| 1 |
!! |
| 2 |
!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
!! |
| 4 |
!! The University of Notre Dame grants you ("Licensee") a |
| 5 |
!! non-exclusive, royalty free, license to use, modify and |
| 6 |
!! redistribute this software in source and binary code form, provided |
| 7 |
!! that the following conditions are met: |
| 8 |
!! |
| 9 |
!! 1. Redistributions of source code must retain the above copyright |
| 10 |
!! notice, this list of conditions and the following disclaimer. |
| 11 |
!! |
| 12 |
!! 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
!! notice, this list of conditions and the following disclaimer in the |
| 14 |
!! documentation and/or other materials provided with the |
| 15 |
!! distribution. |
| 16 |
!! |
| 17 |
!! This software is provided "AS IS," without a warranty of any |
| 18 |
!! kind. All express or implied conditions, representations and |
| 19 |
!! warranties, including any implied warranty of merchantability, |
| 20 |
!! fitness for a particular purpose or non-infringement, are hereby |
| 21 |
!! excluded. The University of Notre Dame and its licensors shall not |
| 22 |
!! be liable for any damages suffered by licensee as a result of |
| 23 |
!! using, modifying or distributing the software or its |
| 24 |
!! derivatives. In no event will the University of Notre Dame or its |
| 25 |
!! licensors be liable for any lost revenue, profit or data, or for |
| 26 |
!! direct, indirect, special, consequential, incidental or punitive |
| 27 |
!! damages, however caused and regardless of the theory of liability, |
| 28 |
!! arising out of the use of or inability to use software, even if the |
| 29 |
!! University of Notre Dame has been advised of the possibility of |
| 30 |
!! such damages. |
| 31 |
!! |
| 32 |
!! SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
!! research, please cite the appropriate papers when you publish your |
| 34 |
!! work. Good starting points are: |
| 35 |
!! |
| 36 |
!! [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
!! [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
!! [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
!! [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
!! |
| 41 |
|
| 42 |
!! Fortran interface to C entry plug. |
| 43 |
|
| 44 |
module simulation |
| 45 |
use definitions |
| 46 |
use status |
| 47 |
use linearAlgebra |
| 48 |
use neighborLists |
| 49 |
use force_globals |
| 50 |
use vector_class |
| 51 |
use atype_module |
| 52 |
use switcheroo |
| 53 |
#ifdef IS_MPI |
| 54 |
use mpiSimulation |
| 55 |
#endif |
| 56 |
|
| 57 |
implicit none |
| 58 |
PRIVATE |
| 59 |
|
| 60 |
#define __FORTRAN90 |
| 61 |
#include "brains/fSimulation.h" |
| 62 |
#include "UseTheForce/fSwitchingFunction.h" |
| 63 |
|
| 64 |
type (simtype), public, save :: thisSim |
| 65 |
|
| 66 |
logical, save :: simulation_setup_complete = .false. |
| 67 |
|
| 68 |
integer, public, save :: nLocal, nGlobal |
| 69 |
integer, public, save :: nGroups, nGroupGlobal |
| 70 |
integer, public, save :: nExcludes = 0 |
| 71 |
integer, public, save :: nOneTwo = 0 |
| 72 |
integer, public, save :: nOneThree = 0 |
| 73 |
integer, public, save :: nOneFour = 0 |
| 74 |
|
| 75 |
integer, allocatable, dimension(:,:), public :: excludes |
| 76 |
