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!! do_Forces.F90 |
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!! module do_Forces |
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!! Calculates Long Range forces. |
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!! @author Charles F. Vardeman II |
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!! @author Matthew Meineke |
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!! @version $Id: do_Forces.F90,v 1.4 2003-03-06 22:08:29 gezelter Exp $, $Date: 2003-03-06 22:08:29 $, $Name: not supported by cvs2svn $, $Revision: 1.4 $ |
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!! @version $Id: do_Forces.F90,v 1.11 2003-03-11 23:13:06 gezelter Exp $, $Date: 2003-03-11 23:13:06 $, $Name: not supported by cvs2svn $, $Revision: 1.11 $ |
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module do_Forces |
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use simulation |
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use definitions |
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use generic_atypes |
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> |
use forceGlobals |
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> |
use atype_typedefs |
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use neighborLists |
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|
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|
19 |
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use lj_FF |
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use lj |
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use sticky_FF |
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use dp_FF |
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use dipole_dipole |
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use gb_FF |
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#ifdef IS_MPI |
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implicit none |
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PRIVATE |
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|
30 |
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!! Number of lj_atypes in lj_atype_list |
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integer, save :: n_atypes = 0 |
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> |
public :: do_force_loop |
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|
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!! Global list of lj atypes in simulation |
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type (atype), pointer :: ListHead => null() |
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type (atype), pointer :: ListTail => null() |
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|
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|
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|
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|
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logical, save :: firstTime = .True. |
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|
37 |
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!! Atype identity pointer lists |
38 |
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#ifdef IS_MPI |
39 |
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!! Row lj_atype pointer list |
40 |
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type (identPtrList), dimension(:), pointer :: identPtrListRow => null() |
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!! Column lj_atype pointer list |
42 |
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type (identPtrList), dimension(:), pointer :: identPtrListColumn => null() |
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#else |
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type(identPtrList ), dimension(:), pointer :: identPtrList => null() |
45 |
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#endif |
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|
47 |
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|
48 |
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!! Logical has lj force field module been initialized? |
49 |
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logical, save :: isFFinit = .false. |
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|
51 |
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!! Use periodic boundry conditions |
52 |
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logical :: wrap = .false. |
53 |
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|
54 |
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!! Potential energy global module variables |
55 |
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#ifdef IS_MPI |
56 |
– |
real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow = 0.0_dp |
57 |
– |
real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol = 0.0_dp |
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|
59 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: muRow = 0.0_dp |
60 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: muCol = 0.0_dp |
61 |
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|
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real(kind = dp), dimension(3,getNrow(plan_row)) :: u_lRow = 0.0_dp |
63 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: u_lCol = 0.0_dp |
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|
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real(kind = dp), dimension(9,getNrow(plan_row)) :: ARow = 0.0_dp |
66 |
