| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | module raffle__distribs | ||
| 2 | !! Module for handling distribution functions. | ||
| 3 | !! | ||
| 4 | !! This module contains the types and subroutines for generating distribution | ||
| 5 | !! fucntions for individual materials. | ||
| 6 | !! The distribution functions are used as fingerprints for atomic structures | ||
| 7 | !! to identify similarities and differences between structures. | ||
| 8 | use raffle__constants, only: real32, pi | ||
| 9 | use raffle__io_utils, only: stop_program, print_warning | ||
| 10 | use raffle__misc, only: strip_null, sort_str | ||
| 11 | use raffle__misc_maths, only: triangular_number | ||
| 12 | use raffle__misc_linalg, only: get_angle, get_improper_dihedral_angle, modu | ||
| 13 | use raffle__geom_rw, only: basis_type, get_element_properties | ||
| 14 | use raffle__geom_extd, only: extended_basis_type | ||
| 15 | use raffle__element_utils, only: & | ||
| 16 | element_type, element_bond_type, & | ||
| 17 | element_database, element_bond_database | ||
| 18 | implicit none | ||
| 19 | |||
| 20 | |||
| 21 | private | ||
| 22 | |||
| 23 | public :: distribs_base_type, distribs_type, get_distrib | ||
| 24 | |||
| 25 | |||
| 26 | type :: distribs_base_type | ||
| 27 | !! Base type for distribution functions. | ||
| 28 | real(real32), dimension(:,:), allocatable :: df_2body | ||
| 29 | !! 2-body distribution function. | ||
| 30 | real(real32), dimension(:,:), allocatable :: df_3body | ||
| 31 | !! 3-body distribution function. | ||
| 32 | real(real32), dimension(:,:), allocatable :: df_4body | ||
| 33 | !! 4-body distribution function. | ||
| 34 | end type distribs_base_type | ||
| 35 | |||
| 36 | type, extends(distribs_base_type) :: distribs_type | ||
| 37 | !! Type for distribution functions. | ||
| 38 | !! | ||
| 39 | !! This type contains the distribution functions for a single atomic | ||
| 40 | !! structure. It also contains other structure properties, including: | ||
| 41 | !! - energy | ||
| 42 | !! - stoichiometry | ||
| 43 | !! - elements | ||
| 44 | !! - number of atoms | ||
| 45 | integer :: num_atoms = 0 | ||
| 46 | !! Number of atoms in the structure. | ||
| 47 | real(real32) :: energy = 0.0_real32 | ||
| 48 | !! Energy of the structure. | ||
| 49 | real(real32) :: energy_above_hull = 0.0_real32 | ||
| 50 | !! Energy above the hull of the structure. | ||
| 51 | logical :: from_host = .false. | ||
| 52 | !! Boolean whether the structure is derived from the host. | ||
| 53 | integer, dimension(:), allocatable :: stoichiometry | ||
| 54 | !! Stoichiometry of the structure. | ||
| 55 | character(len=3), dimension(:), allocatable :: element_symbols | ||
| 56 | !! Elements contained within the structure. | ||
| 57 | integer, dimension(:), allocatable :: num_pairs, num_per_species | ||
| 58 | !! Number of pairs and number of pairs per species. | ||
| 59 | real(real32), dimension(:), allocatable :: weight_pair, weight_per_species | ||
| 60 | !! Weights for the 2-body and species distribution functions. | ||
| 61 | contains | ||
| 62 | procedure, pass(this) :: calculate | ||
| 63 | end type distribs_type | ||
| 64 | |||
| 65 | |||
| 66 | contains | ||
| 67 | |||
| 68 | !############################################################################### | ||
| 69 | 14 | subroutine set_bond_radius_to_default(elements) | |
| 70 | !! Set the bond radius to the default value. | ||
| 71 | !! | ||
| 72 | !! The default value is the average of the covalent radii of the elements. | ||
| 73 | implicit none | ||
| 74 | |||
| 75 | ! Arguments | ||
| 76 | character(len=3), dimension(2), intent(in) :: elements | ||
| 77 | !! Element symbols. | ||
| 78 | |||
| 79 | ! Local variables | ||
| 80 | integer :: idx1, idx2 | ||
| 81 | !! Index of the elements in the element database. | ||
| 82 | real(real32) :: radius, radius1, radius2 | ||
| 83 | !! Average of covalent radii. | ||
| 84 | character(256) :: warn_msg | ||
| 85 | |||
| 86 | |||
| 87 | |||
| 88 | write(warn_msg,'("No bond data for element pair ",A," and ",A)') & | ||
| 89 | 14 | elements(1), elements(2) | |
| 90 | warn_msg = trim(warn_msg) // & | ||
| 91 | achar(13) // achar(10) // & | ||
| 92 |
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14 | "Setting bond to average of covalent radii" |
| 93 | 14 | call print_warning(warn_msg) | |
| 94 |
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14 | if(.not.allocated(element_database)) allocate(element_database(0)) |
| 95 | idx1 = findloc([ element_database(:)%name ], & | ||
| 96 |
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72 | elements(1), dim=1) |
| 97 |
