| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | module raffle__geom_rw | ||
| 2 | !! Module to store, read and write geometry files | ||
| 3 | !! | ||
| 4 | !! This module contains the procedures to read and write geometry files. | ||
| 5 | !! It also contains the derived types used to store the geometry data. | ||
| 6 | use raffle__constants, only: pi,real32 | ||
| 7 | use raffle__io_utils, only: stop_program, print_warning | ||
| 8 | use raffle__misc, only: to_upper, to_lower, jump, icount, strip_null | ||
| 9 | use raffle__misc_linalg, only: modu, inverse_3x3 | ||
| 10 | implicit none | ||
| 11 | |||
| 12 | |||
| 13 | private | ||
| 14 | |||
| 15 | public :: igeom_input, igeom_output | ||
| 16 | public :: basis_type, species_type | ||
| 17 | public :: geom_read, geom_write | ||
| 18 | public :: get_element_properties | ||
| 19 | |||
| 20 | |||
| 21 | integer :: igeom_input = 1 | ||
| 22 | !! geometry input file format | ||
| 23 | !! 1 = VASP | ||
| 24 | ! 2 = CASTEP | ||
| 25 | !! 3 = Quantum Espresso | ||
| 26 | !! 4 = CRYSTAL | ||
| 27 | !! 5 = XYZ | ||
| 28 | !! 6 = extended XYZ | ||
| 29 | integer :: igeom_output = 1 | ||
| 30 | !! geometry output file format | ||
| 31 | |||
| 32 | type :: species_type | ||
| 33 | !! Derived type to store information about a species/element. | ||
| 34 | real(real32), allocatable ,dimension(:,:) :: atom | ||
| 35 | !! The atomic positions of the species. | ||
| 36 | real(real32) :: mass | ||
| 37 | !! The mass of the species. | ||
| 38 | real(real32) :: charge | ||
| 39 | !! The charge of the species. | ||
| 40 | real(real32) :: radius | ||
| 41 | !! The radius of the species. | ||
| 42 | character(len=3) :: name | ||
| 43 | !! The name of the species. | ||
| 44 | integer :: num | ||
| 45 | !! The number of atoms of this species. | ||
| 46 | end type species_type | ||
| 47 | type :: basis_type | ||
| 48 | !! Derived type to store information about a basis. | ||
| 49 | type(species_type), allocatable, dimension(:) :: spec | ||
| 50 | !! Information about each species in the basis. | ||
| 51 | integer :: nspec = 0 | ||
| 52 | !! The number of species in the basis. | ||
| 53 | integer :: natom = 0 | ||
| 54 | !! The number of atoms in the basis. | ||
| 55 | real(real32) :: energy = 0._real32 | ||
| 56 | !! The energy of the basis. | ||
| 57 | real(real32) :: lat(3,3) = 0._real32 | ||
| 58 | !! The lattice vectors of the basis. | ||
| 59 | logical :: lcart = .false. | ||
| 60 | !! Boolean whether the basis is in cartesian coordinates. | ||
| 61 | logical, dimension(3) :: pbc = .true. | ||
| 62 | !! Boolean whether the basis has periodic boundary conditions. | ||
| 63 | character(len=128) :: sysname = "default" | ||
| 64 | !! The name of the system. | ||
| 65 | contains | ||
| 66 | procedure, pass(this) :: allocate_species | ||
| 67 | !! Procedure to allocate the species in the basis. | ||
| 68 | procedure, pass(this) :: convert | ||
| 69 | !! Procedure to convert the basis to cartesian coordinates. | ||
| 70 | procedure, pass(this) :: copy | ||
| 71 | !! Procedure to copy the basis. | ||
| 72 | procedure, pass(this) :: get_lattice_constants | ||
| 73 | !! Procedure to get the lattice constants of the basis. | ||
| 74 | procedure, pass(this) :: remove_atom | ||
| 75 | !! Procedure to remove an atom from the basis. | ||
| 76 | procedure, pass(this) :: remove_atoms | ||
| 77 | !! Procedure to remove atoms from the basis. | ||
| 78 | end type basis_type | ||
| 79 | |||
| 80 | |||
| 81 | interface basis_type | ||
| 82 | module function init_basis_type(basis) result(output) | ||
| 83 | !! Initialise the basis type. | ||
| 84 | type(basis_type), intent(in), optional :: basis | ||
| 85 | !! Optional. Basis to copy. | ||
| 86 | type(basis_type) :: output | ||
| 87 | !! The basis to initialise. | ||
| 88 | end function init_basis_type | ||
| 89 | end interface basis_type | ||
| 90 | |||
| 91 | |||
| 92 | |||
| 93 | contains | ||
| 94 | |||
| 95 | !############################################################################### | ||
| 96 | 1 | module function init_basis_type(basis) result(output) | |
| 97 | !! Initialise the basis type. | ||
| 98 | implicit none | ||
| 99 | |||
| 100 | ! Arguments | ||
| 101 | type(basis_type), intent(in), optional :: basis | ||
| 102 | !! Optional. Basis to copy. | ||
| 103 | type(basis_type) :: output | ||
| 104 | !! The basis to initialise. | ||
| 105 | |||
| 106 | 1 | if(present(basis)) call output%copy(basis) | |
| 107 | |||
| 108 |
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17 | end function init_basis_type |
| 109 | !############################################################################### | ||
| 110 | |||
| 111 | |||
| 112 | !############################################################################### | ||
| 113 | 4 | subroutine allocate_species( & | |
| 114 | this, num_species, & | ||
| 115 |
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4 | species_symbols, species_count, atoms ) |
| 116 | !! Allocate the species in the basis. | ||
| 117 | implicit none | ||
| 118 | |||
| 119 | ! Arguments | ||
| 120 | class(basis_type), intent(inout) :: this | ||
| 121 | !! Parent. The basis to allocate the species in. | ||
| 122 | integer, intent(in), optional :: num_species | ||
| 123 | !! Optional. The number of species in the basis. | ||
| 124 | character(3), dimension(:), intent(in), optional :: species_symbols | ||
| 125 | !! Optional. The symbols of the species. | ||
| 126 | integer, dimension(:), intent(in), optional :: species_count | ||
| 127 | !! Optional. The number of atoms of each species. | ||
| 128 | real(real32), dimension(:,:), intent(in), optional :: atoms | ||
| 129 | !! Optional. The atomic positions of the species. | ||
| 130 | |||
| 131 | ! Local variables | ||
| 132 | integer :: i, istart, iend | ||
| 133 | !! Loop index. | ||
| 134 | |||
| 135 |
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4 | if(present(num_species)) this%nspec = num_species |
| 136 | |||
| 137 |
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13 | if(allocated(this%spec)) deallocate(this%spec) |
| 138 |
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10 | allocate(this%spec(this%nspec)) |
| 139 | |||
| 140 |
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4 | species_check: if(present(species_symbols))then |
| 141 |
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1 | if(size(species_symbols).ne.this%nspec) exit species_check |
| 142 |
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3 | this%spec(:)%name = species_symbols |
| 143 | end if species_check | ||
| 144 | |||
| 145 |
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4 | natom_check: if(present(species_count))then |
| 146 |
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1 | if(size(species_count).ne.this%nspec) exit natom_check |
| 147 |
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3 | this%spec(:)%num = species_count |
| 148 | 1 | istart = 1 | |
| 149 |
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3 | do i = 1, this%nspec |
| 150 | 2 | iend = istart + this%spec(i)%num - 1 | |
| 151 |
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2 | allocate(this%spec(i)%atom(this%spec(i)%num,3)) |
| 152 |
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2 | if(present(atoms))then |
| 153 |
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19 | this%spec(i)%atom = atoms(istart:iend,:3) |
| 154 | end if | ||
| 155 | 3 | istart = iend + 1 | |
| 156 | end do | ||
| 157 | end if natom_check | ||
| 158 | |||
| 159 |
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10 | do i = 1, this%nspec |
| 160 | call get_element_properties( & | ||
| 161 | this%spec(i)%name, & | ||
| 162 | mass = this%spec(i)%mass, & | ||
| 163 | charge = this%spec(i)%charge, & | ||
| 164 | 10 | radius = this%spec(i)%radius ) | |
| 165 | end do | ||
| 166 | |||
| 167 | 4 | end subroutine allocate_species | |
| 168 | !############################################################################### | ||
| 169 | |||
| 170 | |||
| 171 | !############################################################################### | ||
| 172 |
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48 | subroutine geom_read(UNIT, basis, length, iostat) |
| 173 | !! Read geometry from a file. | ||
| 174 | implicit none | ||
| 175 | |||
| 176 | ! Arguments | ||
| 177 | integer, intent(in) :: UNIT | ||
| 178 | !! The unit number of the file to read from. | ||
| 179 | type(basis_type), intent(out) :: basis | ||
| 180 | !! The basis to read the geometry into. | ||
| 181 | integer, optional, intent(in) :: length | ||
| 182 | !! Optional. The dimension of the basis atom positions. | ||
| 183 | integer, optional, intent(out) :: iostat | ||
| 184 | !! Optional. The I/O status of the read. | ||
| 185 | |||
| 186 | ! Local variables | ||
| 187 | integer :: i | ||
| 188 | !! Loop index. | ||
| 189 | integer :: length_ | ||
| 190 | !! The dimension of the basis atom positions. | ||
| 191 | integer :: iostat_ | ||
| 192 | !! The I/O status of the read. | ||
| 193 | |||
| 194 | |||
| 195 | 3 | length_ = 3 | |
| 196 | 3 | iostat_ = 0 | |
| 197 |
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3 | if(present(length)) length_=length |
| 198 | |||
| 199 | 2 | select case(igeom_input) | |
| 200 | case(1) | ||
| 201 | 2 | call VASP_geom_read(UNIT, basis, length_, iostat_) | |
| 202 | case(2) | ||
| 203 | ✗ | call CASTEP_geom_read(UNIT, basis, length_) | |
| 204 | case(3) | ||
| 205 | ✗ | call QE_geom_read(UNIT, basis, length_) | |
| 206 | case(4) | ||
| 207 | ✗ | call stop_program("Not yet set up for CRYSTAL") | |
| 208 | ✗ | return | |
| 209 | case(5) | ||
| 210 | ✗ | call XYZ_geom_read(UNIT, basis, length_, iostat_) | |
| 211 | ✗ | call print_warning("XYZ file format does not contain lattice data") | |
| 212 | case(6) | ||
| 213 |
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3 | call extXYZ_geom_read(UNIT, basis, length_, iostat_) |
| 214 | end select | ||
| 215 |
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3 | if(iostat_.ne.0) then |
| 216 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 217 | ✗ | return | |
| 218 | else | ||
| 219 |
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3 | if(present(iostat)) iostat = 0 |
| 220 | end if | ||
| 221 |
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3 | if(length_.eq.4)then |
| 222 | ✗ | do i = 1, basis%nspec | |
| 223 | ✗ | basis%spec(i)%atom(:,4)=1._real32 | |
| 224 | end do | ||
| 225 | end if | ||
| 226 |
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6 | do i = 1, basis%nspec |
| 227 | call get_element_properties( & | ||
| 228 | basis%spec(i)%name, & | ||
| 229 | mass = basis%spec(i)%mass, & | ||
| 230 | charge = basis%spec(i)%charge, & | ||
| 231 | 6 | radius = basis%spec(i)%radius ) | |
| 232 | end do | ||
| 233 | |||
| 234 | end subroutine geom_read | ||
| 235 | !############################################################################### | ||
| 236 | |||
| 237 | |||
| 238 | !############################################################################### | ||
| 239 | 2 | subroutine geom_write(UNIT, basis) | |
| 240 | !! Write geometry to a file. | ||
| 241 | implicit none | ||
| 242 | |||
| 243 | ! Arguments | ||
| 244 | integer, intent(in) :: UNIT | ||
| 245 | !! The unit number of the file to write to. | ||
| 246 | class(basis_type), intent(in) :: basis | ||
| 247 | !! The basis to write the geometry from. | ||
| 248 | |||
| 249 | ! MAKE IT CHANGE HERE IF USER SPECIFIES LCART OR NOT | ||
| 250 | ! AND GIVE IT THE CASTEP AND QE OPTION OF LABC ! | ||
| 251 | |||
| 252 | 1 | select case(igeom_output) | |
| 253 | case(1) | ||
| 254 | 1 | call VASP_geom_write(UNIT,basis) | |
| 255 | case(2) | ||
| 256 | ✗ | call CASTEP_geom_write(UNIT,basis) | |
| 257 | case(3) | ||
| 258 | ✗ | call QE_geom_write(UNIT,basis) | |
| 259 | case(4) | ||
| 260 | ✗ | call stop_program("ERROR: Not yet set up for CRYSTAL") | |
| 261 | ✗ | return | |
| 262 | case(5) | ||
| 263 | ✗ | call XYZ_geom_write(UNIT,basis) | |
| 264 | case(6) | ||
| 265 |
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2 | call extXYZ_geom_write(UNIT,basis) |
| 266 | end select | ||
| 267 | |||
| 268 | end subroutine geom_write | ||
| 269 | !############################################################################### | ||