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real(kind = dp), dimension(9,getNcol(plan_col)) :: ACol = 0.0_dp |
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|
68 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow = 0.0_dp |
69 |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: fTemp1 = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: tTemp1 = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: fTemp2 = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: tTemp2 = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: fTemp = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: tTemp = 0.0_dp |
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|
77 |
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real(kind = dp), dimension(3,getNrow(plan_row)) :: tRow = 0.0_dp |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: tCol = 0.0_dp |
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|
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real(kind = dp), dimension(3,getNrow(plan_row)) :: rflRow = 0.0_dp |
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real(kind = dp), dimension(3,getNcol(plan_col)) :: rflCol = 0.0_dp |
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real(kind = dp), dimension(3,getNlocal()) :: rflTemp = 0.0_dp |
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|
84 |
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real(kind = dp), dimension(getNrow(plan_row)) :: eRow = 0.0_dp |
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real(kind = dp), dimension(getNcol(plan_col)) :: eCol = 0.0_dp |
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|
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real(kind = dp), dimension(getNlocal()) :: eTemp = 0.0_dp |
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#endif |
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real(kind = dp) :: pe = 0.0_dp |
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real(kind = dp), dimension(3,natoms) :: fTemp = 0.0_dp |
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real(kind = dp), dimension(3,natoms) :: tTemp = 0.0_dp |
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real(kind = dp), dimension(3,natoms) :: rflTemp = 0.0_dp |
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real(kind = dp), dimension(9) :: tauTemp = 0.0_dp |
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|
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logical :: do_preForce = .false. |
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logical :: do_postForce = .false. |
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|
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|
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|
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!! Public methods and data |
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public :: new_atype |
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public :: do_forceLoop |
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public :: init_FF |
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|
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contains |
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!! Adds a new lj_atype to the list. |
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subroutine new_atype(ident,mass,epsilon,sigma, & |
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is_LJ,is_Sticky,is_DP,is_GB,w0,v0,dipoleMoment,status) |
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real( kind = dp ), intent(in) :: mass |
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real( kind = dp ), intent(in) :: epsilon |
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real( kind = dp ), intent(in) :: sigma |
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real( kind = dp ), intent(in) :: w0 |
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real( kind = dp ), intent(in) :: v0 |
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real( kind = dp ), intent(in) :: dipoleMoment |
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|
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integer, intent(in) :: ident |
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integer, intent(out) :: status |
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integer, intent(in) :: is_Sticky |
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integer, intent(in) :: is_DP |
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integer, intent(in) :: is_GB |
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integer, intent(in) :: is_LJ |
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|
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|
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type (atype), pointer :: the_new_atype |
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integer :: alloc_error |
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integer :: atype_counter = 0 |
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integer :: alloc_size |
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integer :: err_stat |
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status = 0 |
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|
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|
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|
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! allocate a new atype |
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allocate(the_new_atype,stat=alloc_error) |
139 |