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14 | if(idx1.lt.1)then |
| 98 | 1 | call get_element_properties(elements(1), radius=radius1) | |
| 99 | element_database = [ element_database, & | ||
| 100 |
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6 | element_type(name=elements(1), radius=radius1) ] |
| 101 | 1 | idx1 = size(element_database) | |
| 102 | end if | ||
| 103 | idx2 = findloc([ element_database(:)%name ], & | ||
| 104 |
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74 | elements(2), dim=1) |
| 105 |
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14 | if(idx2.lt.1)then |
| 106 | 1 | call get_element_properties(elements(2), radius=radius2) | |
| 107 | element_database = [ element_database, & | ||
| 108 |
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9 | element_type(name=elements(2), radius=radius2) ] |
| 109 | 1 | idx2 = size(element_database) | |
| 110 | end if | ||
| 111 | radius = ( element_database(idx1)%radius + & | ||
| 112 | 14 | element_database(idx2)%radius ) / 2._real32 | |
| 113 |
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14 | if(.not.allocated(element_bond_database)) & |
| 114 |
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6 | allocate(element_bond_database(0)) |
| 115 | element_bond_database = [ element_bond_database, & | ||
| 116 | element_bond_type(elements=[ & | ||
| 117 | elements(1), & | ||
| 118 | elements(2) & | ||
| 119 | ], radius=radius) & | ||
| 120 |
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133 | ] |
| 121 | call sort_str( & | ||
| 122 | element_bond_database(size(element_bond_database))%element & | ||
| 123 | 14 | ) | |
| 124 | |||
| 125 | 14 | end subroutine set_bond_radius_to_default | |
| 126 | !############################################################################### | ||
| 127 | |||
| 128 | |||
| 129 | !############################################################################### | ||
| 130 | 27 | subroutine calculate(this, basis, & | |
| 131 | nbins, width, sigma, cutoff_min, cutoff_max, radius_distance_tol) | ||
| 132 | !! Calculate the distribution functions for the container. | ||
| 133 | !! | ||
| 134 | !! This procedure calculates the 2-, 3-, and 4-body distribution function | ||
| 135 | !! for a given atomic structure (i.e. basis). | ||
| 136 | implicit none | ||
| 137 | |||
| 138 | ! Arguments | ||
| 139 | class(distribs_type), intent(inout) :: this | ||
| 140 | !! Parent of the procedure. Instance of distribution functions container. | ||
| 141 | type(basis_type), intent(in) :: basis | ||
| 142 | !! Atomic structure. | ||
| 143 | integer, dimension(3), intent(in), optional :: nbins | ||
| 144 | !! Optional. Number of bins for the distribution functions. | ||
| 145 | real(real32), dimension(3), intent(in), optional :: width, sigma | ||
| 146 | !! Optional. Width and sigma for the distribution functions. | ||
| 147 | real(real32), dimension(3), intent(in), optional :: cutoff_min, cutoff_max | ||
| 148 | !! Optional. Cutoff minimum and maximum for the distribution functions. | ||
| 149 | real(real32), dimension(4), intent(in), optional :: radius_distance_tol | ||
| 150 | !! Tolerance for the distance between atoms for 3- and 4-body. | ||
| 151 | |||
| 152 | ! Local variables | ||
| 153 | integer, dimension(3) :: nbins_ | ||
| 154 | !! Number of bins for the distribution functions. | ||
| 155 | real(real32), dimension(3) :: sigma_ | ||
| 156 | !! Sigma for the distribution functions. | ||
| 157 | real(real32), dimension(3) :: width_ | ||
| 158 | !! Width of the bins for the distribution functions. | ||
| 159 | real(real32), dimension(3) :: cutoff_min_ | ||
| 160 | !! Cutoff minimum for the distribution functions. | ||
| 161 | real(real32), dimension(3) :: cutoff_max_ | ||
| 162 | !! Cutoff maximum for the distribution functions. | ||
| 163 | 27 | type(element_bond_type), dimension(:), allocatable :: bond_info | |
| 164 | !! Bond information for radii. | ||
| 165 | real(real32), dimension(4) :: radius_distance_tol_ | ||
| 166 | !! Tolerance for the distance between atoms for 3- and 4-body. | ||
| 167 | |||
| 168 | |||
| 169 | integer :: i, b, itmp1, idx | ||
| 170 | !! Loop index. | ||
| 171 | integer :: is, js, ia, ja, ka, la | ||
| 172 | !! Loop index. | ||
| 173 | integer :: num_pairs | ||
| 174 | !! Number of pairs and angles. | ||
| 175 | real(real32) :: bondlength | ||
| 176 | !! Temporary real variables. | ||
| 177 | logical :: success | ||
| 178 | !! Boolean for success. | ||
| 179 |
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432 | type(extended_basis_type) :: basis_extd |
| 180 | !! Extended basis of the system. | ||