integer, allocatable, dimension(:), public :: molMembershipList |
| 77 |
integer, allocatable, dimension(:), public :: groupListRow |
| 78 |
integer, allocatable, dimension(:), public :: groupStartRow |
| 79 |
integer, allocatable, dimension(:), public :: groupListCol |
| 80 |
integer, allocatable, dimension(:), public :: groupStartCol |
| 81 |
integer, allocatable, dimension(:), public :: groupListLocal |
| 82 |
integer, allocatable, dimension(:), public :: groupStartLocal |
| 83 |
integer, allocatable, dimension(:), public :: nSkipsForLocalAtom |
| 84 |
integer, allocatable, dimension(:,:), public :: skipsForLocalAtom |
| 85 |
integer, allocatable, dimension(:), public :: nSkipsForRowAtom |
| 86 |
integer, allocatable, dimension(:,:), public :: skipsForRowAtom |
| 87 |
integer, allocatable, dimension(:), public :: nTopoPairsForAtom |
| 88 |
integer, allocatable, dimension(:,:), public :: toposForAtom |
| 89 |
integer, allocatable, dimension(:,:), public :: topoDistance |
| 90 |
real(kind=dp), allocatable, dimension(:), public :: mfactRow |
| 91 |
real(kind=dp), allocatable, dimension(:), public :: mfactCol |
| 92 |
real(kind=dp), allocatable, dimension(:), public :: mfactLocal |
| 93 |
|
| 94 |
real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
| 95 |
real(kind=dp), save :: DangerRcut |
| 96 |
logical, public, save :: boxIsOrthorhombic |
| 97 |
|
| 98 |
public :: SimulationSetup |
| 99 |
public :: getNlocal |
| 100 |
public :: setBox |
| 101 |
public :: checkBox |
| 102 |
public :: SimUsesPBC |
| 103 |
public :: SimUsesAtomicVirial |
| 104 |
public :: SimUsesDirectionalAtoms |
| 105 |
public :: SimUsesMetallicAtoms |
| 106 |
public :: SimRequiresSkipCorrection |
| 107 |
public :: SimRequiresSelfCorrection |
| 108 |
public :: setHmatDangerousRcutValue |
| 109 |
|
| 110 |
contains |
| 111 |
|
| 112 |
subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, & |
| 113 |
CnExcludes, Cexcludes, CnOneTwo, ConeTwo, CnOneThree, ConeThree, & |
| 114 |
CnOneFour, ConeFour, CmolMembership, Cmfact, CnGroups, & |
| 115 |
CglobalGroupMembership, status) |
| 116 |
|
| 117 |
type (simtype) :: setThisSim |
| 118 |
integer, intent(inout) :: CnGlobal, CnLocal |
| 119 |
integer, dimension(CnLocal), intent(inout) :: c_idents |
| 120 |
|
| 121 |
integer :: CnExcludes |
| 122 |
integer, dimension(2,CnExcludes), intent(in) :: Cexcludes |
| 123 |
integer :: CnOneTwo |
| 124 |
integer, dimension(2,CnOneTwo), intent(in) :: ConeTwo |
| 125 |
integer :: CnOneThree |
| 126 |
integer, dimension(2,CnOneThree), intent(in) :: ConeThree |
| 127 |
integer :: CnOneFour |
| 128 |
integer, dimension(2,CnOneFour), intent(in) :: ConeFour |
| 129 |
|
| 130 |
integer, dimension(CnGlobal),intent(in) :: CmolMembership |
| 131 |
!! Result status, success = 0, status = -1 |
| 132 |
integer, intent(out) :: status |
| 133 |
integer :: i, j, me, thisStat, alloc_stat, myNode, id1, id2 |
| 134 |
integer :: ia, jend |
| 135 |
|
| 136 |
!! mass factors used for molecular cutoffs |
| 137 |
real ( kind = dp ), dimension(CnLocal) :: Cmfact |
| 138 |
integer, intent(in):: CnGroups |
| 139 |
integer, dimension(CnGlobal), intent(in):: CglobalGroupMembership |
| 140 |
integer :: maxSkipsForLocalAtom, maxToposForAtom, glPointer |
| 141 |
integer :: maxSkipsForRowAtom |
| 142 |
|
| 143 |