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if (alloc_error /= 0 ) then |
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status = -1 |
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return |
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end if |
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|
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! assign our new atype information |
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the_new_atype%mass = mass |
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the_new_atype%epsilon = epsilon |
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the_new_atype%sigma = sigma |
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< |
the_new_atype%sigma2 = sigma * sigma |
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< |
the_new_atype%sigma6 = the_new_atype%sigma2 * the_new_atype%sigma2 & |
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< |
* the_new_atype%sigma2 |
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< |
the_new_atype%w0 = w0 |
152 |
< |
the_new_atype%v0 = v0 |
153 |
< |
the_new_atype%dipoleMoment = dipoleMoment |
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|
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!! Does force loop over i,j pairs. Calls do_pair to calculates forces. |
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> |
!-------------------------------------------------------------> |
36 |
> |
subroutine do_force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror) |
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> |
!! Position array provided by C, dimensioned by getNlocal |
38 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: q |
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> |
!! Rotation Matrix for each long range particle in simulation. |
40 |
> |
real( kind = dp), dimension(9,getNlocal()) :: A |
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|
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! assume that this atype will be successfully added |
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< |
the_new_atype%atype_ident = ident |
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< |
the_new_atype%atype_number = n_lj_atypes + 1 |
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> |
!! Magnitude dipole moment |
43 |
> |
real( kind = dp ), dimension(3,getNlocal()) :: mu |
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> |
!! Unit vectors for dipoles (lab frame) |
45 |
> |
real( kind = dp ), dimension(3,getNlocal()) :: u_l |
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> |
!! Force array provided by C, dimensioned by getNlocal |
47 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: f |
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!! Torsion array provided by C, dimensioned by getNlocal |
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> |
real( kind = dp ), dimension(3,getNlocal()) :: t |
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|
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if ( is_Sticky /= 0 ) the_new_atype%is_Sticky = .true. |
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if ( is_GB /= 0 ) the_new_atype%is_GB = .true. |
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if ( is_LJ /= 0 ) the_new_atype%is_LJ = .true. |
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if ( is_DP /= 0 ) the_new_atype%is_DP = .true. |
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> |
!! Stress Tensor |
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real( kind = dp), dimension(9) :: tau |
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|
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real ( kind = dp ) :: potE |
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> |
logical ( kind = 2) :: do_pot |
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> |
integer :: FFerror |
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|
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call add_atype(the_new_atype,ListHead,ListTail,err_stat) |
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if (err_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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n_atypes = n_atypes + 1 |
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|
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|
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end subroutine new_atype |
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|
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|
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subroutine init_FF(nComponents,ident, status) |
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!! Number of components in ident array |
179 |
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integer, intent(inout) :: nComponents |
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!! Array of identities nComponents long corresponding to |
181 |
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!! ljatype ident. |
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integer, dimension(nComponents),intent(inout) :: ident |
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!! Result status, success = 0, error = -1 |
184 |
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integer, intent(out) :: Status |
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|
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integer :: alloc_stat |
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|
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integer :: thisStat |
