module mod_nonbonded use mod_memory, only: rp, ip, lp use mod_neighbor_list, only: ommp_neigh_list use mod_constants, only: OMMP_STR_CHAR_MAX use mod_adjacency_mat, only: yale_sparse use mod_topology, only: ommp_topology_type use mod_constants, only: OMMP_VDWTYPE_LJ, & OMMP_VDWTYPE_BUF714, & OMMP_RADRULE_ARITHMETIC, & OMMP_RADRULE_CUBIC, & OMMP_RADTYPE_RMIN, & OMMP_EPSRULE_GEOMETRIC, & OMMP_EPSRULE_HHG implicit none private integer(ip), parameter :: pair_allocation_chunk = 16 type ommp_nonbonded_type !! Derived type for storing the information relative to the calculation !! of non-bonding interactions type(ommp_topology_type), pointer :: top !! Data structure for topology logical(lp) :: use_nl !! Flag for using neighbors list type(ommp_neigh_list) :: nl !! Neighbor list struture real(rp), allocatable, dimension(:) :: vdw_r !! VdW radii for the atoms of the system real(rp), allocatable, dimension(:) :: vdw_e !! Vdw energies for the atoms of fthe system real(rp), allocatable, dimension(:) :: vdw_f !! Scale factor for displacing the interaction center integer(ip) :: npair = 0 !! Number of nonbonded pair parameters logical(lp), allocatable :: vdw_pair_mask_a(:,:), vdw_pair_mask_b(:,:) !! Mask to apply a pair parameter to a pair of atoms dimension is !! Natoms x Nparams real(rp), allocatable :: vdw_pair_r(:) !! Radii for the VdW atom pairs real(rp), allocatable :: vdw_pair_e(:) !! VdW energies for atom pairs real(rp), dimension(4) :: vdw_screening = [0.0, 0.0, 1.0, 1.0] !! Screening factors for 1,2 1,3 and 1,4 neighbours. !! Default vaules from tinker manual. real(rp) :: radf = 1.0 !! Scal factor for atomic radii/diameters (1.0 is used for diameters, !! 2.0 for radii) integer(ip) :: radrule !! Flag for the radius rule to be used integer(ip) :: radtype !! Flag for the radius type integer(ip) :: vdwtype !! Flag for the vdW type integer(ip) :: epsrule !! Flag for eps rule !!TODO end type ommp_nonbonded_type abstract interface subroutine vdw_term(Rij, Rij0, Eij, V) use mod_memory, only: rp real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(inout) :: V end subroutine end interface abstract interface subroutine vdw_gterm(Rij, Rij0, Eij, Rijgrad) use mod_memory, only: rp real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(out) :: Rijgrad end subroutine end interface public :: ommp_nonbonded_type public :: vdw_init, vdw_terminate, vdw_set_pair, vdw_remove_potential public :: vdw_set_cutoff public :: vdw_potential, vdw_geomgrad public :: vdw_potential_inter, vdw_geomgrad_inter public :: vdw_potential_inter_restricted, vdw_geomgrad_inter_restricted contains subroutine vdw_init(vdw, top, vdw_type, radius_rule, radius_size, & radius_type, epsrule, cutoff) !! Initialize the non-bonded object allocating the parameters vectors use mod_memory, only: mallocate use mod_io, only: fatal_error use mod_neighbor_list, only: nl_init use mod_constants, only: OMMP_DEFAULT_NL_SUB implicit none type(ommp_nonbonded_type), intent(inout) :: vdw type(ommp_topology_type), intent(in), target :: top character(len=*) :: vdw_type, radius_rule, radius_size, radius_type, & epsrule real(rp) :: cutoff select case(trim(vdw_type)) case("lennard-jones") vdw%vdwtype = OMMP_VDWTYPE_LJ continue case("buckingham") call fatal_error("VdW type buckingham is not implemented") case("buffered-14-7") vdw%vdwtype = OMMP_VDWTYPE_BUF714 continue case("mm3-hbond") call fatal_error("VdW type mm3-hbond is not implemented") case("gaussian") call fatal_error("VdW type gaussian is not implemented") case default call fatal_error("VdW type specified is not understood") end select select case(trim(radius_rule)) case("arithmetic") vdw%radrule = OMMP_RADRULE_ARITHMETIC continue case("geometric") call fatal_error("radiusrule geometric is not implemented") case("cubic-mean") vdw%radrule = OMMP_RADRULE_CUBIC continue case default call fatal_error("radiusrule specified is not understood") end select select case(trim(radius_size)) case("radius") vdw%radf = 2.0 continue case("diameter") vdw%radf = 1.0 continue case default call fatal_error("radiussize specified is not understood") end select select case(trim(radius_type)) case("sigma") call fatal_error("radiustype sigma is not implemented") case("r-min") vdw%radtype = OMMP_RADTYPE_RMIN continue case default call fatal_error("radiustype specified is not understood") end select select case(trim(epsrule)) case("geometric") vdw%epsrule = OMMP_EPSRULE_GEOMETRIC