| 1 |
module lj_module |
| 2 |
use definitions, ONLY : DP,ndim |
| 3 |
use parameter |
| 4 |
use simulation |
| 5 |
use second_deriv |
| 6 |
use status, ONLY: error,info,warning |
| 7 |
use force_utilities |
| 8 |
#ifdef MPI |
| 9 |
use mpi_module |
| 10 |
#endif |
| 11 |
|
| 12 |
integer, parameter :: n_ljatypes = 12 |
| 13 |
real( kind = DP ),allocatable, dimension(:) :: lj_eps |
| 14 |
real( kind = DP ),allocatable, dimension(:) :: lj_sigma |
| 15 |
integer, allocatable, dimension(:) :: ljatype ! to be fixed in a module |
| 16 |
|
| 17 |
|
| 18 |
|
| 19 |
|
| 20 |
public :: lj_eps,lj_sigma |
| 21 |
public :: calc_lj_forces,initialize_lj |
| 22 |
private :: mass_weight |
| 23 |
|
| 24 |
contains |
| 25 |
|
| 26 |
subroutine allocate_lj_module(n_size_atype) |
| 27 |
integer, intent(in) :: n_size_atype |
| 28 |
|
| 29 |
allocate(ljatype(n_size_atype)) |
| 30 |
allocate(lj_eps(n_size_atype)) |
| 31 |
allocate(lj_sigma(n_size_atype)) |
| 32 |
end subroutine allocate_lj_module |
| 33 |
|
| 34 |
subroutine deallocate_lj_module() |
| 35 |
deallocate(lj_eps) |
| 36 |
deallocate(lj_sigma) |
| 37 |
deallocate(ljatype) |
| 38 |
end subroutine deallocate_lj_module |
| 39 |
|
| 40 |
subroutine calc_lj_forces(update_nlist, nmflag,pe) |
| 41 |
|
| 42 |
! include 'headers/sizes.h' |
| 43 |
! include 'headers/fileio.h' |
| 44 |
|
| 45 |
|
| 46 |
#ifdef MPI |
| 47 |
real( kind = DP ), dimension(3,ncol) :: efr |
| 48 |
real( kind = DP ) :: pot_local |
| 49 |
#else |
| 50 |
real( kind = DP ), dimension(3,natoms) :: efr |
| 51 |
#endif |
| 52 |
|
| 53 |
real( kind = DP ), intent(out), optional :: pe |
| 54 |
logical, intent(in) :: nmflag |
| 55 |
logical, intent(in) :: update_nlist |
| 56 |
logical :: do_pot |
| 57 |
|
| 58 |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
| 59 |
integer :: nlist |
| 60 |
integer :: j_start |
| 61 |
integer :: tag_i,tag_j |
| 62 |
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
| 63 |
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
| 64 |
|
| 65 |
|
| 66 |
|
| 67 |
|
| 68 |
#ifndef MPI |
| 69 |
integer :: nrow |
| 70 |
integer :: ncol |
| 71 |
|
| 72 |
nrow = natoms - 1 |
| 73 |
ncol = natoms |
| 74 |
#else |
| 75 |
j_start = 1 |
| 76 |
#endif |
| 77 |
|
| 78 |
|
| 79 |
do_pot = .false. |
| 80 |
if (present(pe)) do_pot = .true. |
| 81 |
|
| 82 |
#ifndef MPI |
| 83 |
if (do_pot) pot = 0.0E0_DP |
| 84 |
f = 0.0E0_DP |
| 85 |
e = 0.0E0_DP |
| 86 |
#else |
| 87 |
f_row = 0.0E0_DP |
