UseTheForce/DarkSide/eam.F90

!!
!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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!! non-exclusive, royalty free, license to use, modify and
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!! that the following conditions are met:
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!! 1. Acknowledgement of the program authors must be made in any
!!    publication of scientific results based in part on use of the
!!    program.  An acceptable form of acknowledgement is citation of
!!    the article in which the program was described (Matthew
!!    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
!!    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
!!    Parallel Simulation Engine for Molecular Dynamics,"
!!    J. Comput. Chem. 26, pp. 252-271 (2005))
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!! 2. Redistributions of source code must retain the above copyright
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module eam
  use definitions
  use simulation
  use force_globals
  use status
  use atype_module
  use vector_class
  use interpolation
#ifdef IS_MPI
  use mpiSimulation
#endif
  implicit none
  PRIVATE
#define __FORTRAN90
#include "UseTheForce/DarkSide/fInteractionMap.h"

  logical, save :: EAM_FF_initialized = .false.
  integer, save :: EAM_Mixing_Policy
  real(kind = dp), save :: EAM_rcut
  logical, save :: haveRcut = .false.

  character(len = statusMsgSize) :: errMesg
  integer :: eam_err

  character(len = 200) :: errMsg
  character(len=*), parameter :: RoutineName =  "EAM MODULE"
  !! Logical that determines if eam arrays should be zeroed
  logical :: cleanme = .true.

  type, private :: EAMtype
     integer           :: eam_atype       
     real( kind = DP ) :: eam_lattice        
     real( kind = DP ) :: eam_rcut     
     integer           :: eam_atype_map
     type(cubicSpline) :: rho 
     type(cubicSpline) :: Z
     type(cubicSpline) :: F
     type(cubicSpline) :: phi
  end type EAMtype

  !! Arrays for derivatives used in force calculation
  real( kind = dp), dimension(:), allocatable :: frho
  real( kind = dp), dimension(:), allocatable :: rho
  real( kind = dp), dimension(:), allocatable :: dfrhodrho

  !! Arrays for MPI storage
#ifdef IS_MPI
  real( kind = dp),save, dimension(:), allocatable :: dfrhodrho_col
  real( kind = dp),save, dimension(:), allocatable :: dfrhodrho_row
  real( kind = dp),save, dimension(:), allocatable :: frho_row
  real( kind = dp),save, dimension(:), allocatable :: frho_col
  real( kind = dp),save, dimension(:), allocatable :: rho_row
  real( kind = dp),save, dimension(:), allocatable :: rho_col
  real( kind = dp),save, dimension(:), allocatable :: rho_tmp
#endif

  type, private :: EAMTypeList
     integer           :: n_eam_types = 0
     integer           :: currentAddition = 0

     type (EAMtype), pointer  :: EAMParams(:) => null()
     integer, pointer         :: atidToEAMType(:) => null()
  end type EAMTypeList

  type (eamTypeList), save :: EAMList

  !! standard eam stuff  


  public :: init_EAM_FF
  public :: setCutoffEAM
  public :: do_eam_pair
  public :: newEAMtype
  public :: calc_eam_prepair_rho
  public :: calc_eam_preforce_Frho
  public :: clean_EAM
  public :: destroyEAMTypes
  public :: getEAMCut
  public :: lookupEAMSpline
  public :: lookupEAMSpline1d

contains

  subroutine newEAMtype(lattice_constant,eam_nrho,eam_drho,eam_nr,&
       eam_dr,rcut,eam_Z_r,eam_rho_r,eam_F_rho, c_ident, status)
    real (kind = dp )                      :: lattice_constant
    integer                                :: eam_nrho
    real (kind = dp )                      :: eam_drho
    integer                                :: eam_nr
    real (kind = dp )                      :: eam_dr
    real (kind = dp )                      :: rcut
    real (kind = dp ), dimension(eam_nr)   :: eam_Z_r, rvals
    real (kind = dp ), dimension(eam_nr)   :: eam_rho_r, eam_phi_r
    real (kind = dp ), dimension(eam_nrho) :: eam_F_rho, rhovals
    integer                                :: c_ident
    integer                                :: status

    integer                                :: nAtypes,nEAMTypes,myATID
    integer                                :: maxVals
    integer                                :: alloc_stat
    integer                                :: current, j
    integer,pointer                        :: Matchlist(:) => null()

    status = 0

    !! Assume that atypes has already been set and get the total number of types in atypes
    !! Also assume that every member of atypes is a EAM model.