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integer :: i |
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|
191 |
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integer :: myNode |
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#ifdef IS_MPI |
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integer, allocatable, dimension(:) :: identRow |
194 |
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integer, allocatable, dimension(:) :: identCol |
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< |
integer :: nrow |
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integer :: ncol |
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real( kind = DP ) :: pot_local |
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#endif |
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status = 0 |
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|
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|
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real( kind = DP ) :: pe |
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logical :: update_nlist |
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|
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|
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!! if were're not in MPI, we just update ljatypePtrList |
67 |
< |
#ifndef IS_MPI |
68 |
< |
call create_IdentPtrlst(ident,ListHead,identPtrList,thisStat) |
206 |
< |
if ( thisStat /= 0 ) then |
207 |
< |
status = -1 |
208 |
< |
return |
209 |
< |
endif |
210 |
< |
|
66 |
> |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
67 |
> |
integer :: nlist |
68 |
> |
integer :: j_start |
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|
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! if were're in MPI, we also have to worry about row and col lists |
71 |
< |
#else |
72 |
< |
|
73 |
< |
! We can only set up forces if mpiSimulation has been setup. |
216 |
< |
if (.not. isMPISimSet()) then |
217 |
< |
write(default_error,*) "MPI is not set" |
218 |
< |
status = -1 |
219 |
< |
return |
220 |
< |
endif |
221 |
< |
nrow = getNrow(plan_row) |
222 |
< |
ncol = getNcol(plan_col) |
223 |
< |
mynode = getMyNode() |
224 |
< |
!! Allocate temperary arrays to hold gather information |
225 |
< |
allocate(identRow(nrow),stat=alloc_stat) |
226 |
< |
if (alloc_stat /= 0 ) then |
227 |
< |
status = -1 |
228 |
< |
return |
229 |
< |
endif |
70 |
> |
real( kind = DP ) :: r_ij, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
71 |
> |
|
72 |
> |
real( kind = DP ) :: rx_ij, ry_ij, rz_ij, rijsq |
73 |
> |
real( kind = DP ) :: rlistsq, rcutsq, rlist, rcut |
74 |
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|
75 |
< |
allocate(identCol(ncol),stat=alloc_stat) |
76 |
< |
if (alloc_stat /= 0 ) then |
77 |
< |
status = -1 |
78 |
< |
return |
79 |
< |
endif |
75 |
> |
! a rig that need to be fixed. |
76 |
> |
#ifdef IS_MPI |
77 |
> |
real( kind = dp ) :: pe_local |
78 |
> |
integer :: nlocal |
79 |
> |
#endif |
80 |
> |
integer :: nrow |
81 |
> |
integer :: ncol |
82 |
> |
integer :: natoms |
83 |
> |
integer :: neighborListSize |
84 |
> |
integer :: listerror |
85 |
> |
!! should we calculate the stress tensor |
86 |
> |
logical :: do_stress = .false. |
87 |
> |
FFerror = 0 |
88 |
|
|
89 |
< |
!! Gather idents into row and column idents |
90 |
< |
|
91 |
< |
call gather(ident,identRow,plan_row) |
92 |
< |
call gather(ident,identCol,plan_col) |
241 |
< |
|
242 |
< |
|
243 |
< |
!! Create row and col pointer lists |
244 |
< |
|
245 |
< |
call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat) |
246 |
< |
if (thisStat /= 0 ) then |
247 |
< |
status = -1 |
89 |
> |
! Make sure we are properly initialized. |
90 |
> |
if (.not. isFFInit) then |
91 |
> |
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
92 |
> |
FFerror = -1 |
93 |
|
return |
94 |
|
endif |
95 |
< |
|
96 |
< |
call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat) |
97 |
< |
if (thisStat /= 0 ) then |
98 |
< |
status = -1 |
95 |
> |
#ifdef IS_MPI |
96 |
> |
if (.not. isMPISimSet()) then |
97 |
> |
write(default_error,*) "ERROR: mpiSimulation has not been properly initialized" |
98 |
> |
FFerror = -1 |
99 |
|
return |
100 |
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endif |
256 |
– |
|
257 |
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!! free temporary ident arrays |
258 |
– |
if (allocated(identCol)) then |
259 |
– |
deallocate(identCol) |
260 |
– |
end if |
261 |
– |
if (allocated(identCol)) then |
262 |
– |
deallocate(identRow) |
263 |
– |
endif |
264 |
– |
|
101 |
|
#endif |
102 |
|
|
103 |
< |
call initForce_Modules(thisStat) |
104 |
< |
if (thisStat /= 0) then |
105 |
< |
status = -1 |
106 |
< |
return |
271 |
< |
endif |
272 |
< |
|
273 |
< |
!! Create neighbor lists |
274 |
< |
call expandList(thisStat) |
275 |
< |
if (thisStat /= 0) then |
276 |
< |
status = -1 |
277 |
< |
return |
278 |
< |
endif |
279 |
< |
|
280 |
< |
isFFinit = .true. |
281 |
< |
|
282 |
< |
|
283 |
< |
end subroutine init_FF |
284 |
< |
|
285 |
< |
|
286 |
< |
|
287 |
< |
|
288 |
< |
subroutine initForce_Modules(thisStat) |
289 |
< |
integer, intent(out) :: thisStat |
290 |
< |
integer :: my_status |
103 |
> |
!! initialize local variables |
104 |
> |
natoms = getNlocal() |
105 |
> |
call getRcut(rcut,rcut2=rcutsq) |
106 |
> |
call getRlist(rlist,rlistsq) |
107 |
|
|
108 |
< |
thisStat = 0 |
109 |
< |
call init_lj_FF(ListHead,my_status) |
294 |
< |
if (my_status /= 0) then |
295 |
< |
thisStat = -1 |
296 |
< |
return |
297 |
< |
end if |
298 |
< |