| 181 |
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432 | type(extended_basis_type) :: neighbour_basis |
| 182 | !! Basis for storing neighbour data. | ||
| 183 | real(real32), dimension(3) :: eta | ||
| 184 | !! Parameters for the distribution functions. | ||
| 185 | 27 | real(real32), allocatable, dimension(:) :: angle_list, bondlength_list, & | |
| 186 | 27 | distance | |
| 187 | !! Temporary real arrays. | ||
| 188 | 27 | integer, allocatable, dimension(:,:) :: pair_index | |
| 189 | !! Index of element pairs. | ||
| 190 | |||
| 191 | |||
| 192 | !--------------------------------------------------------------------------- | ||
| 193 | ! initialise optional variables | ||
| 194 | !--------------------------------------------------------------------------- | ||
| 195 |
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27 | if(present(cutoff_min))then |
| 196 | 27 | cutoff_min_ = cutoff_min | |
| 197 | else | ||
| 198 | ✗ | cutoff_min_ = [0.5_real32, 0._real32, 0._real32] | |
| 199 | end if | ||
| 200 |
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27 | if(present(cutoff_max))then |
| 201 | 27 | cutoff_max_ = cutoff_max | |
| 202 | else | ||
| 203 | ✗ | cutoff_max_ = [6._real32, pi, pi] | |
| 204 | end if | ||
| 205 |
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27 | if(present(width))then |
| 206 | 27 | width_ = width | |
| 207 | else | ||
| 208 | ✗ | width_ = [0.25_real32, pi/64._real32, pi/64._real32] | |
| 209 | end if | ||
| 210 |
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27 | if(present(sigma))then |
| 211 | 27 | sigma_ = sigma | |
| 212 | else | ||
| 213 | ✗ | sigma_ = [0.1_real32, 0.1_real32, 0.1_real32] | |
| 214 | end if | ||
| 215 |
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27 | if(present(nbins))then |
| 216 | ✗ | nbins_ = nbins | |
| 217 | ✗ | width_ = ( cutoff_max_ - cutoff_min_ )/real( nbins_ - 1, real32 ) | |
| 218 | else | ||
| 219 |
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108 | nbins_ = 1 + nint( (cutoff_max_ - cutoff_min_)/width_ ) |
| 220 | end if | ||
| 221 |
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27 | if(present(radius_distance_tol))then |
| 222 | 27 | radius_distance_tol_ = radius_distance_tol | |
| 223 | else | ||
| 224 | ✗ | radius_distance_tol_ = [1.5_real32, 2.5_real32, 3._real32, 6._real32] | |
| 225 | end if | ||
| 226 | |||
| 227 | |||
| 228 | |||
| 229 | !--------------------------------------------------------------------------- | ||
| 230 | ! get the number of pairs of species | ||
| 231 | ! (this uses a combination calculator with repetition) | ||
| 232 | !--------------------------------------------------------------------------- | ||
| 233 | num_pairs = nint( & | ||
| 234 | gamma(real(basis%nspec + 2, real32)) / & | ||
| 235 | ( gamma(real(basis%nspec, real32)) * gamma( 3._real32 ) ) & | ||
| 236 | 27 | ) | |
| 237 |
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27 | allocate(this%element_symbols(basis%nspec)) |
| 238 |
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61 | do is = 1, basis%nspec |
| 239 | 61 | this%element_symbols(is) = strip_null(basis%spec(is)%name) | |
| 240 | end do | ||
| 241 | 27 | i = 0 | |
| 242 |
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69 | allocate(bond_info(num_pairs)) |
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27 | allocate(pair_index(basis%nspec,basis%nspec)) |
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61 | do is = 1, basis%nspec, 1 |
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103 | do js = is, basis%nspec, 1 |
| 246 | 42 | i = i + 1 | |
| 247 | 42 | pair_index(js,is) = i | |
| 248 | 42 | pair_index(is,js) = i | |
| 249 | call bond_info(i)%set( & | ||
| 250 | this%element_symbols(is), & | ||
| 251 | this%element_symbols(js), success & | ||
| 252 | 42 | ) | |
| 253 |
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42 | if(success) cycle |
| 254 | call set_bond_radius_to_default( [ & | ||
| 255 | this%element_symbols(is), & | ||
| 256 | this%element_symbols(js) & | ||
| 257 |
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42 | ] ) |
| 258 | call bond_info(i)%set( & | ||
| 259 | this%element_symbols(is), & | ||
| 260 | this%element_symbols(js), success & | ||
| 261 | 48 | ) | |
| 262 | end do | ||
| 263 | end do | ||
| 264 | |||
| 265 | |||
| 266 | !--------------------------------------------------------------------------- | ||
| 267 | ! get the stoichiometry, energy, and number of atoms | ||
| 268 | !--------------------------------------------------------------------------- | ||
| 269 |
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61 | this%stoichiometry = basis%spec(:)%num |