| 270 | |||
| 271 | |||
| 272 | !############################################################################### | ||
| 273 |
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32 | subroutine VASP_geom_read(UNIT, basis, length, iostat) |
| 274 | !! Read the structure in vasp poscar style format. | ||
| 275 | implicit none | ||
| 276 | |||
| 277 | ! Arguments | ||
| 278 | integer, intent(in) :: UNIT | ||
| 279 | !! The unit number of the file to read from. | ||
| 280 | type(basis_type), intent(out) :: basis | ||
| 281 | !! The basis to read the geometry into. | ||
| 282 | integer, intent(in), optional :: length | ||
| 283 | !! Optional. The dimension of the basis atom positions. | ||
| 284 | integer, intent(out), optional :: iostat | ||
| 285 | !! Optional. The I/O status of the read. | ||
| 286 | |||
| 287 | integer :: Reason | ||
| 288 | !! The I/O status of the read. | ||
| 289 | integer :: pos, count | ||
| 290 | !! Temporary integer variables. | ||
| 291 | real(real32) :: scal | ||
| 292 | !! The scaling factor of the lattice. | ||
| 293 | character(len=100) :: lspec | ||
| 294 | !! The species names and number of each atomic species. | ||
| 295 | character(len=1024) :: buffer | ||
| 296 | !! Temporary character variable. | ||
| 297 | integer :: i, j, k | ||
| 298 | !! Loop index. | ||
| 299 | integer :: length_ | ||
| 300 | !! The dimension of the basis atom positions. | ||
| 301 | integer :: iostat_ | ||
| 302 | !! The I/O status of the read. | ||
| 303 | |||
| 304 | |||
| 305 | 2 | length_ = 3 | |
| 306 | 2 | iostat_ = 0 | |
| 307 | !--------------------------------------------------------------------------- | ||
| 308 | ! determine dimension of basis (include translation dimension for symmetry?) | ||
| 309 | !--------------------------------------------------------------------------- | ||
| 310 |
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2 | if(present(length)) length_ = length |
| 311 | |||
| 312 | |||
| 313 | !--------------------------------------------------------------------------- | ||
| 314 | ! read system name | ||
| 315 | !--------------------------------------------------------------------------- | ||
| 316 | 2 | read(UNIT,'(A)',iostat=Reason) basis%sysname | |
| 317 |
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2 | if(Reason.ne.0)then |
| 318 | ✗ | write(0,'("ERROR: The file is not in POSCAR format.")') | |
| 319 | ✗ | write(0,*) "Expected system name, got: ",trim(basis%sysname) | |
| 320 | ✗ | iostat_ = 1 | |
| 321 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 322 | ✗ | return | |
| 323 | end if | ||
| 324 | 2 | read(UNIT,*) scal | |
| 325 | |||
| 326 | |||
| 327 | !--------------------------------------------------------------------------- | ||
| 328 | ! read lattice | ||
| 329 | !--------------------------------------------------------------------------- | ||
| 330 |
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8 | do i = 1, 3 |
| 331 |
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26 | read(UNIT,*) (basis%lat(i,j),j=1,3) |
| 332 | end do | ||
| 333 |
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26 | basis%lat=scal*basis%lat |
| 334 | |||
| 335 | |||
| 336 | !--------------------------------------------------------------------------- | ||
| 337 | ! read species names and number of each atomic species | ||
| 338 | !--------------------------------------------------------------------------- | ||
| 339 | 2 | read(UNIT,'(A)') lspec | |
| 340 | 2 | basis%nspec = icount(lspec) | |
| 341 |
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4 | allocate(basis%spec(basis%nspec)) |
| 342 |
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2 | if(verify(lspec,' 0123456789').ne.0) then |
| 343 | 2 | count=0;pos=1 | |
| 344 | 2 | speccount: do | |
| 345 | 4 | i=verify(lspec(pos:), ' ') | |
| 346 |
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4 | if (i.eq.0) exit speccount |
| 347 | 2 | count=count+1 | |
| 348 | 2 | pos=i+pos-1 | |
| 349 | 2 | i=scan(lspec(pos:), ' ') | |
| 350 |
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2 | if (i.eq.0) exit speccount |
| 351 |
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2 | basis%spec(count)%name=lspec(pos:pos+i-1) |
| 352 | 2 | pos=i+pos-1 | |
| 353 | end do speccount | ||
| 354 | |||
| 355 |
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4 | read(UNIT,*) (basis%spec(j)%num,j=1,basis%nspec) |
| 356 | else !only numbers | ||
| 357 | ✗ | do count = 1, basis%nspec | |
| 358 | ✗ | write(basis%spec(count)%name,'(I0)') count | |
| 359 | end do | ||
| 360 | ✗ | read(lspec,*) (basis%spec(j)%num,j=1,basis%nspec) | |
| 361 | end if | ||
| 362 | |||
| 363 | |||
| 364 | !--------------------------------------------------------------------------- | ||
| 365 | ! determines whether input basis is in direct or cartesian coordinates | ||
| 366 | !--------------------------------------------------------------------------- | ||
| 367 | 2 | basis%lcart=.false. | |
| 368 | 2 | read(UNIT,'(A)') buffer | |
| 369 |
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2 | buffer = to_lower(buffer) |
| 370 |
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2 | if(verify(trim(buffer),'direct').eq.0) basis%lcart=.false. |
| 371 |
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2 | if(verify(trim(buffer),'cartesian').eq.0) basis%lcart=.true. |
| 372 | |||
| 373 | |||
| 374 | !--------------------------------------------------------------------------- | ||
| 375 | ! read basis | ||
| 376 | !--------------------------------------------------------------------------- | ||
| 377 |
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4 | do i = 1, basis%nspec |
| 378 |
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2 | allocate(basis%spec(i)%atom(basis%spec(i)%num,length_)) |
| 379 |
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56 | basis%spec(i)%atom(:,:)=0._real32 |
| 380 |
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20 | do j = 1, basis%spec(i)%num |
| 381 |
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66 | read(UNIT,*) (basis%spec(i)%atom(j,k),k=1,3) |
| 382 | end do | ||
| 383 | end do | ||
| 384 | |||
| 385 | |||
| 386 | !--------------------------------------------------------------------------- | ||
| 387 | ! convert basis if in cartesian coordinates | ||
| 388 | !--------------------------------------------------------------------------- | ||
| 389 |
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2 | if(basis%lcart) call basis%convert() |
| 390 | |||
| 391 | |||
| 392 | !--------------------------------------------------------------------------- | ||
| 393 | ! normalise basis to between 0 and 1 in direct coordinates | ||
| 394 | !--------------------------------------------------------------------------- | ||
| 395 |
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4 | do i = 1, basis%nspec |
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20 | do j = 1, basis%spec(i)%num |
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66 | do k = 1, 3 |
| 398 | basis%spec(i)%atom(j,k)=& | ||
| 399 |
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64 | basis%spec(i)%atom(j,k)-floor(basis%spec(i)%atom(j,k)) |
| 400 | end do | ||
| 401 | end do | ||
| 402 | end do | ||
| 403 |
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4 | basis%natom=sum(basis%spec(:)%num) |
| 404 | |||
| 405 |
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2 | if(present(iostat)) iostat = iostat_ |
| 406 | |||
| 407 | end subroutine VASP_geom_read | ||
| 408 | !############################################################################### | ||
| 409 | |||
| 410 | |||
| 411 | !############################################################################### | ||
| 412 | 1 | subroutine VASP_geom_write(UNIT, basis, cartesian) | |
| 413 | !! Write the structure in vasp poscar style format. | ||
| 414 | implicit none | ||
| 415 | |||
| 416 | ! Arguments | ||
| 417 | integer, intent(in) :: UNIT | ||
| 418 | !! The unit number of the file to write to. | ||
| 419 | class(basis_type), intent(in) :: basis | ||
| 420 | !! The basis to write the geometry from. | ||
| 421 | logical, intent(in), optional :: cartesian | ||
| 422 | !! Optional. Whether to write the basis in cartesian coordinates. | ||
| 423 | |||
| 424 | ! Local variables | ||
| 425 | integer :: i,j | ||
| 426 | !! Loop index. | ||
| 427 | character(100) :: fmt | ||
| 428 | !! Format string. | ||
| 429 | character(10) :: string | ||
| 430 | !! String to determine whether to write in direct or cartesian coordinates. | ||
| 431 | |||
| 432 | |||
| 433 | 1 | string="Direct" | |
| 434 |
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1 | if(present(cartesian))then |
| 435 | ✗ | if(cartesian) string="Cartesian" | |
| 436 | end if | ||
| 437 | |||
| 438 |
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1 | write(UNIT,'(A)') trim(adjustl(basis%sysname)) |
| 439 | 1 | write(UNIT,'(F15.9)') 1._real32 | |
| 440 |
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4 | do i = 1, 3 |
| 441 | 4 | write(UNIT,'(3(F15.9))') basis%lat(i,:) | |
| 442 | end do | ||
| 443 | 1 | write(fmt,'("(",I0,"(A,1X))")') basis%nspec | |
| 444 |
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2 | write(UNIT,trim(adjustl(fmt))) (adjustl(basis%spec(j)%name),j=1,basis%nspec) |
| 445 | 1 | write(fmt,'("(",I0,"(I0,5X))")') basis%nspec | |
| 446 |
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2 | write(UNIT,trim(adjustl(fmt))) (basis%spec(j)%num,j=1,basis%nspec) |
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1 | write(UNIT,'(A)') trim(adjustl(string)) |
| 448 |
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2 | do i = 1, basis%nspec |
| 449 |
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10 | do j = 1, basis%spec(i)%num |
| 450 |
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33 | write(UNIT,'(3(F15.9))') basis%spec(i)%atom(j,1:3) |
| 451 | end do | ||
| 452 | end do | ||
| 453 | |||
| 454 | 1 | end subroutine VASP_geom_write | |
| 455 | !############################################################################### | ||
| 456 | |||
| 457 | |||
| 458 | !############################################################################### | ||
| 459 | ✗ | subroutine QE_geom_read(UNIT,basis,length) | |
| 460 | !! Read the structure in Quantum Espresso style format. | ||
| 461 | implicit none | ||
| 462 | |||
| 463 | ! Arguments | ||
| 464 | integer, intent(in) :: UNIT | ||
| 465 | !! The unit number of the file to read from. | ||
| 466 | type(basis_type), intent(out) :: basis | ||
| 467 | !! The basis to read the geometry into. | ||
| 468 | integer, intent(in), optional :: length | ||
| 469 | !! Optional. The dimension of the basis atom positions. | ||
| 470 | |||
| 471 | ! Local variables | ||
| 472 | integer :: Reason | ||
| 473 | !! The I/O status of the read. | ||
| 474 | integer :: i, j, k, iline | ||
| 475 | !! Loop index. | ||
| 476 | integer :: length_ = 3 | ||
| 477 | !! The dimension of the basis atom positions. | ||
| 478 | integer, dimension(1000) :: tmp_natom | ||
| 479 | !! Temporary array to store the number of atoms of each species. | ||
| 480 | real(real32), dimension(3) :: tmpvec | ||
| 481 | !! Temporary array to store the atomic positions. | ||
| 482 | character(len=3) :: ctmp | ||
| 483 | !! Temporary character variable. | ||
| 484 | character(256) :: stop_msg | ||
| 485 | !! Error message. | ||
| 486 | character(len=3), dimension(1000) :: tmp_spec | ||
| 487 | !! Temporary array to store the species names. | ||
| 488 | character(len=1024) :: buffer, buffer2 | ||
| 489 | !! Temporary character variables. | ||
| 490 | |||
| 491 | |||
| 492 | !--------------------------------------------------------------------------- | ||
| 493 | ! determine dimension of basis (include translation dimension for symmetry?) | ||
| 494 | !--------------------------------------------------------------------------- | ||
| 495 | ✗ | if(present(length)) length_ = length | |
| 496 | ✗ | basis%lcart = .false. | |
| 497 | ✗ | basis%sysname = "Converted_from_geom_file" | |
| 498 | |||
| 499 | |||
| 500 | !--------------------------------------------------------------------------- | ||
| 501 | ! read lattice | ||
