| 1 |
!-------------------------------------------------------------------- |
| 2 |
! Module INIT_SYSTEM |
| 3 |
! Initializes and builds system if necessary |
| 4 |
! Author: Charles F. Vardeman II and J. Daniel Gezelter |
| 5 |
!-------------------------------------------------------------------- |
| 6 |
|
| 7 |
|
| 8 |
module init_simulation |
| 9 |
use definitions, ONLY : DP, machdep_lnblnk |
| 10 |
use parameter |
| 11 |
use simulation |
| 12 |
use sprng_mod, ONLY : get_random_sprng |
| 13 |
use model_module |
| 14 |
use status, ONLY: error,info, warning |
| 15 |
#ifdef MPI |
| 16 |
use mpi_module |
| 17 |
#endif |
| 18 |
implicit none |
| 19 |
PRIVATE |
| 20 |
|
| 21 |
public :: nano_build_system |
| 22 |
|
| 23 |
integer :: nsolute |
| 24 |
integer :: nsolvent |
| 25 |
integer :: ncore |
| 26 |
integer :: nshell |
| 27 |
integer :: n_vacancy |
| 28 |
real( kind = DP ) :: solvent_x |
| 29 |
real( kind = DP ), parameter :: rhoconv = 1.661E0_DP |
| 30 |
|
| 31 |
type :: unit_cell |
| 32 |
private |
| 33 |
real( kind = DP ), dimension(4) :: sx,sy,sz |
| 34 |
real( kind = DP ), dimension(4) :: s_ex,s_ey,s_ez |
| 35 |
integer :: number_of_cells |
| 36 |
real( kind = DP ) :: cell_length |
| 37 |
end type unit_cell |
| 38 |
|
| 39 |
|
| 40 |
|
| 41 |
|
| 42 |
contains |
| 43 |
|
| 44 |
! inteface to module, builds the right system |
| 45 |
subroutine nano_build_system(assign_positions) |
| 46 |
type (unit_cell) :: system_cell |
| 47 |
logical, intent(in) :: assign_positions |
| 48 |
integer :: n_interface |
| 49 |
! integer :: n_vacancy |
| 50 |
logical :: found |
| 51 |
logical :: random_cluster |
| 52 |
logical, allocatable, dimension(:) :: vacancy |
| 53 |
real( kind = DP ),parameter :: small_number = 1.0d-6 |
| 54 |
real( kind = DP ) :: dbl_n_interface |
| 55 |
real( kind = DP ) :: junk |
| 56 |
real( kind = DP ) :: scale |
| 57 |
character(len=80) :: msg |
| 58 |
integer :: i |
| 59 |
integer :: tester |
| 60 |
integer :: orig_nmol |
| 61 |
#ifndef MPI |
| 62 |
integer, parameter :: node = 0 |
| 63 |
#endif |
| 64 |
|
| 65 |
random_cluster = .false. |
| 66 |
|
| 67 |
|
| 68 |
|
| 69 |
|
| 70 |
call build_fcc_unit_cell(system_cell) |
| 71 |
|
| 72 |
call get_nmol(system_cell,nmol,n_interface) |
| 73 |
|
| 74 |
|
| 75 |
!! generate vacancy if necessary |
| 76 |
dbl_n_interface = real(n_interface,KIND(DP)) |
| 77 |
if (sim_type == 'liquid') then |
| 78 |
n_vacancy = 0 |
| 79 |
else |
| 80 |
n_vacancy = idint(dbl_n_interface * vacancy_fraction) |
| 81 |
endif |
| 82 |
|
| 83 |
if (n_vacancy /= 0) then |
| 84 |
allocate(vacancy(n_interface)) |
| 85 |
do i = 1, n_interface |
| 86 |
vacancy(i) = .false. |
| 87 |
enddo |
| 88 |
|
| 89 |
do i = 1, n_vacancy |
| 90 |
found = .false. |
| 91 |
gen_vacancy: do |
| 92 |
if (found) exit gen_vacancy |
| 93 |
|
| 94 |
tester = 1 + idint(dbl_n_interface*get_random_sprng()) |
| 95 |
|
| 96 |
if (.not.vacancy(tester)) then |
| 97 |
vacancy(tester) = .true. |
| 98 |
found = .true. |
| 99 |
end if |
| 100 |
end do gen_vacancy |
| 101 |
end do |
| 102 |
orig_nmol = nmol |
| 103 |
nmol = nmol - n_vacancy |
| 104 |
end if |
| 105 |
|
| 106 |
|
| 107 |
#ifdef MPI |
| 108 |
call setup_parallel_mol(nmol) |
| 109 |
call allocate_nmol_arrays(maxmol_local) |
