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!! |
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!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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!! |
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!! The University of Notre Dame grants you ("Licensee") a |
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!! non-exclusive, royalty free, license to use, modify and |
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!! redistribute this software in source and binary code form, provided |
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!! that the following conditions are met: |
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!! |
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!! 1. Acknowledgement of the program authors must be made in any |
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!! publication of scientific results based in part on use of the |
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!! program. An acceptable form of acknowledgement is citation of |
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!! the article in which the program was described (Matthew |
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!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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!! Parallel Simulation Engine for Molecular Dynamics," |
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!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
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!! |
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!! 2. Redistributions of source code must retain the above copyright |
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!! notice, this list of conditions and the following disclaimer. |
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!! |
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!! 3. Redistributions in binary form must reproduce the above copyright |
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!! notice, this list of conditions and the following disclaimer in the |
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!! documentation and/or other materials provided with the |
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!! distribution. |
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!! |
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!! This software is provided "AS IS," without a warranty of any |
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!! kind. All express or implied conditions, representations and |
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!! warranties, including any implied warranty of merchantability, |
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!! fitness for a particular purpose or non-infringement, are hereby |
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!! excluded. The University of Notre Dame and its licensors shall not |
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!! be liable for any damages suffered by licensee as a result of |
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!! using, modifying or distributing the software or its |
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!! derivatives. In no event will the University of Notre Dame or its |
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!! licensors be liable for any lost revenue, profit or data, or for |
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!! direct, indirect, special, consequential, incidental or punitive |
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!! damages, however caused and regardless of the theory of liability, |
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!! arising out of the use of or inability to use software, even if the |
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!! University of Notre Dame has been advised of the possibility of |
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!! such damages. |
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!! |
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|
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|
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module gb_pair |
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use force_globals |
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use definitions |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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< |
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> |
|
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implicit none |
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|
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PRIVATE |
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subroutine set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
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real( kind = dp ), intent(in) :: sigma, l2b_ratio, eps, eps_ratio |
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real( kind = dp ), intent(in) :: mu, nu |
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< |
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> |
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gb_sigma = sigma |