| 88 |
f_col = 0.0E0_DP |
| 89 |
|
| 90 |
pot_local = 0.0E0_DP |
| 91 |
|
| 92 |
e_row = 0.0E0_DP |
| 93 |
e_col = 0.0E0_DP |
| 94 |
e_tmp = 0.0E0_DP |
| 95 |
#endif |
| 96 |
efr = 0.0E0_DP |
| 97 |
|
| 98 |
! communicate MPI positions |
| 99 |
#ifdef MPI |
| 100 |
call gather(q,q_row,plan_row3) |
| 101 |
call gather(q,q_col,plan_col3) |
| 102 |
#endif |
| 103 |
|
| 104 |
if (update_nlist) then |
| 105 |
|
| 106 |
! save current configuration, contruct neighbor list, |
| 107 |
! and calculate forces |
| 108 |
call save_nlist() |
| 109 |
|
| 110 |
nlist = 0 |
| 111 |
|
| 112 |
do i = 1, nrow |
| 113 |
point(i) = nlist + 1 |
| 114 |
#ifdef MPI |
| 115 |
tag_i = tag_row(i) |
| 116 |
rxi = q_row(1,i) |
| 117 |
ryi = q_row(2,i) |
| 118 |
rzi = q_row(3,i) |
| 119 |
#else |
| 120 |
j_start = i + 1 |
| 121 |
rxi = q(1,i) |
| 122 |
ryi = q(2,i) |
| 123 |
rzi = q(3,i) |
| 124 |
#endif |
| 125 |
|
| 126 |
inner: do j = j_start, ncol |
| 127 |
#ifdef MPI |
| 128 |
tag_j = tag_col(j) |
| 129 |
if (newtons_thrd) then |
| 130 |
if (tag_i <= tag_j) then |
| 131 |
if (mod(tag_i + tag_j,2) == 0) cycle inner |
| 132 |
else |
| 133 |
if (mod(tag_i + tag_j,2) == 1) cycle inner |
| 134 |
endif |
| 135 |
endif |
| 136 |
|
| 137 |
rxij = wrap(rxi - q_col(1,j), 1) |
| 138 |
ryij = wrap(ryi - q_col(2,j), 2) |
| 139 |
rzij = wrap(rzi - q_col(3,j), 3) |
| 140 |
#else |
| 141 |
rxij = wrap(rxi - q(1,j), 1) |
| 142 |
ryij = wrap(ryi - q(2,j), 2) |
| 143 |
rzij = wrap(rzi - q(3,j), 3) |
| 144 |
#endif |
| 145 |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 146 |
|
| 147 |
#ifdef MPI |
| 148 |
if (rijsq <= rlstsq .AND. & |
| 149 |
tag_j /= tag_i) then |
| 150 |
#else |
| 151 |
if (rijsq < rlstsq) then |
| 152 |
#endif |
| 153 |
|
| 154 |
nlist = nlist + 1 |
| 155 |
list(nlist) = j |
| 156 |
|
| 157 |
|
| 158 |
if (rijsq < rcutsq) then |
| 159 |
|
| 160 |
r = dsqrt(rijsq) |
| 161 |
|
| 162 |
call LJ_mix(r,pot,dudr,d2,i,j) |
| 163 |
#ifdef MPI |
| 164 |
e_row(i) = e_row(i) + pot*0.5 |
| 165 |
e_col(i) = e_col(i) + pot*0.5 |
| 166 |
#else |
| 167 |
if (do_pot) pe = pe + pot |
| 168 |
#endif |
| 169 |
efr(1,j) = -rxij |
| 170 |
efr(2,j) = -ryij |
| 171 |
efr(3,j) = -rzij |
| 172 |
|
| 173 |
do dim = 1, 3 |
| 174 |
|
| 175 |
drdx1 = efr(j,dim) / r |
| 176 |
ftmp = dudr * drdx1 |
| 177 |
|
| 178 |
#ifdef MPI |
| 179 |
f_col(dim,j) = f_col(dim,j) - ftmp |
| 180 |
f_row(dim,i) = f_row(dim,i) + ftmp |
| 181 |
#else |
| 182 |
f(dim,j) = f(dim,j) - ftmp |