| 110 |
#else |
| 111 |
call allocate_nmol_arrays(nmol) |
| 112 |
nmol_local = nmol |
| 113 |
#endif |
| 114 |
|
| 115 |
|
| 116 |
if (sim_type == 'liquid' .OR. & |
| 117 |
dabs(r_shell-r_core).lt.small_number) then |
| 118 |
call generate_model() |
| 119 |
random_cluster = .true. |
| 120 |
elseif (n_vacancy /= 0) then |
| 121 |
call generate_model(this_cell=system_cell,vacancy = vacancy) |
| 122 |
else |
| 123 |
call generate_model(this_cell=system_cell) |
| 124 |
endif |
| 125 |
|
| 126 |
!! set box length |
| 127 |
if (sim_type == "liquid") then |
| 128 |
scale = (total_mass*rhoconv/density)**(1.0E0_DP/3.0E0_DP) |
| 129 |
box(1) = scale |
| 130 |
box(2) = scale |
| 131 |
box(3) = scale |
| 132 |
else !! For cluster box length is set to 1, wrap handles |
| 133 |
!! selecting the right pbc. |
| 134 |
box(1) = 1 |
| 135 |
box(2) = 1 |
| 136 |
box(3) = 1 |
| 137 |
endif |
| 138 |
|
| 139 |
if (assign_positions) then |
| 140 |
if (n_vacancy /= 0) then |
| 141 |
call build_positions(system_cell,vacancy=vacancy) |
| 142 |
else |
| 143 |
call build_positions(system_cell) |
| 144 |
end if |
| 145 |
endif |
| 146 |
|
| 147 |
!! write out what we just did.... |
| 148 |
if (assign_positions) then |
| 149 |
call info("BUILD_SYSTEM", & |
| 150 |
"Built new system with the following...") |
| 151 |
else |
| 152 |
call info("BUILD_SYSTEM", & |
| 153 |
"Initialized system with the following...") |
| 154 |
endif |
| 155 |
#ifdef MPI |
| 156 |
call info("BUILD_SYSTEM", & |
| 157 |
"MPI parallel calculations") |
| 158 |
#endif |
| 159 |
write(msg,'(a18,i11)') '# nmol = ', nmol |
| 160 |
call info("BUILD_SYSTEM",trim(msg)) |
| 161 |
write(msg,'(a18,i11)') '# natoms = ', natoms |
| 162 |
call info("BUILD_SYSTEM",trim(msg)) |
| 163 |
write(msg,'(a18,es12.3,a10)') 'lattice spacing = ', system_cell%cell_length, & |
| 164 |
" angstroms" |
| 165 |
call info("BUILD_SYSTEM",trim(msg)) |
| 166 |
|
| 167 |
select case (sim_type) |
| 168 |
case ("cluster") |
| 169 |
call info("BUILD_SYSTEM","Built cluster with the following") |
| 170 |
write(msg,'(a8,i11,a24)') '# using ', 2*system_cell%number_of_cells + 1, & |
| 171 |
' cells in each direction' |
| 172 |
call info('BUILD_SYSTEM',trim(msg)) |
| 173 |
write(msg,'(a18,f6.2,a12)') "Particle radius: ", r_shell, " Angstroms." |
| 174 |
call info('BUILD_SYSTEM',trim(msg)) |
| 175 |
if(random_cluster) then |
| 176 |
call info("BUILD_SYSTEM","Generated random cluster with: ") |
| 177 |
write(msg,'(a13,i11)') '# nsolute = ', nsolute |
| 178 |
call info("BUILD_SYSTEM",trim(msg)) |
| 179 |
write(msg,'(a13,i11)') '# nsolvent = ', nsolvent |
| 180 |
call info("BUILD_SYSTEM",trim(msg)) |
| 181 |
else |
| 182 |
call info("BUILD_SYSTEM","Generated core-shell particle with: ") |
| 183 |
write(msg,'(a13,f6.2,a12)') "Core radius: ", r_core, " Angstroms" |
| 184 |
call info('BUILD_SYSTEM',trim(msg)) |
| 185 |
write(msg,'(a11,i11)') '# ncore = ', ncore |
| 186 |
call info('BUILD_SYSTEM',trim(msg)) |
| 187 |
write(msg,'(a11,i11)') '# nshell = ', nshell |
| 188 |
call info('BUILD_SYSTEM',trim(msg)) |
| 189 |
endif |
| 190 |
if (n_vacancy /= 0) then |
| 191 |
call info("BUILD_SYSTEM","Generated Vacancies with: ") |
| 192 |
write(msg,*) "# mol origonal = ", orig_nmol |
| 193 |
