| 2 |
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!! Corresponds to the force field defined in lj_FF.cpp |
| 3 |
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!! @author Charles F. Vardeman II |
| 4 |
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!! @author Matthew Meineke |
| 5 |
< |
!! @version $Id: lj_FF.F90,v 1.9 2003-01-22 21:45:20 chuckv Exp $, $Date: 2003-01-22 21:45:20 $, $Name: not supported by cvs2svn $, $Revision: 1.9 $ |
| 5 |
> |
!! @version $Id: lj_FF.F90,v 1.11 2003-01-27 18:28:11 chuckv Exp $, $Date: 2003-01-27 18:28:11 $, $Name: not supported by cvs2svn $, $Revision: 1.11 $ |
| 6 |
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| 7 |
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| 8 |
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| 9 |
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module lj_ff |
| 10 |
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use simulation |
| 11 |
< |
use definitions, ONLY : dp, ndim |
| 11 |
> |
use definitions |
| 12 |
> |
use generic_atypes |
| 13 |
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#ifdef IS_MPI |
| 14 |
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use mpiSimulation |
| 15 |
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#endif |
| 19 |
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!! Number of lj_atypes in lj_atype_list |
| 20 |
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integer, save :: n_lj_atypes = 0 |
| 21 |
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|
| 22 |
< |
!! Starting Size for ljMixed Array |
| 23 |
< |
integer, parameter :: ljMixed_blocksize = 10 |
| 22 |
> |
!! Global list of lj atypes in simulation |
| 23 |
> |
type (lj_atype), pointer :: ljListHead => null() |
| 24 |
> |
type (lj_atype), pointer :: ljListTail => null() |
| 25 |
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|
| 24 |
– |
!! Basic atom type for a Lennard-Jones Atom. |
| 25 |
– |
type, public :: lj_atype |
| 26 |
– |
private |
| 27 |
– |
sequence |
| 28 |
– |
!! Unique number for place in linked list |
| 29 |
– |
integer :: atype_number = 0 |
| 30 |
– |
!! Unique indentifier number (ie atomic no, etc) |
| 31 |
– |
integer :: atype_ident = 0 |
| 32 |
– |
!! Mass of Particle |
| 33 |
– |
real ( kind = dp ) :: mass = 0.0_dp |
| 34 |
– |
!! Lennard-Jones epslon |
| 35 |
– |
real ( kind = dp ) :: epslon = 0.0_dp |
| 36 |
– |
!! Lennard-Jones Sigma |
| 37 |
– |
real ( kind = dp ) :: sigma = 0.0_dp |
| 38 |
– |
!! Lennard-Jones Sigma Squared |
| 39 |
– |
real ( kind = dp ) :: sigma2 = 0.0_dp |
| 40 |
– |
!! Lennard-Jones Sigma to sixth |
| 41 |
– |
real ( kind = dp ) :: sigma6 = 0.0_dp |
| 42 |
– |
!! Pointer for linked list creation |
| 43 |
– |
type (lj_atype), pointer :: next => null() |
| 44 |
– |
end type lj_atype |
| 26 |
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|
| 46 |
– |
!! Pointer type for atype ident array |
| 47 |
– |
type, public :: lj_atypePtr |
| 48 |
– |
type (lj_atype), pointer :: this => null() |
| 49 |
– |
end type lj_atypePtr |
| 50 |
– |
|
| 51 |
– |
!! Global list of lj atypes in simulation |
| 52 |
– |
type (lj_atype), pointer :: lj_atype_list => null() |
| 27 |
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!! LJ mixing array |
| 28 |
< |
type (lj_atype), dimension(:,:), allocatable, pointer :: ljMixed =>null() |
| 55 |
< |
!! identity pointer list for force loop. |
| 56 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrList |
| 28 |
> |
type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
| 29 |
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| 30 |
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| 31 |
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!! Neighbor list and commom arrays |
| 36 |
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integer :: nListAllocs = 0 |
| 37 |
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integer, parameter :: maxListAllocs = 5 |
| 38 |
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|
| 67 |
– |
#ifdef IS_MPI |
| 68 |
– |
! Universal routines: All types of force calculations will need these arrays |