#ifdef IS_MPI |
| 144 |
integer, allocatable, dimension(:) :: c_idents_Row |
| 145 |
integer, allocatable, dimension(:) :: c_idents_Col |
| 146 |
integer :: nAtomsInRow, nGroupsInRow, aid |
| 147 |
integer :: nAtomsInCol, nGroupsInCol, gid |
| 148 |
#endif |
| 149 |
|
| 150 |
simulation_setup_complete = .false. |
| 151 |
status = 0 |
| 152 |
|
| 153 |
! copy C struct into fortran type |
| 154 |
|
| 155 |
nLocal = CnLocal |
| 156 |
nGlobal = CnGlobal |
| 157 |
nGroups = CnGroups |
| 158 |
|
| 159 |
thisSim = setThisSim |
| 160 |
|
| 161 |
nExcludes = CnExcludes |
| 162 |
|
| 163 |
call InitializeForceGlobals(nLocal, thisStat) |
| 164 |
if (thisStat /= 0) then |
| 165 |
write(default_error,*) "SimSetup: InitializeForceGlobals error" |
| 166 |
status = -1 |
| 167 |
return |
| 168 |
endif |
| 169 |
|
| 170 |
call InitializeSimGlobals(thisStat) |
| 171 |
if (thisStat /= 0) then |
| 172 |
write(default_error,*) "SimSetup: InitializeSimGlobals error" |
| 173 |
status = -1 |
| 174 |
return |
| 175 |
endif |
| 176 |
|
| 177 |
#ifdef IS_MPI |
| 178 |
! We can only set up forces if mpiSimulation has been setup. |
| 179 |
if (.not. isMPISimSet()) then |
| 180 |
write(default_error,*) "MPI is not set" |
| 181 |
status = -1 |
| 182 |
return |
| 183 |
endif |
| 184 |
nAtomsInRow = getNatomsInRow(plan_atom_row) |
| 185 |
nAtomsInCol = getNatomsInCol(plan_atom_col) |
| 186 |
nGroupsInRow = getNgroupsInRow(plan_group_row) |
| 187 |
nGroupsInCol = getNgroupsInCol(plan_group_col) |
| 188 |
mynode = getMyNode() |
| 189 |
|
| 190 |
call gather(c_idents, c_idents_Row, plan_atom_row) |
| 191 |
call gather(c_idents, c_idents_Col, plan_atom_col) |
| 192 |
|
| 193 |
do i = 1, nAtomsInRow |
| 194 |
me = getFirstMatchingElement(atypes, "c_ident", c_idents_Row(i)) |
| 195 |
atid_Row(i) = me |
| 196 |
enddo |
| 197 |
|
| 198 |
do i = 1, nAtomsInCol |
| 199 |
me = getFirstMatchingElement(atypes, "c_ident", c_idents_Col(i)) |
| 200 |
atid_Col(i) = me |
| 201 |
enddo |
| 202 |
|
| 203 |
#endif |
| 204 |
|
| 205 |
#ifdef IS_MPI |
| 206 |
allocate(groupStartRow(nGroupsInRow+1),stat=alloc_stat) |
| 207 |
if (alloc_stat /= 0 ) then |
| 208 |
status = -1 |
| 209 |
return |
| 210 |
endif |
| 211 |
allocate(groupStartCol(nGroupsInCol+1),stat=alloc_stat) |
| 212 |
if (alloc_stat /= 0 ) then |
| 213 |
status = -1 |
| 214 |
return |
| 215 |
endif |
| 216 |
allocate(groupListRow(nAtomsInRow),stat=alloc_stat) |
| 217 |
if (alloc_stat /= 0 ) then |
| 218 |
status = -1 |
| 219 |
return |
| 220 |
endif |
| 221 |
allocate(groupListCol(nAtomsInCol),stat=alloc_stat) |
| 222 |
if (alloc_stat /= 0 ) then |
| 223 |
status = -1 |
| 224 |
return |
| 225 |
endif |
| 226 |
allocate(mfactRow(nAtomsInRow),stat=alloc_stat) |
| 227 |
if (alloc_stat /= 0 ) then |
| 228 |
status = -1 |
| 229 |
return |
| 230 |
endif |
| 231 |
allocate(mfactCol(nAtomsInCol),stat=alloc_stat) |
| 232 |
if (alloc_stat /= 0 ) then |
| 233 |
status = -1 |
| 234 |
return |
| 235 |
endif |
| 236 |
allocate(mfactLocal(nLocal),stat=alloc_stat) |
| 237 |
if (alloc_stat /= 0 ) then |
| 238 |
status = -1 |
| 239 |
return |
| 240 |
endif |
| 241 |
|
| 242 |
glPointer = 1 |
| 243 |
|
| 244 |
do i = 1, nGroupsInRow |
| 245 |
|
| 246 |
gid = GroupRowToGlobal(i) |
| 247 |
groupStartRow(i) = glPointer |
| 248 |
|
| 249 |