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gb_l2b_ratio = l2b_ratio |
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gb_eps = eps |
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|
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|
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subroutine do_gb_pair(atom1, atom2, d, r, r2, sw, vpair, fpair, & |
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pot, u_l, f, t, do_pot) |
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< |
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pot, A, f, t, do_pot) |
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|
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integer, intent(in) :: atom1, atom2 |
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integer :: id1, id2 |
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real (kind=dp), intent(inout) :: r, r2 |
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real (kind=dp), dimension(3), intent(in) :: d |
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real (kind=dp), dimension(3), intent(inout) :: fpair |
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real (kind=dp) :: pot, sw, vpair |
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< |
real (kind=dp), dimension(3,nLocal) :: u_l |
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> |
real (kind=dp), dimension(9,nLocal) :: A |
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real (kind=dp), dimension(3,nLocal) :: f |
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real (kind=dp), dimension(3,nLocal) :: t |
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logical, intent(in) :: do_pot |
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real(kind=dp) :: term2a, term2b, term2u1x, term2u1y, term2u1z |
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real(kind=dp) :: term2u2x, term2u2y, term2u2z |
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real(kind=dp) :: yick1, yick2, mess1, mess2 |
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s2 = (gb_l2b_ratio)**2 |
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emu = (gb_eps_ratio)**(1.0d0/gb_mu) |
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|
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r4 = r2*r2 |
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|
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#ifdef IS_MPI |
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ul1(1) = u_l_Row(1,atom1) |
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ul1(2) = u_l_Row(2,atom1) |
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ul1(3) = u_l_Row(3,atom1) |
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> |
ul1(1) = A_Row(3,atom1) |
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ul1(2) = A_Row(6,atom1) |
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> |
ul1(3) = A_Row(9,atom1) |
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|
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ul2(1) = u_l_Col(1,atom2) |
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ul2(2) = u_l_Col(2,atom2) |
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ul2(3) = u_l_Col(3,atom2) |
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> |
ul2(1) = A_Col(3,atom2) |
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> |
ul2(2) = A_Col(6,atom2) |
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> |
ul2(3) = A_Col(9,atom2) |
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#else |
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< |
ul1(1) = u_l(1,atom1) |
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< |
ul1(2) = u_l(2,atom1) |
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< |
ul1(3) = u_l(3,atom1) |
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> |
ul1(1) = A(3,atom1) |
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> |
ul1(2) = A(6,atom1) |
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> |
ul1(3) = A(9,atom1) |
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|
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< |
ul2(1) = u_l(1,atom2) |
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ul2(2) = u_l(2,atom2) |
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ul2(3) = u_l(3,atom2) |
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ul2(1) = A(3,atom2) |
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ul2(2) = A(6,atom2) |
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ul2(3) = A(9,atom2) |
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#endif |
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< |
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> |
|
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dru1dx = ul1(1) |
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dru2dx = ul2(1) |
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dru1dy = ul1(2) |
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dru2dy = ul2(2) |
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dru1dz = ul1(3) |
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dru2dz = ul2(3) |
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drdx = d(1) / r |
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drdy = d(2) / r |
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drdz = d(3) / r |