| 502 | !--------------------------------------------------------------------------- | ||
| 503 | ✗ | rewind UNIT | |
| 504 | ✗ | cellparam: do | |
| 505 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 506 | ✗ | if(Reason.ne.0)then | |
| 507 | call stop_program( & | ||
| 508 | "An issue with the QE input file format has been encountered." & | ||
| 509 | ✗ | ) | |
| 510 | ✗ | return | |
| 511 | end if | ||
| 512 | ✗ | if(index(trim(buffer),"ibrav").ne.0)then | |
| 513 | write(stop_msg,*) & | ||
| 514 | "Internal error in QE_geom_read" // & | ||
| 515 | achar(13) // achar(10) // & | ||
| 516 | ✗ | " Subroutine not yet set up to read IBRAV lattices" | |
| 517 | ✗ | call stop_program(stop_msg) | |
| 518 | ✗ | return | |
| 519 | end if | ||
| 520 | ✗ | if(verify("CELL_PARAMETERS",buffer).eq.0) then | |
| 521 | ✗ | exit cellparam | |
| 522 | end if | ||
| 523 | end do cellparam | ||
| 524 | ✗ | do i = 1, 3 | |
| 525 | ✗ | read(UNIT,*) (basis%lat(i,j),j=1,3) | |
| 526 | end do | ||
| 527 | |||
| 528 | |||
| 529 | !--------------------------------------------------------------------------- | ||
| 530 | ! determines whether input basis is in direct or cartesian coordinates | ||
| 531 | !--------------------------------------------------------------------------- | ||
| 532 | ✗ | iline=0 | |
| 533 | ✗ | rewind UNIT | |
| 534 | ✗ | basfind: do | |
| 535 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 536 | ✗ | iline=iline+1 | |
| 537 | ✗ | if(verify("ATOMIC_POSITIONS",buffer).eq.0)then | |
| 538 | ✗ | backspace(UNIT) | |
| 539 | ✗ | read(UNIT,*) buffer,buffer2 | |
| 540 | ✗ | if(verify("crystal",buffer2).eq.0) basis%lcart = .false. | |
| 541 | ✗ | if(verify("angstrom",buffer2).eq.0) basis%lcart = .true. | |
| 542 | ✗ | exit basfind | |
| 543 | end if | ||
| 544 | end do basfind | ||
| 545 | |||
| 546 | |||
| 547 | !--------------------------------------------------------------------------- | ||
| 548 | ! read basis | ||
| 549 | !--------------------------------------------------------------------------- | ||
| 550 | ✗ | basis%natom = 0 | |
| 551 | ✗ | basis%nspec = 0 | |
| 552 | ✗ | tmp_natom = 1 | |
| 553 | ✗ | basread: do | |
| 554 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 555 | ✗ | read(buffer,*) ctmp | |
| 556 | ✗ | if(Reason.ne.0) exit | |
| 557 | ✗ | if(trim(ctmp).eq.'') exit | |
| 558 | ✗ | if(verify(buffer,' 0123456789').eq.0) exit | |
| 559 | ✗ | basis%natom = basis%natom + 1 | |
| 560 | ✗ | if(.not.any(tmp_spec(1:basis%nspec).eq.ctmp))then | |
| 561 | ✗ | basis%nspec = basis%nspec + 1 | |
| 562 | ✗ | tmp_spec(basis%nspec) = ctmp | |
| 563 | else | ||
| 564 | ✗ | where(tmp_spec(1:basis%nspec).eq.ctmp) | |
| 565 | tmp_natom(1:basis%nspec) = tmp_natom(1:basis%nspec) + 1 | ||
| 566 | end where | ||
| 567 | end if | ||
| 568 | end do basread | ||
| 569 | |||
| 570 | ✗ | allocate(basis%spec(basis%nspec)) | |
| 571 | ✗ | basis%spec(1:basis%nspec)%name = tmp_spec(1:basis%nspec) | |
| 572 | ✗ | do i = 1, basis%nspec | |
| 573 | ✗ | basis%spec(i)%num = 0 | |
| 574 | ✗ | allocate(basis%spec(i)%atom(tmp_natom(i),length_)) | |
| 575 | end do | ||
| 576 | |||
| 577 | ✗ | call jump(UNIT,iline) | |
| 578 | ✗ | basread2: do i = 1, basis%natom | |
| 579 | ✗ | read(UNIT,*,iostat=Reason) ctmp,tmpvec(1:3) | |
| 580 | ✗ | do j = 1, basis%nspec | |
| 581 | ✗ | if(basis%spec(j)%name.eq.ctmp)then | |
| 582 | ✗ | basis%spec(j)%num = basis%spec(j)%num + 1 | |
| 583 | ✗ | basis%spec(j)%atom(basis%spec(j)%num,1:3) = tmpvec(1:3) | |
| 584 | ✗ | exit | |
| 585 | end if | ||
| 586 | end do | ||
| 587 | end do basread2 | ||
| 588 | |||
| 589 | |||
| 590 | !--------------------------------------------------------------------------- | ||
| 591 | ! convert basis if in cartesian coordinates | ||
| 592 | !--------------------------------------------------------------------------- | ||
| 593 | ✗ | if(basis%lcart) call basis%convert() | |
| 594 | |||
| 595 | |||
| 596 | !--------------------------------------------------------------------------- | ||
| 597 | ! normalise basis to between 0 and 1 in direct coordinates | ||
| 598 | !--------------------------------------------------------------------------- | ||
| 599 | ✗ | do i = 1, basis%nspec | |
| 600 | ✗ | do j = 1, basis%spec(i)%num | |
| 601 | ✗ | do k = 1, 3 | |
| 602 | basis%spec(i)%atom(j,k) = & | ||
| 603 | ✗ | basis%spec(i)%atom(j,k) - floor( basis%spec(i)%atom(j,k) ) | |
| 604 | end do | ||
| 605 | end do | ||
| 606 | end do | ||
| 607 | ✗ | basis%natom=sum(basis%spec(:)%num) | |
| 608 | |||
| 609 | end subroutine QE_geom_read | ||
| 610 | !############################################################################### | ||
| 611 | |||
| 612 | |||
| 613 | !############################################################################### | ||
| 614 | ✗ | subroutine QE_geom_write(UNIT, basis, cartesian) | |
| 615 | !! Write the structure in Quantum Espresso style format. | ||
| 616 | implicit none | ||
| 617 | |||
| 618 | ! Arguments | ||
| 619 | integer, intent(in) :: UNIT | ||
| 620 | !! The unit number of the file to write to. | ||
| 621 | class(basis_type), intent(in) :: basis | ||
| 622 | !! The basis to write the geometry from. | ||
| 623 | logical, intent(in), optional :: cartesian | ||
| 624 | !! Optional. Whether to write the basis in cartesian coordinates. | ||
| 625 | |||
| 626 | ! Local variables | ||
| 627 | integer :: i,j | ||
| 628 | !! Loop index. | ||
| 629 | character(10) :: string | ||
| 630 | !! String to determine whether to write in crystal or angstrom coordinates. | ||
| 631 | |||
| 632 | |||
| 633 | ✗ | string="crystal" | |
| 634 | ✗ | if(present(cartesian))then | |
| 635 | ✗ | if(cartesian) string="angstrom" | |
| 636 | end if | ||
| 637 | |||
| 638 | |||
| 639 | ✗ | write(UNIT,'("CELL_PARAMETERS angstrom")') | |
| 640 | ✗ | do i = 1, 3 | |
| 641 | ✗ | write(UNIT,'(3(F15.9))') basis%lat(i,:) | |
| 642 | end do | ||
| 643 | ✗ | write(UNIT,'("ATOMIC_SPECIES")') | |
| 644 | ✗ | do i = 1, basis%nspec | |
| 645 | ✗ | write(UNIT,'(A)') trim(adjustl(basis%spec(i)%name)) | |
| 646 | end do | ||
| 647 | ✗ | write(UNIT,'("ATOMIC_POSITIONS",1X,A)') trim(adjustl(string)) | |
| 648 | ✗ | do i = 1, basis%nspec | |
| 649 | ✗ | do j = 1, basis%spec(i)%num | |
| 650 | write(UNIT,'(A5,1X,3(F15.9))') & | ||
| 651 | ✗ | basis%spec(i)%name,basis%spec(i)%atom(j,1:3) | |
| 652 | end do | ||
| 653 | end do | ||
| 654 | |||
| 655 | ✗ | end subroutine QE_geom_write | |
| 656 | !############################################################################### | ||
| 657 | |||
| 658 | |||
| 659 | !############################################################################### | ||
| 660 | ✗ | subroutine CASTEP_geom_read(UNIT, basis, length) | |
| 661 | !! Read the structure in CASTEP style format. | ||
| 662 | implicit none | ||
| 663 | |||
| 664 | ! Arguments | ||
| 665 | integer, intent(in) :: UNIT | ||
| 666 | !! The unit number of the file to read from. | ||
| 667 | type(basis_type), intent(out) :: basis | ||
| 668 | !! The basis to read the geometry into. | ||
| 669 | integer, intent(in), optional :: length | ||
| 670 | !! Optional. The dimension of the basis atom positions. | ||
| 671 | |||
| 672 | ! Local variables | ||
| 673 | integer :: Reason | ||
| 674 | !! The I/O status of the read. | ||
| 675 | integer :: i, j, k, iline | ||
| 676 | !! Loop index. | ||
| 677 | integer :: length_ = 3 | ||
| 678 | !! The dimension of the basis atom positions. | ||
| 679 | integer :: itmp1 | ||
| 680 | !! Temporary integer variable. | ||
| 681 | character(len=3) :: ctmp | ||
| 682 | !! Temporary character variable. | ||
| 683 | character(len=20) :: units | ||
| 684 | !! Units of the lattice vectors. | ||
| 685 | character(len=200) :: buffer, store | ||
| 686 | !! Temporary character variables. | ||
| 687 | logical :: labc | ||
| 688 | !! Logical variable to determine whether the lattice is in abc or | ||
| 689 | !! cartesian coordinates. | ||
| 690 | integer, dimension(1000) :: tmp_natom | ||
| 691 | !! Temporary array to store the number of atoms of each species. | ||
| 692 | real(real32), dimension(3) :: abc, angle, dvtmp1 | ||
| 693 | !! Temporary arrays to store the lattice vectors. | ||
| 694 | character(len=3), dimension(1000) :: tmp_spec | ||
| 695 | !! Temporary array to store the species names. | ||
| 696 | |||
| 697 | |||
| 698 | !--------------------------------------------------------------------------- | ||
| 699 | ! determine dimension of basis (include translation dimension for symmetry?) | ||
| 700 | !--------------------------------------------------------------------------- | ||
| 701 | ✗ | if(present(length)) length_ = length | |
| 702 | |||
| 703 | |||
| 704 | !--------------------------------------------------------------------------- | ||
| 705 | ! reading loop of file | ||
| 706 | !--------------------------------------------------------------------------- | ||
| 707 | ✗ | tmp_spec = "" | |
| 708 | ✗ | tmp_natom = 0 | |
| 709 | ✗ | iline = 0 | |
| 710 | ✗ | labc = .true. | |
| 711 | ✗ | basis%sysname = "from CASTEP" | |
| 712 | ✗ | rewind(UNIT) | |
| 713 | ✗ | readloop: do | |
| 714 | ✗ | iline=iline+1 | |
| 715 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 716 | ✗ | if(Reason.ne.0) exit | |
| 717 | ✗ | buffer=to_upper(buffer) | |
| 718 | ✗ | if(scan(trim(adjustl(buffer)),'%').ne.1) cycle readloop | |
| 719 | ✗ | if(index(trim(adjustl(buffer)),'%END').eq.1) cycle readloop | |
| 720 | ✗ | read(buffer,*) store, buffer | |
| 721 | ✗ | if(trim(buffer).eq.'') cycle readloop | |
| 722 | !------------------------------------------------------------------------ | ||
| 723 | ! read lattice | ||
| 724 | !------------------------------------------------------------------------ | ||
| 725 | ✗ | lattice_if: if(index(trim(buffer),"LATTICE").eq.1)then | |
| 726 | ✗ | if(index(trim(buffer),"ABC").ne.0) labc = .true. | |
| 727 | ✗ | if(index(trim(buffer),"CART").ne.0) labc = .false. | |
| 728 | ✗ | store = "" | |
| 729 | ✗ | itmp1 = 0 | |
| 730 | ✗ | lattice_loop: do | |
| 731 | ✗ | itmp1 = itmp1 + 1 | |
| 732 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 733 | ✗ | if(Reason.ne.0) exit lattice_loop | |
| 734 | ✗ | if(scan(trim(adjustl(buffer)),'%').eq.1) exit lattice_loop | |
| 735 | ✗ | if(itmp1.eq.5)then | |
| 736 | call stop_program( & | ||
| 737 | "Too many lines in LATTICE block of structure file" & | ||
| 738 | ✗ | ) | |
| 739 | ✗ | return | |
| 740 | end if | ||
| 741 | ✗ | store=trim(store)//" "//trim(buffer) | |
| 742 | end do lattice_loop | ||
| 743 | ✗ | iline=iline+itmp1 | |
| 744 | |||
| 745 | ✗ | if(labc)then | |
| 746 | ✗ | read(store,*) units,(abc(i),i=1,3), (angle(j),j=1,3) | |
| 747 | ✗ | basis%lat = convert_abc_to_lat(abc,angle,.false.) | |
| 748 | else | ||
| 749 | ✗ | read(store,*) units,(basis%lat(i,:),i=1,3) | |
| 750 | end if | ||
| 751 | ✗ | cycle readloop | |
| 752 | end if lattice_if | ||
| 753 | |||
| 754 | !------------------------------------------------------------------------ | ||
| 755 | ! read basis | ||
| 756 | !------------------------------------------------------------------------ | ||
| 757 | ✗ | basis_if: if(index(trim(buffer),"POSITIONS").eq.1) then | |
| 758 | ✗ | if(index(trim(buffer),"ABS").ne.0) basis%lcart=.true. | |
| 759 | ✗ | if(index(trim(buffer),"FRAC").ne.0) basis%lcart=.false. | |
| 760 | ✗ | itmp1 = 0 | |
| 761 | ✗ | basis_loop1: do | |
| 762 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 763 | ✗ | if(Reason.ne.0) exit basis_loop1 | |
| 764 | ✗ | if(scan(trim(adjustl(buffer)),'%').eq.1) exit basis_loop1 | |
| 765 | ✗ | read(buffer,*) ctmp | |
| 766 | ✗ | if(trim(ctmp).eq.'') exit | |
| 767 | ✗ | if(verify(buffer,' 0123456789').eq.0) exit | |
| 768 | ✗ | basis%natom = basis%natom + 1 | |
| 769 | ✗ | if(.not.any(tmp_spec(1:basis%nspec).eq.ctmp))then | |
| 770 | ✗ | basis%nspec = basis%nspec+1 | |
| 771 | ✗ | tmp_natom(basis%nspec) = 1 | |
| 772 | ✗ | tmp_spec(basis%nspec) = ctmp | |
| 773 | else | ||
| 774 | ✗ | where(tmp_spec(1:basis%nspec).eq.ctmp) | |
| 775 | tmp_natom(1:basis%nspec) = tmp_natom(1:basis%nspec) + 1 | ||
| 776 | end where | ||
| 777 | end if | ||
| 778 | end do basis_loop1 | ||
| 779 | |||
| 780 | ✗ | allocate(basis%spec(basis%nspec)) | |
| 781 | ✗ | basis%spec(1:basis%nspec)%name = tmp_spec(1:basis%nspec) | |
