| 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. Acknowledgement of the program authors must be made in any |
| 10 |
!! publication of scientific results based in part on use of the |
| 11 |
!! program. An acceptable form of acknowledgement is citation of |
| 12 |
!! the article in which the program was described (Matthew |
| 13 |
!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
!! Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
!! |
| 18 |
!! 2. Redistributions of source code must retain the above copyright |
| 19 |
!! notice, this list of conditions and the following disclaimer. |
| 20 |
!! |
| 21 |
!! 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
!! notice, this list of conditions and the following disclaimer in the |
| 23 |
!! documentation and/or other materials provided with the |
| 24 |
!! distribution. |
| 25 |
!! |
| 26 |
!! This software is provided "AS IS," without a warranty of any |
| 27 |
!! kind. All express or implied conditions, representations and |
| 28 |
!! warranties, including any implied warranty of merchantability, |
| 29 |
!! fitness for a particular purpose or non-infringement, are hereby |
| 30 |
!! excluded. The University of Notre Dame and its licensors shall not |
| 31 |
!! be liable for any damages suffered by licensee as a result of |
| 32 |
!! using, modifying or distributing the software or its |
| 33 |
!! derivatives. In no event will the University of Notre Dame or its |
| 34 |
!! licensors be liable for any lost revenue, profit or data, or for |
| 35 |
!! direct, indirect, special, consequential, incidental or punitive |
| 36 |
!! damages, however caused and regardless of the theory of liability, |
| 37 |
!! arising out of the use of or inability to use software, even if the |
| 38 |
!! University of Notre Dame has been advised of the possibility of |
| 39 |
!! such damages. |
| 40 |
!! |
| 41 |
|
| 42 |
|
| 43 |
!! Calculates Long Range forces Lennard-Jones interactions. |
| 44 |
!! @author Charles F. Vardeman II |
| 45 |
!! @author Matthew Meineke |
| 46 |
!! @version $Id: LJ.F90,v 1.10 2005-04-13 20:36:45 chuckv Exp $, $Date: 2005-04-13 20:36:45 $, $Name: not supported by cvs2svn $, $Revision: 1.10 $ |
| 47 |
|
| 48 |
|
| 49 |
module lj |
| 50 |
use atype_module |
| 51 |
use switcheroo |
| 52 |
use vector_class |
| 53 |
use simulation |
| 54 |
use status |
| 55 |
#ifdef IS_MPI |
| 56 |
use mpiSimulation |
| 57 |
#endif |
| 58 |
use force_globals |
| 59 |
|
| 60 |
implicit none |
| 61 |
PRIVATE |
| 62 |
|
| 63 |
integer, parameter :: DP = selected_real_kind(15) |
| 64 |
|
| 65 |
type, private :: LjType |
| 66 |
integer :: c_ident |
| 67 |
integer :: atid |
| 68 |
real(kind=dp) :: sigma |
| 69 |
real(kind=dp) :: epsilon |
| 70 |
logical :: soft_pot |
| 71 |
end type LjType |
| 72 |
|
| 73 |
type(LjType), dimension(:), allocatable :: ParameterMap |
| 74 |
|
| 75 |
logical, save :: haveMixingMap = .false. |
| 76 |
|
| 77 |
type :: MixParameters |