| 270 | 27 | this%energy = basis%energy | |
| 271 | 27 | this%num_atoms = basis%natom | |
| 272 | |||
| 273 | |||
| 274 | !--------------------------------------------------------------------------- | ||
| 275 | ! calculate the gaussian width and allocate the distribution functions | ||
| 276 | !--------------------------------------------------------------------------- | ||
| 277 |
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108 | eta = 1._real32 / ( 2._real32 * sigma_**2._real32 ) |
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69 | allocate(this%num_pairs(num_pairs), source = 0) |
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61 | allocate(this%num_per_species(basis%nspec), source = 0) |
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69 | allocate(this%weight_pair(num_pairs), source = 0._real32) |
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61 | allocate(this%weight_per_species(basis%nspec), source = 0._real32) |
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9351 | allocate(this%df_2body(nbins_(1), num_pairs), source = 0._real32) |
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2815 | allocate(this%df_3body(nbins_(2), basis%nspec), source = 0._real32) |
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2815 | allocate(this%df_4body(nbins_(3), basis%nspec), source = 0._real32) |
| 285 | |||
| 286 | |||
| 287 | !--------------------------------------------------------------------------- | ||
| 288 | ! create the extended basis and neighbour basis | ||
| 289 | !--------------------------------------------------------------------------- | ||
| 290 | 27 | call basis_extd%copy(basis) | |
| 291 | 27 | call basis_extd%create_images( max_bondlength = cutoff_max_(1) ) | |
| 292 |
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27 | allocate(bondlength_list(basis_extd%natom+basis_extd%num_images)) |
| 293 | |||
| 294 |
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54 | allocate(neighbour_basis%spec(1)) |
| 295 |
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54 | allocate(neighbour_basis%image_spec(1)) |
| 296 | ✗ | allocate(neighbour_basis%spec(1)%atom( & | |
| 297 | sum(basis_extd%spec(:)%num)+sum(basis_extd%image_spec(:)%num), 3 & | ||
| 298 |
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95 | ) ) |
| 299 | ✗ | allocate(neighbour_basis%image_spec(1)%atom( & | |
| 300 | sum(basis_extd%spec(:)%num)+sum(basis_extd%image_spec(:)%num), 3 & | ||
| 301 |
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95 | ) ) |
| 302 | 27 | neighbour_basis%nspec = basis%nspec | |
| 303 | 27 | neighbour_basis%natom = 0 | |
| 304 | 27 | neighbour_basis%num_images = 0 | |
| 305 |
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351 | neighbour_basis%lat = basis%lat |
| 306 | |||
| 307 | |||
| 308 | !--------------------------------------------------------------------------- | ||
| 309 | ! calculate the distribution functions | ||
| 310 | !--------------------------------------------------------------------------- | ||
| 311 |
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61 | do is = 1, basis%nspec |
| 312 |
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246 | do ia = 1, basis%spec(is)%num |
| 313 |
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185 | allocate(distance(basis_extd%natom+basis_extd%num_images)) |
| 314 | 185 | neighbour_basis%spec(1)%num = 0 | |
| 315 | 185 | neighbour_basis%image_spec(1)%num = 0 | |
| 316 |
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420 | do js = 1, basis%nspec |
| 317 | 235 | itmp1 = 0 | |
| 318 | |||
| 319 | !------------------------------------------------------------------ | ||
| 320 | ! loop over all atoms inside the unit cell | ||
| 321 | !------------------------------------------------------------------ | ||
| 322 |
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1612 | atom_loop: do ja = 1, basis_extd%spec(js)%num |
| 323 | |||
| 324 | associate( vector => matmul( & | ||
| 325 | [ & | ||
| 326 | basis_extd%spec(js)%atom(ja,1:3) - & | ||
| 327 | basis_extd%spec(is)%atom(ia,1:3) & | ||
| 328 | ], basis_extd%lat ) & | ||
| 329 | 235 | ) | |
| 330 | 1377 | bondlength = modu( vector ) | |
| 331 | |||
| 332 | if( & | ||
| 333 | 1377 | bondlength .lt. cutoff_min_(1) .or. & | |
| 334 | bondlength .gt. cutoff_max_(1) & | ||
| 335 | 185 | ) cycle atom_loop | |
| 336 | |||
| 337 | ! add 2-body bond to store if within tolerances for 3-body | ||
| 338 | ! distance | ||
| 339 | if( & | ||
| 340 | bondlength .ge. ( & | ||
| 341 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 342 | radius_distance_tol_(1) & | ||