call info("BUILD_SYSTEM",trim(msg)) |
| 194 |
write(msg,'(a21,f6.2,a1)') "A vacancy percent of: ", vacancy_fraction*100,"%" |
| 195 |
call info("BUILD_SYSTEM",trim(msg)) |
| 196 |
write(msg,'(a21,f6.2,a31)') "A vacancy radius of: ", vacancy_radius, & |
| 197 |
" angstroms from the interface." |
| 198 |
call info("BUILD_SYSTEM",trim(msg)) |
| 199 |
write(msg,*) "Total # of atoms at interface: ", n_interface |
| 200 |
call info("BUILD_SYSTEM",trim(msg)) |
| 201 |
write(msg,'(a14,i5,a25)') "Resulting in: ", n_vacancy, & |
| 202 |
" particles being removed." |
| 203 |
call info("BUILD_SYSTEM",trim(msg)) |
| 204 |
|
| 205 |
end if |
| 206 |
case("liquid") |
| 207 |
call info("BUILD_SYSTEM","Generated liquid with the following: ") |
| 208 |
write(msg,'(a13,i11)') '# nsolute = ', nsolute |
| 209 |
call info("BUILD_SYSTEM",trim(msg)) |
| 210 |
write(msg,'(a13,i11)') '# nsolvent = ', nsolvent |
| 211 |
call info("BUILD_SYSTEM",trim(msg)) |
| 212 |
call info("BUILD_SYSTEM","Periodic Boundary Conditions") |
| 213 |
write(msg,'(a11,es30.16)') 'boxX = ', box(1) |
| 214 |
call info("BUILD_SYSTEM",trim(msg)) |
| 215 |
write(msg,'(a11,es30.16)') 'boxY = ', box(2) |
| 216 |
call info("BUILD_SYSTEM",trim(msg)) |
| 217 |
write(msg,'(a11,es30.16)') 'boxZ = ', box(3) |
| 218 |
call info("BUILD_SYSTEM",trim(msg)) |
| 219 |
write(msg,'(a12,es30.16)') 'total_mass = ', total_mass |
| 220 |
call info("BUILD_SYSTEM",trim(msg)) |
| 221 |
write(msg,'(a12,es30.16)') 'rhoconv = ', rhoconv |
| 222 |
call info("BUILD_SYSTEM",trim(msg)) |
| 223 |
|
| 224 |
junk = total_mass*rhoconv/(box(1)*box(2)*box(3)) |
| 225 |
write(msg,'(a11,es12.3)') 'density = ', junk |
| 226 |
call info('BUILD_SYSTEM',trim(msg)) |
| 227 |
junk = dble(nmol)/(box(1)*box(2)*box(3)) |
| 228 |
write(msg,'(a11,es12.3)') 'ndensity = ', junk |
| 229 |
call info('BUILD_SYSTEM',trim(msg)) |
| 230 |
end select |
| 231 |
|
| 232 |
if (allocated(vacancy)) & |
| 233 |
deallocate(vacancy) |
| 234 |
#ifdef MPI |
| 235 |
call allocate_mpi_arrays(max_local) |
| 236 |
#endif |
| 237 |
end subroutine nano_build_system |
| 238 |
|
| 239 |
|
| 240 |
|
| 241 |
|
| 242 |
|
| 243 |
!-----------------Utility subroutines---------------------- |
| 244 |
|
| 245 |
!builds FCC unit cell |
| 246 |
subroutine build_fcc_unit_cell(this_cell) |
| 247 |
type (unit_cell), intent(out) :: this_cell |
| 248 |
|
| 249 |
real( kind = DP ) :: cell2, rroot3 |
| 250 |
|
| 251 |
|
| 252 |
call info("INIT_SYSTEM", "Creating unit cell ...") |
| 253 |
select case(sim_type) |
| 254 |
case ("cluster") |
| 255 |
this_cell%cell_length = cell |
| 256 |
this_cell%number_of_cells = & |
| 257 |
2.0E0_DP*r_shell/this_cell%cell_length |
| 258 |
case ("liquid") |
| 259 |
this_cell%number_of_cells = ncells |
| 260 |
this_cell%cell_length = & |
| 261 |
1.0E0_DP / real(this_cell%number_of_cells,KIND(DP)) |
| 262 |
end select |
| 263 |
|
| 264 |
cell2 = 0.5E0_DP * this_cell%cell_length |
| 265 |
rroot3 = 1.0E0_DP/ dsqrt(3.0E0_DP) |
| 266 |
|
| 267 |
|
| 268 |
! molecule 1 |
| 269 |
|
| 270 |
this_cell%sx(1) = 0.0E0_DP |
| 271 |
this_cell%sy(1) = 0.0E0_DP |
| 272 |
this_cell%sz(1) = 0.0E0_DP |
| 273 |
this_cell%s_ex(1) = RROOT3 |
| 274 |
this_cell%s_ey(1) = RROOT3 |
| 275 |
this_cell%s_ez(1) = RROOT3 |
| 276 |
|
| 277 |