continue case("arithmetic") call fatal_error("epsilonrule arithmetic is not implemented") case("harmonic") call fatal_error("epsilonrule harmonic is not implemented") case("w-h") call fatal_error("epsilonrule w-h is not implemented") case("hhg") vdw%epsrule = OMMP_EPSRULE_HHG continue case default call fatal_error("epsilonrule specified is not understood") end select vdw%top => top call mallocate('vdw_init [vdw_r]', top%mm_atoms, vdw%vdw_r) call mallocate('vdw_init [vdw_e]', top%mm_atoms, vdw%vdw_e) call mallocate('vdw_init [vdw_f]', top%mm_atoms, vdw%vdw_f) call mallocate('vdw_init [vdw_pair_mask_a]', & top%mm_atoms, pair_allocation_chunk,vdw%vdw_pair_mask_a) call mallocate('vdw_init [vdw_pair_mask_b]', & top%mm_atoms, pair_allocation_chunk,vdw%vdw_pair_mask_b) call mallocate('vdw_init [vdw_pair_r]', pair_allocation_chunk, & vdw%vdw_pair_r) call mallocate('vdw_init [vdw_pair_e]', pair_allocation_chunk, & vdw%vdw_pair_e) vdw%vdw_f = 1.0_rp if(cutoff > 0.0) then vdw%use_nl = .true. if(vdw%use_nl) call nl_init(vdw%nl, top%cmm, cutoff, OMMP_DEFAULT_NL_SUB) else vdw%use_nl = .false. end if end subroutine vdw_init subroutine vdw_set_cutoff(vdw, cutoff, subdivision) use mod_neighbor_list, only: nl_terminate, nl_init implicit none type(ommp_nonbonded_type), intent(inout) :: vdw real(rp), intent(in) :: cutoff integer(ip), intent(in) :: subdivision if(vdw%use_nl) then ! This is re-initialization, old stuff should be cleaned. call nl_terminate(vdw%nl) end if if(cutoff > 0.0) then vdw%use_nl = .true. call nl_init(vdw%nl, vdw%top%cmm, cutoff, subdivision) else vdw%use_nl = .false. end if end subroutine subroutine vdw_terminate(vdw) use mod_memory, only: mfree use mod_adjacency_mat, only: matfree use mod_neighbor_list, only: nl_terminate implicit none type(ommp_nonbonded_type), intent(inout) :: vdw call mfree('vdw_terminate [vdw_r]', vdw%vdw_r) call mfree('vdw_terminate [vdw_e]', vdw%vdw_e) call mfree('vdw_terminate [vdw_f]', vdw%vdw_f) call mfree('vdw_terminate [vdw_pair_r]', vdw%vdw_pair_r) call mfree('vdw_terminate [vdw_pair_e]', vdw%vdw_pair_e) call mfree('vdw_terminate [vdw_pair_mask_b]', vdw%vdw_pair_mask_a) call mfree('vdw_terminate [vdw_pair_mask_b]', vdw%vdw_pair_mask_b) if(vdw%use_nl) call nl_terminate(vdw%nl) end subroutine subroutine vdw_remove_potential(vdw, i) !! Remove the VdW interaction from the specified atom !! the atom will not interact anymore with any other atom implicit none type(ommp_nonbonded_type), intent(inout) :: vdw integer(ip), intent(in) :: i vdw%vdw_e(i) = 0.0 ! TODO do it also for pair interactions end subroutine subroutine vdw_set_pair(vdw, mask_a, mask_b, r, e) use mod_io, only: ommp_message, fatal_error use mod_constants, only: OMMP_VERBOSE_LOW use mod_memory, only: mallocate, mfree implicit none type(ommp_nonbonded_type), intent(inout) :: vdw !! Nonbonded data structure logical(lp), intent(in) :: mask_a(vdw%top%mm_atoms) logical(lp), intent(in) :: mask_b(vdw%top%mm_atoms) real(rp), intent(in) :: r !! Equilibrium distance for the pair real(rp), intent(in) :: e !! Depth of the potential integer(ip) :: oldsize, newsize logical(lp), allocatable :: ltmp(:,:) real(rp), allocatable :: rtmp(:) character(len=OMMP_STR_CHAR_MAX) :: msg oldsize = size(vdw%vdw_pair_r) if(vdw%npair >= oldsize) then newsize = oldsize + pair_allocation_chunk call mallocate('vdw_set_pair [rtmp]', oldsize, rtmp) call mallocate('vdw_set_pair [ltmp]',vdw%top%mm_atoms, oldsize, ltmp) rtmp = vdw%vdw_pair_r call mfree('vdw_set_pair [vdw%vdw_pair_r]', vdw%vdw_pair_r) call mallocate('vdw_set_pair [vdw%vdw_pair_r]', newsize, vdw%vdw_pair_r) vdw%vdw_pair_r(1:oldsize) = rtmp rtmp = vdw%vdw_pair_e call mfree('vdw_set_pair [vdw%vdw_pair_e]', vdw%vdw_pair_e) call mallocate('vdw_set_pair [vdw%vdw_pair_e]', newsize, vdw%vdw_pair_e) vdw%vdw_pair_e(1:oldsize) = rtmp ltmp = vdw%vdw_pair_mask_a call mfree('vdw_set_pair [vdw_pair_mask_a]', vdw%vdw_pair_mask_a) call mallocate('vdw_set_pair [vdw_pair_mask_a]', & vdw%top%mm_atoms, newsize, vdw%vdw_pair_mask_a) vdw%vdw_pair_mask_a(:,1:oldsize) = ltmp ltmp = vdw%vdw_pair_mask_b call mfree('vdw_set_pair [vdw_pair_mask_b]', vdw%vdw_pair_mask_b) call mallocate('vdw_set_pair [vdw_pair_mask_b]', & vdw%top%mm_atoms, newsize, vdw%vdw_pair_mask_b) vdw%vdw_pair_mask_b(:,1:oldsize) = ltmp call mfree('vdw_set_pair [rtmp]', rtmp) call mfree('vdw_set_pair [ltmp]', ltmp) end if vdw%npair = vdw%npair + 1 vdw%vdw_pair_mask_a(:,vdw%npair) = mask_a