| 183 |
f(dim,i) = f(dim,i) + ftmp |
| 184 |
#endif |
| 185 |
if (nmflag) then |
| 186 |
idim = 3 * (i-1) + dim |
| 187 |
jdim = 3 * (j-1) + dim |
| 188 |
|
| 189 |
do dim2 = 1, 3 |
| 190 |
|
| 191 |
kt1 = d2 * efr(dim,j) * efr(dim2,j)/r/r |
| 192 |
kt2 = - dudr * efr(dim,j) * efr(dim2,j)/r/r/r |
| 193 |
|
| 194 |
if (dim.eq.dim2) then |
| 195 |
kt3 = dudr / r |
| 196 |
else |
| 197 |
kt3 = 0.0E0_DP |
| 198 |
endif |
| 199 |
|
| 200 |
! The factor of 2 below is to compensate for |
| 201 |
! overcounting. |
| 202 |
! Mass weighting is done separately... |
| 203 |
|
| 204 |
ktmp = (kt1+kt2+kt3)/2.0E0_DP |
| 205 |
idim2 = 3 * (i-1) + dim2 |
| 206 |
jdim2 = 3 * (j-1) + dim2 |
| 207 |
|
| 208 |
d(idim, idim2) = d(idim,idim2) + ktmp |
| 209 |
d(idim2, idim) = d(idim2,idim) + ktmp |
| 210 |
|
| 211 |
d(idim, jdim2) = d(idim,jdim2) - ktmp |
| 212 |
d(idim2, jdim) = d(idim2,jdim) - ktmp |
| 213 |
|
| 214 |
d(jdim, idim2) = d(jdim,idim2) - ktmp |
| 215 |
d(jdim2, idim) = d(jdim2,idim) - ktmp |
| 216 |
|
| 217 |
d(jdim, jdim2) = d(jdim,jdim2) + ktmp |
| 218 |
d(jdim2, jdim) = d(jdim2,jdim) + ktmp |
| 219 |
|
| 220 |
enddo |
| 221 |
endif |
| 222 |
enddo |
| 223 |
endif |
| 224 |
endif |
| 225 |
enddo inner |
| 226 |
enddo |
| 227 |
#ifdef MPI |
| 228 |
point(nrow + 1) = nlist + 1 |
| 229 |
#else |
| 230 |
point(natoms) = nlist + 1 |
| 231 |
#endif |
| 232 |
|
| 233 |
else |
| 234 |
! use the list to find the neighbors |
| 235 |
do i = 1, nrow |
| 236 |
JBEG = POINT(i) |
| 237 |
JEND = POINT(i+1) - 1 |
| 238 |
! check thiat molecule i has neighbors |
| 239 |
if (jbeg .le. jend) then |
| 240 |
#ifdef MPI |
| 241 |
rxi = q_row(1,i) |
| 242 |
ryi = q_row(2,i) |
| 243 |
rzi = q_row(3,i) |
| 244 |
#else |
| 245 |
rxi = q(1,i) |
| 246 |
ryi = q(2,i) |
| 247 |
rzi = q(3,i) |
| 248 |
#endif |
| 249 |
do jnab = jbeg, jend |
| 250 |
j = list(jnab) |
| 251 |
#ifdef MPI |
| 252 |
rxij = wrap(rxi - q_col(1,j), 1) |
| 253 |
ryij = wrap(ryi - q_col(2,j), 2) |
| 254 |
rzij = wrap(rzi - q_col(3,j), 3) |
| 255 |
#else |
| 256 |
rxij = wrap(rxi - q(1,j), 1) |
| 257 |
ryij = wrap(ryi - q(2,j), 2) |
| 258 |
rzij = wrap(rzi - q(3,j), 3) |
| 259 |
#endif |
| 260 |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 261 |
|
| 262 |
if (rijsq < rcutsq) then |
| 263 |
|
| 264 |
r = dsqrt(rijsq) |
| 265 |
|
| 266 |
call LJ_mix(r,pot,dudr,d2,i,j) |
| 267 |
#ifdef MPI |
| 268 |
e_row(i) = e_row(i) + pot*0.5 |
| 269 |
e_col(i) = e_col(i) + pot*0.5 |