| 78 |
real(kind=DP) :: sigma |
| 79 |
real(kind=DP) :: epsilon |
| 80 |
real(kind=dp) :: sigma6 |
| 81 |
real(kind=dp) :: tp6 |
| 82 |
real(kind=dp) :: tp12 |
| 83 |
real(kind=dp) :: delta |
| 84 |
logical :: soft_pot |
| 85 |
end type MixParameters |
| 86 |
|
| 87 |
type(MixParameters), dimension(:,:), allocatable :: MixingMap |
| 88 |
|
| 89 |
real(kind=DP), save :: LJ_rcut |
| 90 |
logical, save :: have_rcut = .false. |
| 91 |
logical, save :: LJ_do_shift = .false. |
| 92 |
logical, save :: useGeometricDistanceMixing = .false. |
| 93 |
|
| 94 |
!! Public methods and data |
| 95 |
|
| 96 |
public :: setCutoffLJ |
| 97 |
public :: useGeometricMixing |
| 98 |
public :: do_lj_pair |
| 99 |
public :: newLJtype |
| 100 |
public :: getSigma |
| 101 |
public :: getEpsilon |
| 102 |
public :: destroyLJTypes |
| 103 |
|
| 104 |
contains |
| 105 |
|
| 106 |
subroutine newLJtype(c_ident, sigma, epsilon, soft_pot, status) |
| 107 |
integer,intent(in) :: c_ident |
| 108 |
real(kind=dp),intent(in) :: sigma |
| 109 |
real(kind=dp),intent(in) :: epsilon |
| 110 |
integer, intent(in) :: soft_pot |
| 111 |
integer,intent(out) :: status |
| 112 |
integer :: nATypes, myATID |
| 113 |
integer, pointer :: MatchList(:) => null() |
| 114 |
|
| 115 |
status = 0 |
| 116 |
|
| 117 |
myATID = getFirstMatchingElement(atypes, "c_ident", c_ident) |
| 118 |
|
| 119 |
if (.not.allocated(ParameterMap)) then |
| 120 |
|
| 121 |
!call getMatchingElementList(atypes, "is_LennardJones", .true., & |
| 122 |
! nLJTypes, MatchList) |
| 123 |
nAtypes = getSize(atypes) |
| 124 |
if (nAtypes == 0) then |
| 125 |
status = -1 |
| 126 |
return |
| 127 |
end if |
| 128 |
|
| 129 |
if (.not. allocated(ParameterMap)) then |
| 130 |
allocate(ParameterMap(nAtypes)) |
| 131 |
endif |
| 132 |
|
| 133 |
end if |
| 134 |
|
| 135 |
if (myATID .gt. size(ParameterMap)) then |
| 136 |
status = -1 |
| 137 |
return |
| 138 |
endif |
| 139 |
|
| 140 |
! set the values for ParameterMap for this atom type: |
| 141 |
|
| 142 |
ParameterMap(myATID)%c_ident = c_ident |
| 143 |
ParameterMap(myATID)%atid = myATID |
| 144 |
ParameterMap(myATID)%epsilon = epsilon |
| 145 |
ParameterMap(myATID)%sigma = sigma |
| 146 |
if (soft_pot == 1) then |
| 147 |
ParameterMap(myATID)%soft_pot = .true. |
| 148 |
else |
| 149 |
ParameterMap(myATID)%soft_pot = .false. |
| 150 |
endif |
| 151 |
end subroutine newLJtype |
| 152 |
|
| 153 |
function getSigma(atid) result (s) |
| 154 |
integer, intent(in) :: atid |
| 155 |
integer :: localError |
| 156 |
real(kind=dp) :: s |
| 157 |
|
| 158 |
if (.not.allocated(ParameterMap)) then |
| 159 |
call handleError("LJ", "no ParameterMap was present before first call of getSigma!") |
| 160 |
return |
| 161 |
end if |
| 162 |
|
| 163 |
s = ParameterMap(atid)%sigma |
| 164 |
end function getSigma |
| 165 |
|
| 166 |
function getEpsilon(atid) result (e) |
| 167 |
integer, intent(in) :: atid |
| 168 |
integer :: localError |
| 169 |