vdw%vdw_pair_mask_b(:,vdw%npair) = mask_b vdw%vdw_pair_r(vdw%npair) = r vdw%vdw_pair_e(vdw%npair) = e end subroutine vdw_set_pair subroutine vdw_lennard_jones(Rij, Rij0, Eij, V) implicit none real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(inout) :: V real(rp) :: sigma_ov_r sigma_ov_r = Rij0 / Rij V = V + Eij*(sigma_ov_r**12 - 2_rp*sigma_ov_r**6) end subroutine vdw_lennard_jones subroutine vdw_lennard_jones_Rijgrad(Rij, Rij0, Eij, Rijgrad) implicit none real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(out) :: Rijgrad real(rp) :: sigma_ov_r sigma_ov_r = Rij0 / Rij Rijgrad = -12.0 * Eij * (sigma_ov_r ** 12 - sigma_ov_r ** 6) / Rij end subroutine vdw_lennard_jones_Rijgrad subroutine vdw_buffered_7_14(Rij, Rij0, Eij, V) !! Compute the dispersion-repulsion energy using the buffered 7-14 !! potential. Details can be found in ref: 10.1021/jp027815 implicit none real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(inout) :: V real(rp) :: rho real(rp), parameter :: delta = 0.07, gam = 0.12 integer(ip), parameter :: n = 14, m = 7 rho = Rij / Rij0 V = V + Eij*((1+delta)/(rho+delta))**(n-m) * ((1+gam)/(rho**m+gam)-2) end subroutine vdw_buffered_7_14 subroutine vdw_buffered_7_14_Rijgrad(Rij, Rij0, Eij, Rijgrad) !! Compute the gradient of vdw energy (using the buffered 7-14 !! potential ref: 10.1021/jp027815) with respect to the distance !! between the two atoms (Rij). implicit none real(rp), intent(in) :: Rij real(rp), intent(in) :: Rij0 real(rp), intent(in) :: Eij real(rp), intent(out) :: Rijgrad real(rp) :: rho, rhom real(rp), parameter :: delta = 0.07, gam = 0.12 integer(ip), parameter :: n = 14, m = 7 rho = Rij / Rij0 rhom = rho**m Rijgrad = Eij * ((delta+1)/(delta+rho))**(n-m) * & (rho*(gam+rhom)*(m-n)*(1-2*rhom-gam) - & rhom*m*(delta+rho)*(gam+1)) / & (rho*(delta+rho)*(gam+rhom)**2) Rijgrad = Rijgrad / Rij0 end subroutine vdw_buffered_7_14_Rijgrad pure function get_Rij0(vdw, i, j) result(Rij0) use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in), target :: vdw !! Nonbonded data structure integer(ip), intent(in) :: i, j !! Indices of interacting atoms real(rp) :: Rij0 if(vdw%vdw_r(i) < eps_rp .and. vdw%vdw_r(j) < eps_rp) then Rij0 = 0.0 return end if select case(vdw%radrule) case(OMMP_RADRULE_ARITHMETIC) Rij0 = vdw%radf*(vdw%vdw_r(i) + vdw%vdw_r(j))/2 case(OMMP_RADRULE_CUBIC) Rij0 = (vdw%vdw_r(i)**3 + vdw%vdw_r(j)**3) / & (vdw%vdw_r(i)**2 + vdw%vdw_r(j)**2) case default Rij0 = 0.0 end select end function pure function get_eij(vdw, i, j) result(eij) use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in) :: vdw !! Nonbonded data structure integer(ip), intent(in) :: i, j !! Indices of interacting atoms real(rp) :: eij if(vdw%vdw_e(i) < eps_rp .and. vdw%vdw_e(j) < eps_rp) then eij = 0.0 return end if select case(vdw%epsrule) case(OMMP_EPSRULE_GEOMETRIC) eij = sqrt(vdw%vdw_e(i)*vdw%vdw_e(j)) case(OMMP_EPSRULE_HHG) eij = (4*vdw%vdw_e(i)*vdw%vdw_e(j)) / & (vdw%vdw_e(i)**0.5 + vdw%vdw_e(j)**0.5)**2 case default eij = 0.0 end select end function pure function get_Rij0_inter(vdw1, vdw2, i, j) result(Rij0) use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in), target :: vdw1, vdw2 !! Nonbonded data structure integer(ip), intent(in) :: i, j !! Indices of interacting atoms real(rp) :: Rij0 if(abs(vdw1%radrule - vdw2%radrule) > eps_rp .or. & abs(vdw1%radf - vdw2%radf) > eps_rp) then Rij0 = 0.0 return end if if(vdw1%vdw_r(i) < eps_rp .and. vdw2%vdw_r(j) < eps_rp) then Rij0 = 0.0 return end if select case(vdw1%radrule) case(OMMP_RADRULE_ARITHMETIC) Rij0 = vdw1%radf*(vdw1%vdw_r(i) + vdw2%vdw_r(j))/2 case(OMMP_RADRULE_CUBIC) Rij0 = (vdw1%vdw_r(i)**3 + vdw2%vdw_r(j)**3) / & (vdw1%vdw_r(i)**2 + vdw2%vdw_r(j)**2) case default Rij0 = 0.0 end select end function pure function get_eij_inter(vdw1, vdw2, i, j) result(eij) use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in) :: vdw1, vdw2 !! Nonbonded data structure integer(ip), intent(in) :: i, j !! Indices of interacting atoms real(rp) :: eij if(vdw1%epsrule /= vdw2%epsrule) then eij = 0.0 return end if if(vdw1%vdw_e(i) < eps_rp .and. vdw2%vdw_e(j) < eps_rp) then eij = 0.0 return end if select case(vdw1%epsrule) case(OMMP_EPSRULE_GEOMETRIC) eij = sqrt(vdw1%vdw_e(i)*vdw2%vdw_e(j)) case(OMMP_EPSRULE_HHG) eij = (4*vdw1%vdw_e(i)*vdw2%vdw_e(j)) / & (vdw1%vdw_e(i)**0.5 + vdw2%vdw_e(j)**0.5)**2 case default eij = 0.0 end select end function subroutine