| 782 | ✗ | do i = 1, basis%nspec | |
| 783 | ✗ | basis%spec(i)%num = 0 | |
| 784 | ✗ | allocate(basis%spec(i)%atom(tmp_natom(i),length_)) | |
| 785 | end do | ||
| 786 | |||
| 787 | ✗ | call jump(UNIT,iline) | |
| 788 | ✗ | basis_loop2: do i = 1, basis%natom | |
| 789 | ✗ | read(UNIT,'(A)',iostat=Reason) buffer | |
| 790 | ✗ | if(Reason.ne.0)then | |
| 791 | ✗ | call stop_program("Internal error in assigning the basis") | |
| 792 | ✗ | return | |
| 793 | end if | ||
| 794 | ✗ | read(buffer,*) ctmp,dvtmp1(1:3) | |
| 795 | ✗ | species_loop: do j = 1, basis%nspec | |
| 796 | ✗ | if(basis%spec(j)%name.eq.ctmp)then | |
| 797 | ✗ | basis%spec(j)%num = basis%spec(j)%num + 1 | |
| 798 | ✗ | basis%spec(j)%atom(basis%spec(j)%num,1:3) = dvtmp1(1:3) | |
| 799 | ✗ | exit species_loop | |
| 800 | end if | ||
| 801 | end do species_loop | ||
| 802 | end do basis_loop2 | ||
| 803 | |||
| 804 | end if basis_if | ||
| 805 | end do readloop | ||
| 806 | |||
| 807 | |||
| 808 | !--------------------------------------------------------------------------- | ||
| 809 | ! convert basis if in cartesian coordinates | ||
| 810 | !--------------------------------------------------------------------------- | ||
| 811 | ✗ | if(basis%lcart) call basis%convert() | |
| 812 | |||
| 813 | |||
| 814 | !--------------------------------------------------------------------------- | ||
| 815 | ! normalise basis to between 0 and 1 in direct coordinates | ||
| 816 | !--------------------------------------------------------------------------- | ||
| 817 | ✗ | do i = 1, basis%nspec | |
| 818 | ✗ | do j = 1, basis%spec(i)%num | |
| 819 | ✗ | do k = 1, 3 | |
| 820 | basis%spec(i)%atom(j,k) = & | ||
| 821 | ✗ | basis%spec(i)%atom(j,k) - floor( basis%spec(i)%atom(j,k) ) | |
| 822 | end do | ||
| 823 | end do | ||
| 824 | end do | ||
| 825 | ✗ | basis%natom=sum(basis%spec(:)%num) | |
| 826 | |||
| 827 | end subroutine CASTEP_geom_read | ||
| 828 | !############################################################################### | ||
| 829 | |||
| 830 | |||
| 831 | !############################################################################### | ||
| 832 | ✗ | subroutine CASTEP_geom_write(UNIT, basis, labc, cartesian) | |
| 833 | !! Write the structure in CASTEP style format. | ||
| 834 | implicit none | ||
| 835 | |||
| 836 | ! Arguments | ||
| 837 | integer :: UNIT | ||
| 838 | !! The unit number of the file to write to. | ||
| 839 | class(basis_type), intent(in) :: basis | ||
| 840 | !! The basis to write the geometry from. | ||
| 841 | logical, intent(in), optional :: labc | ||
| 842 | !! Optional. Boolean whether to write the lattice in abc format. | ||
| 843 | logical, intent(in), optional :: cartesian | ||
| 844 | !! Optional. Boolean whether to write basis in cartesian coordinates. | ||
| 845 | |||
| 846 | ! Local variables | ||
| 847 | integer :: i, j | ||
| 848 | !! Loop index. | ||
| 849 | real(real32), dimension(2,3) :: abc_angle | ||
| 850 | !! Temporary arrays to store the lattice vectors. | ||
| 851 | character(4) :: string_lat, string_bas | ||
| 852 | !! Strings specifying lattice and basis format | ||
| 853 | character(len=256) :: stop_msg | ||
| 854 | !! Error message. | ||
| 855 | |||
| 856 | |||
| 857 | ✗ | string_lat="CART" | |
| 858 | ✗ | if(present(labc))then | |
| 859 | ✗ | if(labc) string_lat="ABC" | |
| 860 | end if | ||
| 861 | |||
| 862 | ✗ | string_bas="FRAC" | |
| 863 | ✗ | if(present(cartesian))then | |
| 864 | ✗ | if(cartesian)then | |
| 865 | ✗ | string_bas="ABS" | |
| 866 | write(stop_msg,*) & | ||
| 867 | "Internal error in CASTEP_geom_write" // & | ||
| 868 | achar(13) // achar(10) // & | ||
| 869 | ✗ | " Subroutine not yet set up to output cartesian coordinates" | |
| 870 | ✗ | call stop_program(stop_msg) | |
| 871 | ✗ | return | |
| 872 | end if | ||
| 873 | end if | ||
| 874 | |||
| 875 | ✗ | write(UNIT,'("%block LATTICE_",A)') trim(string_lat) | |
| 876 | ✗ | write(UNIT,'("ang")') | |
| 877 | ✗ | if(present(labc))then | |
| 878 | ✗ | if(labc)then | |
| 879 | ✗ | abc_angle = convert_lat_to_abc(basis%lat) | |
| 880 | ✗ | write(UNIT,'(3(F15.9))') abc_angle(1,:) | |
| 881 | ✗ | write(UNIT,'(3(F15.9))') abc_angle(2,:) | |
| 882 | ✗ | goto 10 | |
| 883 | end if | ||
| 884 | end if | ||
| 885 | ✗ | do i = 1, 3 | |
| 886 | ✗ | write(UNIT,'(3(F15.9))') basis%lat(i,:) | |
| 887 | end do | ||
| 888 | |||
| 889 | ✗ | 10 write(UNIT,'("%endblock LATTICE_",A)') trim(string_lat) | |
| 890 | |||
| 891 | ✗ | write(UNIT,*) | |
| 892 | ✗ | write(UNIT,'("%block POSITIONS_",A)') trim(string_bas) | |
| 893 | ✗ | do i = 1, basis%nspec | |
| 894 | ✗ | do j = 1, basis%spec(i)%num | |
| 895 | write(UNIT,'(A5,1X,3(F15.9))') & | ||
| 896 | ✗ | basis%spec(i)%name,basis%spec(i)%atom(j,1:3) | |
| 897 | end do | ||
| 898 | end do | ||
| 899 | ✗ | write(UNIT,'("%endblock POSITIONS_",A)') trim(string_bas) | |
| 900 | |||
| 901 | end subroutine CASTEP_geom_write | ||
| 902 | !############################################################################### | ||
| 903 | |||
| 904 | |||
| 905 | !############################################################################### | ||
| 906 | ✗ | subroutine XYZ_geom_read(UNIT, basis, length, iostat) | |
| 907 | !! Read the structure in xyz style format. | ||
| 908 | implicit none | ||
| 909 | |||
| 910 | ! Arguments | ||
| 911 | integer, intent(in) :: UNIT | ||
| 912 | !! The unit number of the file to read from. | ||
| 913 | type(basis_type), intent(out) :: basis | ||
| 914 | !! The basis to read the geometry into. | ||
| 915 | integer, intent(in), optional :: length | ||
| 916 | !! Optional. The dimension of the basis atom positions. | ||
| 917 | integer, intent(out), optional :: iostat | ||
| 918 | !! Optional. The I/O status of the read. | ||
| 919 | |||
| 920 | ! Local variables | ||
| 921 | integer :: Reason | ||
| 922 | !! The I/O status of the read. | ||
| 923 | integer :: i, j | ||
| 924 | !! Loop index. | ||
| 925 | ✗ | integer, allocatable, dimension(:) :: tmp_num | |
| 926 | !! Temporary array to store the number of atoms of each species. | ||
| 927 | real(real32), dimension(3) :: vec | ||
| 928 | !! Temporary array to store the atomic positions. | ||
| 929 | ✗ | real(real32), allocatable, dimension(:,:,:) :: tmp_bas | |
| 930 | !! Temporary array to store the atomic positions. | ||
| 931 | character(len=3) :: ctmp | ||
| 932 | !! Temporary character variable. | ||
| 933 | ✗ | character(len=3), allocatable, dimension(:) :: tmp_spec | |
| 934 | !! Temporary array to store the species names. | ||
| 935 | integer :: length_ | ||
| 936 | !! The dimension of the basis atom positions. | ||
| 937 | integer :: iostat_ | ||
| 938 | !! The I/O status of the read. | ||
| 939 | |||
| 940 | |||
| 941 | ✗ | length_ = 3 | |
| 942 | ✗ | iostat_ = 0 | |
| 943 | ✗ | if(present(length)) length_ = length | |
| 944 | |||
| 945 | |||
| 946 | ✗ | read(UNIT,*,iostat=Reason) basis%natom | |
| 947 | ✗ | if(Reason.ne.0)then | |
| 948 | ✗ | write(0,'("ERROR: The file is not in xyz format.")') | |
| 949 | ✗ | iostat_ = 1 | |
| 950 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 951 | ✗ | return | |
| 952 | end if | ||
| 953 | ✗ | read(UNIT,'(A)',iostat=Reason) basis%sysname | |
| 954 | |||
| 955 | |||
| 956 | !--------------------------------------------------------------------------- | ||
| 957 | ! read basis | ||
| 958 | !--------------------------------------------------------------------------- | ||
| 959 | ✗ | allocate(tmp_spec(basis%natom)) | |
| 960 | ✗ | allocate(tmp_num(basis%natom)) | |
| 961 | ✗ | allocate(tmp_bas(basis%natom,basis%natom,length_)) | |
| 962 | ✗ | tmp_num(:) = 0 | |
| 963 | ✗ | tmp_spec = "" | |
| 964 | ✗ | tmp_bas = 0 | |
| 965 | ✗ | basis%nspec = 0 | |
| 966 | ✗ | do i = 1, basis%natom | |
| 967 | ✗ | read(UNIT,*,iostat=Reason) ctmp,vec(1:3) | |
| 968 | ✗ | if(.not.any(tmp_spec(1:basis%nspec).eq.ctmp))then | |
| 969 | ✗ | basis%nspec = basis%nspec + 1 | |
| 970 | ✗ | tmp_spec(basis%nspec) = ctmp | |
| 971 | ✗ | tmp_bas(basis%nspec,1,1:3) = vec(1:3) | |
| 972 | ✗ | tmp_num(basis%nspec) = 1 | |
| 973 | else | ||
| 974 | ✗ | checkspec: do j = 1, basis%nspec | |
| 975 | ✗ | if(tmp_spec(j).eq.ctmp)then | |
| 976 | ✗ | tmp_num(j) = tmp_num(j)+1 | |
| 977 | ✗ | tmp_bas(j,tmp_num(j),1:3) = vec(1:3) | |
| 978 | ✗ | exit checkspec | |
| 979 | end if | ||
| 980 | end do checkspec | ||
| 981 | end if | ||
| 982 | end do | ||
| 983 | |||
| 984 | |||
| 985 | !--------------------------------------------------------------------------- | ||
| 986 | ! move basis from temporary basis to main basis. | ||
| 987 | ! done to allow for correct allocation of number of and per species | ||
| 988 | !--------------------------------------------------------------------------- | ||
| 989 | ✗ | allocate(basis%spec(basis%nspec)) | |
| 990 | ✗ | do i = 1, basis%nspec | |
| 991 | ✗ | basis%spec(i)%name = tmp_spec(i) | |
| 992 | ✗ | basis%spec(i)%num = tmp_num(i) | |
| 993 | ✗ | allocate(basis%spec(i)%atom(tmp_num(i),length_)) | |
| 994 | ✗ | basis%spec(i)%atom(:,:) = 0 | |
| 995 | ✗ | basis%spec(i)%atom(1:tmp_num(i),1:3) = tmp_bas(i,1:tmp_num(i),1:3) | |
| 996 | end do | ||
| 997 | |||
| 998 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 999 | |||
| 1000 | ✗ | end subroutine XYZ_geom_read | |
| 1001 | !############################################################################### | ||
| 1002 | |||
| 1003 | |||
| 1004 | !############################################################################### | ||
| 1005 | ✗ | subroutine XYZ_geom_write(UNIT,basis) | |
| 1006 | !! Write the structure in xyz style format. | ||
| 1007 | implicit none | ||
| 1008 | |||
| 1009 | ! Arguments | ||
| 1010 | integer, intent(in) :: UNIT | ||
| 1011 | !! The unit number of the file to write to. | ||
| 1012 | class(basis_type), intent(in) :: basis | ||
| 1013 | !! The basis to write the geometry from. | ||
| 1014 | |||
| 1015 | ! Local variables | ||
| 1016 | integer :: i, j | ||
| 1017 | !! Loop index. | ||
| 1018 | |||
| 1019 | |||
| 1020 | ✗ | write(UNIT,'("I0")') basis%natom | |
| 1021 | ✗ | write(UNIT,'("A")') basis%sysname | |
| 1022 | ✗ | do i = 1, basis%nspec | |
| 1023 | ✗ | do j = 1, basis%spec(i)%num | |
| 1024 | write(UNIT,'(A5,1X,3(F15.9))') & | ||
| 1025 | ✗ | basis%spec(i)%name,basis%spec(i)%atom(j,1:3) | |
| 1026 | end do | ||
| 1027 | end do | ||
| 1028 | |||
| 1029 | ✗ | end subroutine XYZ_geom_write | |
| 1030 | !############################################################################### | ||
| 1031 | |||
| 1032 | |||
| 1033 | !############################################################################### | ||
| 1034 |
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|
16 | subroutine extXYZ_geom_read(UNIT, basis, length, iostat) |
| 1035 | !! Read the structure in extended xyz style format. | ||
| 1036 | implicit none | ||
| 1037 | |||
| 1038 | ! Arguments | ||
| 1039 | integer, intent(in) :: UNIT | ||
| 1040 | !! The unit number of the file to read from. | ||
| 1041 | type(basis_type), intent(out) :: basis | ||
| 1042 | !! The basis to read the geometry into. | ||
| 1043 | integer, intent(in), optional :: length | ||
| 1044 | !! Optional. The dimension of the basis atom positions. | ||
| 1045 | integer, intent(out), optional :: iostat | ||
| 1046 | !! Optional. The I/O status of the read. | ||
| 1047 | |||
| 1048 | ! Local variables | ||
| 1049 | integer :: Reason | ||
| 1050 | !! The I/O status of the read. | ||
| 1051 | integer :: i, j | ||
| 1052 | !! Loop index. | ||
| 1053 | integer :: index1, index2 | ||
| 1054 | !! Index variables. | ||
| 1055 | 1 | integer, allocatable, dimension(:) :: tmp_num | |
| 1056 | !! Temporary array to store the number of atoms of each species. | ||
| 1057 | real(real32), dimension(3) :: vec | ||
| 1058 | !! Temporary array to store the atomic positions. | ||
| 1059 | 1 | real(real32), allocatable, dimension(:,:,:) :: tmp_bas | |
| 1060 | !! Temporary array to store the atomic positions. | ||
| 1061 | character(len=3) :: ctmp | ||
| 1062 | !! Temporary character variable. | ||
| 1063 |
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1 | character(len=3), allocatable, dimension(:) :: tmp_spec |
| 1064 | !! Temporary array to store the species names. | ||
| 1065 | character(len=1024) :: buffer | ||
| 1066 | !! Temporary character variable. | ||