do j = 1, nAtomsInRow |
| 250 |
aid = AtomRowToGlobal(j) |
| 251 |
if (CglobalGroupMembership(aid) .eq. gid) then |
| 252 |
groupListRow(glPointer) = j |
| 253 |
glPointer = glPointer + 1 |
| 254 |
endif |
| 255 |
enddo |
| 256 |
enddo |
| 257 |
groupStartRow(nGroupsInRow+1) = nAtomsInRow + 1 |
| 258 |
|
| 259 |
glPointer = 1 |
| 260 |
|
| 261 |
do i = 1, nGroupsInCol |
| 262 |
|
| 263 |
gid = GroupColToGlobal(i) |
| 264 |
groupStartCol(i) = glPointer |
| 265 |
|
| 266 |
do j = 1, nAtomsInCol |
| 267 |
aid = AtomColToGlobal(j) |
| 268 |
if (CglobalGroupMembership(aid) .eq. gid) then |
| 269 |
groupListCol(glPointer) = j |
| 270 |
glPointer = glPointer + 1 |
| 271 |
endif |
| 272 |
enddo |
| 273 |
enddo |
| 274 |
groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1 |
| 275 |
|
| 276 |
mfactLocal = Cmfact |
| 277 |
|
| 278 |
call gather(mfactLocal, mfactRow, plan_atom_row) |
| 279 |
call gather(mfactLocal, mfactCol, plan_atom_col) |
| 280 |
|
| 281 |
if (allocated(mfactLocal)) then |
| 282 |
deallocate(mfactLocal) |
| 283 |
end if |
| 284 |
#else |
| 285 |
allocate(groupStartRow(nGroups+1),stat=alloc_stat) |
| 286 |
if (alloc_stat /= 0 ) then |
| 287 |
status = -1 |
| 288 |
return |
| 289 |
endif |
| 290 |
allocate(groupStartCol(nGroups+1),stat=alloc_stat) |
| 291 |
if (alloc_stat /= 0 ) then |
| 292 |
status = -1 |
| 293 |
return |
| 294 |
endif |
| 295 |
allocate(groupListRow(nLocal),stat=alloc_stat) |
| 296 |
if (alloc_stat /= 0 ) then |
| 297 |
status = -1 |
| 298 |
return |
| 299 |
endif |
| 300 |
allocate(groupListCol(nLocal),stat=alloc_stat) |
| 301 |
if (alloc_stat /= 0 ) then |
| 302 |
status = -1 |
| 303 |
return |
| 304 |
endif |
| 305 |
allocate(mfactRow(nLocal),stat=alloc_stat) |
| 306 |
if (alloc_stat /= 0 ) then |
| 307 |
status = -1 |
| 308 |
return |
| 309 |
endif |
| 310 |
allocate(mfactCol(nLocal),stat=alloc_stat) |
| 311 |
if (alloc_stat /= 0 ) then |
| 312 |
status = -1 |
| 313 |
return |
| 314 |
endif |
| 315 |
allocate(mfactLocal(nLocal),stat=alloc_stat) |
| 316 |
if (alloc_stat /= 0 ) then |
| 317 |
status = -1 |
| 318 |
return |
| 319 |
endif |
| 320 |
|
| 321 |
glPointer = 1 |
| 322 |
do i = 1, nGroups |
| 323 |
groupStartRow(i) = glPointer |
| 324 |
groupStartCol(i) = glPointer |
| 325 |
do j = 1, nLocal |
| 326 |
if (CglobalGroupMembership(j) .eq. i) then |
| 327 |
groupListRow(glPointer) = j |
| 328 |
groupListCol(glPointer) = j |
| 329 |
glPointer = glPointer + 1 |
| 330 |
endif |
| 331 |
enddo |
| 332 |
enddo |
| 333 |
groupStartRow(nGroups+1) = nLocal + 1 |
| 334 |
groupStartCol(nGroups+1) = nLocal + 1 |
| 335 |
|
| 336 |
do i = 1, nLocal |
| 337 |
mfactRow(i) = Cmfact(i) |
| 338 |
mfactCol(i) = Cmfact(i) |
| 339 |
end do |
| 340 |
|
| 341 |
#endif |
| 342 |
|
| 343 |
! We build the local atid's for both mpi and nonmpi |
| 344 |
do i = 1, nLocal |
| 345 |
me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
| 346 |
atid(i) = me |
| 347 |
c_idents_local(i) = c_idents(i) |
| 348 |
enddo |
| 349 |
|
| 350 |
do i = 1, nExcludes |
| 351 |
excludes(1,i) = Cexcludes(1,i) |
| 352 |
excludes(2,i) = Cexcludes(2,i) |
| 353 |
enddo |
| 354 |
|
| 355 |
#ifdef IS_MPI |
| 356 |
allocate(nSkipsForRowAtom(nAtomsInRow), stat=alloc_stat) |
| 357 |
#endif |
| 358 |
|
| 359 |
allocate(nSkipsForLocalAtom(nLocal), stat=alloc_stat) |