vdw_potential(vdw, V) !! Compute the dispersion repulsion energy for the whole system !! using a double loop algorithm use mod_io, only : fatal_error use mod_profiling, only: time_push, time_pull use mod_constants, only: eps_rp use mod_memory, only: mallocate, mfree use mod_neighbor_list, only: get_ith_nl implicit none type(ommp_nonbonded_type), intent(in), target :: vdw !! Nonbonded data structure real(rp), intent(inout) :: V !! Potential, result will be added integer(ip) :: i, j, jc, l, ipair, ineigh, nthreads, ithread, nn real(rp) :: eij, rij0, rij, ci(3), cj(3), s, vtmp type(ommp_topology_type), pointer :: top procedure(vdw_term), pointer :: vdw_func integer(ip), allocatable :: nl_neigh(:,:) real(rp), allocatable :: nl_r(:,:) integer :: omp_get_num_threads, omp_get_thread_num call time_push() !$omp parallel nthreads = omp_get_num_threads() !$omp end parallel top => vdw%top select case(vdw%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_func => vdw_lennard_jones case(OMMP_VDWTYPE_BUF714) vdw_func => vdw_buffered_7_14 case default vdw_func => vdw_buffered_7_14 call fatal_error("Unexpected error in vdw_potential") end select if(vdw%use_nl) then call mallocate('vdw_potential [rneigh]', top%mm_atoms, nthreads, nl_r) call mallocate('vdw_potential [nl_neigh]', top%mm_atoms, nthreads, nl_neigh) end if !$omp parallel do default(shared) reduction(+:v) schedule(dynamic) & !$omp private(i,j,jc,ineigh,ithread,nn,s,ci,cj,ipair,l,Eij,Rij0,Rij,vtmp) do i=1, top%mm_atoms ithread = omp_get_thread_num() + 1 if(abs(vdw%vdw_f(i) - 1.0_rp) < eps_rp) then ci = top%cmm(:,i) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top%conn(1)%ri(i+1) - top%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms") end if ineigh = top%conn(1)%ci(top%conn(1)%ri(i)) ci = top%cmm(:,ineigh) + (top%cmm(:,i) - top%cmm(:,ineigh)) & * vdw%vdw_f(i) endif ! If neighbor list are enabled get the one for the current if(vdw%use_nl) call get_ith_nl(vdw%nl, i, top%cmm, & nl_neigh(:,ithread), & nl_r(:,ithread), nn) do jc=1, top%mm_atoms ! If the two atoms aren't neighbors, just skip the loop if(vdw%use_nl) then if(jc > nn) exit !! All neighbors done! j = nl_neigh(jc,ithread) if(j <= i) cycle else ! Skip all iteration with j <= i if(jc > i) then j = jc else cycle end if end if ! Compute the screening factor for this pair s = 1.0_rp do ineigh=1,4 ! Look if j is at distance ineigh from i if(any(top%conn(ineigh)%ci(top%conn(ineigh)%ri(i): & top%conn(ineigh)%ri(i+1)-1) == j)) then s = vdw%vdw_screening(ineigh) ! Exit the loop exit end if end do if(s > eps_rp) then ipair = -1 do l=1, vdw%npair if((vdw%vdw_pair_mask_a(i,l) .and. vdw%vdw_pair_mask_b(j,l)) .or. & (vdw%vdw_pair_mask_a(j,l) .and. vdw%vdw_pair_mask_b(i,l))) then ipair = l exit end if end do if(ipair > 0) then Rij0 = vdw%vdw_pair_r(ipair) eij = vdw%vdw_pair_e(ipair) else Rij0 = get_Rij0(vdw, i, j) eij = get_eij(vdw, i, j) end if if(abs(vdw%vdw_f(j) - 1.0_rp) < eps_rp) then cj = top%cmm(:,j) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top%conn(1)%ri(j+1) - top%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms") end if ineigh = top%conn(1)%ci(top%conn(1)%ri(j)) cj = top%cmm(:,ineigh) + & (top%cmm(:,j) - top%cmm(:,ineigh)) * vdw%vdw_f(j) endif Rij = norm2(ci-cj) if(Rij < eps_rp) then call fatal_error("Requesting non-bonded potential for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if vtmp = 0.0_rp call vdw_func(Rij, Rij0, Eij, vtmp) v = v + vtmp*s end if end do end do if(vdw%use_nl) then call mfree('vdw_potential [rneigh]', nl_r) call mfree('vdw_potential [nl_neigh]', nl_neigh) end if call time_pull('VdW potential calculation') end subroutine vdw_potential subroutine vdw_geomgrad(vdw, grad) !! Compute the dispersion repulsion geometric gradients for the whole system !! using a double loop algorithm use mod_io, only : fatal_error use mod_constants, only: eps_rp use mod_jacobian_mat, only: Rij_jacobian use mod_profiling, only: time_push, time_pull use mod_memory, only: mallocate, mfree use mod_neighbor_list, only: get_ith_nl implicit none type(ommp_nonbonded_type), intent(in), target :: vdw !! Nonbonded data structure real(rp), intent(inout) :: grad(3,vdw%top%mm_atoms) !! Gradients, result will be added integer(ip) :: i, j, l, ipair, ineigh, ineigh_i, ineigh_j, jc, & nn, ithread, nthreads real(rp) :: eij, rij0, rij, ci(3), cj(3), s, J_i(3), J_j(3), Rijg, & f_i, f_j logical :: skip type(ommp_topology_type), pointer :: top procedure(vdw_gterm), pointer :: vdw_gfunc integer(ip), allocatable :: nl_neigh(:,:) real(rp), allocatable :: nl_r(:,:) integer :: omp_get_num_threads, omp_get_thread_num call time_push() !