| 69 |
– |
! Arrays specific to a type of force calculation should be declared in that module. |
| 70 |
– |
real( kind = dp ), allocatable, dimension(:,:) :: qRow |
| 71 |
– |
real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
| 39 |
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|
| 40 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: fRow |
| 41 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
| 42 |
< |
|
| 43 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrListRow |
| 44 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrListColumn |
| 40 |
> |
!! Atype identity pointer lists |
| 41 |
> |
#ifdef IS_MPI |
| 42 |
> |
!! Row lj_atype pointer list |
| 43 |
> |
type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null() |
| 44 |
> |
!! Column lj_atype pointer list |
| 45 |
> |
type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
| 46 |
> |
#else |
| 47 |
> |
type( lj_identPtrList ), dimension(:), pointer :: identPtrList => null() |
| 48 |
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#endif |
| 49 |
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|
| 50 |
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|
| 51 |
+ |
!! Logical has lj force field module been initialized? |
| 52 |
+ |
logical, save :: isljFFinit = .false. |
| 53 |
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|
| 82 |
– |
logical :: isljFFinit = .false. |
| 54 |
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| 84 |
– |
|
| 55 |
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!! Public methods and data |
| 56 |
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public :: new_lj_atype |
| 57 |
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public :: do_lj_ff |
| 58 |
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public :: getLjPot |
| 59 |
< |
|
| 59 |
> |
public :: init_ljFF |
| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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contains |
| 65 |
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| 66 |
< |
subroutine new_lj_atype(ident,mass,epslon,sigma,status) |
| 66 |
> |
!! Adds a new lj_atype to the list. |
| 67 |
> |
subroutine new_lj_atype(ident,mass,epsilon,sigma,status) |
| 68 |
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real( kind = dp ), intent(in) :: mass |
| 69 |
< |
real( kind = dp ), intent(in) :: epslon |
| 69 |
> |
real( kind = dp ), intent(in) :: epsilon |
| 70 |
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real( kind = dp ), intent(in) :: sigma |
| 71 |
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integer, intent(in) :: ident |
| 72 |
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integer, intent(out) :: status |
| 73 |
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|
| 74 |
< |
type (lj_atype), pointer :: this_lj_atype |
| 104 |
< |
type (lj_atype), pointer :: lj_atype_ptr |
| 105 |
< |
|
| 106 |
< |
type (lj_atype), allocatable, dimension(:,:), pointer :: thisMix |
| 107 |
< |
type (lj_atype), allocatable, dimension(:,:), pointer :: oldMix |
| 74 |
> |
type (lj_atype), pointer :: newLJ_atype |
| 75 |
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integer :: alloc_error |
| 76 |
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integer :: atype_counter = 0 |
| 77 |
|
integer :: alloc_size |
| 78 |
< |
|
| 78 |
> |
integer :: err_stat |
| 79 |
|
status = 0 |
| 80 |
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|
| 81 |
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| 82 |
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|
| 83 |
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! allocate a new atype |
| 84 |
< |
allocate(this_lj_atype,stat=alloc_error) |
| 84 |
> |
allocate(newLJ_atype,stat=alloc_error) |
| 85 |
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if (alloc_error /= 0 ) then |
| 86 |
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status = -1 |
| 87 |
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return |
| 88 |
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end if |
| 89 |