| 1067 | integer :: length_ = 3 | ||
| 1068 | !! The dimension of the basis atom positions. | ||
| 1069 | integer :: iostat_ = 0 | ||
| 1070 | !! The I/O status of the read. | ||
| 1071 | |||
| 1072 | |||
| 1073 | 1 | basis%lcart=.true. | |
| 1074 |
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1 | if(present(length)) length_ = length |
| 1075 | |||
| 1076 | |||
| 1077 | !--------------------------------------------------------------------------- | ||
| 1078 | ! read system information | ||
| 1079 | !--------------------------------------------------------------------------- | ||
| 1080 | 1 | read(UNIT,*,iostat=Reason) basis%natom | |
| 1081 |
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1 | if(Reason.ne.0)then |
| 1082 | ✗ | write(0,'("ERROR: The file is not in xyz format.")') | |
| 1083 | ✗ | iostat_ = 1 | |
| 1084 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 1085 | ✗ | return | |
| 1086 | end if | ||
| 1087 | 1 | read(UNIT,'(A)',iostat=Reason) buffer | |
| 1088 |
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1 | if(Reason.ne.0)then |
| 1089 | ✗ | write(0,'("ERROR: The file is not in xyz format.")') | |
| 1090 | ✗ | iostat_ = 1 | |
| 1091 | ✗ | if(present(iostat)) iostat = iostat_ | |
| 1092 | ✗ | return | |
| 1093 | end if | ||
| 1094 | 1 | index1 = index(buffer,'Lattice="') + 9 | |
| 1095 | 1 | index2 = index(buffer(index1:),'"') + index1 - 2 | |
| 1096 |
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|
13 | read(buffer(index1:index2),*) ( ( basis%lat(i,j), j = 1, 3), i = 1, 3) |
| 1097 | |||
| 1098 | 1 | index1 = index(buffer,'free_energy=') + 12 | |
| 1099 | 1 | read(buffer(index1:),*) basis%energy | |
| 1100 | |||
| 1101 | |||
| 1102 | !--------------------------------------------------------------------------- | ||
| 1103 | ! read basis | ||
| 1104 | !--------------------------------------------------------------------------- | ||
| 1105 |
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1 | allocate(tmp_spec(basis%natom)) |
| 1106 |
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1 | allocate(tmp_num(basis%natom)) |
| 1107 |
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1 | allocate(tmp_bas(basis%natom,basis%natom,length_)) |
| 1108 |
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9 | tmp_num(:) = 0 |
| 1109 |
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9 | tmp_spec = "" |
| 1110 |
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|
220 | tmp_bas = 0 |
| 1111 | 1 | basis%nspec = 0 | |
| 1112 |
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9 | do i = 1, basis%natom |
| 1113 | 8 | read(UNIT,*,iostat=Reason) ctmp, vec(1:3) | |
| 1114 |
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9 | if(.not.any(tmp_spec(1:basis%nspec).eq.ctmp))then |
| 1115 | 1 | basis%nspec=basis%nspec+1 | |
| 1116 |
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1 | tmp_spec(basis%nspec) = trim(adjustl(ctmp)) |
| 1117 |
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4 | tmp_bas(basis%nspec,1,1:3) = vec(1:3) |
| 1118 | 1 | tmp_num(basis%nspec) = 1 | |
| 1119 | else | ||
| 1120 |
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7 | checkspec: do j = 1, basis%nspec |
| 1121 |
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7 | if(tmp_spec(j).eq.ctmp)then |
| 1122 | 7 | tmp_num(j) = tmp_num(j) + 1 | |
| 1123 |
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|
28 | tmp_bas(j,tmp_num(j),1:3) = vec(1:3) |
| 1124 | 7 | exit checkspec | |
| 1125 | end if | ||
| 1126 | end do checkspec | ||
| 1127 | end if | ||
| 1128 | end do | ||
| 1129 | |||
| 1130 | |||
| 1131 | !--------------------------------------------------------------------------- | ||
| 1132 | ! move basis from temporary basis to main basis. | ||
| 1133 | ! done to allow for correct allocation of number of and per species | ||
| 1134 | !--------------------------------------------------------------------------- | ||
| 1135 |
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2 | allocate(basis%spec(basis%nspec)) |
| 1136 | 1 | basis%sysname = "" | |
| 1137 |
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2 | do i = 1, basis%nspec |
| 1138 | 1 | basis%spec(i)%name = tmp_spec(i) | |
| 1139 | 1 | basis%spec(i)%num = tmp_num(i) | |
| 1140 |
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1 | allocate(basis%spec(i)%atom(tmp_num(i),length_)) |
| 1141 |
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28 | basis%spec(i)%atom(:,:) = 0 |
| 1142 |
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28 | basis%spec(i)%atom(1:tmp_num(i),1:3) = tmp_bas(i,1:tmp_num(i),1:3) |
| 1143 |
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1 | write(buffer,'(I0,A)') basis%spec(i)%num,trim(basis%spec(i)%name) |
| 1144 |
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1 | basis%sysname = basis%sysname//trim(buffer) |
| 1145 |
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2 | if(i.lt.basis%nspec) basis%sysname = trim(adjustl(basis%sysname))//"_" |
| 1146 | end do | ||
| 1147 | |||
| 1148 |
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1 | if(present(iostat)) iostat = iostat_ |
| 1149 | |||
| 1150 |
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|
1 | end subroutine extXYZ_geom_read |
| 1151 | !############################################################################### | ||
| 1152 | |||
| 1153 | |||
| 1154 | !############################################################################### | ||
| 1155 | 1 | subroutine extXYZ_geom_write(UNIT, basis) | |
| 1156 | !! Write the structure in extended xyz style format. | ||
| 1157 | implicit none | ||
| 1158 | |||
| 1159 | ! Arguments | ||
| 1160 | integer, intent(in) :: UNIT | ||
| 1161 | !! The unit number of the file to write to. | ||
| 1162 | class(basis_type), intent(in) :: basis | ||
| 1163 | !! The basis to write the geometry from. | ||
| 1164 | |||
| 1165 | ! Local variables | ||
| 1166 | integer :: i, j | ||
| 1167 | !! Loop index. | ||
| 1168 | |||
| 1169 | |||
| 1170 | 1 | write(UNIT,'(I0)') basis%natom | |
| 1171 | write(UNIT,'(A,8(F0.8,1X),F0.8,A)', advance="no") & | ||
| 1172 |
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|
13 | 'Lattice="',((basis%lat(i,j),j=1,3),i=1,3),'"' |
| 1173 | 1 | write(UNIT,'(A,F0.8)', advance="no") ' free_energy=',basis%energy | |
| 1174 | 1 | write(UNIT,'(A)', advance="no") ' pbc="T T T"' | |
| 1175 |
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|
1 | if(basis%lcart)then |
| 1176 | ✗ | do i = 1, basis%nspec | |
| 1177 | ✗ | do j = 1, basis%spec(i)%num | |
| 1178 | write(UNIT,'(A8,3(1X, F16.8))') & | ||
| 1179 | ✗ | basis%spec(i)%name,basis%spec(i)%atom(j,1:3) | |
| 1180 | end do | ||
| 1181 | end do | ||
| 1182 | else | ||
| 1183 |
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|
2 | do i = 1, basis%nspec |
| 1184 |
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10 | do j = 1, basis%spec(i)%num |
| 1185 | 8 | write(UNIT,'(A8,3(1X, F16.8))') basis%spec(i)%name, & | |
| 1186 |
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|
41 | matmul(basis%spec(i)%atom(j,1:3),basis%lat) |
| 1187 | end do | ||
| 1188 | end do | ||
| 1189 | end if | ||
| 1190 | |||
| 1191 | 1 | end subroutine extXYZ_geom_write | |
| 1192 | !############################################################################### | ||
| 1193 | |||
| 1194 | |||
| 1195 | !############################################################################### | ||
| 1196 | 1 | subroutine convert(this) | |
| 1197 | !! Convert the basis between direct and cartesian coordinates. | ||
| 1198 | implicit none | ||
| 1199 | |||
| 1200 | ! Arguments | ||
| 1201 | class(basis_type), intent(inout) :: this | ||
| 1202 | !! Parent. The basis to convert. | ||
| 1203 | |||
| 1204 | ! Local variables | ||
| 1205 | integer :: is, ia | ||
| 1206 | !! Loop index. | ||
| 1207 | real(real32), dimension(3,3) :: lattice | ||
| 1208 | !! The reciprocal lattice vectors. | ||
| 1209 | |||
| 1210 | |||
| 1211 |
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1 | if(this%lcart)then |
| 1212 | ✗ | lattice = inverse_3x3( this%lat ) | |
| 1213 | else | ||
| 1214 |
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|
13 | lattice = this%lat |
| 1215 | end if | ||
| 1216 | |||
| 1217 | 1 | this%lcart = .not.this%lcart | |
| 1218 |
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|
2 | do is = 1, this%nspec |
| 1219 |
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|
10 | do ia = 1, this%spec(is)%num |
| 1220 | this%spec(is)%atom(ia,1:3) = & | ||
| 1221 |
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|
33 | matmul( this%spec(is)%atom(ia,1:3), lattice ) |
| 1222 | end do | ||
| 1223 | end do | ||
| 1224 | |||
| 1225 | 1 | end subroutine convert | |
| 1226 | !############################################################################### | ||
| 1227 | |||
| 1228 | |||
| 1229 | !############################################################################# | ||
| 1230 | ✗ | function convert_abc_to_lat(abc,angle,radians) result(lattice) | |
| 1231 | !! Convert the lattice from abc and αβγ to lattice matrix. | ||
| 1232 | implicit none | ||
| 1233 | |||
| 1234 | ! Arguments | ||
| 1235 | real(real32), dimension(3), intent(in) :: abc, angle | ||
| 1236 | !! lattice constants | ||
| 1237 | logical, intent(in), optional :: radians | ||
| 1238 | !! Optional. Boolean whether angles are in radians. | ||
| 1239 | real(real32), dimension(3,3) :: lattice | ||
| 1240 | !! The lattice matrix. | ||
| 1241 | |||
| 1242 | ! Local variables | ||
| 1243 | real(real32), dimension(3) :: in_angle | ||
| 1244 | !! The lattice angles in radians. | ||
| 1245 | |||
| 1246 | |||
| 1247 | |||
| 1248 | ✗ | in_angle = angle | |
| 1249 | ✗ | if(present(radians))then | |
| 1250 | ✗ | if(.not.radians) in_angle = angle*pi/180._real32 | |
| 1251 | end if | ||
| 1252 | |||
| 1253 | ✗ | lattice=0._real32 | |
| 1254 | |||
| 1255 | ✗ | lattice(1,1)=abc(1) | |
| 1256 | ✗ | lattice(2,:2)=(/abc(2)*cos(in_angle(3)),abc(2)*sin(in_angle(3))/) | |
| 1257 | |||
| 1258 | ✗ | lattice(3,1) = abc(3)*cos(in_angle(2)) | |
| 1259 | lattice(3,2) = abc(3)*(cos(in_angle(1)) - cos(in_angle(2))*& | ||
| 1260 | ✗ | cos(in_angle(3)))/sin(in_angle(3)) | |
| 1261 | lattice(3,3) = sqrt(abc(3)**2._real32 - & | ||
| 1262 | lattice(3,1)**2._real32 - & | ||
| 1263 | ✗ | lattice(3,2)**2._real32) | |
| 1264 | |||
| 1265 | ✗ | end function convert_abc_to_lat | |
| 1266 | !############################################################################### | ||
| 1267 | |||
| 1268 | |||
| 1269 | !############################################################################### | ||
| 1270 | ✗ | function convert_lat_to_abc(lattice, radians) result(abc_angle) | |
| 1271 | !! Convert the lattice from lattice matrix to abc and αβγ. | ||
| 1272 | implicit none | ||
| 1273 | |||
| 1274 | ! Arguments | ||
| 1275 | real(real32), dimension(3,3), intent(in) :: lattice | ||
| 1276 | !! The lattice matrix. | ||
| 1277 | logical, intent(in), optional :: radians | ||
| 1278 | !! Optional. Boolean whether to return angles in radians. | ||
| 1279 | real(real32), dimension(2,3) :: abc_angle | ||
| 1280 | !! The lattice constants and angles. | ||
| 1281 | |||
| 1282 | ! Local variables | ||
| 1283 | integer :: i | ||
| 1284 | !! Loop index. | ||
| 1285 | |||
| 1286 | |||
| 1287 | ✗ | do i = 1, 3 | |
| 1288 | ✗ | abc_angle(1,i)=modu(lattice(i,:)) | |
| 1289 | end do | ||
| 1290 | ✗ | do i = 1, 3 | |
| 1291 | end do | ||
| 1292 | abc_angle(2,1)=acos(dot_product(lattice(2,:),lattice(3,:))/& | ||
| 1293 | ✗ | (abc_angle(1,2)*abc_angle(1,3))) | |
| 1294 | abc_angle(2,3)=acos(dot_product(lattice(1,:),lattice(3,:))/& | ||
| 1295 | ✗ | (abc_angle(1,1)*abc_angle(1,3))) | |
| 1296 | abc_angle(2,3)=acos(dot_product(lattice(1,:),lattice(2,:))/& | ||
| 1297 | ✗ | (abc_angle(1,1)*abc_angle(1,2))) | |
| 1298 | |||
| 1299 | ✗ | if(present(radians))then | |
| 1300 | ✗ | if(.not.radians) abc_angle(2,:)=abc_angle(2,:)*180._real32/pi | |
| 1301 | end if | ||
| 1302 | |||
| 1303 | ✗ | end function convert_lat_to_abc | |
| 1304 | !############################################################################### | ||
| 1305 | |||
| 1306 | |||
| 1307 | !############################################################################### | ||