$omp parallel nthreads = omp_get_num_threads() !$omp end parallel top => vdw%top select case(vdw%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_gfunc => vdw_lennard_jones_Rijgrad case(OMMP_VDWTYPE_BUF714) vdw_gfunc => vdw_buffered_7_14_Rijgrad case default vdw_gfunc => vdw_buffered_7_14_Rijgrad call fatal_error("Unexpected error in vdw_geomgrad") end select if(vdw%use_nl) then call mallocate('vdw_geomgrad [rneigh]', top%mm_atoms, nthreads, nl_r) call mallocate('vdw_geomgrad [nl_neigh]', top%mm_atoms, nthreads, nl_neigh) end if !$omp parallel do default(shared) schedule(dynamic) & !$omp private(i,j,ci,cj,ineigh,ineigh_i,ineigh_j,f_i,f_j,s,ipair,l) & !$omp private(Eij,Rij0,Rijg,Rij,J_i,J_j,skip,jc,nn,ithread) do i=1, top%mm_atoms ithread = omp_get_thread_num() + 1 if(abs(vdw%vdw_f(i) - 1.0) < eps_rp) then ci = top%cmm(:,i) ineigh_i = 0 ! This is needed later for force projection f_i = 1.0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top%conn(1)%ri(i+1) - top%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms") end if ineigh_i = top%conn(1)%ci(top%conn(1)%ri(i)) f_i = vdw%vdw_f(i) ci = top%cmm(:,ineigh_i) + (top%cmm(:,i) - & top%cmm(:,ineigh_i)) * f_i endif if(vdw%use_nl) call get_ith_nl(vdw%nl, i, top%cmm, & nl_neigh(:,ithread), & nl_r(:,ithread), nn) do jc=1, top%mm_atoms ! If the two atoms aren't neighbors, just skip the loop if(vdw%use_nl) then if(jc > nn) exit !! All neighbors done! j = nl_neigh(jc,ithread) if(j <= i) cycle else ! Skip all iteration with j <= i if(jc > i) then j = jc else cycle end if end if ! Compute the screening factor for this pair s = 1.0_rp do ineigh=1,4 ! Look if j is at distance ineigh from i if(any(top%conn(ineigh)%ci(top%conn(ineigh)%ri(i): & top%conn(ineigh)%ri(i+1)-1) == j)) then s = vdw%vdw_screening(ineigh) ! Exit the loop exit end if end do if(s > eps_rp) then if(abs(vdw%vdw_f(j) - 1.0) < eps_rp) then cj = top%cmm(:,j) ineigh_j = 0 ! This is needed later for force projection f_j = 1.0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top%conn(1)%ri(j+1) - top%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms") end if ineigh_j = top%conn(1)%ci(top%conn(1)%ri(j)) f_j = vdw%vdw_f(j) cj = top%cmm(:,ineigh_j) + & (top%cmm(:,j) - top%cmm(:,ineigh_j)) * f_j endif ! if all atoms in the interaction are frozen ! just skip to next iteration if(top%use_frozen) then skip = .true. skip = skip .and. top%frozen(i) skip = skip .and. top%frozen(j) if(ineigh_i > 0) skip = skip .and. top%frozen(ineigh_i) if(ineigh_j > 0) skip = skip .and. top%frozen(ineigh_j) if(skip) cycle end if ipair = -1 do l=1, vdw%npair if((vdw%vdw_pair_mask_a(i,l) .and. vdw%vdw_pair_mask_b(j,l)) .or. & (vdw%vdw_pair_mask_a(j,l) .and. vdw%vdw_pair_mask_b(i,l))) then ipair = l exit end if end do if(ipair > 0) then Rij0 = vdw%vdw_pair_r(ipair) eij = vdw%vdw_pair_e(ipair) else Rij0 = get_Rij0(vdw, i, j) eij = get_eij(vdw, i, j) end if call Rij_jacobian(ci, cj, Rij, J_i, J_j) if(Rij < eps_rp) then call fatal_error("Requesting non-bonded gradients for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if call vdw_gfunc(Rij, Rij0, Eij, Rijg) Rijg = Rijg * s if(ineigh_i == 0) then if(.not. (top%use_frozen .and. top%frozen(i))) then !$omp atomic update grad(1,i) = grad(1,i) + J_i(1) * Rijg !$omp atomic update grad(2,i) = grad(2,i) + J_i(2) * Rijg !$omp atomic update grad(3,i) = grad(3,i) + J_i(3) * Rijg end if else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top%use_frozen .and. top%frozen(i))) then !$omp atomic update grad(1,i) = grad(1,i) + J_i(1) * Rijg * f_i !$omp atomic update grad(2,i) = grad(2,i) + J_i(2) * Rijg * f_i !$omp atomic update grad(3,i) = grad(3,i) + J_i(3) * Rijg * f_i end if if(.not. (top%use_frozen .and. top%frozen(ineigh_i))) then !$omp atomic update grad(1,ineigh_i) = grad(1,ineigh_i) + J_i(1) * Rijg * (1-f_i) !$omp atomic update grad(2,ineigh_i) = grad(2,ineigh_i) + J_i(2) * Rijg * (1-f_i) !$omp atomic update grad(3,ineigh_i) = grad(3,ineigh_i) + J_i(3) * Rijg * (1-f_i) end if end if if(ineigh_j == 0) then if(.not. (top%use_frozen .and. top%frozen(j))) then !$omp atomic update grad(1,j) = grad(1,j) + J_j(1) * Rijg !$omp atomic update grad(2,j) = grad(2,j) + J_j(2) * Rijg !