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|
| 90 |
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! assign our new lj_atype information |
| 91 |
< |
this_lj_atype%mass = mass |
| 92 |
< |
this_lj_atype%epslon = epslon |
| 93 |
< |
this_lj_atype%sigma = sigma |
| 94 |
< |
this_lj_atype%sigma2 = sigma * sigma |
| 95 |
< |
this_lj_atype%sigma6 = this_lj_atype%sigma2 * this_lj_atype%sigma2 & |
| 96 |
< |
* this_lj_atype%sigma2 |
| 91 |
> |
newLJ_atype%mass = mass |
| 92 |
> |
newLJ_atype%epsilon = epsilon |
| 93 |
> |
newLJ_atype%sigma = sigma |
| 94 |
> |
newLJ_atype%sigma2 = sigma * sigma |
| 95 |
> |
newLJ_atype%sigma6 = newLJ_atype%sigma2 * newLJ_atype%sigma2 & |
| 96 |
> |
* newLJ_atype%sigma2 |
| 97 |
|
! assume that this atype will be successfully added |
| 98 |
< |
this_lj_atype%atype_ident = ident |
| 99 |
< |
this_lj_atype%number = n_lj_atypes + 1 |
| 98 |
> |
newLJ_atype%atype_ident = ident |
| 99 |
> |
newLJ_atype%atype_number = n_lj_atypes + 1 |
| 100 |
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|
| 101 |
< |
|
| 102 |
< |
! First time through allocate a array of size ljMixed_blocksize |
| 103 |
< |
if(.not. associated(ljMixed)) then |
| 104 |
< |
allocate(thisMix(ljMixed_blocksize,ljMixed_blocksize)) |
| 138 |
< |
if (alloc_error /= 0 ) then |
| 139 |
< |
status = -1 |
| 140 |
< |
return |
| 141 |
< |
end if |
| 142 |
< |
ljMixed => thisMix |
| 143 |
< |
! If we have outgrown ljMixed_blocksize, allocate a new matrix twice the size and |
| 144 |
< |
! point ljMix at the new matrix. |
| 145 |
< |
else if( (n_lj_atypes + 1) > size(ljMixed)) then |
| 146 |
< |
alloc_size = 2*size(ljMix) |
| 147 |
< |
allocate(thisMix(alloc_size,alloc_size)) |
| 148 |
< |
if (alloc_error /= 0 ) then |
| 149 |
< |
status = -1 |
| 150 |
< |
return |
| 151 |
< |
end if |
| 152 |
< |
! point oldMix at old ljMixed array |
| 153 |
< |
oldMix => ljMixed |
| 154 |
< |
! Copy oldMix into new Mixed array |
| 155 |
< |
thisMix = oldMix |
| 156 |
< |
! Point ljMixed at new array |
| 157 |
< |
ljMixed => thisMix |
| 158 |
< |
! Free old array so we don't have a memory leak |
| 159 |
< |
deallocate(oldMix) |
| 101 |
> |
call add_atype(newLJ_atype,ljListHead,ljListTail,err_stat) |
| 102 |
> |
if (err_stat /= 0 ) then |
| 103 |
> |
status = -1 |
| 104 |
> |
return |
| 105 |
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endif |
| 161 |
– |
|
| 162 |
– |
|
| 163 |
– |
|
| 164 |
– |
|
| 165 |
– |
|
| 166 |
– |
! Find bottom of atype master list |
| 167 |
– |
! if lj_atype_list is null then we are at the top of the list. |
| 168 |
– |
if (.not. associated(lj_atype_list)) then |
| 169 |
– |
lj_atype_ptr => this_lj_atype |
| 170 |
– |
atype_counter = 1 |
| 106 |
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|
| 172 |
– |
else ! we need to find the bottom of the list to insert new atype |
| 173 |
– |
lj_atype_ptr => lj_atype_list%next |
| 174 |
– |
atype_counter = 1 |
| 175 |
– |
find_end: do |
| 176 |
– |
if (.not. associated(lj_atype_ptr%next)) then |
| 177 |
– |
exit find_end |
| 178 |
– |
end if |
| 179 |
– |
! Set up mixing for new atype and current atype in list |
| 180 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
| 181 |
– |
calcLJMix("sigma",this_lj_atype%sigma, & |
| 182 |
– |
lj_atype_prt%sigma) |
| 183 |
– |
|
| 184 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
| 185 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
| 186 |
– |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
| 187 |
– |
|
| 188 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
| 189 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 190 |
– |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 191 |
– |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
| 192 |
– |
|
| 193 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epslon = & |
| 194 |
– |
calcLJMix("epslon",this_lj_atype%epslon, & |
| 195 |
– |
lj_atype_prt%epslon) |
| 196 |
– |
|
| 197 |
– |
! Advance to next pointer |
| 198 |
– |
lj_atype_ptr => lj_atype_ptr%next |
| 199 |
– |
atype_counter = atype_counter + 1 |
| 200 |
– |
|
| 201 |
– |
end do find_end |
| 202 |