real(kind=dp) :: e |
| 170 |
|
| 171 |
if (.not.allocated(ParameterMap)) then |
| 172 |
call handleError("LJ", "no ParameterMap was present before first call of getEpsilon!") |
| 173 |
return |
| 174 |
end if |
| 175 |
|
| 176 |
e = ParameterMap(atid)%epsilon |
| 177 |
end function getEpsilon |
| 178 |
|
| 179 |
|
| 180 |
subroutine setCutoffLJ(rcut, do_shift, status) |
| 181 |
logical, intent(in):: do_shift |
| 182 |
integer :: status, myStatus |
| 183 |
real(kind=dp) :: rcut |
| 184 |
|
| 185 |
#define __FORTRAN90 |
| 186 |
#include "UseTheForce/fSwitchingFunction.h" |
| 187 |
|
| 188 |
status = 0 |
| 189 |
|
| 190 |
LJ_rcut = rcut |
| 191 |
LJ_do_shift = do_shift |
| 192 |
call set_switch(LJ_SWITCH, rcut, rcut) |
| 193 |
have_rcut = .true. |
| 194 |
|
| 195 |
return |
| 196 |
end subroutine setCutoffLJ |
| 197 |
|
| 198 |
subroutine useGeometricMixing() |
| 199 |
useGeometricDistanceMixing = .true. |
| 200 |
haveMixingMap = .false. |
| 201 |
return |
| 202 |
end subroutine useGeometricMixing |
| 203 |
|
| 204 |
subroutine createMixingMap(status) |
| 205 |
integer :: nATIDs |
| 206 |
integer :: status |
| 207 |
integer :: i |
| 208 |
integer :: j |
| 209 |
real ( kind = dp ) :: Sigma_i, Sigma_j |
| 210 |
real ( kind = dp ) :: Epsilon_i, Epsilon_j |
| 211 |
real ( kind = dp ) :: rcut6 |
| 212 |
logical :: i_is_LJ, j_is_LJ |
| 213 |
|
| 214 |
status = 0 |
| 215 |
|
| 216 |
if (.not. allocated(ParameterMap)) then |
| 217 |
call handleError("LJ", "no ParameterMap was present before call of createMixingMap!") |
| 218 |
status = -1 |
| 219 |
return |
| 220 |
endif |
| 221 |
|
| 222 |
nATIDs = size(ParameterMap) |
| 223 |
|
| 224 |
if (nATIDs == 0) then |
| 225 |
status = -1 |
| 226 |
return |
| 227 |
end if |
| 228 |
|
| 229 |
if (.not. allocated(MixingMap)) then |
| 230 |
allocate(MixingMap(nATIDs, nATIDs)) |
| 231 |
endif |
| 232 |
|
| 233 |
if (.not.have_rcut) then |
| 234 |
status = -1 |
| 235 |
return |
| 236 |
endif |
| 237 |
|
| 238 |
rcut6 = LJ_rcut**6 |
| 239 |
|
| 240 |
! This loops through all atypes, even those that don't support LJ forces. |
| 241 |
do i = 1, nATIDs |
| 242 |
call getElementProperty(atypes, i, "is_LennardJones", i_is_LJ) |
| 243 |
if (i_is_LJ) then |
| 244 |
Epsilon_i = ParameterMap(i)%epsilon |
| 245 |
Sigma_i = ParameterMap(i)%sigma |
| 246 |
|
| 247 |
! do self mixing rule |
| 248 |
MixingMap(i,i)%sigma = Sigma_i |
| 249 |
MixingMap(i,i)%sigma6 = Sigma_i ** 6 |
| 250 |
MixingMap(i,i)%tp6 = (MixingMap(i,i)%sigma6)/rcut6 |
| 251 |
MixingMap(i,i)%tp12 = (MixingMap(i,i)%tp6) ** 2 |
| 252 |
MixingMap(i,i)%epsilon = Epsilon_i |
| 253 |
MixingMap(i,i)%delta = -4.0_DP * MixingMap(i,i)%epsilon * & |
| 254 |
(MixingMap(i,i)%tp12 - MixingMap(i,i)%tp6) |
| 255 |
MixingMap(i,i)%soft_pot = ParameterMap(i)%soft_pot |
| 256 |
|
| 257 |
do j = i + 1, nATIDs |
| 258 |
call getElementProperty(atypes, j, "is_LennardJones", j_is_LJ) |
| 259 |
|
| 260 |
if (j_is_LJ) then |
| 261 |
Epsilon_j = ParameterMap(j)%epsilon |