|
299 |
< |
end subroutine initForce_Modules |
300 |
< |
|
301 |
< |
|
302 |
< |
|
303 |
< |
|
304 |
< |
!! FORCE routine Calculates Lennard Jones forces. |
305 |
< |
!-------------------------------------------------------------> |
306 |
< |
subroutine do_force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror) |
307 |
< |
!! Position array provided by C, dimensioned by getNlocal |
308 |
< |
real ( kind = dp ), dimension(3,getNlocal()) :: q |
309 |
< |
!! Rotation Matrix for each long range particle in simulation. |
310 |
< |
real( kind = dp), dimension(9,getNlocal()) :: A |
311 |
< |
|
312 |
< |
!! Magnitude dipole moment |
313 |
< |
real( kind = dp ), dimension(3,getNlocal()) :: mu |
314 |
< |
!! Unit vectors for dipoles (lab frame) |
315 |
< |
real( kind = dp ), dimension(3,getNlocal()) :: u_l |
316 |
< |
!! Force array provided by C, dimensioned by getNlocal |
317 |
< |
real ( kind = dp ), dimension(3,getNlocal()) :: f |
318 |
< |
!! Torsion array provided by C, dimensioned by getNlocal |
319 |
< |
real( kind = dp ), dimension(3,getNlocal()) :: t |
320 |
< |
|
321 |
< |
!! Stress Tensor |
322 |
< |
real( kind = dp), dimension(9) :: tau |
323 |
< |
|
324 |
< |
real ( kind = dp ) :: potE |
325 |
< |
logical ( kind = 2) :: do_pot |
326 |
< |
integer :: FFerror |
327 |
< |
|
108 |
> |
!! See if we need to update neighbor lists |
109 |
> |
call check(q, update_nlist) |
110 |
|
|
111 |
< |
type(atype), pointer :: Atype_i |
112 |
< |
type(atype), pointer :: Atype_j |
111 |
> |
!--------------WARNING........................... |
112 |
> |
! Zero variables, NOTE:::: Forces are zeroed in C |
113 |
> |
! Zeroing them here could delete previously computed |
114 |
> |
! Forces. |
115 |
> |
!------------------------------------------------ |
116 |
> |
call zero_module_variables() |
117 |
|
|
118 |
< |
|
333 |
< |
|
334 |
< |
|
335 |
< |
|
336 |
< |
|
337 |
< |
#ifdef IS_MPI |
338 |
< |
real( kind = DP ) :: pot_local |
339 |
< |
|
340 |
< |
!! Local arrays needed for MPI |
341 |
< |
|
342 |
< |
#endif |
343 |
< |
|
344 |
< |
|
345 |
< |
|
346 |
< |
real( kind = DP ) :: pe |
347 |
< |
logical :: update_nlist |
348 |
< |
|
349 |
< |
|
350 |
< |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
351 |
< |
integer :: nlist |
352 |
< |
integer :: j_start |
353 |
< |
|
354 |
< |
real( kind = DP ) :: r_ij, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
355 |
< |
|
356 |
< |
real( kind = DP ) :: rx_ij, ry_ij, rz_ij, rijsq |
357 |
< |
real( kind = DP ) :: rlistsq, rcutsq,rlist,rcut |
358 |
< |
|
359 |
< |
real( kind = DP ) :: dielectric = 0.0_dp |
360 |
< |
|
361 |
< |
! a rig that need to be fixed. |
362 |
< |
#ifdef IS_MPI |
363 |
< |
real( kind = dp ) :: pe_local |
364 |
< |
integer :: nlocal |
365 |
< |
#endif |
366 |
< |
integer :: nrow |
367 |
< |
integer :: ncol |
368 |
< |
integer :: natoms |
369 |
< |
integer :: neighborListSize |
370 |
< |
integer :: listerror |
371 |
< |
!! should we calculate the stress tensor |
372 |
< |
logical :: do_stress = .false. |
373 |
< |
|
374 |
< |
|
375 |
< |
FFerror = 0 |
376 |
< |
|
377 |
< |
! Make sure we are properly initialized. |
378 |
< |
if (.not. isFFInit) then |
379 |
< |
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
380 |
< |
FFerror = -1 |
381 |
< |
return |
382 |
< |
endif |
383 |
< |
#ifdef IS_MPI |
384 |
< |
if (.not. isMPISimSet()) then |
385 |
< |
write(default_error,*) "ERROR: mpiSimulation has not been properly initialized" |
386 |
< |
FFerror = -1 |
387 |
< |
return |
388 |
< |
endif |
389 |
< |
#endif |
390 |
< |
|
391 |
< |
!! initialize local variables |
392 |
< |
natoms = getNlocal() |
393 |
< |
call getRcut(rcut,rcut2=rcutsq) |
394 |
< |
call getRlist(rlist,rlistsq) |
395 |
< |
|
396 |
< |
!! Find ensemble |
397 |
< |
if (isEnsemble("NPT")) do_stress = .true. |
398 |
< |
!! set to wrap |
399 |
< |
if (isPBC()) wrap = .true. |
400 |
< |
|
401 |
< |
|
402 |
< |
|
403 |
< |
|
404 |
< |
!! See if we need to update neighbor lists |
405 |
< |
call check(q,update_nlist) |
406 |
< |
|
407 |
< |
!--------------WARNING........................... |
408 |
< |
! Zero variables, NOTE:::: Forces are zeroed in C |
409 |
< |
! Zeroing them here could delete previously computed |
410 |
< |
! Forces. |
411 |
< |
!------------------------------------------------ |
412 |
< |
call zero_module_variables() |
413 |
< |
|
414 |
< |
|
415 |
< |
! communicate MPI positions |
118 |
> |
! communicate MPI positions |
119 |
|
#ifdef IS_MPI |
120 |
< |
call gather(q,qRow,plan_row3d) |
121 |
< |
call gather(q,qCol,plan_col3d) |
122 |
< |
|
123 |
< |
call gather(mu,muRow,plan_row3d) |
124 |
< |
call gather(mu,muCol,plan_col3d) |
125 |
< |
|
126 |
< |
call gather(u_l,u_lRow,plan_row3d) |
127 |
< |
call gather(u_l,u_lCol,plan_col3d) |
425 |
< |
|
426 |
< |
call gather(A,ARow,plan_row_rotation) |
427 |
< |
call gather(A,ACol,plan_col_rotation) |
120 |
> |
call gather(q,q_Row,plan_row3d) |
121 |
> |
call gather(q,q_Col,plan_col3d) |
122 |
> |
|
123 |
> |
call gather(u_l,u_l_Row,plan_row3d) |
124 |
> |
call gather(u_l,u_l_Col,plan_col3d) |
125 |
> |
|
126 |
> |
call gather(A,A_Row,plan_row_rotation) |
127 |
> |
call gather(A,A_Col,plan_col_rotation) |
128 |
|
#endif |
129 |
|
|
130 |
|
|
145 |
|
|
146 |
|
do i = 1, nrow |
147 |
|
point(i) = nlist + 1 |
448 |
– |
Atype_i => identPtrListRow(i)%this |
148 |
|
|
149 |
|
inner: do j = 1, ncol |
451 |
– |
Atype_j => identPtrListColumn(j)%this |
150 |
|
|
151 |
< |
call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),& |
152 |
< |
rxij,ryij,rzij,rijsq,r) |
153 |
< |
|
154 |
< |