– |
end if |
| 203 |
– |
|
| 204 |
– |
|
| 205 |
– |
|
| 206 |
– |
|
| 207 |
– |
! Insert new atype at end of list |
| 208 |
– |
lj_atype_ptr => this_lj_atype |
| 209 |
– |
! Increment number of atypes |
| 210 |
– |
|
| 107 |
|
n_lj_atypes = n_lj_atypes + 1 |
| 108 |
|
|
| 213 |
– |
! Set up self mixing |
| 109 |
|
|
| 215 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
| 216 |
– |
|
| 217 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma2 = ljMix(n_lj_atypes,n_lj_atypes)%sigma & |
| 218 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma |
| 219 |
– |
|
| 220 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma6 = ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 221 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 222 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 |
| 223 |
– |
|
| 224 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%epslon = this_lj_atype%epslon |
| 225 |
– |
|
| 226 |
– |
|
| 110 |
|
end subroutine new_lj_atype |
| 111 |
|
|
| 112 |
|
|
| 119 |
|
!! Result status, success = 0, error = -1 |
| 120 |
|
integer, intent(out) :: Status |
| 121 |
|
|
| 122 |
+ |
integer :: alloc_stat |
| 123 |
+ |
|
| 124 |
|
integer :: thisStat |
| 125 |
+ |
integer :: i |
| 126 |
|
#ifdef IS_MPI |
| 127 |
|
integer, allocatable, dimension(:) :: identRow |
| 128 |
|
integer, allocatable, dimension(:) :: identCol |
| 131 |
|
integer :: alloc_stat |
| 132 |
|
#endif |
| 133 |
|
status = 0 |
| 248 |
– |
|
| 134 |
|
!! if were're not in MPI, we just update ljatypePtrList |
| 135 |
|
#ifndef IS_MPI |
| 136 |
< |
call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat) |
| 136 |
> |
call create_IdentPtrlst(ident,ljListHead,identPtrList,thisStat) |
| 137 |
|
if ( thisStat /= 0 ) then |
| 138 |
|
status = -1 |
| 139 |
|
return |
| 140 |
|
endif |
| 141 |
+ |
|
| 142 |
|
!! Allocate pointer lists |
| 143 |
|
allocate(point(nComponents),stat=alloc_stat) |
| 144 |
|
if (alloc_stat /=0) then |
| 178 |
|
call gather(ident,identCol,plan_col) |
| 179 |
|
|
| 180 |
|
!! Create row and col pointer lists |
| 181 |
< |
call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat) |
| 181 |
> |
call create_IdentPtrlst(identRow,ljListTail,identPtrListRow,thisStat) |
| 182 |
|
if (thisStat /= 0 ) then |
| 183 |
|
status = -1 |
| 184 |
|
return |
| 185 |
|
endif |
| 186 |
|
|
| 187 |
< |
call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat) |
| 187 |
> |
call create_IdentPtrlst(identCol,ljListTail,identPtrListCol,thisStat) |
| 188 |
|
if (thisStat /= 0 ) then |
| 189 |
|
status = -1 |
| 190 |
|
return |
| 194 |
|
deallocate(identCol) |
| 195 |
|
deallocate(identRow) |
| 196 |
|
|
| 311 |
– |
!! Allocate Simulation arrays |
| 312 |
– |
!! NOTE: This bit of code should be fixed, it can cause large |
| 313 |
– |
!! memory fragmentation if call repeatedly |
| 197 |
|
|
| 315 |
– |
if (.not.allocated(qRow)) then |
| 316 |
– |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 317 |
– |
if (alloc_stat /= 0 ) then |
| 318 |
– |
status = -1 |
| 319 |
– |
return |
| 320 |
– |
endif |
| 321 |
– |
else |
| 322 |
– |
deallocate(qrow) |
| 323 |
– |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 324 |
– |
if (alloc_stat /= 0 ) then |
| 325 |
– |
status = -1 |
| 326 |
– |
return |
| 327 |
– |
endif |
| 328 |
– |
endif |
| 329 |
– |
|
| 330 |
– |
if (.not.allocated(3,qCol)) then |
| 331 |
– |
allocate(qCol(ncol),stat=alloc_stat) |
| 332 |
– |
if (alloc_stat /= 0 ) then |
| 333 |
– |
status = -1 |
| 334 |
– |
return |
| 335 |
– |
endif |
| 336 |
– |
else |
| 337 |
– |
deallocate(qCol) |
| 338 |
– |
allocate(qCol(3,ncol),stat=alloc_stat) |
| 339 |
– |
if (alloc_stat /= 0 ) then |
| 340 |
– |
status = -1 |
| 341 |
– |
return |
| 342 |
– |
endif |
| 343 |
– |
endif |
| 344 |
– |
|
| 345 |
– |
if (.not.allocated(fRow)) then |
| 346 |
– |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 347 |
– |
if (alloc_stat /= 0 ) then |
| 348 |
– |
status = -1 |
| 349 |
– |
return |
| 350 |
– |
endif |
| 351 |
– |
else |
| 352 |
– |
deallocate(fRow) |
| 353 |
– |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 354 |
– |