    ! check to see if this is the first time into 
    if (.not.associated(EAMList%EAMParams)) then
       call getMatchingElementList(atypes, "is_EAM", .true., nEAMtypes, MatchList)
       EAMList%n_eam_types = nEAMtypes
       allocate(EAMList%EAMParams(nEAMTypes))
       nAtypes = getSize(atypes)
       allocate(EAMList%atidToEAMType(nAtypes))
    end if

    EAMList%currentAddition = EAMList%currentAddition + 1
    current = EAMList%currentAddition

    myATID =  getFirstMatchingElement(atypes, "c_ident", c_ident)
    EAMList%atidToEAMType(myATID) = current

    EAMList%EAMParams(current)%eam_atype    = c_ident
    EAMList%EAMParams(current)%eam_lattice  = lattice_constant
    EAMList%EAMParams(current)%eam_rcut     = rcut

    ! Build array of r values
    do j = 1, eam_nr
       rvals(j) = real(j-1,kind=dp) * eam_dr
    end do
    
    ! Build array of rho values
    do j = 1, eam_nrho
       rhovals(j) = real(j-1,kind=dp) * eam_drho
    end do

    ! convert from eV to kcal / mol:
    do j = 1, eam_nrho
       eam_F_rho(j) = eam_F_rho(j) * 23.06054E0_DP
    end do
    
    ! precompute the pair potential and get it into kcal / mol:
    eam_phi_r(1) = 0.0E0_DP
    do j = 2, eam_nr
       eam_phi_r(j) = 331.999296E0_DP * (eam_Z_r(j)**2) / rvals(j)
    enddo

    call newSpline(EAMList%EAMParams(current)%rho, rvals, eam_rho_r, .true.)
    call newSpline(EAMList%EAMParams(current)%Z,   rvals, eam_Z_r, .true.)
    call newSpline(EAMList%EAMParams(current)%F, rhovals, eam_F_rho, .true.)
    call newSpline(EAMList%EAMParams(current)%phi, rvals, eam_phi_r, .true.)
  end subroutine newEAMtype


  ! kills all eam types entered and sets simulation to uninitalized
  subroutine destroyEAMtypes()
    integer :: i
    type(EAMType), pointer :: tempEAMType=>null()

    do i = 1, EAMList%n_eam_types
       tempEAMType => eamList%EAMParams(i)
       call deallocate_EAMType(tempEAMType)
    end do
    if(associated( eamList%EAMParams)) deallocate( eamList%EAMParams)
    eamList%EAMParams => null()

    eamList%n_eam_types = 0
    eamList%currentAddition = 0
  end subroutine destroyEAMtypes

  function getEAMCut(atomID) result(cutValue)
    integer, intent(in) :: atomID
    integer :: eamID
    real(kind=dp) :: cutValue
    
    eamID = EAMList%atidToEAMType(atomID)
    cutValue = EAMList%EAMParams(eamID)%eam_rcut
  end function getEAMCut

  subroutine init_EAM_FF(status)
    integer :: status
    integer :: i,j
    real(kind=dp) :: current_rcut_max
#ifdef IS_MPI
    integer :: nAtomsInRow
    integer :: nAtomsInCol
#endif
    integer :: alloc_stat
    integer :: number_r, number_rho

    status = 0
    if (EAMList%currentAddition == 0) then
       call handleError("init_EAM_FF","No members in EAMList")
       status = -1
       return
    end if
    