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! do some dot products: |
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! NB the r in these dot products is the actual intermolecular vector, |
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! and is not the unit vector in that direction. |
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rdotu1 = d(1)*ul1(1) + d(2)*ul1(2) + d(3)*ul1(3) |
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rdotu2 = d(1)*ul2(1) + d(2)*ul2(2) + d(3)*ul2(3) |
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u1dotu2 = ul1(1)*ul2(1) + ul1(2)*ul2(2) + ul1(3)*ul2(3) |
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! We note however, that there are some major typos in that Appendix |
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! of the Luckhurst paper, particularly in equations A23, A29 and A31 |
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! We have attempted to correct them below. |
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dotsum = rdotu1+rdotu2 |
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dotdiff = rdotu1-rdotu2 |
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ds2 = dotsum*dotsum |
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dd2 = dotdiff*dotdiff |
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opXdot = 1.0d0 + Chi*u1dotu2 |
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omXdot = 1.0d0 - Chi*u1dotu2 |
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opXpdot = 1.0d0 + ChiPrime*u1dotu2 |
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omXpdot = 1.0d0 - ChiPrime*u1dotu2 |
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line1a = dotsum/opXdot |
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line1bx = dru1dx + dru2dx |
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line1by = dru1dy + dru2dy |
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line1bz = dru1dz + dru2dz |
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line2a = dotdiff/omXdot |
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line2bx = dru1dx - dru2dx |
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line2by = dru1dy - dru2dy |
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line2bz = dru1dz - dru2dz |
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term1x = -Chi*(line1a*line1bx + line2a*line2bx)/r2 |
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term1y = -Chi*(line1a*line1by + line2a*line2by)/r2 |
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term1z = -Chi*(line1a*line1bz + line2a*line2bz)/r2 |
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line3a = ds2/opXdot |
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line3b = dd2/omXdot |
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line3 = Chi*(line3a + line3b)/r4 |
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line3x = d(1)*line3 |
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line3y = d(2)*line3 |
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line3z = d(3)*line3 |
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dgdx = term1x + line3x |
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dgdy = term1y + line3y |
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dgdz = term1z + line3z |
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term1u2x = 2.0d0*(line1a-line2a)*d(1) |
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term1u2y = 2.0d0*(line1a-line2a)*d(2) |
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term1u2z = 2.0d0*(line1a-line2a)*d(3) |
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term2a = -line3a/opXdot |
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term2b = line3b/omXdot |
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term2u1x = Chi*ul2(1)*(term2a + term2b) |
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term2u1y = Chi*ul2(2)*(term2a + term2b) |
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term2u1z = Chi*ul2(3)*(term2a + term2b) |
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term2u2x = Chi*ul1(1)*(term2a + term2b) |
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term2u2y = Chi*ul1(2)*(term2a + term2b) |
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term2u2z = Chi*ul1(3)*(term2a + term2b) |
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pref = -Chi*0.5d0/r2 |
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dgdu1x = pref*(term1u1x+term2u1x) |
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dgdu2z = pref*(term1u2z+term2u2z) |
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g = 1.0d0 - Chi*(line3a + line3b)/(2.0d0*r2) |
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< |
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> |
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BigR = (r - gb_sigma*(g**(-0.5d0)) + gb_sigma)/gb_sigma |
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Ri = 1.0d0/BigR |
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Ri2 = Ri*Ri |
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dBigRdu2x = dgdu2x*gfact |
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dBigRdu2y = dgdu2y*gfact |
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dBigRdu2z = dgdu2z*gfact |
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> |