if (alloc_stat /= 0 ) then |
| 355 |
– |
status = -1 |
| 356 |
– |
return |
| 357 |
– |
endif |
| 358 |
– |
endif |
| 359 |
– |
|
| 360 |
– |
if (.not.allocated(fCol)) then |
| 361 |
– |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 362 |
– |
if (alloc_stat /= 0 ) then |
| 363 |
– |
status = -1 |
| 364 |
– |
return |
| 365 |
– |
endif |
| 366 |
– |
else |
| 367 |
– |
deallocate(fCol) |
| 368 |
– |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 369 |
– |
if (alloc_stat /= 0 ) then |
| 370 |
– |
status = -1 |
| 371 |
– |
return |
| 372 |
– |
endif |
| 373 |
– |
endif |
| 198 |
|
!! Allocate neighbor lists for mpi simulations. |
| 199 |
|
if (.not. allocated(point)) then |
| 200 |
|
allocate(point(nrow),stat=alloc_stat) |
| 226 |
|
|
| 227 |
|
#endif |
| 228 |
|
|
| 229 |
< |
|
| 229 |
> |
call createMixingList(thisStat) |
| 230 |
> |
if (thisStat /= 0) then |
| 231 |
> |
status = -1 |
| 232 |
> |
return |
| 233 |
> |
endif |
| 234 |
|
isljFFinit = .true. |
| 235 |
|
|
| 408 |
– |
|
| 236 |
|
end subroutine init_ljFF |
| 237 |
|
|
| 238 |
|
|
| 239 |
|
|
| 240 |
|
|
| 241 |
|
|
| 415 |
– |
!! Takes an ident array and creates an atype pointer list |
| 416 |
– |
!! based on those identities |
| 417 |
– |
subroutine new_ljatypePtrList(mysize,ident,PtrList,status) |
| 418 |
– |
integer, intent(in) :: mysize |
| 419 |
– |
integer, intent(in) :: ident |
| 420 |
– |
integer, optional :: status |
| 421 |
– |
type(lj_atypePtr), dimension(:) :: PtrList |
| 242 |
|
|
| 243 |
< |
integer :: thisIdent |
| 243 |
> |
subroutine createMixingList(status) |
| 244 |
> |
integer :: listSize |
| 245 |
> |
integer :: status |
| 246 |
|
integer :: i |
| 247 |
< |
integer :: alloc_error |
| 426 |
< |
type (lj_atype), pointer :: tmpPtr |
| 247 |
> |
integer :: j |
| 248 |
|
|
| 249 |
< |
if (present(status)) status = 0 |
| 249 |
> |
integer :: outerCounter = 0 |
| 250 |
> |
integer :: innerCounter = 0 |
| 251 |
> |
type (lj_atype), pointer :: tmpPtrOuter => null() |
| 252 |
> |
type (lj_atype), pointer :: tmpPtrInner => null() |
| 253 |
> |
status = 0 |
| 254 |
|
|
| 255 |
< |
! First time through, allocate list |
| 256 |
< |
if (.not.(allocated)) then |
| 257 |
< |
allocate(PtrList(mysize)) |
| 255 |
> |
listSize = getListLen(ljListHead) |
| 256 |
> |
if (listSize == 0) then |
| 257 |
> |
status = -1 |
| 258 |
> |
return |
| 259 |
> |
end if |
| 260 |
> |
|
| 261 |
> |
|
| 262 |
> |
if (.not. associated(ljMixed)) then |
| 263 |
> |
allocate(ljMixed(listSize,listSize)) |
| 264 |
|
else |
| 265 |
< |
! We want to creat a new ident list so free old list |
| 266 |
< |
deallocate(PrtList) |
| 267 |
< |
allocate(PtrList(mysize)) |
| 437 |
< |
endif |
| 265 |
> |
status = -1 |
| 266 |
> |
return |
| 267 |
> |
end if |
| 268 |
|
|
| 269 |
< |
! Match pointer list |
| 270 |
< |
do i = 1, mysize |
| 271 |
< |
thisIdent = ident(i) |
| 272 |
< |
call getLJatype(thisIdent,tmpPtr) |
| 273 |
< |
|
| 274 |
< |
if (.not. associated(tmpPtr)) then |
| 275 |
< |
status = -1 |
| 276 |
< |
return |
| 269 |
> |
|
| 270 |
> |
write(*,*) "Creating mixing list" |
| 271 |
> |
tmpPtrOuter => ljListHead |
| 272 |
> |
tmpPtrInner => tmpPtrOuter%next |
| 273 |
> |
do while (associated(tmpPtrOuter)) |
| 274 |
> |
outerCounter = outerCounter + 1 |
| 275 |
> |
write(*,*) "Outer index is: ", outerCounter |
| 276 |
> |
write(*,*) "For atype: ", tmpPtrOuter%atype_ident |
| 277 |
> |
! do self mixing rule |
| 278 |
> |
ljMixed(outerCounter,outerCounter)%sigma = tmpPtrOuter%sigma |
| 279 |
> |
|
| 280 |
> |
ljMixed(outerCounter,outerCounter)%sigma2 = ljMixed(outerCounter,outerCounter)%sigma & |
| 281 |
> |
* ljMixed(outerCounter,outerCounter)%sigma |
| 282 |
> |
|
| 283 |
> |
ljMixed(outerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,outerCounter)%sigma2 & |
| 284 |
> |
* ljMixed(outerCounter,outerCounter)%sigma2 & |
| 285 |
> |
* ljMixed(outerCounter,outerCounter)%sigma2 |
| 286 |
> |
|
| 287 |
> |
ljMixed(outerCounter,outerCounter)%epsilon = tmpPtrOuter%epsilon |
| 288 |
> |
|
| 289 |
> |
innerCounter = outerCounter + 1 |
| 290 |
> |
do while (associated(tmpPtrInner)) |
| 291 |