| 1308 | ✗ | function get_lattice_constants(this, radians) result(output) | |
| 1309 | !! Convert the lattice from lattice matrix to abc and αβγ. | ||
| 1310 | implicit none | ||
| 1311 | |||
| 1312 | ! Arguments | ||
| 1313 | class(basis_type), intent(in) :: this | ||
| 1314 | !! Parent. The basis. | ||
| 1315 | logical, intent(in), optional :: radians | ||
| 1316 | !! Optional. Boolean whether to return angles in radians. | ||
| 1317 | real(real32), dimension(2,3) :: output | ||
| 1318 | !! The lattice constants and angles. | ||
| 1319 | |||
| 1320 | ! Local variables | ||
| 1321 | logical :: radians_ | ||
| 1322 | !! Boolean whether to return angles in radians. | ||
| 1323 | |||
| 1324 | |||
| 1325 | ✗ | radians_ = .true. | |
| 1326 | ✗ | if(present(radians)) radians_ = radians | |
| 1327 | |||
| 1328 | ✗ | output = convert_lat_to_abc(this%lat, radians_) | |
| 1329 | |||
| 1330 | ✗ | end function get_lattice_constants | |
| 1331 | !############################################################################### | ||
| 1332 | |||
| 1333 | |||
| 1334 | !############################################################################### | ||
| 1335 | 63 | subroutine copy(this, basis, length) | |
| 1336 | !! Copy the basis. | ||
| 1337 | implicit none | ||
| 1338 | |||
| 1339 | ! Arguments | ||
| 1340 | class(basis_type), intent(inout) :: this | ||
| 1341 | !! Parent. The basis to copy into. | ||
| 1342 | class(basis_type), intent(in) :: basis | ||
| 1343 | !! The basis to copy from. | ||
| 1344 | integer, intent(in), optional :: length | ||
| 1345 | !! The dimension of the basis atom positions. | ||
| 1346 | |||
| 1347 | |||
| 1348 | ! Local variables | ||
| 1349 | integer :: i | ||
| 1350 | !! Loop index. | ||
| 1351 | integer :: length_, length_input | ||
| 1352 | !! The dimension of the basis atom positions. | ||
| 1353 | |||
| 1354 | |||
| 1355 | !--------------------------------------------------------------------------- | ||
| 1356 | ! determines whether user wants output basis extra translational dimension | ||
| 1357 | !--------------------------------------------------------------------------- | ||
| 1358 | 63 | length_input = size(basis%spec(1)%atom(1,:),dim=1) | |
| 1359 |
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63 | if(present(length))then |
| 1360 | ✗ | length_ = length | |
| 1361 | else | ||
| 1362 | 63 | length_ = length_input | |
| 1363 | end if | ||
| 1364 | |||
| 1365 | |||
| 1366 | !--------------------------------------------------------------------------- | ||
| 1367 | ! if already allocated, deallocates output basis | ||
| 1368 | !--------------------------------------------------------------------------- | ||
| 1369 |
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63 | if(allocated(this%spec))then |
| 1370 | ✗ | do i = 1, this%nspec | |
| 1371 | ✗ | if(allocated(this%spec(i)%atom)) deallocate(this%spec(i)%atom) | |
| 1372 | end do | ||
| 1373 | ✗ | deallocate(this%spec) | |
| 1374 | end if | ||
| 1375 | |||
| 1376 | |||
| 1377 | !--------------------------------------------------------------------------- | ||
| 1378 | ! allocates output basis and clones data from input basis to output basis | ||
| 1379 | !--------------------------------------------------------------------------- | ||
| 1380 |
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139 | allocate(this%spec(basis%nspec)) |
| 1381 |
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139 | do i = 1, basis%nspec |
| 1382 | ✗ | allocate(this%spec(i)%atom(& | |
| 1383 |
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76 | basis%spec(i)%num,length_)) |
| 1384 | |||
| 1385 |
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|
1795 | this%spec(i)%atom(:,:3) = basis%spec(i)%atom(:,:3) |
| 1386 |
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76 | if(length_input.eq.length_)then |
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|
1795 | this%spec(i)%atom(:,:length_) = basis%spec(i)%atom(:,:length_) |
| 1388 | ✗ | elseif(length_input.gt.length_)then | |
| 1389 | ✗ | this%spec(i)%atom(:,:3) = basis%spec(i)%atom(:,:3) | |
| 1390 | ✗ | elseif(length_input.lt.length_)then | |
| 1391 | ✗ | this%spec(i)%atom(:,:3) = basis%spec(i)%atom(:,:3) | |
| 1392 | ✗ | this%spec(i)%atom(:,4) = 1._real32 | |
| 1393 | end if | ||
| 1394 | 76 | this%spec(i)%num = basis%spec(i)%num | |
| 1395 | 76 | this%spec(i)%name = strip_null(basis%spec(i)%name) | |
| 1396 | |||
| 1397 | 76 | this%spec(i)%mass = basis%spec(i)%mass | |
| 1398 | 76 | this%spec(i)%charge = basis%spec(i)%charge | |
| 1399 | 139 | this%spec(i)%radius = basis%spec(i)%radius | |
| 1400 | end do | ||
| 1401 | 63 | this%nspec = basis%nspec | |
| 1402 | 63 | this%natom = basis%natom | |
| 1403 | 63 | this%lcart = basis%lcart | |
| 1404 | 63 | this%sysname = basis%sysname | |
| 1405 | 63 | this%energy = basis%energy | |
| 1406 |
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|
819 | this%lat = basis%lat |
| 1407 |
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|
252 | this%pbc = basis%pbc |
| 1408 | |||
| 1409 | 63 | end subroutine copy | |
| 1410 | !############################################################################### | ||
| 1411 | |||
| 1412 | |||
| 1413 | !############################################################################### | ||
| 1414 | 8 | subroutine remove_atom(this, ispec, iatom) | |
| 1415 | !! Remove an atom from the basis. | ||
| 1416 | implicit none | ||
| 1417 | |||
| 1418 | ! Arguments | ||
| 1419 | class(basis_type), intent(inout) :: this | ||
| 1420 | !! Parent. The basis. | ||
| 1421 | integer, intent(in) :: ispec, iatom | ||
| 1422 | !! The species and atom to remove. | ||
| 1423 | |||
| 1424 | ! Local variables | ||
| 1425 | integer :: i | ||
| 1426 | !! Loop index. | ||
| 1427 | 8 | real(real32), dimension(:,:), allocatable :: atom | |
| 1428 | !! Temporary array to store the atomic positions. | ||
| 1429 | |||
| 1430 | |||
| 1431 | !--------------------------------------------------------------------------- | ||
| 1432 | ! remove atom from basis | ||
| 1433 | !--------------------------------------------------------------------------- | ||
| 1434 |
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16 | do i = 1, this%nspec |
| 1435 |
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16 | if(i.eq.ispec)then |
| 1436 |
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8 | if(iatom.gt.this%spec(i)%num)then |
| 1437 | ✗ | call stop_program("Atom to remove does not exist") | |
| 1438 | ✗ | return | |
| 1439 | end if | ||
| 1440 |
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|
8 | allocate(atom(this%spec(i)%num-1,size(this%spec(i)%atom,2))) |
| 1441 |
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|
299 | atom(1:iatom-1:1,:) = this%spec(i)%atom(1:iatom-1:1,:) |
| 1442 | atom(iatom:this%spec(i)%num-1:1,:) = & | ||
| 1443 |
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|
185 | this%spec(i)%atom(iatom+1:this%spec(i)%num:1,:) |
| 1444 |
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|
452 | this%spec(i)%atom = atom |
| 1445 |
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|
8 | deallocate(atom) |
| 1446 | 8 | this%spec(i)%num = this%spec(i)%num - 1 | |
| 1447 | 8 | this%natom = this%natom - 1 | |
| 1448 |
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8 | if(this%spec(i)%num.eq.0)then |
| 1449 | ✗ | deallocate(this%spec(i)%atom) | |
| 1450 | ✗ | if(this%nspec.eq.0)then | |
| 1451 | ✗ | deallocate(this%spec) | |
| 1452 | ✗ | this%lcart = .true. | |
| 1453 | ✗ | this%sysname = "" | |
| 1454 | ✗ | this%energy = 0._real32 | |
| 1455 | ✗ | this%lat = 0._real32 | |
| 1456 | ✗ | this%pbc = .true. | |
| 1457 | end if | ||
| 1458 | end if | ||
| 1459 | end if | ||
| 1460 | end do | ||
| 1461 | |||
| 1462 |
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|
8 | end subroutine remove_atom |
| 1463 | !############################################################################### | ||
| 1464 | |||
| 1465 | |||
| 1466 | !############################################################################### | ||
| 1467 |
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|
2 | subroutine remove_atoms(this, atoms) |
| 1468 | !! Remove atoms from the basis. | ||
| 1469 | use raffle__misc, only: swap | ||
| 1470 | implicit none | ||
| 1471 | |||
| 1472 | ! Arguments | ||
| 1473 | class(basis_type), intent(inout) :: this | ||
| 1474 | !! Parent. The basis. | ||
| 1475 | integer, dimension(:,:), intent(in) :: atoms | ||
| 1476 | !! The atoms to remove (2, number of atoms to remove) | ||
| 1477 | !! 1st value of 1st dimension is the species number | ||
| 1478 | !! 2nd value of 1st dimension is the atom number | ||
| 1479 | !! 2nd dimension is the number of atoms to remove | ||
| 1480 | |||
| 1481 | ! Local variables | ||
| 1482 | integer :: is, ia, i | ||
| 1483 | !! Loop index. | ||
| 1484 | integer :: n, m, start_idx, end_idx, loc | ||
| 1485 | !! Index variables. | ||
| 1486 | integer :: num_species | ||
| 1487 | !! The number of species. | ||
| 1488 | 2 | integer, dimension(:,:), allocatable :: atoms_ordered | |
| 1489 | !! The atoms to remove ordered by species and atom | ||
| 1490 | real(real32), dimension(:,:), allocatable :: atom | ||
| 1491 | !! Temporary array to store the atomic positions. | ||
| 1492 | |||
| 1493 | |||
| 1494 | !--------------------------------------------------------------------------- | ||
| 1495 | ! reorder atoms to remove | ||
| 1496 | !--------------------------------------------------------------------------- | ||
| 1497 |
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|
26 | allocate(atoms_ordered, source=atoms) |
| 1498 | 2 | n = size(atoms_ordered, 1) | |
| 1499 | 2 | m = size(atoms_ordered, 2) | |
| 1500 | |||
| 1501 |
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10 | do i = 1, m |
| 1502 |
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|
14 | loc = maxloc(atoms_ordered(1, i:n), dim=1) + i - 1 |
| 1503 |
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10 | if (loc .ne. i) then |
| 1504 | 4 | call swap(atoms_ordered(1, i), atoms_ordered(1, loc)) | |
| 1505 | 4 | call swap(atoms_ordered(2, i), atoms_ordered(2, loc)) | |
| 1506 | end if | ||
| 1507 | end do | ||
| 1508 | 2 | num_species = this%nspec | |
| 1509 |
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4 | do is = 1, num_species |
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2 | start_idx = findloc(atoms_ordered(1, :), is, dim=1) |
| 1511 |
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✗ Branch 3 not taken.
|
2 | end_idx = findloc(atoms_ordered(1, :), is, dim=1, back=.true.) |
| 1512 |
1/2✗ Branch 0 not taken.
✓ Branch 1 taken 2 times.
|
2 | if (start_idx .eq. 0) cycle |
| 1513 |
2/2✓ Branch 0 taken 8 times.
✓ Branch 1 taken 2 times.
|
12 | do ia = start_idx, end_idx, 1 |
| 1514 | loc = maxloc( & | ||
| 1515 | atoms_ordered(2, ia:end_idx), & | ||
| 1516 | dim=1 & | ||
| 1517 |
5/6✓ Branch 0 taken 8 times.
✗ Branch 1 not taken.
✓ Branch 2 taken 20 times.
✓ Branch 3 taken 8 times.
✓ Branch 4 taken 11 times.
✓ Branch 5 taken 9 times.
|
28 | ) + ia - 1 |
| 1518 |
2/2✓ Branch 0 taken 2 times.
✓ Branch 1 taken 6 times.
|
10 | if (loc .ne. ia) then |
| 1519 | 2 | call swap(atoms_ordered(1, ia), atoms_ordered(1, loc)) | |
| 1520 | 2 | call swap(atoms_ordered(2, ia), atoms_ordered(2, loc)) | |
| 1521 | end if | ||
| 1522 | end do | ||
| 1523 | end do | ||
| 1524 | |||
| 1525 | |||
| 1526 | !--------------------------------------------------------------------------- | ||
| 1527 | ! remove atoms from basis | ||
| 1528 | !--------------------------------------------------------------------------- | ||
| 1529 |
2/2✓ Branch 0 taken 8 times.
✓ Branch 1 taken 2 times.
|
10 | do i = 1, size(atoms_ordered, 2) |
| 1530 | 10 | call this%remove_atom(atoms_ordered(1, i), atoms_ordered(2, i)) | |
| 1531 | end do | ||
| 1532 | |||
| 1533 |
2/2✓ Branch 0 taken 2 times.
✓ Branch 1 taken 2 times.
|
4 | do is = 1, this%nspec |
| 1534 |
1/2✗ Branch 0 not taken.
✓ Branch 1 taken 2 times.
|
4 | if (this%spec(is)%num .eq. 0) then |
| 1535 | ✗ | this%spec = [ this%spec(1:is-1), this%spec(is+1:) ] | |
| 1536 | ✗ | this%nspec = this%nspec - 1 | |
| 1537 | end if | ||
| 1538 | end do | ||
| 1539 | |||
| 1540 |
1/2✓ Branch 0 taken 2 times.