! molecule 3 |
| 278 |
|
| 279 |
this_cell%sx(3) = cell2 |
| 280 |
this_cell%sy(3) = cell2 |
| 281 |
this_cell%sz(3) = 0.0E0_DP |
| 282 |
this_cell%s_ex(3) = RROOT3 |
| 283 |
this_cell%s_ey(3) = -RROOT3 |
| 284 |
this_cell%s_ez(3) = -RROOT3 |
| 285 |
|
| 286 |
! molecule 2 |
| 287 |
|
| 288 |
this_cell%sx(2) = 0.0E0_DP |
| 289 |
this_cell%sy(2) = cell2 |
| 290 |
this_cell%sz(2) = cell2 |
| 291 |
this_cell%s_ex(2) = -RROOT3 |
| 292 |
this_cell%s_ey(2) = RROOT3 |
| 293 |
this_cell%s_ez(2) = -RROOT3 |
| 294 |
|
| 295 |
! molecule 4 |
| 296 |
|
| 297 |
this_cell%sx(4) = cell2 |
| 298 |
this_cell%sy(4) = 0.0E0_DP |
| 299 |
this_cell%sz(4) = cell2 |
| 300 |
this_cell%s_ex(4) = -RROOT3 |
| 301 |
this_cell%s_ey(4) = -RROOT3 |
| 302 |
this_cell%s_ez(4) = RROOT3 |
| 303 |
|
| 304 |
|
| 305 |
|
| 306 |
|
| 307 |
|
| 308 |
end subroutine build_fcc_unit_cell |
| 309 |
|
| 310 |
!! Subroutine counts or calculates the number of molecules in |
| 311 |
!! this simulation. |
| 312 |
subroutine get_nmol(this_cell,number_of_molecules, number_at_interface) |
| 313 |
! argument declarations |
| 314 |
type (unit_cell), intent(in) :: this_cell |
| 315 |
integer, intent(out) :: number_of_molecules |
| 316 |
integer, intent(out) :: number_at_interface |
| 317 |
|
| 318 |
! integers |
| 319 |
integer :: ix, iy, iz !cell indexes |
| 320 |
integer :: iref |
| 321 |
integer :: number_in_lattice |
| 322 |
! reals |
| 323 |
integer :: nc |
| 324 |
real( kind = DP ) :: rx,ry,rz |
| 325 |
real( kind = DP ) :: dist |
| 326 |
|
| 327 |
!! r_core = core radius in declared in parameter_mod |
| 328 |
!! r_shell = shell radius in declared in parameter_mod |
| 329 |
!! vacancy_radius = radius arround interface to create vacancies |
| 330 |
|
| 331 |
number_of_molecules = 0 |
| 332 |
number_at_interface = 0 |
| 333 |
number_in_lattice = 0 |
| 334 |
|
| 335 |
select case (sim_type) |
| 336 |
case ('liquid') |
| 337 |
number_of_molecules = 4 * & |
| 338 |
this_cell%number_of_cells* & |
| 339 |
this_cell%number_of_cells* & |
| 340 |
this_cell%number_of_cells |
| 341 |
case ('cluster') |
| 342 |
nc = this_cell%number_of_cells |
| 343 |
do iz = -nc, nc, 1 |
| 344 |
do iy = -nc, nc, 1 |
| 345 |
do ix = -nc, nc, 1 |
| 346 |
do iref = 1, 4 |
| 347 |
number_in_lattice = & |
| 348 |
number_in_lattice + 1 |
| 349 |
rx = this_cell%sx(iref) + this_cell%cell_length & |
| 350 |
* (dble( ix ) - 0.5E0_DP) |
| 351 |
ry = this_cell%sy(iref) + this_cell%cell_length & |
| 352 |
* (dble( iy ) - 0.5E0_DP) |
| 353 |
rz = this_cell%sz(iref) + this_cell%cell_length & |
| 354 |
* (dble( iz ) - 0.5E0_DP) |
| 355 |
dist = dsqrt(rx*rx + ry*ry + rz*rz) |
| 356 |
if (dist.le.r_shell) then |
| 357 |
number_of_molecules = & |
| 358 |
number_of_molecules + 1 |
| 359 |
endif |
| 360 |
if ((dist.ge.r_core-vacancy_radius/2.0E0_DP).and. & |
| 361 |
(dist.le.r_core+vacancy_radius/2.0E0_DP)) then |
| 362 |
number_at_interface = & |
| 363 |
number_at_interface + 1 |
| 364 |
endif |
| 365 |
end do |
| 366 |
end do |
| 367 |
end do |
| 368 |
end do |
| 369 |
end select |
| 370 |
end subroutine get_nmol |
| 371 |
|
| 372 |
|
| 373 |
subroutine generate_model(this_cell,vacancy) |
| 374 |
|
| 375 |
! Arguments! |
| 376 |
!! optional -- only if generating cluster |
| 377 |