> |
|
| 292 |
> |
write(*,*) "Entered inner loop for: ", innerCounter |
| 293 |
> |
ljMixed(outerCounter,innerCounter)%sigma = & |
| 294 |
> |
calcLJMix("sigma",tmpPtrOuter%sigma, & |
| 295 |
> |
tmpPtrInner%sigma) |
| 296 |
> |
|
| 297 |
> |
ljMixed(outerCounter,innerCounter)%sigma2 = & |
| 298 |
> |
ljMixed(outerCounter,innerCounter)%sigma & |
| 299 |
> |
* ljMixed(outerCounter,innerCounter)%sigma |
| 300 |
> |
|
| 301 |
> |
ljMixed(outerCounter,innerCounter)%sigma6 = & |
| 302 |
> |
ljMixed(outerCounter,innerCounter)%sigma2 & |
| 303 |
> |
* ljMixed(outerCounter,innerCounter)%sigma2 & |
| 304 |
> |
* ljMixed(outerCounter,innerCounter)%sigma2 |
| 305 |
> |
|
| 306 |
> |
ljMixed(outerCounter,innerCounter)%epsilon = & |
| 307 |
> |
calcLJMix("epsilon",tmpPtrOuter%epsilon, & |
| 308 |
> |
tmpPtrInner%epsilon) |
| 309 |
> |
ljMixed(innerCounter,outerCounter)%sigma = ljMixed(outerCounter,innerCounter)%sigma |
| 310 |
> |
ljMixed(innerCounter,outerCounter)%sigma2 = ljMixed(outerCounter,innerCounter)%sigma2 |
| 311 |
> |
ljMixed(innerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,innerCounter)%sigma6 |
| 312 |
> |
ljMixed(innerCounter,outerCounter)%epsilon = ljMixed(outerCounter,innerCounter)%epsilon |
| 313 |
> |
|
| 314 |
> |
|
| 315 |
> |
tmpPtrInner => tmpPtrInner%next |
| 316 |
> |
innerCounter = innerCounter + 1 |
| 317 |
> |
end do |
| 318 |
> |
! advance pointers |
| 319 |
> |
tmpPtrOuter => tmpPtrOuter%next |
| 320 |
> |
if (associated(tmpPtrOuter)) then |
| 321 |
> |
tmpPtrInner => tmpPtrOuter%next |
| 322 |
|
endif |
| 323 |
|
|
| 449 |
– |
PtrList(i)%this => tmpPtr |
| 324 |
|
end do |
| 325 |
|
|
| 326 |
< |
end subroutine new_ljatypePtrList |
| 326 |
> |
end subroutine createMixingList |
| 327 |
|
|
| 454 |
– |
!! Finds a lj_atype based upon numerical ident |
| 455 |
– |
!! returns a null pointer if error |
| 456 |
– |
subroutine getLJatype(ident,ljAtypePtr) |
| 457 |
– |
integer, intent(in) :: ident |
| 458 |
– |
type (lj_atype), intent(out),pointer :: ljAtypePtr => null() |
| 459 |
– |
|
| 460 |
– |
type (lj_atype), pointer :: tmplj_atype_ptr => null() |
| 328 |
|
|
| 462 |
– |
if(.not. associated(lj_atype_list)) return |
| 329 |
|
|
| 464 |
– |
! Point at head of list. |
| 465 |
– |
tmplj_atype_ptr => lj_atype_list |
| 466 |
– |
find_ident: do |
| 467 |
– |
if (.not.associated(tmplj_atype_ptr)) then |
| 468 |
– |
exit find_ident |
| 469 |
– |
else if( lj_atype_ptr%atype_ident == ident) |
| 470 |
– |
ljAtypePtr => tmplj_atype_ptr |
| 471 |
– |
exit find_ident |
| 472 |
– |
endif |
| 473 |
– |
tmplj_atype_ptr => tmplj_atype_ptr%next |
| 474 |
– |
end do find_ident |
| 330 |
|
|
| 331 |
< |
end subroutine getLJatype |
| 331 |
> |
|
| 332 |
> |
|
| 333 |
|
|
| 334 |
|
|
| 335 |
|
!! FORCE routine Calculates Lennard Jones forces. |
| 336 |
|
!-------------------------------------------------------------> |
| 337 |
|
subroutine do_lj_ff(q,f,potE,do_pot) |
| 338 |
< |
real ( kind = dp ), dimension(ndim,) :: q |
| 339 |
< |
real ( kind = dp ), dimension(ndim,nLRparticles) :: f |
| 338 |
> |
!! Position array provided by C, dimensioned by getNlocal |
| 339 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: q |
| 340 |
> |
!! Force array provided by C, dimensioned by getNlocal |
| 341 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: f |
| 342 |
|
real ( kind = dp ) :: potE |
| 343 |
|
logical ( kind = 2) :: do_pot |
| 344 |
|
|
| 346 |
|
type(lj_atype), pointer :: ljAtype_j |
| 347 |
|
|
| 348 |
|
#ifdef MPI |
| 349 |
< |
real( kind = DP ), dimension(3,ncol) :: efr |
| 349 |
> |
real( kind = DP ), dimension(3,getNcol()) :: efr |
| 350 |
|
real( kind = DP ) :: pot_local |
| 351 |
|
#else |
| 352 |
< |
! real( kind = DP ), dimension(3,natoms) :: efr |
| 352 |
> |
real( kind = DP ), dimension(3,getNlocal()) :: efr |
| 353 |
|
#endif |
| 354 |
|
|
| 355 |
+ |
!! Local arrays needed for MPI |
| 356 |
+ |
#ifdef IS_MPI |
| 357 |
+ |
real(kind = dp), dimension(3:getNrow()) :: qRow |
| 358 |
+ |
real(kind = dp), dimension(3:getNcol()) :: qCol |
| 359 |
+ |
|
| 360 |
+ |
real(kind = dp), dimension(3:getNrow()) :: fRow |