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! Now, we must do it again for g(ChiPrime) and dgpdx |
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line1a = dotsum/opXpdot |
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line3x = d(1)*line3 |
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line3y = d(2)*line3 |
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line3z = d(3)*line3 |
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> |
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dgpdx = term1x + line3x |
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dgpdy = term1y + line3y |
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dgpdz = term1z + line3z |
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< |
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> |
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term1u1x = 2.0d0*(line1a+line2a)*d(1) |
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term1u1y = 2.0d0*(line1a+line2a)*d(2) |
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term1u1z = 2.0d0*(line1a+line2a)*d(3) |
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term1u2x = 2.0d0*(line1a-line2a)*d(1) |
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term1u2y = 2.0d0*(line1a-line2a)*d(2) |
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term1u2z = 2.0d0*(line1a-line2a)*d(3) |
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< |
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> |
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term2a = -line3a/opXpdot |
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term2b = line3b/omXpdot |
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< |
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> |
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term2u1x = ChiPrime*ul2(1)*(term2a + term2b) |
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term2u1y = ChiPrime*ul2(2)*(term2a + term2b) |
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term2u1z = ChiPrime*ul2(3)*(term2a + term2b) |
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term2u2x = ChiPrime*ul1(1)*(term2a + term2b) |
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term2u2y = ChiPrime*ul1(2)*(term2a + term2b) |
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term2u2z = ChiPrime*ul1(3)*(term2a + term2b) |
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< |
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> |
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pref = -ChiPrime*0.5d0/r2 |
| 307 |
< |
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| 307 |
> |
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| 308 |
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dgpdu1x = pref*(term1u1x+term2u1x) |
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dgpdu1y = pref*(term1u1y+term2u1y) |
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dgpdu1z = pref*(term1u1z+term2u1z) |
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dgpdu2x = pref*(term1u2x+term2u2x) |
| 312 |
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dgpdu2y = pref*(term1u2y+term2u2y) |
| 313 |
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dgpdu2z = pref*(term1u2z+term2u2z) |
| 314 |
< |
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| 314 |
> |
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| 315 |
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gp = 1.0d0 - ChiPrime*(line3a + line3b)/(2.0d0*r2) |
| 316 |
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gmu = gp**gb_mu |
| 317 |
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gpi = 1.0d0 / gp |
| 318 |
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gmum = gmu*gpi |
| 319 |
< |
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| 319 |
> |
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| 320 |
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! write(*,*) atom1, atom2, Chi, u1dotu2 |
| 321 |
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curlyE = 1.0d0/dsqrt(1.0d0 - Chi*Chi*u1dotu2*u1dotu2) |
| 322 |
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|
| 323 |
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dcE = (curlyE**3)*Chi*Chi*u1dotu2 |
| 324 |
< |
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| 324 |
> |
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| 325 |
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dcEdu1x = dcE*ul2(1) |
| 326 |
|
dcEdu1y = dcE*ul2(2) |
| 327 |
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dcEdu1z = dcE*ul2(3) |
| 328 |
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dcEdu2x = dcE*ul1(1) |
| 329 |
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dcEdu2y = dcE*ul1(2) |
| 330 |
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dcEdu2z = dcE*ul1(3) |
| 331 |
< |
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| 331 |
> |
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| 332 |
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enu = curlyE**gb_nu |
| 333 |
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enum = enu/curlyE |
| 334 |
< |
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| 334 |
> |
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| 335 |
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eps = gb_eps*enu*gmu |
| 336 |
|
|
| 337 |