type (unit_cell), intent(in), optional :: this_cell |
| 378 |
logical,intent(in), dimension(:), optional :: vacancy |
| 379 |
!arrays |
| 380 |
character(len=10), allocatable, dimension(:) :: model_tmp |
| 381 |
! real variables |
| 382 |
real( kind = DP ) :: dist |
| 383 |
real( kind = DP ) :: rx,ry,rz |
| 384 |
real( kind = DP ) :: mtot_local |
| 385 |
! integers counters |
| 386 |
integer :: i, ntmp,j |
| 387 |
integer :: tester |
| 388 |
integer :: atom_count |
| 389 |
integer :: ncount |
| 390 |
logical :: record_start |
| 391 |
integer :: ix,iy,iz |
| 392 |
integer :: iref |
| 393 |
integer :: nc |
| 394 |
integer :: iinterface |
| 395 |
integer :: atom |
| 396 |
character(len=10) :: this_model |
| 397 |
integer :: this_atype |
| 398 |
logical :: found |
| 399 |
|
| 400 |
|
| 401 |
#ifndef MPI |
| 402 |
integer :: nmol_local |
| 403 |
#endif |
| 404 |
record_start = .true. |
| 405 |
allocate (model_tmp(nmol)) |
| 406 |
|
| 407 |
|
| 408 |
!! this_cell is the unit cell which we only need to |
| 409 |
!! build the model for the core-shell cluster |
| 410 |
!! else we build a random model.... |
| 411 |
if (.not. present(this_cell)) then |
| 412 |
call info('GENERATE_RANDOM_MODEL', & |
| 413 |
'Generating random configuration....') |
| 414 |
!! check for problems with cluster model |
| 415 |
|
| 416 |
if (sim_type == 'cluster') then |
| 417 |
if (core_model /= solute_model .AND. & |
| 418 |
shell_model /= solvent_model) then |
| 419 |
call error('GENERATE_RANDOM_MODEL', & |
| 420 |
'Cluster models and Solvent Models are different') |
| 421 |
end if |
| 422 |
end if |
| 423 |
|
| 424 |
nsolute = idint(solute_x*dble(nmol)) |
| 425 |
nsolvent = nmol - nsolute |
| 426 |
solute_x = dble(nsolute)/dble(nmol) |
| 427 |
solvent_x = 1.0E0_DP - solute_x |
| 428 |
|
| 429 |
|
| 430 |
|
| 431 |
|
| 432 |
do i = 1, nmol |
| 433 |
model_tmp(i) = solvent_model |
| 434 |
enddo |
| 435 |
|
| 436 |
|
| 437 |
if (solvent_model /= solute_model) then |
| 438 |
do i = 1, nsolute |
| 439 |
found = .false. |
| 440 |
do |
| 441 |
if (found) exit |
| 442 |
tester = 1+idint(dble(nmol)*get_random_sprng()) |
| 443 |
|
| 444 |
if (model_tmp(tester).ne.solute_model) then |
| 445 |
model_tmp(tester) = solute_model |
| 446 |
found = .true. |
| 447 |
endif |
| 448 |
end do |
| 449 |
enddo |
| 450 |
endif |
| 451 |
|
| 452 |
|
| 453 |
ntmp = 0 |
| 454 |
nlocal = 0 |
| 455 |
atom_count = 0 |
| 456 |
|
| 457 |
do i = 1, nmol |
| 458 |
atom_count = atom_count + & |
| 459 |
model_na(model_tmp(i)) |
| 460 |
#ifdef MPI |
| 461 |
if (i.ge.nmol_start.and. & |
| 462 |
i.le.nmol_end) then |
| 463 |
ntmp = i - nmol_start + 1 |
| 464 |
#else |
| 465 |
ntmp = i |
| 466 |
#endif |
| 467 |
model(ntmp) = model_tmp(i) |
| 468 |
na(ntmp) = model_na(model(ntmp)) |
| 469 |
#ifdef MPI |
| 470 |
if (record_start) then |
| 471 |
nstart = atom_count - na(ntmp) + 1 |
| 472 |
record_start = .false. |
| 473 |
end if |
| 474 |
#endif |
| 475 |
|
| 476 |
do j = 1,na(ntmp) |
| 477 |
nlocal = nlocal + 1 |
| 478 |
atom_index(ntmp,j) = nlocal |
| 479 |
end do |
| 480 |
#ifdef MPI |
| 481 |
endif |
| 482 |
#endif |
| 483 |
end do |
| 484 |
|
| 485 |
else ! generate core-shell cluster |
| 486 |
call info("GENERATE_MODEL","Generating Cluster Model ...") |