| 270 |
#else |
| 271 |
if (do_pot) pe = pe + pot |
| 272 |
#endif |
| 273 |
|
| 274 |
|
| 275 |
efr(1,j) = -rxij |
| 276 |
efr(2,j) = -ryij |
| 277 |
efr(3,j) = -rzij |
| 278 |
|
| 279 |
do dim = 1, 3 |
| 280 |
|
| 281 |
drdx1 = efr(j,dim) / r |
| 282 |
ftmp = dudr * drdx1 |
| 283 |
#ifdef MPI |
| 284 |
f_col(dim,j) = f_col(dim,j) - ftmp |
| 285 |
f_row(dim,i) = f_row(dim,i) + ftmp |
| 286 |
#else |
| 287 |
f(dim,j) = f(dim,j) - ftmp |
| 288 |
f(dim,i) = f(dim,i) + ftmp |
| 289 |
#endif |
| 290 |
if (nmflag) then |
| 291 |
idim = 3 * (i-1) + dim |
| 292 |
jdim = 3 * (j-1) + dim |
| 293 |
|
| 294 |
do dim2 = 1, 3 |
| 295 |
|
| 296 |
kt1 = d2 * efr(dim,j) * efr(dim2,j)/r/r |
| 297 |
kt2 = - dudr * efr(dim,j) * efr(dim2,j)/r/r/r |
| 298 |
|
| 299 |
if (dim.eq.dim2) then |
| 300 |
kt3 = dudr / r |
| 301 |
else |
| 302 |
kt3 = 0.0E0_DP |
| 303 |
endif |
| 304 |
|
| 305 |
! The factor of 2 below is to compensate for |
| 306 |
! overcounting. |
| 307 |
! Mass weighting is done separately... |
| 308 |
|
| 309 |
ktmp = (kt1+kt2+kt3)/2.0E0_DP |
| 310 |
idim2 = 3 * (i-1) + dim2 |
| 311 |
jdim2 = 3 * (j-1) + dim2 |
| 312 |
|
| 313 |
d(idim, idim2) = d(idim,idim2) + ktmp |
| 314 |
d(idim2, idim) = d(idim2,idim) + ktmp |
| 315 |
|
| 316 |
d(idim, jdim2) = d(idim,jdim2) - ktmp |
| 317 |
d(idim2, jdim) = d(idim2,jdim) - ktmp |
| 318 |
|
| 319 |
d(jdim, idim2) = d(jdim,idim2) - ktmp |
| 320 |
d(jdim2, idim) = d(jdim2,idim) - ktmp |
| 321 |
|
| 322 |
d(jdim, jdim2) = d(jdim,jdim2) + ktmp |
| 323 |
d(jdim2, jdim) = d(jdim2,jdim) + ktmp |
| 324 |
|
| 325 |
enddo |
| 326 |
endif |
| 327 |
enddo |
| 328 |
|
| 329 |
endif |
| 330 |
enddo |
| 331 |
endif |
| 332 |
enddo |
| 333 |
endif |
| 334 |
|
| 335 |
#ifdef MPI |
| 336 |
!!distribute forces |
| 337 |
call scatter(f_row,f,plan_row3) |
| 338 |
if (newtons_thrd) then |
| 339 |
call scatter(f_col,f_tmp,plan_col3) |
| 340 |
do i = 1,nlocal |
| 341 |
do dim = 1,3 |
| 342 |
f(dim,i) = f(dim,i) + f_tmp(dim,i) |
| 343 |
end do |
| 344 |
end do |
| 345 |
endif |
| 346 |
|
| 347 |
|
| 348 |
if (do_pot) then |
| 349 |
! scatter/gather pot_row into the members of my column |
| 350 |
call scatter(e_row,e_tmp,plan_row) |
| 351 |
|
| 352 |
! scatter/gather pot_local into all other procs |
| 353 |
! add resultant to get total pot |
| 354 |
do i = 1, nlocal |
| 355 |
pot_local = pot_local + e_tmp(i) |
| 356 |
enddo |
| 357 |
if (newtons_thrd) then |
| 358 |
e_tmp = 0.0E0_DP |
| 359 |