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yick1 = gb_eps*enu*gb_mu*gmum |
| 343 |
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depsdu2x = yick1*dgpdu2x + yick2*dcEdu2x |
| 344 |
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depsdu2y = yick1*dgpdu2y + yick2*dcEdu2y |
| 345 |
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depsdu2z = yick1*dgpdu2z + yick2*dcEdu2z |
| 346 |
< |
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| 346 |
> |
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| 347 |
|
R126 = Ri12 - Ri6 |
| 348 |
|
R137 = 6.0d0*Ri7 - 12.0d0*Ri13 |
| 349 |
< |
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| 349 |
> |
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| 350 |
|
mess1 = gmu*R137 |
| 351 |
|
mess2 = R126*gb_mu*gmum |
| 352 |
< |
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| 352 |
> |
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| 353 |
|
dUdx = 4.0d0*gb_eps*enu*(mess1*dBigRdx + mess2*dgpdx)*sw |
| 354 |
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dUdy = 4.0d0*gb_eps*enu*(mess1*dBigRdy + mess2*dgpdy)*sw |
| 355 |
|
dUdz = 4.0d0*gb_eps*enu*(mess1*dBigRdz + mess2*dgpdz)*sw |
| 356 |
< |
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| 356 |
> |
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| 357 |
|
dUdu1x = 4.0d0*(R126*depsdu1x + eps*R137*dBigRdu1x)*sw |
| 358 |
|
dUdu1y = 4.0d0*(R126*depsdu1y + eps*R137*dBigRdu1y)*sw |
| 359 |
|
dUdu1z = 4.0d0*(R126*depsdu1z + eps*R137*dBigRdu1z)*sw |
| 360 |
|
dUdu2x = 4.0d0*(R126*depsdu2x + eps*R137*dBigRdu2x)*sw |
| 361 |
|
dUdu2y = 4.0d0*(R126*depsdu2y + eps*R137*dBigRdu2y)*sw |
| 362 |
|
dUdu2z = 4.0d0*(R126*depsdu2z + eps*R137*dBigRdu2z)*sw |
| 363 |
< |
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| 363 |
> |
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| 364 |
|
#ifdef IS_MPI |
| 365 |
|
f_Row(1,atom1) = f_Row(1,atom1) + dUdx |
| 366 |
|
f_Row(2,atom1) = f_Row(2,atom1) + dUdy |
| 367 |
|
f_Row(3,atom1) = f_Row(3,atom1) + dUdz |
| 368 |
< |
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| 368 |
> |
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| 369 |
|
f_Col(1,atom2) = f_Col(1,atom2) - dUdx |
| 370 |
|
f_Col(2,atom2) = f_Col(2,atom2) - dUdy |
| 371 |
|
f_Col(3,atom2) = f_Col(3,atom2) - dUdz |
| 372 |
< |
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| 372 |
> |
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| 373 |
|
t_Row(1,atom1) = t_Row(1,atom1) - ul1(2)*dUdu1z + ul1(3)*dUdu1y |
| 374 |
|
t_Row(2,atom1) = t_Row(2,atom1) - ul1(3)*dUdu1x + ul1(1)*dUdu1z |
| 375 |
|
t_Row(3,atom1) = t_Row(3,atom1) - ul1(1)*dUdu1y + ul1(2)*dUdu1x |
| 376 |
< |
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| 376 |
> |
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| 377 |
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t_Col(1,atom2) = t_Col(1,atom2) - ul2(2)*dUdu2z + ul2(3)*dUdu2y |
| 378 |
|
t_Col(2,atom2) = t_Col(2,atom2) - ul2(3)*dUdu2x + ul2(1)*dUdu2z |
| 379 |
|
t_Col(3,atom2) = t_Col(3,atom2) - ul2(1)*dUdu2y + ul2(2)*dUdu2x |
| 381 |
|
f(1,atom1) = f(1,atom1) + dUdx |
| 382 |
|
f(2,atom1) = f(2,atom1) + dUdy |
| 383 |
|
f(3,atom1) = f(3,atom1) + dUdz |
| 384 |
< |
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| 384 |
> |
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| 385 |
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f(1,atom2) = f(1,atom2) - dUdx |
| 386 |
|
f(2,atom2) = f(2,atom2) - dUdy |
| 387 |
|
f(3,atom2) = f(3,atom2) - dUdz |
| 388 |
< |
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| 388 |
> |
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| 389 |
|
t(1,atom1) = t(1,atom1) - ul1(2)*dUdu1z + ul1(3)*dUdu1y |
| 390 |
|
t(2,atom1) = t(2,atom1) - ul1(3)*dUdu1x + ul1(1)*dUdu1z |
| 391 |
|
t(3,atom1) = t(3,atom1) - ul1(1)*dUdu1y + ul1(2)*dUdu1x |
| 392 |
< |
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| 392 |
> |
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| 393 |
|
t(1,atom2) = t(1,atom2) - ul2(2)*dUdu2z + ul2(3)*dUdu2y |
| 394 |
|
t(2,atom2) = t(2,atom2) - ul2(3)*dUdu2x + ul2(1)*dUdu2z |
| 395 |
|
t(3,atom2) = t(3,atom2) - ul2(1)*dUdu2y + ul2(2)*dUdu2x |
| 396 |
|
#endif |
| 397 |
< |
|
| 397 |
> |
|
| 398 |
|
if (do_pot) then |
| 399 |
|
#ifdef IS_MPI |
| 400 |
|
pot_row(atom1) = pot_row(atom1) + 2.0d0*eps*R126*sw |
| 412 |
|
id1 = atom1 |
| 413 |
|
id2 = atom2 |
| 414 |
|
#endif |
| 415 |
< |
|
| 415 |
> |
|
| 416 |
|
if (molMembershipList(id1) .ne. molMembershipList(id2)) then |
| 417 |
< |
|
| 417 |
> |
|
| 418 |
|
fpair(1) = fpair(1) + dUdx |
| 419 |
|
fpair(2) = fpair(2) + dUdy |
| 420 |
|
fpair(3) = fpair(3) + dUdz |
| 421 |
< |
|
| 421 |
> |
|
| 422 |
|
endif |
| 423 |
< |
|
| 423 |
> |
|
| 424 |
|
return |
| 425 |
|
end subroutine do_gb_pair |
| 426 |
|
|
| 427 |
|
end module gb_pair |
| 386 |
– |
|
| 387 |
– |
|
| 388 |
– |
subroutine set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
| 389 |
– |
use definitions, ONLY : dp |
| 390 |
– |
use gb_pair, ONLY : module_set_gb_pair_params => set_gb_pair_params |
| 391 |
– |
real( kind = dp ), intent(inout) :: sigma, l2b_ratio, eps, eps_ratio |
| 392 |
– |
real( kind = dp ), intent(inout) :: mu, nu |
| 393 |
– |
call module_set_gb_pair_params(sigma, l2b_ratio, eps, eps_ratio, mu, nu) |
| 394 |
– |
end subroutine set_gb_pair_params |