! skip the loop if the atoms are identical |
457 |
< |
if (mpi_cycle_jLoop(i,j)) cycle inner: |
458 |
< |
|
151 |
> |
if (check_exclude(i,j)) cycle inner: |
152 |
> |
|
153 |
> |
call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq) |
154 |
> |
|
155 |
|
if (rijsq < rlistsq) then |
156 |
|
|
157 |
|
nlist = nlist + 1 |
166 |
|
endif |
167 |
|
|
168 |
|
list(nlist) = j |
169 |
< |
|
474 |
< |
|
169 |
> |
|
170 |
|
if (rijsq < rcutsq) then |
171 |
< |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
171 |
> |
call do_pair(i, j, rijsq, d) |
172 |
|
endif |
173 |
|
endif |
174 |
|
enddo inner |
184 |
|
JEND = POINT(i+1) - 1 |
185 |
|
! check thiat molecule i has neighbors |
186 |
|
if (jbeg .le. jend) then |
187 |
< |
|
493 |
< |
Atype_i => identPtrListRow(i)%this |
187 |
> |
|
188 |
|
do jnab = jbeg, jend |
189 |
|
j = list(jnab) |
190 |
< |
Atype_j = identPtrListColumn(j)%this |
191 |
< |
call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),& |
192 |
< |
rxij,ryij,rzij,rijsq,r) |
193 |
< |
|
500 |
< |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
190 |
> |
|
191 |
> |
call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq) |
192 |
> |
call do_pair(i, j, rijsq, d) |
193 |
> |
|
194 |
|
enddo |
195 |
|
endif |
196 |
|
enddo |
206 |
|
|
207 |
|
neighborListSize = getNeighborListSize() |
208 |
|
nlist = 0 |
209 |
< |
|
517 |
< |
|
209 |
> |
|
210 |
|
do i = 1, natoms-1 |
211 |
|
point(i) = nlist + 1 |
520 |
– |
Atype_i => identPtrList(i)%this |
212 |
|
|
213 |
|
inner: do j = i+1, natoms |
214 |
< |
Atype_j => identPtrList(j)%this |
215 |
< |
call get_interatomic_vector(i,j,q(:,i),q(:,j),& |
216 |
< |
rxij,ryij,rzij,rijsq,r) |
214 |
> |
|
215 |
> |
if (check_exclude(i,j)) cycle inner: |
216 |
> |
|
217 |
> |
call get_interatomic_vector(q(:,i), q(:,j), d, rijsq) |
218 |
|
|
219 |
|
if (rijsq < rlistsq) then |
220 |
< |
|
220 |
> |
|
221 |
|
nlist = nlist + 1 |
222 |
|
|
223 |
|
if (nlist > neighborListSize) then |
230 |
|
endif |
231 |
|
|
232 |
|
list(nlist) = j |
233 |
< |
|
542 |
< |
|
233 |
> |
|
234 |
|
if (rijsq < rcutsq) then |
235 |
< |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
235 |
> |
call do_pair(i, j, rijsq, d) |
236 |
|
endif |
237 |
|
endif |
238 |
|
enddo inner |
249 |
|
! check thiat molecule i has neighbors |
250 |
|
if (jbeg .le. jend) then |
251 |
|
|
561 |
– |
Atype_i => identPtrList(i)%this |
252 |
|
do jnab = jbeg, jend |
253 |
|
j = list(jnab) |
254 |
< |
Atype_j = identPtrList(j)%this |
255 |
< |
call get_interatomic_vector(i,j,q(:,i),q(:,j),& |
256 |
< |
rxij,ryij,rzij,rijsq,r) |
257 |
< |
call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij) |
254 |
> |
|
255 |
> |
call get_interatomic_vector(q(:,i), q(:,j), d, rijsq) |
256 |
> |
call do_pair(i, j, rijsq, d) |
257 |
> |
|
258 |
|
enddo |
259 |
|
endif |
260 |
|
enddo |
261 |
|
endif |
262 |
< |
|
262 |
> |
|
263 |
|
#endif |
264 |
< |
|
265 |
< |
|
264 |
> |
|
265 |
> |
|
266 |
|
#ifdef IS_MPI |
267 |
|
!! distribute all reaction field stuff (or anything for post-pair): |
268 |
|
call scatter(rflRow,rflTemp1,plan_row3d) |
271 |
|
rflTemp(1:3,i) = rflTemp1(1:3,i) + rflTemp2(1:3,i) |
272 |
|
end do |
273 |
|
#endif |
274 |
< |
|
274 |
> |
|
275 |
|
! This is the post-pair loop: |
276 |
|
#ifdef IS_MPI |
277 |
< |
|
277 |
> |
|
278 |
|
if (system_has_postpair_atoms) then |
279 |
|
do i = 1, nlocal |
280 |
|
Atype_i => identPtrListRow(i)%this |
281 |
|
call do_postpair(i, Atype_i) |
282 |
|
enddo |
283 |
|
endif |
284 |
< |
|
284 |
> |
|
285 |
|
#else |
286 |
< |
|
286 |
> |
|
287 |
|
if (system_has_postpair_atoms) then |
288 |
|
do i = 1, natoms |
289 |
|
Atype_i => identPtr(i)%this |
290 |
|
call do_postpair(i, Atype_i) |
291 |
|
enddo |
292 |
|
endif |
293 |
< |
|
293 |
> |
|
294 |
|
#endif |
295 |
+ |
|
296 |
|
|
606 |
– |
|
607 |
– |
|
608 |
– |
|
297 |
|
#ifdef IS_MPI |
298 |
|
!!distribute forces |
299 |
|
|
300 |
< |
call scatter(fRow,fTemp1,plan_row3d) |
301 |
< |
call scatter(fCol,fTemp2,plan_col3d) |
614 |
< |
|
615 |
< |
|
300 |
> |
call scatter(f_Row,f,plan_row3d) |
301 |
> |
call scatter(f_Col,f_temp,plan_col3d) |
302 |
|
do i = 1,nlocal |
303 |
< |
fTemp(1:3,i) = fTemp1(1:3,i) + fTemp2(1:3,i) |
303 |
> |
f(1:3,i) = f(1:3,i) + f_temp(1:3,i) |
304 |
|
end do |
305 |
|
|
306 |
< |
if (do_torque) then |
307 |
< |
call scatter(tRow,tTemp1,plan_row3d) |
308 |
< |
call scatter(tCol,tTemp2,plan_col3d) |
306 |
> |
if (doTorque()) then |
307 |
> |
call scatter(t_Row,t,plan_row3d) |
308 |
> |
call scatter(t_Col,t_temp,plan_col3d) |
309 |
|
|
310 |
|
do i = 1,nlocal |
311 |
< |
tTemp(1:3,i) = tTemp1(1:3,i) + tTemp2(1:3,i) |
311 |
> |
t(1:3,i) = t(1:3,i) + t_temp(1:3,i) |
312 |
|
end do |
313 |
|
endif |
314 |
< |
|
314 |
> |
|
315 |
|
if (do_pot) then |
316 |
|
! scatter/gather pot_row into the members of my column |
317 |
< |
call scatter(eRow,eTemp,plan_row) |
317 |
> |
call scatter(pot_Row, pot_Temp, plan_row) |
318 |
|
|
319 |
|
! scatter/gather pot_local into all other procs |
320 |
|
! add resultant to get total pot |
321 |
|
do i = 1, nlocal |
322 |
< |
pe_local = pe_local + eTemp(i) |
322 |
> |
pot_local = pot_local + pot_Temp(i) |
323 |
|
enddo |
324 |
|
|
325 |
< |
eTemp = 0.0E0_DP |
326 |
< |
call scatter(eCol,eTemp,plan_col) |
325 |
> |
pot_Temp = 0.0_DP |
326 |
> |
|
327 |
> |
call scatter(pot_Col, pot_Temp, plan_col) |
328 |
|
do i = 1, nlocal |
329 |
< |
pe_local = pe_local + eTemp(i) |
329 |
> |
pot_local = pot_local + pot_Temp(i) |
330 |
|
enddo |
331 |
|
|
332 |
< |
pe = pe_local |
332 |
> |
pot = pot_local |
333 |
|
endif |
647 |
– |
#else |