| 343 |
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1192 | ) .and. & |
| 344 | bondlength .le. ( & | ||
| 345 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 346 | radius_distance_tol_(2) & | ||
| 347 | ) & | ||
| 348 | ) then | ||
| 349 | neighbour_basis%spec(1)%num = & | ||
| 350 | 406 | neighbour_basis%spec(1)%num + 1 | |
| 351 | neighbour_basis%spec(1)%atom( & | ||
| 352 |
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1624 | neighbour_basis%spec(1)%num,1:3) = vector |
| 353 | end if | ||
| 354 | |||
| 355 | ! add 2-body bond to store if within tolerances for 4-body | ||
| 356 | ! distance | ||
| 357 | if( & | ||
| 358 | bondlength .ge. ( & | ||
| 359 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 360 | radius_distance_tol_(3) & | ||
| 361 |
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1192 | ) .and. & |
| 362 | bondlength .le. ( & | ||
| 363 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 364 | radius_distance_tol_(4) & | ||
| 365 | ) & | ||
| 366 | ) then | ||
| 367 | neighbour_basis%image_spec(1)%num = & | ||
| 368 | 724 | neighbour_basis%image_spec(1)%num + 1 | |
| 369 | neighbour_basis%image_spec(1)%atom( & | ||
| 370 |
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2896 | neighbour_basis%image_spec(1)%num,1:3) = vector |
| 371 | end if | ||
| 372 | |||
| 373 | !if(js.lt.js.or.(is.eq.js.and.ja.le.ia)) cycle | ||
| 374 | 1192 | itmp1 = itmp1 + 1 | |
| 375 | 1192 | bondlength_list(itmp1) = bondlength | |
| 376 |
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10831 | distance(itmp1) = 1._real32 |
| 377 | |||
| 378 | end associate | ||
| 379 | end do atom_loop | ||
| 380 | |||
| 381 | |||
| 382 | !------------------------------------------------------------------ | ||
| 383 | ! loop over all image atoms outside of the unit cell | ||
| 384 | !------------------------------------------------------------------ | ||
| 385 |
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70939 | image_loop: do ja = 1, basis_extd%image_spec(js)%num |
| 386 | associate( vector => matmul( & | ||
| 387 | [ & | ||
| 388 | basis_extd%image_spec(js)%atom(ja,1:3) - & | ||
| 389 | basis_extd%spec(is)%atom(ia,1:3) & | ||
| 390 | ], basis_extd%lat ) & | ||
| 391 | 235 | ) | |
| 392 | |||
| 393 | 70704 | bondlength = modu( vector ) | |
| 394 | |||
| 395 | if( & | ||
| 396 | 70704 | bondlength .lt. cutoff_min_(1) .or. & | |
| 397 | bondlength .gt. cutoff_max_(1) & | ||
| 398 | 47478 | ) cycle image_loop | |
| 399 | |||
| 400 | ! add 2-body bond to store if within tolerances for 3-body | ||
| 401 | ! distance | ||
| 402 | if( & | ||
| 403 | bondlength .ge. ( & | ||
| 404 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 405 | radius_distance_tol_(1) & | ||
| 406 |
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23226 | ) .and. & |
| 407 | bondlength .le. ( & | ||
| 408 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 409 | radius_distance_tol_(2) & | ||
| 410 | ) & | ||
| 411 | ) then | ||
| 412 | neighbour_basis%spec(1)%num = & | ||
| 413 | 628 | neighbour_basis%spec(1)%num + 1 | |
| 414 | neighbour_basis%spec(1)%atom( & | ||
| 415 | neighbour_basis%spec(1)%num,1:3 & | ||
| 416 |
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2512 | ) = vector |
| 417 | end if | ||
| 418 | |||
| 419 | ! add 2-body bond to store if within tolerances for 4-body | ||
| 420 | ! distance | ||
| 421 | if( & | ||
| 422 | bondlength .ge. ( & | ||
| 423 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 424 | radius_distance_tol_(3) & | ||
| 425 |
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23226 | ) .and. & |
| 426 | bondlength .le. ( & | ||
| 427 | bond_info(pair_index(is, js))%radius_covalent * & | ||
| 428 | radius_distance_tol_(4) & | ||
| 429 | ) & | ||
| 430 | ) then | ||
| 431 | neighbour_basis%image_spec(1)%num = & | ||
| 432 | 9286 | neighbour_basis%image_spec(1)%num + 1 | |
| 433 | neighbour_basis%image_spec(1)%atom( & | ||
| 434 | neighbour_basis%image_spec(1)%num,1:3 & | ||
| 435 |
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37144 | ) = vector |
| 436 | end if | ||
| 437 | |||
| 438 | 23226 | itmp1 = itmp1 + 1 | |
| 439 | 23226 | bondlength_list(itmp1) = bondlength | |
| 440 |
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518154 | distance(itmp1) = 1._real32 |
| 441 | |||
| 442 | end associate | ||
| 443 | end do image_loop | ||
| 444 | |||
| 445 | !------------------------------------------------------------------ | ||
| 446 | ! calculate the 2-body distribution function contributions from | ||
| 447 | ! atom (is,ia) for species pair (is,js) | ||