| 360 |
|
| 361 |
if (alloc_stat /= 0 ) then |
| 362 |
thisStat = -1 |
| 363 |
write(*,*) 'Could not allocate nSkipsForAtom array' |
| 364 |
return |
| 365 |
endif |
| 366 |
|
| 367 |
#ifdef IS_MPI |
| 368 |
maxSkipsForRowAtom = 0 |
| 369 |
do j = 1, nAtomsInRow |
| 370 |
nSkipsForRowAtom(j) = 0 |
| 371 |
id1 = AtomRowToGlobal(j) |
| 372 |
do i = 1, nExcludes |
| 373 |
if (excludes(1,i) .eq. id1 ) then |
| 374 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 375 |
if (nSkipsForRowAtom(j) .gt. maxSkipsForRowAtom) then |
| 376 |
maxSkipsForRowAtom = nSkipsForRowAtom(j) |
| 377 |
endif |
| 378 |
endif |
| 379 |
if (excludes(2,i) .eq. id1 ) then |
| 380 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 381 |
if (nSkipsForRowAtom(j) .gt. maxSkipsForRowAtom) then |
| 382 |
maxSkipsForRowAtom = nSkipsForRowAtom(j) |
| 383 |
endif |
| 384 |
endif |
| 385 |
end do |
| 386 |
enddo |
| 387 |
#endif |
| 388 |
maxSkipsForLocalAtom = 0 |
| 389 |
do j = 1, nLocal |
| 390 |
nSkipsForLocalAtom(j) = 0 |
| 391 |
#ifdef IS_MPI |
| 392 |
id1 = AtomLocalToGlobal(j) |
| 393 |
#else |
| 394 |
id1 = j |
| 395 |
#endif |
| 396 |
do i = 1, nExcludes |
| 397 |
if (excludes(1,i) .eq. id1 ) then |
| 398 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 399 |
if (nSkipsForLocalAtom(j) .gt. maxSkipsForLocalAtom) then |
| 400 |
maxSkipsForLocalAtom = nSkipsForLocalAtom(j) |
| 401 |
endif |
| 402 |
endif |
| 403 |
if (excludes(2,i) .eq. id1 ) then |
| 404 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 405 |
if (nSkipsForLocalAtom(j) .gt. maxSkipsForLocalAtom) then |
| 406 |
maxSkipsForLocalAtom = nSkipsForLocalAtom(j) |
| 407 |
endif |
| 408 |
endif |
| 409 |
end do |
| 410 |
enddo |
| 411 |
|
| 412 |
#ifdef IS_MPI |
| 413 |
allocate(skipsForRowAtom(nAtomsInRow, maxSkipsForRowAtom), stat=alloc_stat) |
| 414 |
#endif |
| 415 |
allocate(skipsForLocalAtom(nLocal, maxSkipsForLocalAtom), stat=alloc_stat) |
| 416 |
|
| 417 |
if (alloc_stat /= 0 ) then |
| 418 |
write(*,*) 'Could not allocate skipsForAtom arrays' |
| 419 |
return |
| 420 |
endif |
| 421 |
|
| 422 |
#ifdef IS_MPI |
| 423 |
do j = 1, nAtomsInRow |
| 424 |
nSkipsForRowAtom(j) = 0 |
| 425 |
id1 = AtomRowToGlobal(j) |
| 426 |
do i = 1, nExcludes |
| 427 |
if (excludes(1,i) .eq. id1 ) then |
| 428 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 429 |
! exclude lists have global ID's |
| 430 |
id2 = excludes(2,i) |
| 431 |
skipsForRowAtom(j, nSkipsForRowAtom(j)) = id2 |
| 432 |
endif |
| 433 |
if (excludes(2, i) .eq. id1 ) then |
| 434 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 435 |
! exclude lists have global ID's |
| 436 |
id2 = excludes(1,i) |
| 437 |
skipsForRowAtom(j, nSkipsForRowAtom(j)) = id2 |
| 438 |
endif |
| 439 |
end do |
| 440 |
enddo |
| 441 |
#endif |
| 442 |
do j = 1, nLocal |
| 443 |
nSkipsForLocalAtom(j) = 0 |
| 444 |
#ifdef IS_MPI |
| 445 |
id1 = AtomLocalToGlobal(j) |
| 446 |
#else |
| 447 |
id1 = j |
| 448 |
#endif |
| 449 |
do i = 1, nExcludes |
| 450 |
if (excludes(1,i) .eq. id1 ) then |
| 451 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 452 |
! exclude lists have global ID's |
| 453 |
#ifdef IS_MPI |
| 454 |
id2 = AtomGlobalToLocal(excludes(2,i)) |
| 455 |
#else |
| 456 |
id2 = excludes(2,i) |
| 457 |
#endif |
| 458 |