✗ Branch 1 not taken.
|
2 | end subroutine remove_atoms |
| 1541 | !############################################################################### | ||
| 1542 | |||
| 1543 | |||
| 1544 | !############################################################################### | ||
| 1545 | 256 | subroutine get_element_properties(element, charge, mass, radius) | |
| 1546 | !! Set the mass and charge of the element | ||
| 1547 | implicit none | ||
| 1548 | |||
| 1549 | ! Arguments | ||
| 1550 | character(len=3), intent(in) :: element | ||
| 1551 | !! Element name. | ||
| 1552 | real(real32), intent(out), optional :: charge | ||
| 1553 | !! Charge of the element. | ||
| 1554 | real(real32), intent(out), optional :: mass | ||
| 1555 | !! Mass of the element. | ||
| 1556 | real(real32), intent(out), optional :: radius | ||
| 1557 | !! Radius of the element. | ||
| 1558 | |||
| 1559 | ! Local variables | ||
| 1560 | real(real32) :: mass_, charge_, radius_ | ||
| 1561 | !! Mass, charge and radius of the element. | ||
| 1562 | |||
| 1563 | 2 | select case(element) | |
| 1564 | case('H') | ||
| 1565 | 2 | mass_ = 1.00784_real32 | |
| 1566 | 2 | charge_ = 1.0_real32 | |
| 1567 | 2 | radius_ = 0.31_real32 | |
| 1568 | case('He') | ||
| 1569 | 2 | mass_ = 4.0026_real32 | |
| 1570 | 2 | charge_ = 2.0_real32 | |
| 1571 | 2 | radius_ = 0.28_real32 | |
| 1572 | case('Li') | ||
| 1573 | 2 | mass_ = 6.94_real32 | |
| 1574 | 2 | charge_ = 3.0_real32 | |
| 1575 | 2 | radius_ = 1.28_real32 | |
| 1576 | case('Be') | ||
| 1577 | 2 | mass_ = 9.0122_real32 | |
| 1578 | 2 | charge_ = 4.0_real32 | |
| 1579 | 2 | radius_ = 0.96_real32 | |
| 1580 | case('B') | ||
| 1581 | 2 | mass_ = 10.81_real32 | |
| 1582 | 2 | charge_ = 5.0_real32 | |
| 1583 | 2 | radius_ = 0.84_real32 | |
| 1584 | case('C') | ||
| 1585 | 7 | mass_ = 12.011_real32 | |
| 1586 | 7 | charge_ = 6.0_real32 | |
| 1587 | 7 | radius_ = 0.76_real32 | |
| 1588 | case('N') | ||
| 1589 | 2 | mass_ = 14.007_real32 | |
| 1590 | 2 | charge_ = 7.0_real32 | |
| 1591 | 2 | radius_ = 0.71_real32 | |
| 1592 | case('O') | ||
| 1593 | 5 | mass_ = 15.999_real32 | |
| 1594 | 5 | charge_ = 8.0_real32 | |
| 1595 | 5 | radius_ = 0.66_real32 | |
| 1596 | case('F') | ||
| 1597 | 2 | mass_ = 18.998_real32 | |
| 1598 | 2 | charge_ = 9.0_real32 | |
| 1599 | 2 | radius_ = 0.57_real32 | |
| 1600 | case('Ne') | ||
| 1601 | 2 | mass_ = 20.180_real32 | |
| 1602 | 2 | charge_ = 10.0_real32 | |
| 1603 | 2 | radius_ = 0.58_real32 | |
| 1604 | case('Na') | ||
| 1605 | 2 | mass_ = 22.989_real32 | |
| 1606 | 2 | charge_ = 11.0_real32 | |
| 1607 | 2 | radius_ = 1.66_real32 | |
| 1608 | case('Mg') | ||
| 1609 | 3 | mass_ = 24.305_real32 | |
| 1610 | 3 | charge_ = 12.0_real32 | |
| 1611 | 3 | radius_ = 1.41_real32 | |
| 1612 | case('Al') | ||
| 1613 | 2 | mass_ = 26.982_real32 | |
| 1614 | 2 | charge_ = 13.0_real32 | |
| 1615 | 2 | radius_ = 1.21_real32 | |
| 1616 | case('Si') | ||
| 1617 | 6 | mass_ = 28.085_real32 | |
| 1618 | 6 | charge_ = 14.0_real32 | |
| 1619 | 6 | radius_ = 1.11_real32 | |
| 1620 | case('P') | ||
| 1621 | 2 | mass_ = 30.974_real32 | |
| 1622 | 2 | charge_ = 15.0_real32 | |
| 1623 | 2 | radius_ = 1.07_real32 | |
| 1624 | case('S') | ||
| 1625 | 2 | mass_ = 32.06_real32 | |
| 1626 | 2 | charge_ = 16.0_real32 | |
| 1627 | 2 | radius_ = 1.05_real32 | |
| 1628 | case('Cl') | ||
| 1629 | 2 | mass_ = 35.453_real32 | |
| 1630 | 2 | charge_ = 17.0_real32 | |
| 1631 | 2 | radius_ = 1.02_real32 | |
| 1632 | case('Ar') | ||
| 1633 | 2 | mass_ = 39.948_real32 | |
| 1634 | 2 | charge_ = 18.0_real32 | |
| 1635 | 2 | radius_ = 1.06_real32 | |
| 1636 | case('K') | ||
| 1637 | 2 | mass_ = 39.098_real32 | |
| 1638 | 2 | charge_ = 19.0_real32 | |
| 1639 | 2 | radius_ = 2.03_real32 | |
| 1640 | case('Ca') | ||
| 1641 | 2 | mass_ = 40.078_real32 | |
| 1642 | 2 | charge_ = 20.0_real32 | |
| 1643 | 2 | radius_ = 1.74_real32 | |
| 1644 | case('Sc') | ||
| 1645 | 2 | mass_ = 44.956_real32 | |
| 1646 | 2 | charge_ = 21.0_real32 | |
| 1647 | 2 | radius_ = 1.44_real32 | |
| 1648 | case('Ti') | ||
| 1649 | 3 | mass_ = 47.867_real32 | |
| 1650 | 3 | charge_ = 22.0_real32 | |
| 1651 | 3 | radius_ = 1.32_real32 | |
| 1652 | case('V') | ||
| 1653 | 2 | mass_ = 50.942_real32 | |
| 1654 | 2 | charge_ = 23.0_real32 | |
| 1655 | 2 | radius_ = 1.22_real32 | |
| 1656 | case('Cr') | ||
| 1657 | 2 | mass_ = 51.996_real32 | |
| 1658 | 2 | charge_ = 24.0_real32 | |
| 1659 | 2 | radius_ = 1.18_real32 | |
| 1660 | case('Mn') | ||
| 1661 | 2 | mass_ = 54.938_real32 | |
| 1662 | 2 | charge_ = 25.0_real32 | |
| 1663 | 2 | radius_ = 1.17_real32 | |
| 1664 | case('Fe') | ||
| 1665 | 2 | mass_ = 55.845_real32 | |
| 1666 | 2 | charge_ = 26.0_real32 | |
| 1667 | 2 | radius_ = 1.17_real32 | |
| 1668 | case('Co') | ||
| 1669 | 2 | mass_ = 58.933_real32 | |
| 1670 | 2 | charge_ = 27.0_real32 | |
| 1671 | 2 | radius_ = 1.16_real32 | |
| 1672 | case('Ni') | ||
| 1673 | 2 | mass_ = 58.693_real32 | |
| 1674 | 2 | charge_ = 28.0_real32 | |
| 1675 | 2 | radius_ = 1.15_real32 | |
| 1676 | case('Cu') | ||
| 1677 | 2 | mass_ = 63.546_real32 | |
| 1678 | 2 | charge_ = 29.0_real32 | |
| 1679 | 2 | radius_ = 1.17_real32 | |
| 1680 | case('Zn') | ||
| 1681 | 2 | mass_ = 65.38_real32 | |
| 1682 | 2 | charge_ = 30.0_real32 | |
| 1683 | 2 | radius_ = 1.25_real32 | |
| 1684 | case('Ga') | ||
| 1685 | 2 | mass_ = 69.723_real32 | |
| 1686 | 2 | charge_ = 31.0_real32 | |
| 1687 | 2 | radius_ = 1.26_real32 | |
| 1688 | case('Ge') | ||
| 1689 | 2 | mass_ = 72.63_real32 | |
| 1690 | 2 | charge_ = 32.0_real32 | |
| 1691 | 2 | radius_ = 1.22_real32 | |
| 1692 | case('As') | ||
| 1693 | 2 | mass_ = 74.922_real32 | |
| 1694 | 2 | charge_ = 33.0_real32 | |
| 1695 | 2 | radius_ = 1.19_real32 | |
| 1696 | case('Se') | ||
| 1697 | 2 | mass_ = 78.971_real32 | |
| 1698 | 2 | charge_ = 34.0_real32 | |
| 1699 | 2 | radius_ = 1.16_real32 | |
| 1700 | case('Br') | ||
| 1701 | 2 | mass_ = 79.904_real32 | |
| 1702 | 2 | charge_ = 35.0_real32 | |
| 1703 | 2 | radius_ = 1.14_real32 | |
| 1704 | case('Kr') | ||
| 1705 | 2 | mass_ = 83.798_real32 | |
| 1706 | 2 | charge_ = 36.0_real32 | |
| 1707 | 2 | radius_ = 1.12_real32 | |
| 1708 | case('Rb') | ||
| 1709 | 2 | mass_ = 85.468_real32 | |
| 1710 | 2 | charge_ = 37.0_real32 | |
| 1711 | 2 | radius_ = 2.16_real32 | |
| 1712 | case('Sr') | ||
| 1713 | 2 | mass_ = 87.62_real32 | |
| 1714 | 2 | charge_ = 38.0_real32 | |
| 1715 | 2 | radius_ = 1.91_real32 | |
| 1716 | case('Y') | ||
| 1717 | 2 | mass_ = 88.906_real32 | |
| 1718 | 2 | charge_ = 39.0_real32 | |
| 1719 | 2 | radius_ = 1.62_real32 | |
| 1720 | case('Zr') | ||
| 1721 | 2 | mass_ = 91.224_real32 | |
| 1722 | 2 | charge_ = 40.0_real32 | |
| 1723 | 2 | radius_ = 1.45_real32 | |
| 1724 | case('Nb') | ||
| 1725 | 2 | mass_ = 92.906_real32 | |
| 1726 | 2 | charge_ = 41.0_real32 | |
| 1727 | 2 | radius_ = 1.34_real32 | |
| 1728 | case('Mo') | ||
| 1729 | 2 | mass_ = 95.95_real32 | |
| 1730 | 2 | charge_ = 42.0_real32 | |
| 1731 | 2 | radius_ = 1.3_real32 | |
| 1732 | case('Tc') | ||
| 1733 | 2 | mass_ = 98.0_real32 | |
| 1734 | 2 | charge_ = 43.0_real32 | |
| 1735 | 2 | radius_ = 1.27_real32 | |
| 1736 | case('Ru') | ||
| 1737 | 2 | mass_ = 101.07_real32 | |
| 1738 | 2 | charge_ = 44.0_real32 | |
| 1739 | 2 | radius_ = 1.25_real32 | |
| 1740 | case('Rh') | ||
| 1741 | 2 | mass_ = 102.91_real32 | |
| 1742 | 2 | charge_ = 45.0_real32 | |
| 1743 | 2 | radius_ = 1.25_real32 | |
| 1744 | case('Pd') | ||
| 1745 | 2 | mass_ = 106.42_real32 | |
| 1746 | 2 | charge_ = 46.0_real32 | |
| 1747 | 2 | radius_ = 1.28_real32 | |
| 1748 | case('Ag') | ||
| 1749 | 2 | mass_ = 107.87_real32 | |
| 1750 | 2 | charge_ = 47.0_real32 | |
| 1751 | 2 | radius_ = 1.34_real32 | |
| 1752 | case('Cd') | ||
| 1753 | 2 | mass_ = 112.41_real32 | |
| 1754 | 2 | charge_ = 48.0_real32 | |
| 1755 | 2 | radius_ = 1.48_real32 | |
| 1756 | case('In') | ||
| 1757 | 2 | mass_ = 114.82_real32 | |
| 1758 | 2 | charge_ = 49.0_real32 | |
| 1759 | 2 | radius_ = 1.44_real32 | |
| 1760 | case('Sn') | ||
| 1761 | 2 | mass_ = 118.71_real32 | |
| 1762 | 2 | charge_ = 50.0_real32 | |
| 1763 | 2 | radius_ = 1.41_real32 | |
| 1764 | case('Sb') | ||
| 1765 | 2 | mass_ = 121.76_real32 | |
| 1766 | 2 | charge_ = 51.0_real32 | |
| 1767 | 2 | radius_ = 1.38_real32 | |
| 1768 | case('Te') | ||
| 1769 | 2 | mass_ = 127.6_real32 | |
| 1770 | 2 | charge_ = 52.0_real32 | |
| 1771 | 2 | radius_ = 1.35_real32 | |
| 1772 | case('I') | ||
| 1773 | 2 | mass_ = 126.9_real32 | |
| 1774 | 2 | charge_ = 53.0_real32 | |
| 1775 | 2 | radius_ = 1.33_real32 | |
| 1776 | case('Xe') | ||
| 1777 | 2 | mass_ = 131.29_real32 | |
| 1778 | 2 | charge_ = 54.0_real32 | |
| 1779 | 2 | radius_ = 1.31_real32 | |
| 1780 | case('Cs') | ||
| 1781 | 2 | mass_ = 132.91_real32 | |
| 1782 | 2 | charge_ = 55.0_real32 | |
| 1783 | 2 | radius_ = 2.35_real32 | |
| 1784 | case('Ba') | ||
| 1785 | 3 | mass_ = 137.33_real32 | |
| 1786 | 3 | charge_ = 56.0_real32 | |
| 1787 | 3 | radius_ = 1.98_real32 | |
| 1788 | case('La') | ||
| 1789 | 2 | mass_ = 138.91_real32 | |
| 1790 | 2 | charge_ = 57.0_real32 | |
| 1791 | 2 | radius_ = 1.69_real32 | |
| 1792 | case('Ce') | ||
| 1793 | 2 | mass_ = 140.12_real32 | |
| 1794 | 2 | charge_ = 58.0_real32 | |
| 1795 | 2 | radius_ = 1.65_real32 | |
| 1796 | case('Pr') | ||
| 1797 | 2 | mass_ = 140.91_real32 | |
| 1798 | 2 | charge_ = 59.0_real32 | |
| 1799 | 2 | radius_ = 1.65_real32 | |
| 1800 | case('Nd') | ||