| 448 | !------------------------------------------------------------------ | ||
| 449 |
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420 | if(itmp1.gt.0)then |
| 450 | this%df_2body(:,pair_index(is, js)) = & | ||
| 451 | this%df_2body(:,pair_index(is, js)) + & | ||
| 452 | get_distrib( & | ||
| 453 | bondlength_list(:itmp1), & | ||
| 454 | nbins_(1), eta(1), width_(1), & | ||
| 455 | cutoff_min_(1), & | ||
| 456 | scale_list = distance(:itmp1) & | ||
| 457 |
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52170 | ) |
| 458 | this%weight_pair(pair_index(is, js)) = & | ||
| 459 | this%weight_pair(pair_index(is, js)) + & | ||
| 460 | 4._real32 * sum( & | ||
| 461 | ( & | ||
| 462 | bond_info(pair_index(is, js))%radius_covalent / & | ||
| 463 | bondlength_list(:itmp1) ) ** 2 & | ||
| 464 |
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24653 | ) |
| 465 | this%num_pairs(pair_index(is, js)) = & | ||
| 466 | 235 | this%num_pairs(pair_index(is, js)) + itmp1 | |
| 467 | this%weight_per_species(is) = & | ||
| 468 | this%weight_per_species(is) + & | ||
| 469 | 4._real32 * sum( & | ||
| 470 | ( & | ||
| 471 | bond_info(pair_index(is, js))%radius_covalent / & | ||
| 472 | bondlength_list(:itmp1) ) ** 2 & | ||
| 473 |
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24653 | ) |
| 474 | 235 | this%num_per_species(is) = this%num_per_species(is) + itmp1 | |
| 475 | end if | ||
| 476 | |||
| 477 | end do | ||
| 478 |
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185 | deallocate(distance) |
| 479 | |||
| 480 | |||
| 481 | !--------------------------------------------------------------------- | ||
| 482 | ! calculate the 3-body distribution function for atom (is,ia) | ||
| 483 | !--------------------------------------------------------------------- | ||
| 484 |
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185 | if(neighbour_basis%spec(1)%num.le.1) cycle |
| 485 | associate( & | ||
| 486 | num_angles => & | ||
| 487 | triangular_number( neighbour_basis%spec(1)%num - 1 ) & | ||
| 488 | ) | ||
| 489 |
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173 | allocate( angle_list(num_angles), distance(num_angles) ) |
| 490 | end associate | ||
| 491 | 173 | do concurrent ( ja = 1:neighbour_basis%spec(1)%num:1 ) | |
| 492 |
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1207 | do concurrent ( ka = ja + 1:neighbour_basis%spec(1)%num:1 ) |
| 493 | idx = nint( & | ||
| 494 | (ja - 1) * (neighbour_basis%spec(1)%num - ja / 2.0) + & | ||
| 495 | (ka - ja) & | ||
| 496 | 4541 | ) | |
| 497 | angle_list(idx) = get_angle( & | ||
| 498 | [ neighbour_basis%spec(1)%atom(ja,:3) ], & | ||
| 499 | [ neighbour_basis%spec(1)%atom(ka,:3) ] & | ||
| 500 |
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59033 | ) |
| 501 | distance(idx) = & | ||
| 502 | ( & | ||
| 503 | modu(neighbour_basis%spec(1)%atom(ja,:3)) ** 2 * & | ||
| 504 | modu(neighbour_basis%spec(1)%atom(ka,:3)) ** 2 & | ||
| 505 |
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5575 | ) |
| 506 | end do | ||
| 507 | end do | ||
| 508 | ! a NaN in the angle refers to one where two of the vectors are | ||
| 509 | ! parallel, so the angle is undefined | ||
| 510 |
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4714 | do i = 1, size(angle_list) |
| 511 |
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4714 | if(isnan(angle_list(i)))then |
| 512 | ✗ | angle_list(i) = -huge(1._real32) | |
| 513 | ✗ | distance(i) = 1._real32 | |
| 514 | end if | ||
| 515 | end do | ||
| 516 | this%df_3body(:,is) = this%df_3body(:,is) + & | ||
| 517 | get_distrib( & | ||
| 518 | angle_list, & | ||
| 519 | nbins_(2), eta(2), width_(2), & | ||
| 520 | cutoff_min_(2), & | ||
| 521 | scale_list = distance & | ||
| 522 |
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13186 | ) |
| 523 |
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173 | deallocate( angle_list, distance ) |
| 524 | |||
| 525 | |||
| 526 | !--------------------------------------------------------------------- | ||
| 527 | ! calculate the 4-body distribution function for atom (is,ia) | ||
| 528 | !--------------------------------------------------------------------- | ||
| 529 |
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173 | if(neighbour_basis%image_spec(1)%num.eq.0) cycle |
| 530 | associate( & | ||
| 531 | num_angles => & | ||
| 532 | triangular_number( neighbour_basis%spec(1)%num - 1 ) * & | ||
| 533 | neighbour_basis%image_spec(1)%num & | ||
| 534 | ) | ||
| 535 |
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173 | allocate( angle_list(num_angles), distance(num_angles) ) |
| 536 | end associate | ||
| 537 | 173 | idx = 0 | |