| 262 |
Sigma_j = ParameterMap(j)%sigma |
| 263 |
|
| 264 |
! only the distance parameter uses different mixing policies |
| 265 |
if (useGeometricDistanceMixing) then |
| 266 |
! only for OPLS as far as we can tell |
| 267 |
MixingMap(i,j)%sigma = dsqrt(Sigma_i * Sigma_j) |
| 268 |
else |
| 269 |
! everyone else |
| 270 |
MixingMap(i,j)%sigma = 0.5_dp * (Sigma_i + Sigma_j) |
| 271 |
endif |
| 272 |
|
| 273 |
! energy parameter is always geometric mean: |
| 274 |
MixingMap(i,j)%epsilon = dsqrt(Epsilon_i * Epsilon_j) |
| 275 |
|
| 276 |
MixingMap(i,j)%sigma6 = (MixingMap(i,j)%sigma)**6 |
| 277 |
MixingMap(i,j)%tp6 = MixingMap(i,j)%sigma6/rcut6 |
| 278 |
MixingMap(i,j)%tp12 = (MixingMap(i,j)%tp6) ** 2 |
| 279 |
|
| 280 |
MixingMap(i,j)%delta = -4.0_DP * MixingMap(i,j)%epsilon * & |
| 281 |
(MixingMap(i,j)%tp12 - MixingMap(i,j)%tp6) |
| 282 |
|
| 283 |
MixingMap(i,j)%soft_pot = ParameterMap(i)%soft_pot .or. ParameterMap(j)%soft_pot |
| 284 |
|
| 285 |
|
| 286 |
MixingMap(j,i)%sigma = MixingMap(i,j)%sigma |
| 287 |
MixingMap(j,i)%sigma6 = MixingMap(i,j)%sigma6 |
| 288 |
MixingMap(j,i)%tp6 = MixingMap(i,j)%tp6 |
| 289 |
MixingMap(j,i)%tp12 = MixingMap(i,j)%tp12 |
| 290 |
MixingMap(j,i)%epsilon = MixingMap(i,j)%epsilon |
| 291 |
MixingMap(j,i)%delta = MixingMap(i,j)%delta |
| 292 |
MixingMap(j,i)%soft_pot = MixingMap(i,j)%soft_pot |
| 293 |
endif |
| 294 |
end do |
| 295 |
endif |
| 296 |
end do |
| 297 |
|
| 298 |
haveMixingMap = .true. |
| 299 |
|
| 300 |
end subroutine createMixingMap |
| 301 |
|
| 302 |
subroutine do_lj_pair(atom1, atom2, d, rij, r2, sw, vpair, fpair, & |
| 303 |
pot, f, do_pot) |
| 304 |
|
| 305 |
integer, intent(in) :: atom1, atom2 |
| 306 |
real( kind = dp ), intent(in) :: rij, r2 |
| 307 |
real( kind = dp ) :: pot, sw, vpair |
| 308 |
real( kind = dp ), dimension(3,nLocal) :: f |
| 309 |
real( kind = dp ), intent(in), dimension(3) :: d |
| 310 |
real( kind = dp ), intent(inout), dimension(3) :: fpair |
| 311 |
logical, intent(in) :: do_pot |
| 312 |
|
| 313 |
! local Variables |
| 314 |
real( kind = dp ) :: drdx, drdy, drdz |
| 315 |
real( kind = dp ) :: fx, fy, fz |
| 316 |
real( kind = dp ) :: pot_temp, dudr |
| 317 |
real( kind = dp ) :: sigma6 |
| 318 |
real( kind = dp ) :: epsilon |
| 319 |
real( kind = dp ) :: r6 |
| 320 |
real( kind = dp ) :: t6 |
| 321 |
real( kind = dp ) :: t12 |
| 322 |
real( kind = dp ) :: delta |
| 323 |
logical :: soft_pot |
| 324 |
integer :: id1, id2, localError |
| 325 |
|
| 326 |
if (.not.haveMixingMap) then |
| 327 |
localError = 0 |
| 328 |
call createMixingMap(localError) |
| 329 |
if ( localError .ne. 0 ) then |
| 330 |
call handleError("LJ", "MixingMap creation failed!") |
| 331 |
return |
| 332 |
end if |
| 333 |
endif |
| 334 |
|
| 335 |
! Look up the correct parameters in the mixing matrix |
| 336 |
#ifdef IS_MPI |
| 337 |
sigma6 = MixingMap(atid_Row(atom1),atid_Col(atom2))%sigma6 |
| 338 |
epsilon = MixingMap(atid_Row(atom1),atid_Col(atom2))%epsilon |