| 361 |
+ |
real(kind = dp), dimension(3:getNcol()) :: fCol |
| 362 |
+ |
|
| 363 |
+ |
real(kind = dp), dimension(getNrow()) :: eRow |
| 364 |
+ |
real(kind = dp), dimension(getNcol()) :: eCol |
| 365 |
+ |
|
| 366 |
+ |
real(kind = dp), dimension(getNlocal()) :: eTemp |
| 367 |
+ |
#endif |
| 368 |
+ |
|
| 369 |
+ |
|
| 370 |
+ |
|
| 371 |
|
real( kind = DP ) :: pe |
| 372 |
< |
logical, :: update_nlist |
| 372 |
> |
logical :: update_nlist |
| 373 |
|
|
| 374 |
|
|
| 375 |
|
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
| 378 |
|
integer :: tag_i,tag_j |
| 379 |
|
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
| 380 |
|
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
| 381 |
< |
real( kind = DP ) :: rlistsq, rcutsq |
| 381 |
> |
real( kind = DP ) :: rlistsq, rcutsq,rlist,rcut |
| 382 |
|
|
| 383 |
+ |
! a rig that need to be fixed. |
| 384 |
+ |
#ifdef IS_MPI |
| 385 |
+ |
logical :: newtons_thrd = .true. |
| 386 |
+ |
real( kind = dp ) :: pe_local |
| 387 |
+ |
integer :: nlocal |
| 388 |
+ |
#endif |
| 389 |
|
integer :: nrow |
| 390 |
|
integer :: ncol |
| 391 |
+ |
integer :: natoms |
| 392 |
|
|
| 393 |
+ |
! Make sure we are properly initialized. |
| 394 |
|
if (.not. isljFFInit) then |
| 395 |
|
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
| 396 |
|
return |
| 397 |
|
endif |
| 398 |
+ |
#ifdef IS_MPI |
| 399 |
+ |
if (.not. isMPISimSet()) then |
| 400 |
+ |
write(default_error,*) "ERROR: mpiSimulation has not been properly initialized" |
| 401 |
+ |
return |
| 402 |
+ |
endif |
| 403 |
+ |
#endif |
| 404 |
|
|
| 405 |
+ |
!! initialize local variables |
| 406 |
+ |
natoms = getNlocal() |
| 407 |
+ |
call getRcut(rcut,rcut2=rcutsq) |
| 408 |
+ |
call getRlist(rlist,rlistsq) |
| 409 |
|
#ifndef IS_MPI |
| 410 |
|
nrow = natoms - 1 |
| 411 |
|
ncol = natoms |
| 412 |
|
#else |
| 413 |
|
nrow = getNrow(plan_row) |
| 414 |
|
ncol = getNcol(plan_col) |
| 415 |
+ |
nlocal = natoms |
| 416 |
|
j_start = 1 |
| 417 |
|
#endif |
| 418 |
|
|
| 419 |
|
|
| 420 |
+ |
!! See if we need to update neighbor lists |
| 421 |
+ |
call check(q,update_nlist) |
| 422 |
|
|
| 528 |
– |
call check(update_nlist) |
| 529 |
– |
|
| 423 |
|
!--------------WARNING........................... |
| 424 |
|
! Zero variables, NOTE:::: Forces are zeroed in C |
| 425 |
|
! Zeroing them here could delete previously computed |
| 426 |
|
! Forces. |
| 427 |
|
!------------------------------------------------ |
| 428 |
|
#ifndef IS_MPI |
| 429 |
< |
nloops = nloops + 1 |
| 430 |
< |
pot = 0.0E0_DP |
| 431 |
< |
e = 0.0E0_DP |
| 429 |
> |
! nloops = nloops + 1 |
| 430 |
> |
pe = 0.0E0_DP |
| 431 |
> |
|
| 432 |
|
#else |
| 433 |
|
f_row = 0.0E0_DP |
| 434 |
|
f_col = 0.0E0_DP |
| 435 |
|
|
| 436 |
< |
pot_local = 0.0E0_DP |
| 436 |
> |
pe_local = 0.0E0_DP |
| 437 |
|
|
| 438 |
< |
e_row = 0.0E0_DP |
| 439 |
< |
e_col = 0.0E0_DP |
| 440 |
< |
e_tmp = 0.0E0_DP |
| 438 |
> |
eRow = 0.0E0_DP |
| 439 |
> |
eCol = 0.0E0_DP |
| 440 |
> |
eTemp = 0.0E0_DP |
| 441 |
|
#endif |
| 442 |
|
efr = 0.0E0_DP |
| 443 |
|
|
| 447 |
|
call gather(q,qCol,plan_col3) |
| 448 |
|
#endif |
| 449 |
|
|
| 557 |
– |
#ifndef MPI |
| 450 |
|
|
| 559 |
– |
#endif |
| 560 |
– |
|
| 451 |
|
if (update_nlist) then |
| 452 |
|
|
| 453 |
|
! save current configuration, contruct neighbor list, |
| 454 |
|
! and calculate forces |
| 455 |
< |
call save_nlist() |
| 455 |
> |
call save_nlist(q) |
| 456 |
|
|
| 457 |
|
nlist = 0 |
| 458 |
|
|
| 500 |
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 501 |
|
|
| 502 |
|
#ifdef MPI |
| 503 |
< |
if (rijsq <= rlstsq .AND. & |
| 503 |
> |
if (rijsq <= rlistsq .AND. & |
| 504 |
|
tag_j /= tag_i) then |
| 505 |
|
#else |
| 506 |
< |
if (rijsq < rlstsq) then |
| 506 |
> |
if (rijsq < rlistsq) then |
| 507 |
|
#endif |
| 508 |
|
|
| 509 |
|
nlist = nlist + 1 |
| 510 |
|
if (nlist > size(list)) then |
| 511 |
< |
#warning "Change how nlist size is done" |
| 511 |
> |
!! "Change how nlist size is done" |
| 512 |
|
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
| 513 |
|
endif |
| 514 |
|
list(nlist) = j |
| 521 |
|