    !! Allocate arrays for force calculation
    
#ifdef IS_MPI
    nAtomsInRow = getNatomsInRow(plan_atom_row)
    nAtomsInCol = getNatomsInCol(plan_atom_col)
#endif

    if (allocated(frho)) deallocate(frho)
    allocate(frho(nlocal),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

    if (allocated(rho)) deallocate(rho)
    allocate(rho(nlocal),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

    if (allocated(dfrhodrho)) deallocate(dfrhodrho)
    allocate(dfrhodrho(nlocal),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

#ifdef IS_MPI

    if (allocated(rho_tmp)) deallocate(rho_tmp)
    allocate(rho_tmp(nlocal),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

    if (allocated(frho_row)) deallocate(frho_row)
    allocate(frho_row(nAtomsInRow),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if
    if (allocated(rho_row)) deallocate(rho_row)
    allocate(rho_row(nAtomsInRow),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if
    if (allocated(dfrhodrho_row)) deallocate(dfrhodrho_row)
    allocate(dfrhodrho_row(nAtomsInRow),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

    ! Now do column arrays

    if (allocated(frho_col)) deallocate(frho_col)
    allocate(frho_col(nAtomsInCol),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if
    if (allocated(rho_col)) deallocate(rho_col)
    allocate(rho_col(nAtomsInCol),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if
    if (allocated(dfrhodrho_col)) deallocate(dfrhodrho_col)
    allocate(dfrhodrho_col(nAtomsInCol),stat=alloc_stat)
    if (alloc_stat /= 0) then 
       status = -1
       return
    end if

#endif

  end subroutine init_EAM_FF

  subroutine setCutoffEAM(rcut)
    real(kind=dp) :: rcut
    EAM_rcut = rcut
  end subroutine setCutoffEAM

  subroutine clean_EAM()

    ! clean non-IS_MPI first
    frho = 0.0_dp
    rho  = 0.0_dp
    dfrhodrho = 0.0_dp
    ! clean MPI if needed
#ifdef IS_MPI
    frho_row = 0.0_dp
    frho_col = 0.0_dp
    rho_row  = 0.0_dp
    rho_col  = 0.0_dp
    rho_tmp  = 0.0_dp
    dfrhodrho_row = 0.0_dp
    dfrhodrho_col = 0.0_dp
#endif
  end subroutine clean_EAM

  subroutine deallocate_EAMType(thisEAMType)
    type (EAMtype), pointer :: thisEAMType

    call deleteSpline(thisEAMType%F)
    call deleteSpline(thisEAMType%rho)
    call deleteSpline(thisEAMType%phi)
    call deleteSpline(thisEAMType%Z)

  end subroutine deallocate_EAMType

  !! Calculates rho_r
  subroutine calc_eam_prepair_rho(atom1,atom2,d,r,rijsq)
    integer :: atom1, atom2
    real(kind = dp), dimension(3) :: d
    real(kind = dp), intent(inout)               :: r
    real(kind = dp), intent(inout)               :: rijsq
    ! value of electron density rho do to atom i at atom j
    real(kind = dp) :: rho_i_at_j
    ! value of electron density rho do to atom j at atom i
    real(kind = dp) :: rho_j_at_i
    integer :: eam_err
    
    integer :: atid1, atid2 ! Global atid    
    integer :: myid_atom1 ! EAM atid
    integer :: myid_atom2 

    ! check to see if we need to be cleaned at the start of a force loop

#ifdef IS_MPI
    Atid1 = Atid_row(Atom1)
    Atid2 = Atid_col(Atom2)
#else
    Atid1 = Atid(Atom1)
    Atid2 = Atid(Atom2)
#endif

    Myid_atom1 = Eamlist%atidtoeamtype(Atid1)
    Myid_atom2 = Eamlist%atidtoeamtype(Atid2)

    if (r.lt.EAMList%EAMParams(myid_atom1)%eam_rcut) then

       call lookupEAMSpline(EAMList%EAMParams(myid_atom1)%rho, r, &
            rho_i_at_j)