skipsForLocalAtom(j, nSkipsForLocalAtom(j)) = id2 |
| 459 |
endif |
| 460 |
if (excludes(2, i) .eq. id1 ) then |
| 461 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 462 |
! exclude lists have global ID's |
| 463 |
#ifdef IS_MPI |
| 464 |
id2 = AtomGlobalToLocal(excludes(1,i)) |
| 465 |
#else |
| 466 |
id2 = excludes(1,i) |
| 467 |
#endif |
| 468 |
skipsForLocalAtom(j, nSkipsForLocalAtom(j)) = id2 |
| 469 |
endif |
| 470 |
end do |
| 471 |
enddo |
| 472 |
|
| 473 |
do i = 1, nGlobal |
| 474 |
molMemberShipList(i) = CmolMembership(i) |
| 475 |
enddo |
| 476 |
|
| 477 |
#ifdef IS_MPI |
| 478 |
allocate(nTopoPairsForAtom(nAtomsInRow), stat=alloc_stat) |
| 479 |
#else |
| 480 |
allocate(nTopoPairsForAtom(nLocal), stat=alloc_stat) |
| 481 |
#endif |
| 482 |
if (alloc_stat /= 0 ) then |
| 483 |
thisStat = -1 |
| 484 |
write(*,*) 'Could not allocate nTopoPairsForAtom array' |
| 485 |
return |
| 486 |
endif |
| 487 |
|
| 488 |
#ifdef IS_MPI |
| 489 |
jend = nAtomsInRow |
| 490 |
#else |
| 491 |
jend = nLocal |
| 492 |
#endif |
| 493 |
|
| 494 |
do j = 1, jend |
| 495 |
nTopoPairsForAtom(j) = 0 |
| 496 |
#ifdef IS_MPI |
| 497 |
id1 = AtomRowToGlobal(j) |
| 498 |
#else |
| 499 |
id1 = j |
| 500 |
#endif |
| 501 |
do i = 1, CnOneTwo |
| 502 |
if (ConeTwo(1,i) .eq. id1 ) then |
| 503 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 504 |
endif |
| 505 |
if (ConeTwo(2,i) .eq. id1 ) then |
| 506 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 507 |
endif |
| 508 |
end do |
| 509 |
|
| 510 |
do i = 1, CnOneThree |
| 511 |
if (ConeThree(1,i) .eq. id1 ) then |
| 512 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 513 |
endif |
| 514 |
if (ConeThree(2,i) .eq. id1 ) then |
| 515 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 516 |
endif |
| 517 |
end do |
| 518 |
|
| 519 |
do i = 1, CnOneFour |
| 520 |
if (ConeFour(1,i) .eq. id1 ) then |
| 521 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 522 |
endif |
| 523 |
if (ConeFour(2,i) .eq. id1 ) then |
| 524 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 525 |
endif |
| 526 |
end do |
| 527 |
enddo |
| 528 |
|
| 529 |
maxToposForAtom = maxval(nTopoPairsForAtom) |
| 530 |
#ifdef IS_MPI |
| 531 |
allocate(toposForAtom(nAtomsInRow, maxToposForAtom), stat=alloc_stat) |
| 532 |
allocate(topoDistance(nAtomsInRow, maxToposForAtom), stat=alloc_stat) |
| 533 |
#else |
| 534 |
allocate(toposForAtom(nLocal, maxToposForAtom), stat=alloc_stat) |
| 535 |
allocate(topoDistance(nLocal, maxToposForAtom), stat=alloc_stat) |
| 536 |
#endif |
| 537 |
if (alloc_stat /= 0 ) then |
| 538 |
write(*,*) 'Could not allocate topoDistance array' |
| 539 |
return |
| 540 |
endif |
| 541 |
|
| 542 |
#ifdef IS_MPI |
| 543 |
jend = nAtomsInRow |
| 544 |
#else |
| 545 |
jend = nLocal |
| 546 |
#endif |
| 547 |
do j = 1, jend |
| 548 |
nTopoPairsForAtom(j) = 0 |
| 549 |
#ifdef IS_MPI |
| 550 |
id1 = AtomRowToGlobal(j) |
| 551 |
#else |
| 552 |
id1 = j |
| 553 |
#endif |
| 554 |
do i = 1, CnOneTwo |
| 555 |
if (ConeTwo(1,i) .eq. id1 ) then |
| 556 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 557 |
id2 = ConeTwo(2,i) |
| 558 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 559 |
topoDistance(j, nTopoPairsForAtom(j)) = 1 |
| 560 |
endif |
| 561 |
if (ConeTwo(2, i) .eq. id1 ) then |