648 |
– |
! Copy local array into return array for c |
649 |
– |
f = f+fTemp |
650 |
– |
t = t+tTemp |
651 |
– |
#endif |
334 |
|
|
335 |
< |
potE = pe |
335 |
> |
if (doStress()) then |
336 |
> |
mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, & |
337 |
> |
mpi_comm_world,mpi_err) |
338 |
> |
mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, & |
339 |
> |
mpi_comm_world,mpi_err) |
340 |
> |
endif |
341 |
|
|
342 |
+ |
#endif |
343 |
|
|
344 |
< |
if (do_stress) then |
345 |
< |
#ifdef IS_MPI |
346 |
< |
mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, & |
659 |
< |
mpi_comm_world,mpi_err) |
660 |
< |
#else |
661 |
< |
tau = tauTemp |
662 |
< |
#endif |
344 |
> |
if (doStress()) then |
345 |
> |
tau = tau_Temp |
346 |
> |
virial = virial_Temp |
347 |
|
endif |
348 |
|
|
349 |
|
end subroutine do_force_loop |
350 |
|
|
351 |
|
|
668 |
– |
|
669 |
– |
|
670 |
– |
|
671 |
– |
|
672 |
– |
|
673 |
– |
|
674 |
– |
|
675 |
– |
|
352 |
|
!! Calculate any pre-force loop components and update nlist if necessary. |
353 |
|
subroutine do_preForce(updateNlist) |
354 |
|
logical, intent(inout) :: updateNlist |
357 |
|
|
358 |
|
end subroutine do_preForce |
359 |
|
|
684 |
– |
|
685 |
– |
|
686 |
– |
|
687 |
– |
|
688 |
– |
|
689 |
– |
|
690 |
– |
|
691 |
– |
|
692 |
– |
|
693 |
– |
|
694 |
– |
|
695 |
– |
|
360 |
|
!! Calculate any post force loop components, i.e. reaction field, etc. |
361 |
|
subroutine do_postForce() |
362 |
|
|
364 |
|
|
365 |
|
end subroutine do_postForce |
366 |
|
|
367 |
+ |
subroutine do_pair(i, j, rijsq, d) |
368 |
|
|
369 |
+ |
integer, intent(in) :: i, j |
370 |
+ |
real ( kind = dp ), intent(in) :: rijsq |
371 |
+ |
real ( kind = dp ) :: r |
372 |
+ |
real ( kind = dp ), intent(inout) :: d(3) |
373 |
|
|
374 |
+ |
r = sqrt(rijsq) |
375 |
+ |
|
376 |
+ |
logical :: is_LJ_i, is_LJ_j |
377 |
+ |
logical :: is_DP_i, is_DP_j |
378 |
+ |
logical :: is_Sticky_i, is_Sticky_j |
379 |
+ |
integer :: me_i, me_j |
380 |
|
|
381 |
+ |
#ifdef IS_MPI |
382 |
|
|
383 |
+ |
me_i = atid_row(i) |
384 |
+ |
me_j = atid_col(j) |
385 |
|
|
386 |
+ |
#else |
387 |
|
|
388 |
+ |
me_i = atid(i) |
389 |
+ |
me_j = atid(j) |
390 |
|
|
391 |
+ |
#endif |
392 |
|
|
393 |
+ |
call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i) |
394 |
+ |
call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j) |
395 |
|
|
396 |
+ |
if ( is_LJ_i .and. is_LJ_j ) call do_lj_pair(i, j, d, r, pot, f) |
397 |
|
|
398 |
+ |
call getElementProperty(atypes, me_i, "is_DP", is_DP_i) |
399 |
+ |
call getElementProperty(atypes, me_j, "is_DP", is_DP_j) |
400 |
|
|
401 |
+ |
if ( is_DP_i .and. is_DP_j ) then |
402 |
|
|
403 |
< |
|
716 |
< |
|
717 |
< |
|
718 |
< |
|
719 |
< |
subroutine do_pair(atype_i,atype_j,i,j,r_ij,rx_ij,ry_ij,rz_ij) |
720 |
< |
type (atype ), pointer, intent(inout) :: atype_i |
721 |
< |
type (atype ), pointer, intent(inout) :: atype_j |
722 |
< |
integer :: i |
723 |
< |
integer :: j |
724 |
< |
real ( kind = dp ), intent(inout) :: rx_ij |
725 |
< |
real ( kind = dp ), intent(inout) :: ry_ij |
726 |
< |
real ( kind = dp ), intent(inout) :: rz_ij |
727 |
< |
|
728 |
< |
|
729 |
< |
real( kind = dp ) :: fx = 0.0_dp |
730 |
< |
real( kind = dp ) :: fy = 0.0_dp |
731 |
< |
real( kind = dp ) :: fz = 0.0_dp |
732 |
< |
|
733 |
< |
real( kind = dp ) :: drdx = 0.0_dp |
734 |
< |
real( kind = dp ) :: drdy = 0.0_dp |
735 |
< |
real( kind = dp ) :: drdz = 0.0_dp |
736 |
< |
|
403 |
> |
call do_dipole_pair(i, j, d, r, pot, u_l, f, t) |
404 |
|
|
738 |
– |
if (Atype_i%is_LJ .and. Atype_j%is_LJ) then |
739 |
– |
call getLJForce(r,pot,dudr,ljAtype_i,ljAtype_j,fx,fy,fz) |
740 |
– |
endif |
741 |
– |
|
742 |
– |
if (Atype_i%is_dp .and. Atype_j%is_dp) then |
743 |
– |
|
744 |
– |
#ifdef IS_MPI |
745 |
– |
call dipole_dipole(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
746 |
– |
ulRow(:,i), ulCol(:,j), rt, rrf, pot) |
747 |
– |
#else |
748 |
– |
call dipole_dipole(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, & |
749 |
– |
ul(:,i), ul(:,j), rt, rrf, pot) |
750 |
– |
#endif |
751 |
– |
|
405 |
|
if (do_reaction_field) then |
406 |
< |
#ifdef IS_MPI |
754 |
< |
call accumulate_rf(i, j, r_ij, rflRow(:,i), rflCol(:j), & |
755 |
< |
ulRow(:i), ulCol(:,j), rt, rrf) |
756 |
< |
#else |
757 |
< |
call accumulate_rf(i, j, r_ij, rfl(:,i), rfl(:j), & |
758 |
< |
ul(:,i), ul(:,j), rt, rrf) |
759 |
< |
#endif |
406 |
> |
call accumulate_rf(i, j, r_ij) |
407 |
|
endif |
408 |
|
|
762 |
– |
|
409 |
|
endif |
410 |
|
|
411 |
< |
if (Atype_i%is_sticky .and. Atype_j%is_sticky) then |
412 |
< |
call getstickyforce(r,pot,dudr,ljAtype_i,ljAtype_j) |
411 |
> |
call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i) |
412 |
> |
call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j) |
413 |
> |
|
414 |
> |
if ( is_Sticky_i .and. is_Sticky_j ) then |
415 |
> |
call do_sticky_pair(i, j, d, r, pot, u_l, f, t) |
416 |
|
endif |
417 |
|
|
418 |
< |
|
770 |
< |
#ifdef IS_MPI |
771 |
< |
eRow(i) = eRow(i) + pot*0.5 |
772 |
< |
eCol(i) = eCol(i) + pot*0.5 |
773 |
< |
#else |
774 |
< |
pe = pe + pot |
775 |
< |
#endif |
776 |
< |
|
777 |
< |
drdx = -rxij / r |
778 |
< |
drdy = -ryij / r |
779 |
< |
drdz = -rzij / r |
780 |
< |
|
781 |
< |
fx = dudr * drdx |
782 |
< |
fy = dudr * drdy |
783 |
< |
fz = dudr * drdz |
784 |
< |
|
785 |
< |
|
786 |
< |
|
787 |
< |
|
788 |
< |
|
789 |
< |
|
790 |
< |
|
791 |
< |
#ifdef IS_MPI |
792 |
< |
fCol(1,j) = fCol(1,j) - fx |
793 |
< |
fCol(2,j) = fCol(2,j) - fy |
794 |
< |
fCol(3,j) = fCol(3,j) - fz |
795 |
< |
|
796 |
< |
fRow(1,j) = fRow(1,j) + fx |