| 1801 | 2 | mass_ = 144.24_real32 | |
| 1802 | 2 | charge_ = 60.0_real32 | |
| 1803 | 2 | radius_ = 1.64_real32 | |
| 1804 | case('Pm') | ||
| 1805 | 2 | mass_ = 145.0_real32 | |
| 1806 | 2 | charge_ = 61.0_real32 | |
| 1807 | 2 | radius_ = 1.63_real32 | |
| 1808 | case('Sm') | ||
| 1809 | 2 | mass_ = 150.36_real32 | |
| 1810 | 2 | charge_ = 62.0_real32 | |
| 1811 | 2 | radius_ = 1.62_real32 | |
| 1812 | case('Eu') | ||
| 1813 | 2 | mass_ = 152.0_real32 | |
| 1814 | 2 | charge_ = 63.0_real32 | |
| 1815 | 2 | radius_ = 1.85_real32 | |
| 1816 | case('Gd') | ||
| 1817 | 2 | mass_ = 157.25_real32 | |
| 1818 | 2 | charge_ = 64.0_real32 | |
| 1819 | 2 | radius_ = 1.61_real32 | |
| 1820 | case('Tb') | ||
| 1821 | 2 | mass_ = 158.93_real32 | |
| 1822 | 2 | charge_ = 65.0_real32 | |
| 1823 | 2 | radius_ = 1.59_real32 | |
| 1824 | case('Dy') | ||
| 1825 | 2 | mass_ = 162.5_real32 | |
| 1826 | 2 | charge_ = 66.0_real32 | |
| 1827 | 2 | radius_ = 1.59_real32 | |
| 1828 | case('Ho') | ||
| 1829 | 2 | mass_ = 164.93_real32 | |
| 1830 | 2 | charge_ = 67.0_real32 | |
| 1831 | 2 | radius_ = 1.58_real32 | |
| 1832 | case('Er') | ||
| 1833 | 2 | mass_ = 167.26_real32 | |
| 1834 | 2 | charge_ = 68.0_real32 | |
| 1835 | 2 | radius_ = 1.57_real32 | |
| 1836 | case('Tm') | ||
| 1837 | 2 | mass_ = 168.93_real32 | |
| 1838 | 2 | charge_ = 69.0_real32 | |
| 1839 | 2 | radius_ = 1.56_real32 | |
| 1840 | case('Yb') | ||
| 1841 | 2 | mass_ = 173.05_real32 | |
| 1842 | 2 | charge_ = 70.0_real32 | |
| 1843 | 2 | radius_ = 1.74_real32 | |
| 1844 | case('Lu') | ||
| 1845 | 2 | mass_ = 174.97_real32 | |
| 1846 | 2 | charge_ = 71.0_real32 | |
| 1847 | 2 | radius_ = 1.56_real32 | |
| 1848 | case('Hf') | ||
| 1849 | 2 | mass_ = 178.49_real32 | |
| 1850 | 2 | charge_ = 72.0_real32 | |
| 1851 | 2 | radius_ = 1.44_real32 | |
| 1852 | case('Ta') | ||
| 1853 | 2 | mass_ = 180.95_real32 | |
| 1854 | 2 | charge_ = 73.0_real32 | |
| 1855 | 2 | radius_ = 1.34_real32 | |
| 1856 | case('W') | ||
| 1857 | 2 | mass_ = 183.84_real32 | |
| 1858 | 2 | charge_ = 74.0_real32 | |
| 1859 | 2 | radius_ = 1.3_real32 | |
| 1860 | case('Re') | ||
| 1861 | 2 | mass_ = 186.21_real32 | |
| 1862 | 2 | charge_ = 75.0_real32 | |
| 1863 | 2 | radius_ = 1.28_real32 | |
| 1864 | case('Os') | ||
| 1865 | 2 | mass_ = 190.23_real32 | |
| 1866 | 2 | charge_ = 76.0_real32 | |
| 1867 | 2 | radius_ = 1.26_real32 | |
| 1868 | case('Ir') | ||
| 1869 | 2 | mass_ = 192.22_real32 | |
| 1870 | 2 | charge_ = 77.0_real32 | |
| 1871 | 2 | radius_ = 1.27_real32 | |
| 1872 | case('Pt') | ||
| 1873 | 2 | mass_ = 195.08_real32 | |
| 1874 | 2 | charge_ = 78.0_real32 | |
| 1875 | 2 | radius_ = 1.3_real32 | |
| 1876 | case('Au') | ||
| 1877 | 2 | mass_ = 196.97_real32 | |
| 1878 | 2 | charge_ = 79.0_real32 | |
| 1879 | 2 | radius_ = 1.34_real32 | |
| 1880 | case('Hg') | ||
| 1881 | 2 | mass_ = 200.59_real32 | |
| 1882 | 2 | charge_ = 80.0_real32 | |
| 1883 | 2 | radius_ = 1.49_real32 | |
| 1884 | case('Tl') | ||
| 1885 | 2 | mass_ = 204.38_real32 | |
| 1886 | 2 | charge_ = 81.0_real32 | |
| 1887 | 2 | radius_ = 1.48_real32 | |
| 1888 | case('Pb') | ||
| 1889 | 2 | mass_ = 207.2_real32 | |
| 1890 | 2 | charge_ = 82.0_real32 | |
| 1891 | 2 | radius_ = 1.47_real32 | |
| 1892 | case('Bi') | ||
| 1893 | 2 | mass_ = 208.98_real32 | |
| 1894 | 2 | charge_ = 83.0_real32 | |
| 1895 | 2 | radius_ = 1.46_real32 | |
| 1896 | case('Po') | ||
| 1897 | 2 | mass_ = 209.0_real32 | |
| 1898 | 2 | charge_ = 84.0_real32 | |
| 1899 | 2 | radius_ = 1.45_real32 | |
| 1900 | case('At') | ||
| 1901 | 2 | mass_ = 210.0_real32 | |
| 1902 | 2 | charge_ = 85.0_real32 | |
| 1903 | 2 | radius_ = 1.44_real32 | |
| 1904 | case('Rn') | ||
| 1905 | 2 | mass_ = 222.0_real32 | |
| 1906 | 2 | charge_ = 86.0_real32 | |
| 1907 | 2 | radius_ = 1.43_real32 | |
| 1908 | case('Fr') | ||
| 1909 | 2 | mass_ = 223.0_real32 | |
| 1910 | 2 | charge_ = 87.0_real32 | |
| 1911 | 2 | radius_ = 2.6_real32 | |
| 1912 | case('Ra') | ||
| 1913 | 2 | mass_ = 226.0_real32 | |
| 1914 | 2 | charge_ = 88.0_real32 | |
| 1915 | 2 | radius_ = 2.21_real32 | |
| 1916 | case('Ac') | ||
| 1917 | 2 | mass_ = 227.0_real32 | |
| 1918 | 2 | charge_ = 89.0_real32 | |
| 1919 | 2 | radius_ = 1.86_real32 | |
| 1920 | case('Th') | ||
| 1921 | 2 | mass_ = 232.04_real32 | |
| 1922 | 2 | charge_ = 90.0_real32 | |
| 1923 | 2 | radius_ = 1.75_real32 | |
| 1924 | case('Pa') | ||
| 1925 | 2 | mass_ = 231.04_real32 | |
| 1926 | 2 | charge_ = 91.0_real32 | |
| 1927 | 2 | radius_ = 1.61_real32 | |
| 1928 | case('U') | ||
| 1929 | 2 | mass_ = 238.03_real32 | |
| 1930 | 2 | charge_ = 92.0_real32 | |
| 1931 | 2 | radius_ = 1.58_real32 | |
| 1932 | case('Np') | ||
| 1933 | 2 | mass_ = 237.0_real32 | |
| 1934 | 2 | charge_ = 93.0_real32 | |
| 1935 | 2 | radius_ = 1.55_real32 | |
| 1936 | case('Pu') | ||
| 1937 | 2 | mass_ = 244.0_real32 | |
| 1938 | 2 | charge_ = 94.0_real32 | |
| 1939 | 2 | radius_ = 1.53_real32 | |
| 1940 | case('Am') | ||
| 1941 | 2 | mass_ = 243.0_real32 | |
| 1942 | 2 | charge_ = 95.0_real32 | |
| 1943 | 2 | radius_ = 1.51_real32 | |
| 1944 | case('Cm') | ||
| 1945 | 2 | mass_ = 247.0_real32 | |
| 1946 | 2 | charge_ = 96.0_real32 | |
| 1947 | 2 | radius_ = 1.69_real32 | |
| 1948 | case('Bk') | ||
| 1949 | 2 | mass_ = 247.0_real32 | |
| 1950 | 2 | charge_ = 97.0_real32 | |
| 1951 | 2 | radius_ = 1.48_real32 | |
| 1952 | case('Cf') | ||
| 1953 | 2 | mass_ = 251.0_real32 | |
| 1954 | 2 | charge_ = 98.0_real32 | |
| 1955 | 2 | radius_ = 1.47_real32 | |
| 1956 | case('Es') | ||
| 1957 | 2 | mass_ = 252.0_real32 | |
| 1958 | 2 | charge_ = 99.0_real32 | |
| 1959 | 2 | radius_ = 1.46_real32 | |
| 1960 | case('Fm') | ||
| 1961 | 2 | mass_ = 257.0_real32 | |
| 1962 | 2 | charge_ = 100.0_real32 | |
| 1963 | 2 | radius_ = 1.45_real32 | |
| 1964 | case('Md') | ||
| 1965 | 2 | mass_ = 258.0_real32 | |
| 1966 | 2 | charge_ = 101.0_real32 | |
| 1967 | 2 | radius_ = 1.44_real32 | |
| 1968 | case('No') | ||
| 1969 | 2 | mass_ = 259.0_real32 | |
| 1970 | 2 | charge_ = 102.0_real32 | |
| 1971 | 2 | radius_ = 1.43_real32 | |
| 1972 | case('Lr') | ||
| 1973 | 2 | mass_ = 262.0_real32 | |
| 1974 | 2 | charge_ = 103.0_real32 | |
| 1975 | 2 | radius_ = 1.62_real32 | |
| 1976 | case('Rf') | ||
| 1977 | 2 | mass_ = 267.0_real32 | |
| 1978 | 2 | charge_ = 104.0_real32 | |
| 1979 | 2 | radius_ = 1.57_real32 | |
| 1980 | case('Db') | ||
| 1981 | 2 | mass_ = 270.0_real32 | |
| 1982 | 2 | charge_ = 105.0_real32 | |
| 1983 | 2 | radius_ = 1.49_real32 | |
| 1984 | case('Sg') | ||
| 1985 | 2 | mass_ = 271.0_real32 | |
| 1986 | 2 | charge_ = 106.0_real32 | |
| 1987 | 2 | radius_ = 1.43_real32 | |
| 1988 | case('Bh') | ||
| 1989 | 2 | mass_ = 270.0_real32 | |
| 1990 | 2 | charge_ = 107.0_real32 | |
| 1991 | 2 | radius_ = 1.41_real32 | |
| 1992 | case('Hs') | ||
| 1993 | 2 | mass_ = 277.0_real32 | |
| 1994 | 2 | charge_ = 108.0_real32 | |
| 1995 | 2 | radius_ = 1.34_real32 | |
| 1996 | case('Mt') | ||
| 1997 | 2 | mass_ = 276.0_real32 | |
| 1998 | 2 | charge_ = 109.0_real32 | |
| 1999 | 2 | radius_ = 1.29_real32 | |
| 2000 | case('Ds') | ||
| 2001 | 2 | mass_ = 281.0_real32 | |
| 2002 | 2 | charge_ = 110.0_real32 | |
| 2003 | 2 | radius_ = 1.28_real32 | |
| 2004 | case('Rg') | ||
| 2005 | 2 | mass_ = 280.0_real32 | |
| 2006 | 2 | charge_ = 111.0_real32 | |
| 2007 | 2 | radius_ = 1.21_real32 | |
| 2008 | case('Cn') | ||
| 2009 | 2 | mass_ = 285.0_real32 | |
| 2010 | 2 | charge_ = 112.0_real32 | |
| 2011 | 2 | radius_ = 1.22_real32 | |
| 2012 | case('Nh') | ||
| 2013 | 2 | mass_ = 284.0_real32 | |
| 2014 | 2 | charge_ = 113.0_real32 | |
| 2015 | 2 | radius_ = 1.21_real32 | |
| 2016 | case('Fl') | ||
| 2017 | 2 | mass_ = 289.0_real32 | |
| 2018 | 2 | charge_ = 114.0_real32 | |
| 2019 | 2 | radius_ = 1.21_real32 | |
| 2020 | case('Mc') | ||
| 2021 | 2 | mass_ = 288.0_real32 | |
| 2022 | 2 | charge_ = 115.0_real32 | |
| 2023 | 2 | radius_ = 1.21_real32 | |
| 2024 | case('Lv') | ||
| 2025 | 2 | mass_ = 293.0_real32 | |
| 2026 | 2 | charge_ = 116.0_real32 | |
| 2027 | 2 | radius_ = 1.21_real32 | |
| 2028 | case('Ts') | ||
| 2029 | 2 | mass_ = 294.0_real32 | |
| 2030 | 2 | charge_ = 117.0_real32 | |
| 2031 | 2 | radius_ = 1.21_real32 | |
| 2032 | case('Og') | ||
| 2033 | 2 | mass_ = 294.0_real32 | |
| 2034 | 2 | charge_ = 118.0_real32 | |
| 2035 | 2 | radius_ = 1.21_real32 | |
| 2036 | case default | ||
| 2037 | ! handle unknown element | ||
| 2038 | 5 | mass_ = 0.0_real32 | |
| 2039 | 5 | charge_ = 0.0_real32 | |
| 2040 |
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|
256 | radius_ = 0.0_real32 |
| 2041 | end select | ||
| 2042 | |||
| 2043 | !--------------------------------------------------------------------------- | ||
| 2044 | ! Return the values | ||
| 2045 | !--------------------------------------------------------------------------- | ||
| 2046 |
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|
256 | if(present(mass)) mass = mass_ |
| 2047 |
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|
256 | if(present(charge)) charge = charge_ |
| 2048 |
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256 | if(present(radius)) radius = radius_ |
| 2049 | |||
| 2050 | 256 | end subroutine get_element_properties | |
| 2051 | !############################################################################### | ||
| 2052 | |||
| 2053 |
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|
4 | end module raffle__geom_rw |
| 2054 |