| 562 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 563 |
id2 = ConeTwo(1,i) |
| 564 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 565 |
topoDistance(j, nTopoPairsForAtom(j)) = 1 |
| 566 |
endif |
| 567 |
end do |
| 568 |
|
| 569 |
do i = 1, CnOneThree |
| 570 |
if (ConeThree(1,i) .eq. id1 ) then |
| 571 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 572 |
id2 = ConeThree(2,i) |
| 573 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 574 |
topoDistance(j, nTopoPairsForAtom(j)) = 2 |
| 575 |
endif |
| 576 |
if (ConeThree(2, i) .eq. id1 ) then |
| 577 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 578 |
id2 = ConeThree(1,i) |
| 579 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 580 |
topoDistance(j, nTopoPairsForAtom(j)) = 2 |
| 581 |
endif |
| 582 |
end do |
| 583 |
|
| 584 |
do i = 1, CnOneFour |
| 585 |
if (ConeFour(1,i) .eq. id1 ) then |
| 586 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 587 |
id2 = ConeFour(2,i) |
| 588 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 589 |
topoDistance(j, nTopoPairsForAtom(j)) = 3 |
| 590 |
endif |
| 591 |
if (ConeFour(2, i) .eq. id1 ) then |
| 592 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 593 |
id2 = ConeFour(1,i) |
| 594 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 595 |
topoDistance(j, nTopoPairsForAtom(j)) = 3 |
| 596 |
endif |
| 597 |
end do |
| 598 |
enddo |
| 599 |
|
| 600 |
if (status == 0) simulation_setup_complete = .true. |
| 601 |
|
| 602 |
end subroutine SimulationSetup |
| 603 |
|
| 604 |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
| 605 |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
| 606 |
integer :: cBoxIsOrthorhombic |
| 607 |
integer :: smallest, status |
| 608 |
|
| 609 |
Hmat = cHmat |
| 610 |
HmatInv = cHmatInv |
| 611 |
if (cBoxIsOrthorhombic .eq. 0 ) then |
| 612 |
boxIsOrthorhombic = .false. |
| 613 |
else |
| 614 |
boxIsOrthorhombic = .true. |
| 615 |
endif |
| 616 |
|
| 617 |
call checkBox() |
| 618 |
return |
| 619 |
end subroutine setBox |
| 620 |
|
| 621 |
subroutine checkBox() |
| 622 |
|
| 623 |
integer :: i |
| 624 |
real(kind=dp), dimension(3) :: hx, hy, hz, ax, ay, az, piped |
| 625 |
character(len = statusMsgSize) :: errMsg |
| 626 |
|
| 627 |
hx = Hmat(1,:) |
| 628 |
hy = Hmat(2,:) |
| 629 |
hz = Hmat(3,:) |
| 630 |
|
| 631 |
ax = cross_product(hy, hz) |
| 632 |
ay = cross_product(hx, hz) |
| 633 |
az = cross_product(hx, hy) |
| 634 |
|
| 635 |
ax = ax / length(ax) |
| 636 |
ay = ay / length(ay) |
| 637 |
az = az / length(az) |
| 638 |
|
| 639 |
piped(1) = abs(dot_product(ax, hx)) |
| 640 |
piped(2) = abs(dot_product(ay, hy)) |
| 641 |
piped(3) = abs(dot_product(az, hz)) |
| 642 |
|
| 643 |
do i = 1, 3 |
| 644 |
if ((0.5_dp * piped(i)).lt.DangerRcut) then |
| 645 |
write(errMsg, '(a94,f9.4,a1)') 'One of the dimensions of the Periodic ' & |
| 646 |
// 'Box is smaller than ' // newline // tab // & |
| 647 |
'the largest cutoff radius' // & |
| 648 |
' (rCut = ', DangerRcut, ')' |
| 649 |
call handleError("checkBox", errMsg) |
| 650 |
|
| 651 |
end if |
| 652 |
enddo |
| 653 |
return |
| 654 |
end subroutine checkBox |
| 655 |
|
| 656 |
function SimUsesPBC() result(doesit) |
| 657 |
logical :: doesit |
| 658 |
doesit = thisSim%SIM_uses_PBC |
| 659 |