$omp atomic update grad(3,j) = grad(3,j) + J_j(3) * Rijg end if else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top%use_frozen .and. top%frozen(j))) then !$omp atomic update grad(1,j) = grad(1,j) + J_j(1) * Rijg * f_j !$omp atomic update grad(2,j) = grad(2,j) + J_j(2) * Rijg * f_j !$omp atomic update grad(3,j) = grad(3,j) + J_j(3) * Rijg * f_j end if if(.not. (top%use_frozen .and. top%frozen(ineigh_j))) then !$omp atomic update grad(1,ineigh_j) = grad(1,ineigh_j) + J_j(1) * Rijg * (1-f_j) !$omp atomic update grad(2,ineigh_j) = grad(2,ineigh_j) + J_j(2) * Rijg * (1-f_j) !$omp atomic update grad(3,ineigh_j) = grad(3,ineigh_j) + J_j(3) * Rijg * (1-f_j) end if endif end if end do end do call time_pull('VdW gradients calculation') end subroutine subroutine vdw_potential_inter(vdw1, vdw2, V) !! Compute the dispersion repulsion energy for the whole system !! using a double loop algorithm use mod_io, only : fatal_error use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in), target :: vdw1, vdw2 !! Nonbonded data structure real(rp), intent(inout) :: V !! Potential, result will be added integer(ip) :: i, j, ineigh real(rp) :: eij, rij0, rij, ci(3), cj(3), vtmp type(ommp_topology_type), pointer :: top1, top2 procedure(vdw_term), pointer :: vdw_func top1 => vdw1%top top2 => vdw2%top if(vdw1%vdwtype /= vdw2%vdwtype .or. & vdw1%radrule /= vdw2%radrule .or. & vdw1%epsrule /= vdw2%epsrule) then call fatal_error("Requested VdW potential between two incompatible & &VdW groups.") end if select case(vdw1%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_func => vdw_lennard_jones case(OMMP_VDWTYPE_BUF714) vdw_func => vdw_buffered_7_14 case default vdw_func => vdw_buffered_7_14 call fatal_error("Unexpected error in vdw_potential_inter") end select !$omp parallel do default(shared) schedule(dynamic) & !$omp private(i,j,ci,cj,ineigh,Rij,Rij0,Eij,vtmp) reduction(+:v) do i=1, top1%mm_atoms if(abs(vdw1%vdw_f(i) - 1.0_rp) < eps_rp) then ci = top1%cmm(:,i) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top1%conn(1)%ri(i+1) - top1%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms (top1)") end if ineigh = top1%conn(1)%ci(top1%conn(1)%ri(i)) ci = top1%cmm(:,ineigh) + (top1%cmm(:,i) - top1%cmm(:,ineigh)) & * vdw1%vdw_f(i) endif do j=1, top2%mm_atoms Rij0 = get_Rij0_inter(vdw1, vdw2, i, j) eij = get_eij_inter(vdw1, vdw2, i, j) if(abs(vdw2%vdw_f(j) - 1.0_rp) < eps_rp) then cj = top2%cmm(:,j) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top2%conn(1)%ri(j+1) - top2%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms (top2) atom") end if ineigh = top2%conn(1)%ci(top2%conn(1)%ri(j)) cj = top2%cmm(:,ineigh) + & (top2%cmm(:,j) - top2%cmm(:,ineigh)) * vdw2%vdw_f(j) endif Rij = norm2(ci-cj) if(Rij < eps_rp) then call fatal_error("Requesting inter non-bonded potential for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if vtmp = 0.0_rp call vdw_func(Rij, Rij0, Eij, vtmp) v = v + vtmp end do end do end subroutine vdw_potential_inter subroutine vdw_geomgrad_inter(vdw1, vdw2, grad1, grad2) !! Compute the dispersion repulsion energy for the whole system !! using a double loop algorithm use mod_io, only : fatal_error use mod_constants, only: eps_rp use mod_jacobian_mat, only: Rij_jacobian implicit none type(ommp_nonbonded_type), intent(in), target :: vdw1, vdw2 !! Nonbonded data structure real(rp), intent(inout) :: grad1(3,vdw1%top%mm_atoms), & grad2(3,vdw2%top%mm_atoms) !! Potential, result will be added integer(ip) :: i, j, ineigh_i, ineigh_j real(rp) :: eij, rij0, rij, ci(3), cj(3), Rijg, f_i, f_j, & J_i(3), J_j(3) logical :: skip type(ommp_topology_type), pointer :: top1, top2 procedure(vdw_gterm), pointer :: vdw_grad top1 => vdw1%top top2 => vdw2%top if(vdw1%vdwtype /= vdw2%vdwtype .or. & vdw1%radrule /= vdw2%radrule .or. & vdw1%epsrule /= vdw2%epsrule) then call fatal_error("Requested VdW potential between two incompatible & &VdW groups.") end if select case(vdw1%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_grad => vdw_lennard_jones_Rijgrad case(OMMP_VDWTYPE_BUF714) vdw_grad => vdw_buffered_7_14_Rijgrad case default vdw_grad => vdw_buffered_7_14_Rijgrad call fatal_error("Unexpected error in vdw_geomgrad_inter") end select !$omp parallel do default(shared) schedule(dynamic) & !