| 538 | do concurrent ( & | ||
| 539 | ja = 1:neighbour_basis%spec(1)%num:1, & | ||
| 540 | la = 1:neighbour_basis%image_spec(1)%num:1 & | ||
| 541 | 10151 | ) | |
| 542 |
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71459 | do concurrent ( ka = ja + 1:neighbour_basis%spec(1)%num:1 ) |
| 543 | idx = nint( & | ||
| 544 | (ja - 1) * (neighbour_basis%spec(1)%num - ja / 2.0) + & | ||
| 545 | (ka - ja - 1) & | ||
| 546 | 278094 | ) * neighbour_basis%image_spec(1)%num + la | |
| 547 | angle_list(idx) = & | ||
| 548 | get_improper_dihedral_angle( & | ||
| 549 | [ neighbour_basis%spec(1)%atom(ja,:3) ], & | ||
| 550 | [ neighbour_basis%spec(1)%atom(ka,:3) ], & | ||
| 551 | [ neighbour_basis%image_spec(1)%atom(la,:3) ] & | ||
| 552 |
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5283786 | ) |
| 553 | distance(idx) = & | ||
| 554 | modu(neighbour_basis%spec(1)%atom(ja,:3)) ** 2 * & | ||
| 555 | modu(neighbour_basis%spec(1)%atom(ka,:3)) ** 2 * & | ||
| 556 |
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339402 | modu(neighbour_basis%image_spec(1)%atom(la,:3)) ** 2 |
| 557 | end do | ||
| 558 | end do | ||
| 559 | ! a NaN in the angle refers to one where two of the vectors are | ||
| 560 | ! parallel, so the angle is undefined | ||
| 561 |
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278267 | do i = 1, size(angle_list) |
| 562 |
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278267 | if(isnan(angle_list(i)))then |
| 563 | 18230 | angle_list(i) = -huge(1._real32) | |
| 564 | 18230 | distance(i) = 1._real32 | |
| 565 | end if | ||
| 566 | end do | ||
| 567 | this%df_4body(:,is) = this%df_4body(:,is) + & | ||
| 568 | get_distrib( & | ||
| 569 | angle_list, & | ||
| 570 | nbins_(3), eta(3), width_(3), & | ||
| 571 | cutoff_min_(3), & | ||
| 572 | scale_list = distance & | ||
| 573 |
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13186 | ) |
| 574 |
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207 | deallocate( angle_list, distance ) |
| 575 | |||
| 576 | end do | ||
| 577 | end do | ||
| 578 | |||
| 579 | !--------------------------------------------------------------------------- | ||
| 580 | ! apply the cutoff function to the 2-body distribution function | ||
| 581 | !--------------------------------------------------------------------------- | ||
| 582 |
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5994 | do b = 1, nbins_(1) |
| 583 | this%df_2body(b,:) = this%df_2body(b,:) / ( cutoff_min_(1) + & | ||
| 584 |
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15276 | width_(1) * real(b-1, real32) ) ** 2 |
| 585 | end do | ||
| 586 | |||
| 587 | |||
| 588 | !--------------------------------------------------------------------------- | ||
| 589 | ! renormalise the distribution functions so that area under the curve is 1 | ||
| 590 | !--------------------------------------------------------------------------- | ||
| 591 |
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69 | do i = 1, num_pairs |
| 592 |
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2240 | if(any(abs(this%df_2body(:,i)).gt.1.E-6))then |
| 593 |
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18606 | this%df_2body(:,i) = this%df_2body(:,i) / sum(this%df_2body(:,i)) |
| 594 | end if | ||
| 595 | end do | ||
| 596 |
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61 | do is = 1, basis%nspec |
| 597 |
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1069 | if(any(abs(this%df_3body(:,is)).gt.1.E-6))then |
| 598 |
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5149 | this%df_3body(:,is) = this%df_3body(:,is) / sum(this%df_3body(:,is)) |
| 599 | end if | ||
| 600 |
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256 | if(any(abs(this%df_4body(:,is)).gt.1.E-6))then |
| 601 |
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5149 | this%df_4body(:,is) = this%df_4body(:,is) / sum(this%df_4body(:,is)) |
| 602 | end if | ||
| 603 | end do | ||
| 604 | |||
| 605 | |||
| 606 | !--------------------------------------------------------------------------- | ||
| 607 | ! check for NaN in the distribution functions | ||
| 608 | !--------------------------------------------------------------------------- | ||
| 609 |
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9351 | if(any(isnan(this%df_2body)))then |
| 610 | ✗ | call stop_program('NaN in 2-body distribution function') | |
| 611 | end if | ||
| 612 |
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2815 | if(any(isnan(this%df_3body)))then |
| 613 | ✗ | call stop_program('NaN in 3-body distribution function') | |
| 614 | end if | ||
| 615 |