#ifdef  IS_MPI
       rho_col(atom2) = rho_col(atom2) + rho_i_at_j
#else
       rho(atom2) = rho(atom2) + rho_i_at_j
#endif
    endif

    if (r.lt.EAMList%EAMParams(myid_atom2)%eam_rcut) then

       call lookupEAMSpline(EAMList%EAMParams(myid_atom2)%rho, r, &
            rho_j_at_i)

#ifdef  IS_MPI
       rho_row(atom1) = rho_row(atom1) + rho_j_at_i
#else
       rho(atom1) = rho(atom1) + rho_j_at_i
#endif
    endif
  end subroutine calc_eam_prepair_rho


  !! Calculate the functional F(rho) for all local atoms
  subroutine calc_eam_preforce_Frho(nlocal, pot, particle_pot)
    integer :: nlocal
    real(kind=dp) :: pot
    integer :: i, j
    integer :: atom
    real(kind=dp) :: U,U1
    real( kind = dp ), dimension(nlocal) :: particle_pot
    integer :: atype1
    integer :: me, atid1

    cleanme = .true.
    !! Scatter the electron density from  pre-pair calculation back to 
    !! local atoms
#ifdef IS_MPI
    call scatter(rho_row,rho,plan_atom_row,eam_err)
    if (eam_err /= 0 ) then
       write(errMsg,*) " Error scattering rho_row into rho"
       call handleError(RoutineName,errMesg)
    endif
    call scatter(rho_col,rho_tmp,plan_atom_col,eam_err)
    if (eam_err /= 0 ) then
       write(errMsg,*) " Error scattering rho_col into rho"
       call handleError(RoutineName,errMesg)
    endif

    rho(1:nlocal) = rho(1:nlocal) + rho_tmp(1:nlocal)
#endif

    !! Calculate F(rho) and derivative 
    do atom = 1, nlocal
       atid1 = atid(atom)
       me = eamList%atidToEAMtype(atid1)

       call lookupEAMSpline1d(EAMList%EAMParams(me)%F, rho(atom), &
            u, u1)
       
       frho(atom) = u
       dfrhodrho(atom) = u1
       pot = pot + u
       particle_pot(atom) = particle_pot(atom) + u

    enddo

#ifdef IS_MPI
    !! communicate f(rho) and derivatives back into row and column arrays
    call gather(frho,frho_row,plan_atom_row, eam_err)
    if (eam_err /=  0) then
       call handleError("cal_eam_forces()","MPI gather frho_row failure")
    endif
    call gather(dfrhodrho,dfrhodrho_row,plan_atom_row, eam_err)
    if (eam_err /=  0) then
       call handleError("cal_eam_forces()","MPI gather dfrhodrho_row failure")
    endif
    call gather(frho,frho_col,plan_atom_col, eam_err)
    if (eam_err /=  0) then
       call handleError("cal_eam_forces()","MPI gather frho_col failure")
    endif
    call gather(dfrhodrho,dfrhodrho_col,plan_atom_col, eam_err)
    if (eam_err /=  0) then
       call handleError("cal_eam_forces()","MPI gather dfrhodrho_col failure")
    endif
#endif


  end subroutine calc_eam_preforce_Frho
  
  !! Does EAM pairwise Force calculation.  
  subroutine do_eam_pair(atom1, atom2, d, rij, r2, sw, vpair, particle_pot, &
       fpair, pot, f, do_pot)
    !Arguments    
    integer, intent(in) ::  atom1, atom2
    real( kind = dp ), intent(in) :: rij, r2
    real( kind = dp ) :: pot, sw, vpair
    real( kind = dp ), dimension(nLocal) :: particle_pot
    real( kind = dp ), dimension(3,nLocal) :: f
    real( kind = dp ), intent(in), dimension(3) :: d
    real( kind = dp ), intent(inout), dimension(3) :: fpair

    logical, intent(in) :: do_pot

    real( kind = dp ) :: drdx, drdy, drdz
    real( kind = dp ) :: phab, pha, dvpdr
    real( kind = dp ) :: rha, drha, dpha
    real( kind = dp ) :: rhb, drhb, dphb
    real( kind = dp ) :: dudr
    real( kind = dp ) :: rci, rcj
    real( kind = dp ) :: drhoidr, drhojdr
    real( kind = dp ) :: Fx, Fy, Fz
    real( kind = dp ) :: r, phb
    real( kind = dp ) :: fshift1, fshift2, u1, u2