797 |
< |
fRow(2,j) = fRow(2,j) + fy |
798 |
< |
fRow(3,j) = fRow(3,j) + fz |
799 |
< |
#else |
800 |
< |
fTemp(1,j) = fTemp(1,j) - fx |
801 |
< |
fTemp(2,j) = fTemp(2,j) - fy |
802 |
< |
fTemp(3,j) = fTemp(3,j) - fz |
803 |
< |
fTemp(1,i) = fTemp(1,i) + fx |
804 |
< |
fTemp(2,i) = fTemp(2,i) + fy |
805 |
< |
fTemp(3,i) = fTemp(3,i) + fz |
806 |
< |
#endif |
807 |
< |
|
808 |
< |
if (do_stress) then |
809 |
< |
tauTemp(1) = tauTemp(1) + fx * rxij |
810 |
< |
tauTemp(2) = tauTemp(2) + fx * ryij |
811 |
< |
tauTemp(3) = tauTemp(3) + fx * rzij |
812 |
< |
tauTemp(4) = tauTemp(4) + fy * rxij |
813 |
< |
tauTemp(5) = tauTemp(5) + fy * ryij |
814 |
< |
tauTemp(6) = tauTemp(6) + fy * rzij |
815 |
< |
tauTemp(7) = tauTemp(7) + fz * rxij |
816 |
< |
tauTemp(8) = tauTemp(8) + fz * ryij |
817 |
< |
tauTemp(9) = tauTemp(9) + fz * rzij |
818 |
< |
endif |
819 |
< |
|
820 |
< |
|
821 |
< |
|
418 |
> |
|
419 |
|
end subroutine do_pair |
420 |
|
|
421 |
|
|
422 |
< |
|
423 |
< |
|
827 |
< |
|
828 |
< |
|
829 |
< |
|
830 |
< |
|
831 |
< |
|
832 |
< |
|
833 |
< |
|
834 |
< |
|
835 |
< |
|
836 |
< |
|
837 |
< |
|
838 |
< |
|
839 |
< |
subroutine get_interatomic_vector(q_i,q_j,rx_ij,ry_ij,rz_ij,r_sq,r_ij) |
840 |
< |
!---------------- Arguments------------------------------- |
841 |
< |
!! index i |
842 |
< |
|
843 |
< |
!! Position array |
422 |
> |
subroutine get_interatomic_vector(q_i, q_j, d, r_sq) |
423 |
> |
|
424 |
|
real (kind = dp), dimension(3) :: q_i |
425 |
|
real (kind = dp), dimension(3) :: q_j |
846 |
– |
!! x component of vector between i and j |
847 |
– |
real ( kind = dp ), intent(out) :: rx_ij |
848 |
– |
!! y component of vector between i and j |
849 |
– |
real ( kind = dp ), intent(out) :: ry_ij |
850 |
– |
!! z component of vector between i and j |
851 |
– |
real ( kind = dp ), intent(out) :: rz_ij |
852 |
– |
!! magnitude of r squared |
426 |
|
real ( kind = dp ), intent(out) :: r_sq |
854 |
– |
!! magnitude of vector r between atoms i and j. |
855 |
– |
real ( kind = dp ), intent(out) :: r_ij |
856 |
– |
!! wrap into periodic box. |
857 |
– |
logical, intent(in) :: wrap |
858 |
– |
|
859 |
– |
!--------------- Local Variables--------------------------- |
860 |
– |
!! Distance between i and j |
427 |
|
real( kind = dp ) :: d(3) |
862 |
– |
!---------------- END DECLARATIONS------------------------- |
428 |
|
|
864 |
– |
|
865 |
– |
! Find distance between i and j |
429 |
|
d(1:3) = q_i(1:3) - q_j(1:3) |
430 |
< |
|
431 |
< |
! Wrap back into periodic box if necessary |
432 |
< |
if ( wrap ) then |
430 |
> |
|
431 |
> |
! Wrap back into periodic box if necessary |
432 |
> |
if ( isPBC() ) then |
433 |
|
d(1:3) = d(1:3) - thisSim%box(1:3) * sign(1.0_dp,thisSim%box(1:3)) * & |
434 |
|
int(abs(d(1:3)/thisSim%box(1:3) + 0.5_dp) |
435 |
< |
end if |
435 |
> |
endif |
436 |
|
|
874 |
– |
! Find Magnitude of the vector |
437 |
|
r_sq = dot_product(d,d) |
438 |
< |
r_ij = sqrt(r_sq) |
877 |
< |
|
878 |
< |
! Set each component for force calculation |
879 |
< |
rx_ij = d(1) |
880 |
< |
ry_ij = d(2) |
881 |
< |
rz_ij = d(3) |
882 |
< |
|
883 |
< |
|
438 |
> |
|
439 |
|
end subroutine get_interatomic_vector |
440 |
< |
|
440 |
> |
|
441 |
|
subroutine zero_module_variables() |
442 |
|
|
443 |
|
#ifndef IS_MPI |
475 |
|
|
476 |
|
end subroutine zero_module_variables |
477 |
|
|
478 |
< |
#ifdef IS_MPI |
478 |
> |
|
479 |
|
!! Function to properly build neighbor lists in MPI using newtons 3rd law. |
480 |
|
!! We don't want 2 processors doing the same i j pair twice. |
481 |
|
!! Also checks to see if i and j are the same particle. |
482 |
< |
function mpi_cycle_jLoop(i,j) result(do_cycle) |
482 |
> |
function checkExcludes(atom1,atom2) result(do_cycle) |
483 |
|
!--------------- Arguments-------------------------- |
484 |
|
! Index i |
485 |
< |
integer,intent(in) :: i |
485 |
> |
integer,intent(in) :: atom1 |
486 |
|
! Index j |
487 |
< |
integer,intent(in) :: j |
487 |
> |
integer,intent(in), optional :: atom2 |
488 |
|
! Result do_cycle |
489 |
|
logical :: do_cycle |
490 |
|
!--------------- Local variables-------------------- |
491 |
|
integer :: tag_i |
492 |
|
integer :: tag_j |
493 |
< |
!--------------- END DECLARATIONS------------------ |
494 |
< |
tag_i = tagRow(i) |
493 |
> |
integer :: i |
494 |
> |
!--------------- END DECLARATIONS------------------ |
495 |
> |
do_cycle = .false. |
496 |
> |
|
497 |
> |
#ifdef IS_MPI |
498 |
> |
tag_i = tagRow(atom1) |
499 |
> |
#else |
500 |
> |
tag_i = tag(atom1) |
501 |
> |
#endif |
502 |
> |
|
503 |
> |
!! Check global excludes first |
504 |
> |
if (.not. present(atom2)) then |
505 |
> |
do i = 1,nGlobalExcludes |
506 |
> |
if (excludeGlobal(i) == tag_i) then |
507 |
> |
do_cycle = .true. |
508 |
> |
return |
509 |
> |
end if |
510 |
> |
end do |
511 |
> |
return !! return after checking globals |
512 |
> |
end if |
513 |
> |
|
514 |
> |
!! we return if j not present here. |
515 |
|
tag_j = tagColumn(j) |
516 |
|
|
517 |
< |
do_cycle = .false. |
517 |
> |
|
518 |
|
|
519 |
|
if (tag_i == tag_j) then |
520 |
|
do_cycle = .true. |
527 |
|
else |
528 |
|
if (mod(tag_i + tag_j,2) == 1) do_cycle = .true. |
529 |
|
endif |
955 |
– |
end function mpi_cycle_jLoop |
956 |
– |
#endif |
530 |
|
|
531 |
+ |
|
532 |
+ |
|
533 |
+ |
do i = 1, nLocalExcludes |
534 |
+ |
if (tag_i = excludes(1,i) .and. excludes(2,i) < 0) then |
535 |
+ |
do_cycle = .true. |
536 |
+ |
return |
537 |
+ |
end if |
538 |
+ |
end do |
539 |
+ |
|
540 |
+ |
|
541 |
+ |
end function checkExcludes |
542 |
+ |
|
543 |
+ |
|
544 |
|
end module do_Forces |