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2815 | if(any(isnan(this%df_4body)))then |
| 616 | ✗ | call stop_program('NaN in 4-body distribution function') | |
| 617 | end if | ||
| 618 | |||
| 619 |
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|
149 | end subroutine calculate |
| 620 | !############################################################################### | ||
| 621 | |||
| 622 | |||
| 623 | !############################################################################### | ||
| 624 |
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599 | function get_distrib(value_list, nbins, eta, width, cutoff_min, & |
| 625 |
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599 | scale_list ) result(output) |
| 626 | !! Calculate the angular distribution function for a list of values. | ||
| 627 | implicit none | ||
| 628 | |||
| 629 | ! Arguments | ||
| 630 | integer, intent(in) :: nbins | ||
| 631 | !! Number of bins for the distribution functions. | ||
| 632 | real(real32), intent(in) :: eta, width, cutoff_min | ||
| 633 | !! Parameters for the distribution functions. | ||
| 634 | real(real32), dimension(:), intent(in) :: value_list | ||
| 635 | !! List of angles. | ||
| 636 | real(real32), dimension(:), intent(in) :: scale_list | ||
| 637 | !! List of scaling for each angle (distance**3 or distance**4) | ||
| 638 | real(real32), dimension(nbins) :: output | ||
| 639 | !! Distribution function for the list of values. | ||
| 640 | |||
| 641 | ! Local variables | ||
| 642 | integer :: i, j, b, bin | ||
| 643 | !! Loop index. | ||
| 644 | integer :: max_num_steps | ||
| 645 | !! Maximum number of steps. | ||
| 646 | integer, dimension(3,2) :: loop_limits | ||
| 647 | !! Loop limits for the 3-body distribution function. | ||
| 648 | |||
| 649 | |||
| 650 |
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599 | max_num_steps = ceiling( sqrt(16._real32/eta) / width ) |
| 651 |
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82538 | output = 0._real32 |
| 652 | |||
| 653 | !--------------------------------------------------------------------------- | ||
| 654 | ! calculate the distribution function for a list of values | ||
| 655 | !--------------------------------------------------------------------------- | ||
| 656 |
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307670 | do i = 1, size(value_list), 1 |
| 657 | |||
| 658 | !------------------------------------------------------------------------ | ||
| 659 | ! get the bin closest to the value | ||
| 660 | !------------------------------------------------------------------------ | ||
| 661 | 307071 | bin = nint( ( value_list(i) - cutoff_min ) / width ) + 1 | |
| 662 | if( & | ||
| 663 |
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307071 | bin .lt. 1 - max_num_steps .or. & |
| 664 | bin .gt. nbins + max_num_steps & | ||
| 665 | ✗ | ) cycle | |
| 666 | |||
| 667 | |||
| 668 | !------------------------------------------------------------------------ | ||
| 669 | ! calculate the gaussian for this bond | ||
| 670 | !------------------------------------------------------------------------ | ||
| 671 | loop_limits(:,1) = & | ||
| 672 |
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1228284 | [ min(nbins, bin), min(nbins, bin + max_num_steps), 1 ] |
| 673 | loop_limits(:,2) = & | ||
| 674 |
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1228284 | [ max(0, bin - 1), max(1, bin - max_num_steps), -1 ] |
| 675 | |||
| 676 | |||
| 677 | !------------------------------------------------------------------------ | ||
| 678 | ! do forward and backward loops to add gaussian from its centre | ||
| 679 | !------------------------------------------------------------------------ | ||
| 680 | 599 | do concurrent ( j = 1:2 ) | |
| 681 | do concurrent ( & | ||
| 682 | b = loop_limits(1,j):loop_limits(2,j):loop_limits(3,j) & | ||
| 683 |
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921213 | ) |
| 684 | output(b) = output(b) + & | ||
| 685 | exp( & | ||
| 686 | -eta * ( & | ||
| 687 | value_list(i) - & | ||
| 688 | ( width * real(b-1, real32) + cutoff_min ) & | ||
| 689 | ) ** 2._real32 & | ||
| 690 |
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8494816 | ) / scale_list(i) |
| 691 | end do | ||
| 692 | end do | ||
| 693 | end do | ||
| 694 |
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|
82538 | output = output * sqrt( eta / pi ) / real(size(value_list,1),real32) |
| 695 | |||
| 696 | 599 | end function get_distrib | |
| 697 | !############################################################################### | ||
| 698 | |||
| 699 | ✗ | end module raffle__distribs | |
| 700 |