$omp private(i,j,ci,cj,f_i,f_j,ineigh_i,ineigh_j,Eij,Rij0,Rij,Rijg,J_i,J_j,skip) do i=1, top1%mm_atoms if(abs(vdw1%vdw_f(i) - 1.0) < eps_rp) then ci = top1%cmm(:,i) ineigh_i = 0 f_i = 1.0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top1%conn(1)%ri(i+1) - top1%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms") end if ineigh_i = top1%conn(1)%ci(top1%conn(1)%ri(i)) f_i = vdw1%vdw_f(i) ci = top1%cmm(:,ineigh_i) + (top1%cmm(:,i) - top1%cmm(:,ineigh_i)) & * f_i endif do j=1, top2%mm_atoms if(abs(vdw2%vdw_f(j) - 1.0) < eps_rp) then cj = top2%cmm(:,j) ineigh_j = 0 f_j = 1.0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top2%conn(1)%ri(j+1) - top2%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms") end if ineigh_j = top2%conn(1)%ci(top2%conn(1)%ri(j)) f_j = vdw2%vdw_f(j) cj = top2%cmm(:,ineigh_j) + & (top2%cmm(:,j) - top2%cmm(:,ineigh_j)) * f_j endif skip = top1%use_frozen .and. top2%use_frozen if(skip .and. top1%use_frozen) then skip = skip .and. top1%frozen(i) if(ineigh_i > 0) skip = skip .and. top1%frozen(ineigh_i) end if if(skip .and. top2%use_frozen) then skip = skip .and. top2%frozen(j) if(ineigh_j > 0) skip = skip .and. top2%frozen(ineigh_j) end if if(skip) cycle Rij0 = get_Rij0_inter(vdw1, vdw2, i, j) eij = get_eij_inter(vdw1, vdw2, i, j) call Rij_jacobian(ci, cj, Rij, J_i, J_j) if(Rij < eps_rp) then call fatal_error("Requesting inter non-bonded gradients for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if call vdw_grad(Rij, Rij0, Eij, Rijg) !$omp critical if(ineigh_i == 0) then if(.not. (top1%use_frozen .and. top1%frozen(i))) & grad1(:,i) = grad1(:,i) + J_i * Rijg else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top1%use_frozen .and. top1%frozen(i))) & grad1(:,i) = grad1(:,i) + J_i * Rijg * f_i if(.not. (top1%use_frozen .and. top1%frozen(ineigh_i))) & grad1(:,ineigh_i) = grad1(:,ineigh_i) + J_i * Rijg * (1-f_i) end if if(ineigh_j == 0) then if(.not. (top2%use_frozen .and. top2%frozen(j))) & grad2(:,j) = grad2(:,j) + J_j * Rijg else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top2%use_frozen .and. top2%frozen(j))) & grad2(:,j) = grad2(:,j) + J_j * Rijg * f_j if(.not. (top2%use_frozen .and. top2%frozen(ineigh_j))) & grad2(:,ineigh_j) = grad2(:,ineigh_j) + J_j * Rijg * (1-f_j) endif !$omp end critical end do end do end subroutine subroutine vdw_potential_inter_restricted(vdw1, vdw2, pairs, s, n, V) !! Compute the dispersion repulsion energy between two systems vdw1 !! and vdw2 accounting only for the pairs pairs(1,i)--pairs(2,i) and scaling !! each interaction by s(i). use mod_io, only : fatal_error use mod_constants, only: eps_rp implicit none type(ommp_nonbonded_type), intent(in), target :: vdw1, vdw2 !! Nonbonded data structure integer(ip), intent(in) :: n !! number of pairs for which the interaction should be computed integer(ip), intent(in) :: pairs(2,n) !! pairs of atoms for which the interaction should be computed real(rp), intent(in) :: s(:) !! scaling factors for each interaction real(rp), intent(inout) :: V !! Potential, result will be added integer(ip) :: i, j, ineigh, ip real(rp) :: eij, rij0, rij, ci(3), cj(3), vtmp type(ommp_topology_type), pointer :: top1, top2 procedure(vdw_term), pointer :: vdw_func top1 => vdw1%top top2 => vdw2%top if(vdw1%vdwtype /= vdw2%vdwtype .or. & vdw1%radrule /= vdw2%radrule .or. & vdw1%epsrule /= vdw2%epsrule) then call fatal_error("Requested VdW potential between two incompatible & &VdW groups.") end if select case(vdw1%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_func => vdw_lennard_jones case(OMMP_VDWTYPE_BUF714) vdw_func => vdw_buffered_7_14 case default vdw_func => vdw_buffered_7_14 call fatal_error("Unexpected error in vdw_potential_inter_restricted") end select !$omp parallel do default(shared) schedule(dynamic) & !$omp private(i,j,ip,ci,cj,ineigh,Rij,Rij0,Eij,vtmp) reduction(+:v) do ip=1, n i = pairs(1,ip) j = pairs(2,ip) if(abs(vdw1%vdw_f(i) - 1.0_rp) < eps_rp) then ci = top1%cmm(:,i) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top1%conn(1)%ri(i+1) - top1%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms") end if ineigh = top1%conn(1)%ci(top1%conn(1)%ri(i)) ci = top1%cmm(:,ineigh) + (top1%cmm(:,i) - top1%cmm(:,ineigh)) & * vdw1%vdw_f(i) endif Rij0 = get_Rij0_inter(vdw1, vdw2, i, j) eij = get_eij_inter(vdw1, vdw2, i, j) if(abs(vdw2%vdw_f(j) - 1.0_rp) < eps_rp) then cj = top2%cmm(:,j) else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top2%conn(1)%ri(j+1) - top2%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms") end if ineigh = top2%conn(1)%ci(top2%conn(1)%ri(j)) cj = top2%cmm(:,ineigh) + & (top2%cmm(:,j) - top2%cmm(:,ineigh)) * vdw2%vdw_f(j) endif Rij = norm2(ci-cj) if(Rij < eps_rp) then call fatal_error("Requesting inter non-bonded potential for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if vtmp = 0.0_rp call vdw_func(Rij, Rij0, Eij, vtmp) v = v + vtmp * s(ip) end do end subroutine vdw_potential_inter_restricted subroutine vdw_geomgrad_inter_restricted(vdw1, vdw2, pairs, s, n, & grad1, grad2) !! Compute the dispersion repulsion energy for the whole system !! using a double loop algorithm use mod_io, only : fatal_error use mod_constants, only: eps_rp use mod_jacobian_mat, only: Rij_jacobian implicit none type(ommp_nonbonded_type), intent(in), target :: vdw1, vdw2 !! Nonbonded data structure integer(ip), intent(in) :: n !! number of pairs for which the interaction should be computed integer(ip), intent(in) :: pairs(2,n) !! pairs of atoms for which the interaction should be computed real(rp), intent(in) :: s(:) !! scaling factors for each interaction real(rp), intent(inout) :: grad1(3,vdw1%top%mm_atoms), & grad2(3,vdw2%top%mm_atoms) !! Potential, result will be added integer(ip) :: i, j, ineigh_i, ineigh_j, ip real(rp) :: eij, rij0, rij, ci(3), cj(3), Rijg, f_i, f_j, & J_i(3), J_j(3) logical :: skip type(ommp_topology_type), pointer :: top1, top2 procedure(vdw_gterm), pointer :: vdw_grad top1 => vdw1%top top2 => vdw2%top if(vdw1%vdwtype /= vdw2%vdwtype .or. & vdw1%radrule /= vdw2%radrule .or. & vdw1%epsrule /= vdw2%epsrule) then call fatal_error("Requested VdW potential between two incompatible & &VdW groups.") end if select case(vdw1%vdwtype) case(OMMP_VDWTYPE_LJ) vdw_grad => vdw_lennard_jones_Rijgrad case(OMMP_VDWTYPE_BUF714) vdw_grad => vdw_buffered_7_14_Rijgrad case default vdw_grad => vdw_buffered_7_14_Rijgrad call fatal_error("Unexpected error in vdw_geomgrad_inter_restricted") end select do ip=1, n i = pairs(1,ip) j = pairs(2,ip) if(abs(vdw1%vdw_f(i) - 1.0) < eps_rp) then ci = top1%cmm(:,i) ineigh_i = 0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top1%conn(1)%ri(i+1) - top1%conn(1)%ri(i) /= 1) then call fatal_error("Scale factors are only expected for & &monovalent atoms") end if ineigh_i = top1%conn(1)%ci(top1%conn(1)%ri(i)) f_i = vdw1%vdw_f(i) ci = top1%cmm(:,ineigh_i) + (top1%cmm(:,i) - top1%cmm(:,ineigh_i)) & * f_i endif if(abs(vdw2%vdw_f(j) - 1.0) < eps_rp) then cj = top2%cmm(:,j) ineigh_j = 0 else ! Scale factors are used only for monovalent atoms, in that ! case the vdw center is displaced along the axis connecting ! the atom to its neighbour if(top2%conn(1)%ri(j+1) - top2%conn(1)%ri(j) /= 1) then call fatal_error("Scale factors are only expected & & for monovalent atoms") end if ineigh_j = top2%conn(1)%ci(top2%conn(1)%ri(j)) f_j = vdw2%vdw_f(j) cj = top2%cmm(:,ineigh_j) + & (top2%cmm(:,j) - top2%cmm(:,ineigh_j)) * f_j endif skip = top1%use_frozen .and. top2%use_frozen if(skip .and. top1%use_frozen) then skip = skip .and. top1%frozen(i) if(ineigh_i > 0) skip = skip .and. top1%frozen(ineigh_i) end if if(skip .and. top2%use_frozen) then skip = skip .and. top2%frozen(j) if(ineigh_j > 0) skip = skip .and. top2%frozen(ineigh_j) end if if(skip) cycle Rij0 = get_Rij0_inter(vdw1, vdw2, i, j) eij = get_eij_inter(vdw1, vdw2, i, j) * s(ip) call Rij_jacobian(ci, cj, Rij, J_i, J_j) if(Rij < eps_rp) then call fatal_error("Requesting inter non-bonded gradients for two atoms & &placed in the same point, this could be & &an internal bug or a problem in your input & &file, please check.") end if call vdw_grad(Rij, Rij0, Eij, Rijg) if(ineigh_i == 0) then if(.not. (top1%use_frozen .and. top1%frozen(i))) & grad1(:,i) = grad1(:,i) + J_i * Rijg else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top1%use_frozen .and. top1%frozen(i))) & grad1(:,i) = grad1(:,i) + J_i * Rijg * f_i if(.not. (top1%use_frozen .and. top1%frozen(ineigh_i))) & grad1(:,ineigh_i) = grad1(:,ineigh_i) + J_i * Rijg * (1-f_i) end if if(ineigh_j == 0) then if(.not. (top2%use_frozen .and. top2%frozen(j))) & grad2(:,j) = grad2(:,j) + J_j * Rijg else ! If the center is displaced, the forces should be ! projected onto the two atoms that determine the ! position of the center if(.not. (top2%use_frozen .and. top2%frozen(j))) & grad2(:,j) = grad2(:,j) + J_j * Rijg * f_j if(.not. (top2%use_frozen .and. top2%frozen(ineigh_j))) & grad2(:,ineigh_j) = grad2(:,ineigh_j) + J_j * Rijg * (1-f_j) endif end do end subroutine end module mod_nonbonded