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 522 |
|
|
| 523 |
|
#ifdef MPI |
| 524 |
< |
e_row(i) = e_row(i) + pot*0.5 |
| 525 |
< |
e_col(i) = e_col(i) + pot*0.5 |
| 524 |
> |
eRow(i) = eRow(i) + pot*0.5 |
| 525 |
> |
eCol(i) = eCol(i) + pot*0.5 |
| 526 |
|
#else |
| 527 |
|
pe = pe + pot |
| 528 |
|
#endif |
| 599 |
|
|
| 600 |
|
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 601 |
|
#ifdef MPI |
| 602 |
< |
e_row(i) = e_row(i) + pot*0.5 |
| 603 |
< |
e_col(i) = e_col(i) + pot*0.5 |
| 602 |
> |
eRow(i) = eRow(i) + pot*0.5 |
| 603 |
> |
eCol(i) = eCol(i) + pot*0.5 |
| 604 |
|
#else |
| 605 |
< |
if (do_pot) pe = pe + pot |
| 605 |
> |
pe = pe + pot |
| 606 |
|
#endif |
| 607 |
|
|
| 608 |
|
|
| 635 |
|
call scatter(fRow,f,plan_row3) |
| 636 |
|
|
| 637 |
|
call scatter(fCol,f_tmp,plan_col3) |
| 638 |
+ |
|
| 639 |
|
do i = 1,nlocal |
| 640 |
< |
do dim = 1,3 |
| 750 |
< |
f(dim,i) = f(dim,i) + f_tmp(dim,i) |
| 751 |
< |
end do |
| 640 |
> |
f(1:3,i) = f(1:3,i) + f_tmp(1:3,i) |
| 641 |
|
end do |
| 642 |
|
|
| 643 |
|
|
| 649 |
|
! scatter/gather pot_local into all other procs |
| 650 |
|
! add resultant to get total pot |
| 651 |
|
do i = 1, nlocal |
| 652 |
< |
pot_local = pot_local + e_tmp(i) |
| 652 |
> |
pe_local = pe_local + e_tmp(i) |
| 653 |
|
enddo |
| 654 |
|
if (newtons_thrd) then |
| 655 |
|
e_tmp = 0.0E0_DP |
| 656 |
|
call scatter(e_col,e_tmp,plan_col) |
| 657 |
|
do i = 1, nlocal |
| 658 |
< |
pot_local = pot_local + e_tmp(i) |
| 658 |
> |
pe_local = pe_local + e_tmp(i) |
| 659 |
|
enddo |
| 660 |
|
endif |
| 661 |
|
endif |
| 662 |
+ |
potE = pe_local |
| 663 |
|
#endif |
| 664 |
|
|
| 665 |
+ |
potE = pe |
| 666 |
|
|
| 667 |
|
|
| 777 |
– |
|
| 668 |
|
end subroutine do_lj_ff |
| 669 |
|
|
| 670 |
|
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
| 680 |
|
!! Second Derivative, optional, used mainly for normal mode calculations. |
| 681 |
|
real( kind = dp ), intent(out), optional :: d2 |
| 682 |
|
|
| 683 |
< |
type (lj_atype), intent(in), pointer :: atype1 |
| 684 |
< |
type (lj_atype), intent(in), pointer :: atype2 |
| 683 |
> |
type (lj_atype), pointer :: atype1 |
| 684 |
> |
type (lj_atype), pointer :: atype2 |
| 685 |
|
|
| 686 |
|
integer, intent(out), optional :: status |
| 687 |
|
|
| 689 |
|
real( kind = dp ) :: sigma |
| 690 |
|
real( kind = dp ) :: sigma2 |
| 691 |
|
real( kind = dp ) :: sigma6 |
| 692 |
< |
real( kind = dp ) :: epslon |
| 692 |
> |
real( kind = dp ) :: epsilon |
| 693 |
|
|
| 694 |
|
real( kind = dp ) :: rcut |
| 695 |
|
real( kind = dp ) :: rcut2 |
| 714 |
|
if (present(status)) status = 0 |
| 715 |
|
|
| 716 |
|
! Look up the correct parameters in the mixing matrix |
| 717 |
< |
sigma = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma |
| 718 |
< |
sigma2 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma2 |
| 719 |
< |
sigma6 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma6 |
| 720 |
< |
epslon = ljMixed(atype1%atype_ident,atype2_atype_ident)%epslon |
| 717 |
> |
sigma = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma |
| 718 |
> |
sigma2 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma2 |
| 719 |
> |
sigma6 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma6 |
| 720 |
> |
epsilon = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon |
| 721 |
|
|
| 722 |
|
|
| 723 |
|
|
| 737 |
|
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
| 738 |
|
|
| 739 |
|
if (r.le.rcut) then |
| 740 |
< |
u = 4.0E0_DP * epsilon * (t12 - t6) + delta |
| 740 |
> |
pot = 4.0E0_DP * epsilon * (t12 - t6) + delta |
| 741 |
|
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
| 742 |
|
if(doSec) d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
| 743 |
|
else |
| 744 |
< |
u = 0.0E0_DP |
| 744 |
> |
pot = 0.0E0_DP |
| 745 |
|
dudr = 0.0E0_DP |
| 746 |
|
if(doSec) d2 = 0.0E0_DP |
| 747 |
|
endif |
| 770 |
|
|
| 771 |
|
case ("sigma") |
| 772 |
|
myMixParam = 0.5_dp * (param1 + param2) |
| 773 |
< |
case ("epslon") |
| 773 |
> |
case ("epsilon") |
| 774 |
|
myMixParam = sqrt(param1 * param2) |
| 775 |
|
case default |
| 776 |
|
status = -1 |