end function SimUsesPBC |
| 660 |
|
| 661 |
function SimUsesAtomicVirial() result(doesit) |
| 662 |
logical :: doesit |
| 663 |
doesit = thisSim%SIM_uses_AtomicVirial |
| 664 |
end function SimUsesAtomicVirial |
| 665 |
|
| 666 |
function SimUsesDirectionalAtoms() result(doesit) |
| 667 |
logical :: doesit |
| 668 |
doesit = thisSim%SIM_uses_DirectionalAtoms |
| 669 |
end function SimUsesDirectionalAtoms |
| 670 |
|
| 671 |
function SimUsesMetallicAtoms() result(doesit) |
| 672 |
logical :: doesit |
| 673 |
doesit = thisSim%SIM_uses_MetallicAtoms |
| 674 |
end function SimUsesMetallicAtoms |
| 675 |
|
| 676 |
function SimRequiresSkipCorrection() result(doesit) |
| 677 |
logical :: doesit |
| 678 |
doesit = thisSim%SIM_requires_SkipCorrection |
| 679 |
end function SimRequiresSkipCorrection |
| 680 |
|
| 681 |
function SimRequiresSelfCorrection() result(doesit) |
| 682 |
logical :: doesit |
| 683 |
doesit = thisSim%SIM_requires_SelfCorrection |
| 684 |
end function SimRequiresSelfCorrection |
| 685 |
|
| 686 |
subroutine InitializeSimGlobals(thisStat) |
| 687 |
integer, intent(out) :: thisStat |
| 688 |
integer :: alloc_stat |
| 689 |
|
| 690 |
thisStat = 0 |
| 691 |
|
| 692 |
call FreeSimGlobals() |
| 693 |
|
| 694 |
allocate(excludes(2,nExcludes), stat=alloc_stat) |
| 695 |
if (alloc_stat /= 0 ) then |
| 696 |
thisStat = -1 |
| 697 |
return |
| 698 |
endif |
| 699 |
|
| 700 |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
| 701 |
if (alloc_stat /= 0 ) then |
| 702 |
thisStat = -1 |
| 703 |
return |
| 704 |
endif |
| 705 |
|
| 706 |
end subroutine InitializeSimGlobals |
| 707 |
|
| 708 |
subroutine FreeSimGlobals() |
| 709 |
|
| 710 |
!We free in the opposite order in which we allocate in. |
| 711 |
if (allocated(topoDistance)) deallocate(topoDistance) |
| 712 |
if (allocated(toposForAtom)) deallocate(toposForAtom) |
| 713 |
if (allocated(nTopoPairsForAtom)) deallocate(nTopoPairsForAtom) |
| 714 |
if (allocated(skipsForLocalAtom)) deallocate(skipsForLocalAtom) |
| 715 |
if (allocated(nSkipsForLocalAtom)) deallocate(nSkipsForLocalAtom) |
| 716 |
if (allocated(skipsForRowAtom)) deallocate(skipsForRowAtom) |
| 717 |
if (allocated(nSkipsForRowAtom)) deallocate(nSkipsForRowAtom) |
| 718 |
if (allocated(mfactLocal)) deallocate(mfactLocal) |
| 719 |
if (allocated(mfactCol)) deallocate(mfactCol) |
| 720 |
if (allocated(mfactRow)) deallocate(mfactRow) |
| 721 |
if (allocated(groupListCol)) deallocate(groupListCol) |
| 722 |
if (allocated(groupListRow)) deallocate(groupListRow) |
| 723 |
if (allocated(groupStartCol)) deallocate(groupStartCol) |
| 724 |
if (allocated(groupStartRow)) deallocate(groupStartRow) |
| 725 |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
| 726 |
if (allocated(excludes)) deallocate(excludes) |
| 727 |
|
| 728 |
end subroutine FreeSimGlobals |
| 729 |
|
| 730 |
pure function getNlocal() result(n) |
| 731 |
integer :: n |
| 732 |
n = nLocal |
| 733 |
end function getNlocal |
| 734 |
|
| 735 |
subroutine setHmatDangerousRcutValue(dangerWillRobinson) |
| 736 |
real(kind=dp), intent(in) :: dangerWillRobinson |
| 737 |
DangerRcut = dangerWillRobinson |
| 738 |
|
| 739 |
call checkBox() |
| 740 |
|
| 741 |
return |
| 742 |
end subroutine setHmatDangerousRcutValue |
| 743 |
|
| 744 |
end module simulation |
| 745 |
|
