set_gdfs_to_default(3, is) | |
| 2454 | else | ||
| 2455 | 23 | this%in_dataset_3body(is) = .true. | |
| 2456 | end if | ||
| 2457 |
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|
436 | if(all(abs(this%gdf%df_4body(:,is)).lt.1.E-6))then |
| 2458 | 6 | call this%set_gdfs_to_default(4, is) | |
| 2459 | else | ||
| 2460 | 23 | this%in_dataset_4body(is) = .true. | |
| 2461 | end if | ||
| 2462 | end do | ||
| 2463 | |||
| 2464 |
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|
17 | allocate(this%norm_2body(size(this%gdf%df_2body,2))) |
| 2465 |
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|
64 | do j = 1, size(this%gdf%df_2body,2) |
| 2466 |
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|
10481 | this%norm_2body(j) = maxval(this%gdf%df_2body(:,j)) |
| 2467 |
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|
47 | if(abs(this%norm_2body(j)).lt.1.E-6)then |
| 2468 | ✗ | call stop_program( "Zero norm for 2-body distribution function" ) | |
| 2469 | ✗ | return | |
| 2470 | end if | ||
| 2471 | this%gdf%df_2body(:,j) = & | ||
| 2472 |
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10434 | this%gdf%df_2body(:,j) / this%norm_2body(j) |
| 2473 |
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|
10451 | if(any(isnan(this%gdf%df_2body(:,j))))then |
| 2474 | write(err_msg, & | ||
| 2475 | '("NaN in 2-body distribution function for ",A,"-",A,& | ||
| 2476 | &" with norm of ",F0.3)' & | ||
| 2477 | ) & | ||
| 2478 | ✗ | this%bond_info(j)%element(1), & | |
| 2479 | ✗ | this%bond_info(j)%element(2), & | |
| 2480 | ✗ | this%norm_2body(j) | |
| 2481 | ✗ | call stop_program( err_msg ) | |
| 2482 | ✗ | return | |
| 2483 | end if | ||
| 2484 | end do | ||
| 2485 |
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|
17 | allocate(this%norm_3body(size(this%element_info))) |
| 2486 |
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17 | allocate(this%norm_4body(size(this%element_info))) |
| 2487 |
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46 | do is = 1, size(this%element_info) |
| 2488 |
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|
2487 | this%norm_3body(is) = maxval(this%gdf%df_3body(:,is)) |
| 2489 |
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29 | if(abs(this%norm_3body(is)).lt.1.E-6)then |
| 2490 | ✗ | call stop_program( "Zero norm for 3-body distribution function" ) | |
| 2491 | ✗ | return | |
| 2492 | end if | ||
| 2493 |
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|
2487 | this%norm_4body(is) = maxval(this%gdf%df_4body(:,is)) |
| 2494 |
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29 | if(abs(this%norm_4body(is)).lt.1.E-6)then |
| 2495 | ✗ | call stop_program( "Zero norm for 4-body distribution function" ) | |
| 2496 | ✗ | return | |
| 2497 | end if | ||
| 2498 | this%gdf%df_3body(:,is) = & | ||
| 2499 |
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2458 | this%gdf%df_3body(:,is) / this%norm_3body(is) |
| 2500 | this%gdf%df_4body(:,is) = & | ||
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2458 | this%gdf%df_4body(:,is) / this%norm_4body(is) |
| 2502 | |||
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|
2475 | if(any(isnan(this%gdf%df_3body(:,is))))then |
| 2504 | write(err_msg,'("NaN in 3-body distribution function for ",A,& | ||
| 2505 | &" with norm of ",F0.3)' & | ||
| 2506 | ) & | ||
| 2507 | ✗ | this%element_info(is)%name, this%norm_3body(is) | |
| 2508 | ✗ | call stop_program( err_msg ) | |
| 2509 | ✗ | return | |
| 2510 |
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|
2458 | elseif(any(isnan(this%gdf%df_4body(:,is))))then |
| 2511 | write(err_msg,'("NaN in 4-body distribution function for ",A,& | ||
| 2512 | &" with norm of ",F0.3)' & | ||
| 2513 | ) & | ||
| 2514 | ✗ | this%element_info(is)%name, this%norm_4body(is) | |
| 2515 | ✗ | call stop_program( err_msg ) | |
| 2516 | ✗ | return | |
| 2517 | end if | ||
| 2518 | end do | ||
| 2519 | |||
| 2520 | 17 | this%num_evaluated_allocated = size(this%system) | |
| 2521 | 17 | this%num_evaluated = this%num_evaluated + num_evaluated | |
| 2522 | |||
| 2523 | this%viability_3body_default = sum( this%gdf%df_3body ) / & | ||
| 2524 |
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|
2509 | real( size( this%gdf%df_3body ), real32 ) |
| 2525 | this%viability_4body_default = sum( this%gdf%df_4body ) / & | ||
| 2526 |
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|
2509 | real( size( this%gdf%df_4body ), real32 ) |
| 2527 | |||
| 2528 |
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|
17 | end subroutine evolve |
| 2529 | !############################################################################### | ||
| 2530 | |||
| 2531 |
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|
113 | end module raffle__distribs_container |
| 2532 |