call scatter(e_col,e_tmp,plan_col) |
| 360 |
do i = 1, nlocal |
| 361 |
pot_local = pot_local + e_tmp(i) |
| 362 |
enddo |
| 363 |
endif |
| 364 |
|
| 365 |
|
| 366 |
call mpi_reduce(pot_local,pe,1,mpi_double_precision, & |
| 367 |
mpi_sum,0,mpi_comm_world,mpi_err) |
| 368 |
endif |
| 369 |
#endif |
| 370 |
|
| 371 |
|
| 372 |
|
| 373 |
if (nmflag) then |
| 374 |
call mass_weight() |
| 375 |
endif |
| 376 |
|
| 377 |
return |
| 378 |
end subroutine calc_lj_forces |
| 379 |
|
| 380 |
subroutine LJ_mix(r,pot,dudr,d2,atom1,atom2) |
| 381 |
|
| 382 |
! include 'headers/sizes.h' |
| 383 |
! include 'headers/atom.h' |
| 384 |
|
| 385 |
|
| 386 |
integer :: atom1, atom2, id1, id2 |
| 387 |
real( kind = DP ) :: r, pot, dudr, d2 |
| 388 |
real( kind = DP ) :: u1, dudr1, d21 |
| 389 |
real( kind = DP ) :: this_sigma, this_eps |
| 390 |
|
| 391 |
#ifdef MPI |
| 392 |
id1 = ident_row(atom1) |
| 393 |
id2 = ident_col(atom2) |
| 394 |
#else |
| 395 |
id1 = ident(atom1) |
| 396 |
id2 = ident(atom2) |
| 397 |
#endif |
| 398 |
if (id1.eq.id2) then |
| 399 |
this_sigma = lj_sigma(id1) |
| 400 |
this_eps = lj_eps(id1) |
| 401 |
else |
| 402 |
! use Lorentz-Berthelot mixing rules: |
| 403 |
this_sigma = 0.5E0_DP * (lj_sigma(id1) + lj_sigma(id2)) |
| 404 |
this_eps = dsqrt(lj_eps(id1)*lj_eps(id2)) |
| 405 |
endif |
| 406 |
|
| 407 |
call LJ_pot(r, this_sigma, this_eps, u1, dudr1, d21) |
| 408 |
|
| 409 |
pot = u1 |
| 410 |
dudr = dudr1 |
| 411 |
d2 = d21 |
| 412 |
|
| 413 |
return |
| 414 |
end subroutine LJ_mix |
| 415 |
|
| 416 |
subroutine LJ_pot(r, sigma, epsilon, u, dudr, d2) |
| 417 |
|
| 418 |
|
| 419 |
real( kind = DP ) :: r,sigma, epsilon, u, dudr, d2 |
| 420 |
real( kind = DP ) :: sigma2, sigma6, r2, r6, rcut2, rcut6 |
| 421 |
real( kind = DP ) :: t6, t12, tp6, tp12, delta |
| 422 |
|
| 423 |
sigma2 = sigma*sigma |
| 424 |
sigma6 = sigma2*sigma2*sigma2 |
| 425 |
|
| 426 |
r2 = r*r |
| 427 |
r6 = r2*r2*r2 |
| 428 |
|
| 429 |
|
| 430 |
rcut2 = rcut*rcut |
| 431 |
rcut6 = rcut2*rcut2*rcut2 |
| 432 |
|
| 433 |
t6 = sigma6 / r6 |
| 434 |
t12 = t6*t6 |
| 435 |
|
| 436 |
tp6 = sigma6 / rcut6 |
| 437 |
tp12 = tp6*tp6 |
| 438 |
|
| 439 |
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
| 440 |
|
| 441 |
if (r.le.rcut) then |
| 442 |
u = 4.0E0_DP * epsilon * (t12 - t6) + delta |
| 443 |
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
| 444 |
d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
| 445 |
else |
| 446 |
u = 0.0E0_DP |