| 487 |
ncount = 0 |
| 488 |
ntmp = 0 |
| 489 |
atom_count = 0 |
| 490 |
ncore = 0 |
| 491 |
nshell = 0 |
| 492 |
iinterface = 0 |
| 493 |
nlocal = 0 |
| 494 |
nc = this_cell%number_of_cells |
| 495 |
do iz = -nc, nc, 1 |
| 496 |
do iy = -nc, nc, 1 |
| 497 |
do ix = -nc, nc, 1 |
| 498 |
do iref = 1, 4 |
| 499 |
|
| 500 |
rx = this_cell%sx(iref) + & |
| 501 |
this_cell%cell_length * (dble( ix ) - 0.5E0_DP) |
| 502 |
ry = this_cell%sy(iref) + & |
| 503 |
this_cell%cell_length * (dble( iy ) - 0.5E0_DP) |
| 504 |
rz = this_cell%sz(iref) + & |
| 505 |
this_cell%cell_length * (dble( iz ) - 0.5E0_DP) |
| 506 |
|
| 507 |
dist = dsqrt(rx*rx + ry*ry + rz*rz) |
| 508 |
|
| 509 |
|
| 510 |
if ((present(vacancy)).and. & |
| 511 |
(dist.ge.r_core-vacancy_radius/2.0E0_DP).and. & |
| 512 |
(dist.le.r_core+vacancy_radius/2.0E0_DP)) then |
| 513 |
|
| 514 |
iinterface = iinterface + 1 |
| 515 |
if (.not.vacancy(iinterface)) then |
| 516 |
|
| 517 |
|
| 518 |
if (dist.le.r_shell) then |
| 519 |
ncount = ncount + 1 |
| 520 |
if (dist.le.r_core) then |
| 521 |
model_tmp(ncount) = core_model |
| 522 |
ncore = ncore + 1 |
| 523 |
else |
| 524 |
model_tmp(ncount) = shell_model |
| 525 |
nshell = nshell + 1 |
| 526 |
endif |
| 527 |
atom_count = atom_count + & |
| 528 |
model_na(model_tmp(ncount)) |
| 529 |
#ifdef MPI |
| 530 |
if (ncount.ge.nmol_start.and. & |
| 531 |
ncount.le.nmol_end) then |
| 532 |
ntmp = ncount - nmol_start + 1 |
| 533 |
#else |
| 534 |
ntmp = ncount |
| 535 |
#endif |
| 536 |
|
| 537 |
model(ntmp) = model_tmp(ncount) |
| 538 |
na(ntmp) = model_na(model(ntmp)) |
| 539 |
#ifdef MPI |
| 540 |
if (record_start) then |
| 541 |
nstart = atom_count - na(ntmp) + 1 |
| 542 |
record_start = .false. |
| 543 |
end if |
| 544 |
#endif |
| 545 |
|
| 546 |
do j = 1, na(ntmp) |
| 547 |
nlocal = nlocal + 1 |
| 548 |
atom_index(ntmp,j) = nlocal |
| 549 |
enddo |
| 550 |
#ifdef MPI |
| 551 |
endif |
| 552 |
#endif |
| 553 |
endif |
| 554 |
|
| 555 |
endif ! end vacancy(iinterface) |
| 556 |
else ! build core-shell with all particles |
| 557 |
if (dist.le.r_shell) then |
| 558 |
ncount = ncount + 1 |
| 559 |
|
| 560 |
|
| 561 |
if (dist.le.r_core) then |
| 562 |
model_tmp(ncount) = core_model |
| 563 |
ncore = ncore + 1 |
| 564 |
else |
| 565 |
model_tmp(ncount) = shell_model |
| 566 |
nshell = nshell + 1 |
| 567 |
endif |
| 568 |
|
| 569 |
atom_count = atom_count + & |
| 570 |
model_na(model_tmp(ncount)) |
| 571 |
#ifdef MPI |
| 572 |
if (ncount.ge.nmol_start.and. & |
| 573 |
ncount.le.nmol_end) then |
| 574 |
ntmp = ncount - nmol_start + 1 |
| 575 |
#else |
| 576 |
ntmp = ncount |
| 577 |
#endif |
| 578 |
model(ntmp) = model_tmp(ncount) |
| 579 |
na(ntmp) = model_na(model(ntmp)) |
| 580 |
|
| 581 |
#ifdef MPI |
| 582 |
if (record_start) then |
| 583 |
nstart = atom_count - na(ntmp) + 1 |
| 584 |
record_start = .false. |
| 585 |
end if |
| 586 |
#endif |
| 587 |
do j = 1, na(ntmp) |
| 588 |
nlocal = nlocal + 1 |
| 589 |
atom_index(ntmp,j) = nlocal |
| 590 |
enddo |
| 591 |
#ifdef MPI |
| 592 |
endif |
| 593 |
#endif |
| 594 |
endif |
| 595 |
endif !! end present(vacancy) |
| 596 |
end do |
| 597 |
end do |
| 598 |
end do |
| 599 |
end do |
| 600 |
endif |
| 601 |
|
| 602 |
|
| 603 |
|
| 604 |
natoms = atom_count |