| 339 |
delta = MixingMap(atid_Row(atom1),atid_Col(atom2))%delta |
| 340 |
soft_pot = MixingMap(atid_Row(atom1),atid_Col(atom2))%soft_pot |
| 341 |
#else |
| 342 |
sigma6 = MixingMap(atid(atom1),atid(atom2))%sigma6 |
| 343 |
epsilon = MixingMap(atid(atom1),atid(atom2))%epsilon |
| 344 |
delta = MixingMap(atid(atom1),atid(atom2))%delta |
| 345 |
soft_pot = MixingMap(atid(atom1),atid(atom2))%soft_pot |
| 346 |
#endif |
| 347 |
|
| 348 |
r6 = r2 * r2 * r2 |
| 349 |
|
| 350 |
t6 = sigma6/ r6 |
| 351 |
t12 = t6 * t6 |
| 352 |
|
| 353 |
if (soft_pot) then |
| 354 |
pot_temp = 4.0E0_DP * epsilon * t12 |
| 355 |
if (LJ_do_shift) then |
| 356 |
pot_temp = pot_temp + delta |
| 357 |
endif |
| 358 |
|
| 359 |
vpair = vpair + pot_temp |
| 360 |
|
| 361 |
dudr = sw * 24.0E0_DP * epsilon * (-2.0E0_DP)*t12 / rij |
| 362 |
|
| 363 |
else |
| 364 |
pot_temp = 4.0E0_DP * epsilon * (t12 - t6) |
| 365 |
if (LJ_do_shift) then |
| 366 |
pot_temp = pot_temp + delta |
| 367 |
endif |
| 368 |
|
| 369 |
vpair = vpair + pot_temp |
| 370 |
|
| 371 |
dudr = sw * 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / rij |
| 372 |
endif |
| 373 |
|
| 374 |
drdx = d(1) / rij |
| 375 |
drdy = d(2) / rij |
| 376 |
drdz = d(3) / rij |
| 377 |
|
| 378 |
fx = dudr * drdx |
| 379 |
fy = dudr * drdy |
| 380 |
fz = dudr * drdz |
| 381 |
|
| 382 |
|
| 383 |
#ifdef IS_MPI |
| 384 |
if (do_pot) then |
| 385 |
pot_Row(atom1) = pot_Row(atom1) + sw*pot_temp*0.5 |
| 386 |
pot_Col(atom2) = pot_Col(atom2) + sw*pot_temp*0.5 |
| 387 |
endif |
| 388 |
|
| 389 |
f_Row(1,atom1) = f_Row(1,atom1) + fx |
| 390 |
f_Row(2,atom1) = f_Row(2,atom1) + fy |
| 391 |
f_Row(3,atom1) = f_Row(3,atom1) + fz |
| 392 |
|
| 393 |
f_Col(1,atom2) = f_Col(1,atom2) - fx |
| 394 |
f_Col(2,atom2) = f_Col(2,atom2) - fy |
| 395 |
f_Col(3,atom2) = f_Col(3,atom2) - fz |
| 396 |
|
| 397 |
#else |
| 398 |
if (do_pot) pot = pot + sw*pot_temp |
| 399 |
|
| 400 |
f(1,atom1) = f(1,atom1) + fx |
| 401 |
f(2,atom1) = f(2,atom1) + fy |
| 402 |
f(3,atom1) = f(3,atom1) + fz |
| 403 |
|
| 404 |
f(1,atom2) = f(1,atom2) - fx |
| 405 |
f(2,atom2) = f(2,atom2) - fy |
| 406 |
f(3,atom2) = f(3,atom2) - fz |
| 407 |
#endif |
| 408 |
|
| 409 |
#ifdef IS_MPI |
| 410 |
id1 = AtomRowToGlobal(atom1) |
| 411 |
id2 = AtomColToGlobal(atom2) |
| 412 |
#else |
| 413 |
id1 = atom1 |
| 414 |
id2 = atom2 |
| 415 |
#endif |
| 416 |
|
| 417 |
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 418 |
|
| 419 |
fpair(1) = fpair(1) + fx |
| 420 |
fpair(2) = fpair(2) + fy |
| 421 |
fpair(3) = fpair(3) + fz |
| 422 |
|
| 423 |
endif |
| 424 |
|
| 425 |
return |
| 426 |
|
| 427 |
end subroutine do_lj_pair |
| 428 |
|
| 429 |
subroutine destroyLJTypes() |
| 430 |
if(allocated(ParameterMap)) deallocate(ParameterMap) |
| 431 |
if(allocated(MixingMap)) deallocate(MixingMap) |
| 432 |
haveMixingMap = .false. |
| 433 |
end subroutine destroyLJTypes |
| 434 |
|
| 435 |
|
| 436 |
end module lj |