    integer :: id1, id2
    integer  :: mytype_atom1
    integer  :: mytype_atom2
    integer  :: atid1, atid2

    phab = 0.0E0_DP
    dvpdr = 0.0E0_DP

    if (rij .lt. EAM_rcut) then

#ifdef IS_MPI
       atid1 = atid_row(atom1)
       atid2 = atid_col(atom2)
#else
       atid1 = atid(atom1)
       atid2 = atid(atom2)
#endif

       mytype_atom1 = EAMList%atidToEAMType(atid1)
       mytype_atom2 = EAMList%atidTOEAMType(atid2)


       ! get cutoff for atom 1
       rci = EAMList%EAMParams(mytype_atom1)%eam_rcut
       ! get type specific cutoff for atom 2
       rcj = EAMList%EAMParams(mytype_atom2)%eam_rcut

       drdx = d(1)/rij
       drdy = d(2)/rij
       drdz = d(3)/rij

       if (rij.lt.rci) then

          ! Calculate rho and drho for atom1

          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom1)%rho, &
               rij, rha, drha)
          
          ! Calculate Phi(r) for atom1.
          
          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom1)%phi, &
               rij, pha, dpha)

       endif

       if (rij.lt.rcj) then      

          ! Calculate rho and drho for atom2

          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom2)%rho, &
               rij, rhb, drhb)

          ! Calculate Phi(r) for atom2.

          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom2)%phi, &
               rij, phb, dphb)

       endif

       if (rij.lt.rci) then 
          phab = phab + 0.5E0_DP*(rhb/rha)*pha
          dvpdr = dvpdr + 0.5E0_DP*((rhb/rha)*dpha + &
               pha*((drhb/rha) - (rhb*drha/rha/rha)))
       endif

       if (rij.lt.rcj) then
          phab = phab + 0.5E0_DP*(rha/rhb)*phb
          dvpdr = dvpdr + 0.5E0_DP*((rha/rhb)*dphb + &
               phb*((drha/rhb) - (rha*drhb/rhb/rhb)))
       endif

       drhoidr = drha
       drhojdr = drhb

#ifdef IS_MPI
       dudr = drhojdr*dfrhodrho_row(atom1)+drhoidr*dfrhodrho_col(atom2) &
            + dvpdr

#else
       dudr = drhojdr*dfrhodrho(atom1)+drhoidr*dfrhodrho(atom2) &
            + dvpdr
#endif

       fx = dudr * drdx
       fy = dudr * drdy
       fz = dudr * drdz


#ifdef IS_MPI
       if (do_pot) then
          ! particle_pot is the difference between the full potential 
          ! and the full potential without the presence of a particular
          ! particle (atom1).
          !
          ! This reduces the density at other particle locations, so
          ! we need to recompute the density at atom2 assuming atom1
          ! didn't contribute.  This then requires recomputing the
          ! density functional for atom2 as well.
          !
          ! Most of the particle_pot heavy lifting comes from the
          ! pair interaction, and will be handled by vpair.

          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom1)%F, &
               rho_row(atom1)-rhb, &
               fshift1, u1)
          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom2)%F, &
               rho_col(atom2)-rha, &
               fshift2, u2)
          
          ppot_Row(atom1) = ppot_Row(atom1) - frho_row(atom2) + fshift2
          ppot_Col(atom2) = ppot_Col(atom2) - frho_col(atom1) + fshift1


          pot_Row(METALLIC_POT,atom1) = pot_Row(METALLIC_POT,atom1) + phab*0.5
          pot_Col(METALLIC_POT,atom2) = pot_Col(METALLIC_POT,atom2) + phab*0.5
       end if

       f_Row(1,atom1) = f_Row(1,atom1) + fx
       f_Row(2,atom1) = f_Row(2,atom1) + fy
       f_Row(3,atom1) = f_Row(3,atom1) + fz