| 605 |
|
| 606 |
mtot_local = 0.0E0_DP |
| 607 |
total_mass = 0.0E0_DP |
| 608 |
|
| 609 |
do i = 1, nmol |
| 610 |
this_model = model_tmp(i) |
| 611 |
do j = 1,model_na(this_model) |
| 612 |
this_atype = model_atype(this_model,j) |
| 613 |
total_mass = total_mass + atype_mass(this_atype) |
| 614 |
end do |
| 615 |
end do |
| 616 |
|
| 617 |
deallocate(model_tmp) |
| 618 |
|
| 619 |
|
| 620 |
#ifndef MPI |
| 621 |
nmol_local = nmol |
| 622 |
#endif |
| 623 |
|
| 624 |
#ifdef MPI |
| 625 |
call setup_parallel_mpi() |
| 626 |
call allocate_simulation(max_local,ncol) |
| 627 |
#else |
| 628 |
nlocal = natoms |
| 629 |
call allocate_simulation(natoms) |
| 630 |
|
| 631 |
#endif |
| 632 |
|
| 633 |
!! build ident and mass arrays |
| 634 |
do i = 1,nmol_local |
| 635 |
do j = 1, na(i) |
| 636 |
atom = atom_index(i,j) |
| 637 |
ident(atom) = model_atype(model(i), j) |
| 638 |
mass(atom) = atype_mass(ident(atom)) |
| 639 |
mass_local = mass_local + mass(atom) |
| 640 |
|
| 641 |
end do |
| 642 |
end do |
| 643 |
|
| 644 |
! 2-6-2002 Total mass is now calculated on each node to reduce |
| 645 |
! summation error |
| 646 |
!#ifdef MPI |
| 647 |
! call mpi_allreduce(mtot_local,total_mass,1,mpi_double_precision, & |
| 648 |
! mpi_sum,mpi_comm_world,mpi_err) |
| 649 |
!#else |
| 650 |
! total_mass = mtot_local |
| 651 |
!#endif |
| 652 |
|
| 653 |
|
| 654 |
|
| 655 |
end subroutine generate_model |
| 656 |
subroutine build_positions(this_cell,vacancy) |
| 657 |
use file_units, ONLY : next_unit |
| 658 |
logical, intent(in),dimension(:), optional :: vacancy |
| 659 |
type (unit_cell), intent(in) :: this_cell |
| 660 |
integer :: ntemp,ncount,nc |
| 661 |
integer :: ix,iy,iz |
| 662 |
integer :: start_index |
| 663 |
integer :: ntmp |
| 664 |
integer :: iinterface |
| 665 |
integer :: iref |
| 666 |
integer :: vac_unit |
| 667 |
integer :: unit |
| 668 |
character(len=*), parameter :: xyz_coord = "(a3,3es12.4)" |
| 669 |
character(len = 80) :: file |
| 670 |
character(len = 80) :: vac_file |
| 671 |
real( kind = DP ) :: scale |
| 672 |
real( kind = DP ) :: rx,ry,rz |
| 673 |
real( kind = DP ) :: ex,ey,ez |
| 674 |
real( kind = DP ) :: reference |
| 675 |
real( kind = DP ) :: dist |
| 676 |
real( kind = DP ) :: theta |
| 677 |
real( kind = DP ) :: phi |
| 678 |
real( kind = DP ) :: psi |
| 679 |
real( kind = DP ), dimension(3) :: xcom |
| 680 |
|
| 681 |
call info("BUILD_POSITIONS","Building positions of model...") |
| 682 |
|
| 683 |
|
| 684 |
if (sim_type == "liquid") then |
| 685 |
start_index = 1 |
| 686 |
reference = 0.5 |
| 687 |
else |
| 688 |
start_index = - this_cell%number_of_cells |
| 689 |
reference = 0 |
| 690 |
endif |
| 691 |
|
| 692 |
nc = this_cell%number_of_cells |
| 693 |
ncount = 0 |
| 694 |
ntmp = 0 |
| 695 |
iinterface = 0 |
| 696 |
|
| 697 |
!new stuff here |
| 698 |
|
| 699 |
|
| 700 |
|
| 701 |
if (print_vac) then |
| 702 |
vac_unit = next_unit() |
| 703 |
vac_file = file_prefix(1:machdep_lnblnk(file_prefix))//".vac" |
| 704 |
open (unit = vac_unit, status = 'replace', file = vac_file) |
| 705 |
|
| 706 |
write(vac_unit,*) n_vacancy |
| 707 |
write(vac_unit,*) |
| 708 |
|
| 709 |
endif |
| 710 |
|
| 711 |
do iz = start_index, nc, 1 |
| 712 |
do iy = start_index, nc, 1 |