| 447 |
dudr = 0.0E0_DP |
| 448 |
d2 = 0.0E0_DP |
| 449 |
endif |
| 450 |
|
| 451 |
return |
| 452 |
end subroutine LJ_pot |
| 453 |
|
| 454 |
subroutine initialize_lj() |
| 455 |
use model_module |
| 456 |
include 'headers/atom.h' |
| 457 |
|
| 458 |
integer :: n_atypes |
| 459 |
|
| 460 |
n_atypes = get_max_atype() |
| 461 |
call allocate_lj_module(n_atypes) |
| 462 |
|
| 463 |
|
| 464 |
ljatype(1) = H_atom |
| 465 |
ljatype(2) = He_atom |
| 466 |
ljatype(3) = C_atom |
| 467 |
ljatype(4) = N_atom |
| 468 |
ljatype(5) = O_atom |
| 469 |
ljatype(6) = F_atom |
| 470 |
ljatype(7) = Ne_atom |
| 471 |
ljatype(8) = S_atom |
| 472 |
ljatype(9) = Cl_atom |
| 473 |
ljatype(10) = Ar_atom |
| 474 |
ljatype(11) = Br_atom |
| 475 |
ljatype(12) = Kr_atom |
| 476 |
|
| 477 |
lj_sigma(H_atom) = 2.81E0_DP |
| 478 |
lj_sigma(He_atom) = 2.28E0_DP |
| 479 |
lj_sigma(C_atom) = 3.35E0_DP |
| 480 |
lj_sigma(N_atom) = 3.31E0_DP |
| 481 |
lj_sigma(O_atom) = 2.95E0_DP |
| 482 |
lj_sigma(F_atom) = 2.83E0_DP |
| 483 |
lj_sigma(Ne_atom) = 2.72E0_DP |
| 484 |
lj_sigma(S_atom) = 3.52E0_DP |
| 485 |
lj_sigma(Cl_atom) = 3.35E0_DP |
| 486 |
lj_sigma(Ar_atom) = 3.41E0_DP |
| 487 |
lj_sigma(Br_atom) = 3.54E0_DP |
| 488 |
lj_sigma(Kr_atom) = 3.83E0_DP |
| 489 |
|
| 490 |
lj_eps(H_atom) = 0.01708992E0_DP |
| 491 |
lj_eps(He_atom) = 0.02026944E0_DP |
| 492 |
lj_eps(C_atom) = 0.10174464E0_DP |
| 493 |
lj_eps(N_atom) = 0.07412256E0_DP |
| 494 |
lj_eps(O_atom) = 0.12241152E0_DP |
| 495 |
lj_eps(F_atom) = 0.10492416E0_DP |
| 496 |
lj_eps(Ne_atom) = 0.0933984E0_DP |
| 497 |
lj_eps(S_atom) = 0.3636576E0_DP |
| 498 |
lj_eps(Cl_atom) = 0.3447792E0_DP |
| 499 |
lj_eps(Ar_atom) = 0.23806656E0_DP |
| 500 |
lj_eps(Br_atom) = 0.51110784E0_DP |
| 501 |
lj_eps(Kr_atom) = 0.3259008E0_DP |
| 502 |
|
| 503 |
end subroutine initialize_lj |
| 504 |
|
| 505 |
subroutine mass_weight() |
| 506 |
integer ia, ja, dim, dim2, idim, idim2 |
| 507 |
real( kind = DP ) :: mt, m1, m2, wt |
| 508 |
|
| 509 |
|
| 510 |
do ia = 1, natoms |
| 511 |
m1 = mass(ia) |
| 512 |
do ja = 1, natoms |
| 513 |
m2 = mass(ja) |
| 514 |
wt = 1.0E0_DP/dsqrt(m1*m2) |
| 515 |
do dim = 1, 3 |
| 516 |
idim = 3 * (ia-1) + dim |
| 517 |
do dim2 = 1, 3 |
| 518 |
idim2 = 3 * (ja-1) + dim2 |
| 519 |
d(idim,idim2) = d(idim,idim2)*wt |
| 520 |
enddo |
| 521 |
enddo |
| 522 |
enddo |
| 523 |
enddo |
| 524 |
|
| 525 |
end subroutine mass_weight |
| 526 |
|
| 527 |
|
| 528 |
|
| 529 |
|
| 530 |
end module lj_module |