       f_Col(1,atom2) = f_Col(1,atom2) - fx
       f_Col(2,atom2) = f_Col(2,atom2) - fy
       f_Col(3,atom2) = f_Col(3,atom2) - fz
#else

       if(do_pot) then
          ! particle_pot is the difference between the full potential 
          ! and the full potential without the presence of a particular
          ! particle (atom1).
          !
          ! This reduces the density at other particle locations, so
          ! we need to recompute the density at atom2 assuming atom1
          ! didn't contribute.  This then requires recomputing the
          ! density functional for atom2 as well.
          !
          ! Most of the particle_pot heavy lifting comes from the
          ! pair interaction, and will be handled by vpair.

          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom1)%F, &
               rho(atom1)-rhb, &
               fshift1, u1)
          call lookupEAMSpline1d(EAMList%EAMParams(mytype_atom2)%F, &
               rho(atom2)-rha, &
               fshift2, u2)
          
          particle_pot(atom1) = particle_pot(atom1) - frho(atom2) + fshift2
          particle_pot(atom2) = particle_pot(atom2) - frho(atom1) + fshift1

          pot = pot + phab
       end if

       f(1,atom1) = f(1,atom1) + fx
       f(2,atom1) = f(2,atom1) + fy
       f(3,atom1) = f(3,atom1) + fz

       f(1,atom2) = f(1,atom2) - fx
       f(2,atom2) = f(2,atom2) - fy
       f(3,atom2) = f(3,atom2) - fz
#endif

       vpair = vpair + phab

#ifdef IS_MPI
       id1 = AtomRowToGlobal(atom1)
       id2 = AtomColToGlobal(atom2)
#else
       id1 = atom1
       id2 = atom2
#endif

       if (molMembershipList(id1) .ne. molMembershipList(id2)) then

          fpair(1) = fpair(1) + fx
          fpair(2) = fpair(2) + fy
          fpair(3) = fpair(3) + fz

       endif
    endif
  end subroutine do_eam_pair

  subroutine lookupEAMSpline(cs, xval, yval)
    
    implicit none

    type (cubicSpline), intent(in) :: cs
    real( kind = DP ), intent(in)  :: xval
    real( kind = DP ), intent(out) :: yval
    real( kind = DP ) ::  dx
    integer :: i, j
    !
    !  Find the interval J = [ cs%x(J), cs%x(J+1) ] that contains 
    !  or is nearest to xval.
    
    j = MAX(1, MIN(cs%n-1, int((xval-cs%x(1)) * cs%dx_i) + 1))
    
    dx = xval - cs%x(j)
    yval = cs%y(j) + dx*(cs%b(j) + dx*(cs%c(j) + dx*cs%d(j)))
    
    return
  end subroutine lookupEAMSpline

  subroutine lookupEAMSpline1d(cs, xval, yval, dydx)
    
    implicit none

    type (cubicSpline), intent(in) :: cs
    real( kind = DP ), intent(in)  :: xval
    real( kind = DP ), intent(out) :: yval, dydx
    real( kind = DP ) :: dx
    integer :: i, j
    
    !  Find the interval J = [ cs%x(J), cs%x(J+1) ] that contains 
    !  or is nearest to xval.


    j = MAX(1, MIN(cs%n-1, int((xval-cs%x(1)) * cs%dx_i) + 1))
    
    dx = xval - cs%x(j)
    yval = cs%y(j) + dx*(cs%b(j) + dx*(cs%c(j) + dx*cs%d(j)))

    dydx = cs%b(j) + dx*(2.0d0 * cs%c(j) + 3.0d0 * dx * cs%d(j))
       
    return
  end subroutine lookupEAMSpline1d

end module eam
Revision:	1309
Committed:	Tue Oct 21 18:23:31 2008 UTC (16 years, 9 months ago) by gezelter
File size:	22278 byte(s)
Log Message:	many changes to keep track of particle potentials for both bonded and non-bonded interactions