| 713 |
do ix = start_index, nc, 1 |
| 714 |
do iref = 1, 4 |
| 715 |
|
| 716 |
rx = this_cell%sx(iref) + & |
| 717 |
this_cell%cell_length * (dble( ix ) - 0.5E0_DP) |
| 718 |
ry = this_cell%sy(iref) + & |
| 719 |
this_cell%cell_length * (dble( iy ) - 0.5E0_DP) |
| 720 |
rz = this_cell%sz(iref) + & |
| 721 |
this_cell%cell_length * (dble( iz ) - 0.5E0_DP) |
| 722 |
|
| 723 |
ex = this_cell%s_ex(iref) |
| 724 |
ey = this_cell%s_ey(iref) |
| 725 |
ez = this_cell%s_ez(iref) |
| 726 |
|
| 727 |
dist = dsqrt(rx*rx + ry*ry + rz*rz) |
| 728 |
if ((present(vacancy)).and. & |
| 729 |
(dist.ge.r_core-vacancy_radius/2.0E0_DP).and. & |
| 730 |
(dist.le.r_core+vacancy_radius/2.0E0_DP)) then |
| 731 |
|
| 732 |
iinterface = iinterface + 1 |
| 733 |
|
| 734 |
if (.not.vacancy(iinterface)) then |
| 735 |
|
| 736 |
ncount = ncount + 1 |
| 737 |
#ifdef MPI |
| 738 |
if(ncount.ge.nmol_start.and. & |
| 739 |
ncount.le.nmol_end) then |
| 740 |
ntmp = ncount - nmol_start + 1 |
| 741 |
#else |
| 742 |
ntmp = ncount |
| 743 |
#endif |
| 744 |
rx = box(1)*(rx - reference) |
| 745 |
ry = box(2)*(ry - reference) |
| 746 |
rz = box(3)*(rz - reference) |
| 747 |
|
| 748 |
|
| 749 |
xcom(1) = rx |
| 750 |
xcom(2) = ry |
| 751 |
xcom(3) = rz |
| 752 |
|
| 753 |
theta = cos(ez) |
| 754 |
phi = 0.0E0_DP |
| 755 |
psi = dtan(ex/ey) |
| 756 |
call set_pos(ntmp, xcom, theta, phi, psi) |
| 757 |
#ifdef MPI |
| 758 |
end if |
| 759 |
#endif |
| 760 |
|
| 761 |
!new stuff here |
| 762 |
|
| 763 |
|
| 764 |
|
| 765 |
|
| 766 |
elseif (print_vac) then |
| 767 |
rx = box(1)*(rx - reference) |
| 768 |
ry = box(2)*(ry - reference) |
| 769 |
rz = box(3)*(rz - reference) |
| 770 |
write(unit = vac_unit,fmt = xyz_coord) "Ar", rx, ry, rz |
| 771 |
|
| 772 |
endif |
| 773 |
|
| 774 |
else |
| 775 |
!! this will build either a liquid or a cluster |
| 776 |
!! without any vacancies |
| 777 |
if (is_shell(dist)) then |
| 778 |
ncount = ncount + 1 |
| 779 |
#ifdef MPI |
| 780 |
if(ncount.ge.nmol_start.and. & |
| 781 |
ncount.le.nmol_end) then |
| 782 |
ntmp = ncount - nmol_start +1 |
| 783 |
#else |
| 784 |
ntmp = ncount |
| 785 |
#endif |
| 786 |
rx = box(1)*(rx - reference) |
| 787 |
ry = box(2)*(ry - reference) |
| 788 |
rz = box(3)*(rz - reference) |
| 789 |
|
| 790 |
xcom(1) = rx |
| 791 |
xcom(2) = ry |
| 792 |
xcom(3) = rz |
| 793 |
|
| 794 |
theta = dacos(ez) |
| 795 |
phi = 0.0E0_DP |
| 796 |
psi = tan(ex/ey) |
| 797 |
|
| 798 |
call set_pos(ntmp, xcom, theta, phi, psi) |
| 799 |
#ifdef MPI |
| 800 |
endif |
| 801 |
#endif |
| 802 |
endif |
| 803 |
|
| 804 |
|
| 805 |
endif |
| 806 |
end do |
| 807 |
end do |
| 808 |
end do |
| 809 |
end do |
| 810 |
close(vac_unit) |
| 811 |
|
| 812 |
end subroutine build_positions |
| 813 |
|
| 814 |
|
| 815 |
function is_shell(dist) result(make_shell) |
| 816 |
real( kind = DP ), intent(in) :: dist |
| 817 |
logical :: make_shell |
| 818 |
|
| 819 |
if (sim_type == "liquid") then |
| 820 |
make_shell = .true. |
| 821 |
return |
| 822 |
elseif (dist <= r_shell) then |
| 823 |
make_shell = .true. |
| 824 |
return |
| 825 |
else |
| 826 |
make_shell = .false. |
| 827 |
endif |
| 828 |
|
| 829 |
return |
| 830 |
end function is_shell |
| 831 |
|
| 832 |
|
| 833 |
end module init_simulation |
