| 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 1.10 2003-01-24 21:36:52 chuckv Exp $, $Date: 2003-01-24 21:36:52 $, $Name: not supported by cvs2svn $, $Revision: 1.10 $ |
| 5 |
> |
!! @version $Id: lj_FF.F90,v 1.17 2003-02-03 21:15:59 chuckv Exp $, $Date: 2003-02-03 21:15:59 $, $Name: not supported by cvs2svn $, $Revision: 1.17 $ |
| 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 |
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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 ) :: epsilon = 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 |
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type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
| 55 |
– |
!! identity pointer list for force loop. |
| 56 |
– |
type (lj_atypePtr), dimension(:), pointer :: identPtrList => 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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|
| 39 |
< |
#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 |
< |
!! Row position array. |
| 71 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: qRow |
| 72 |
< |
!! Column position array. |
| 73 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
| 39 |
> |
logical, save :: firstTime = .True. |
| 40 |
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|
| 41 |
< |
!! Row Force array. |
| 42 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: fRow |
| 77 |
< |
!! Column Force Array. |
| 78 |
< |
real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
| 79 |
< |
|
| 80 |
< |
!! Row potential energy array |
| 81 |
< |
real( kind = dp ), allocatable, dimension(:) :: eRow |
| 82 |
< |
!! Column potential energy array |
| 83 |
< |
real( kind = dp ), allocatable, dimension(:) :: eColumn |
| 84 |
< |
|
| 85 |
< |
|
| 41 |
> |
!! Atype identity pointer lists |
| 42 |
> |
#ifdef IS_MPI |
| 43 |
|
!! Row lj_atype pointer list |
| 44 |
< |
type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null() |
| 44 |
> |
type (lj_identPtrList), dimension(:), pointer :: identPtrListRow => null() |
| 45 |
|
!! Column lj_atype pointer list |
| 46 |
< |
type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
| 46 |
> |
type (lj_identPtrList), dimension(:), pointer :: identPtrListColumn => null() |
| 47 |
> |
#else |
| 48 |
> |
type( lj_identPtrList ), dimension(:), pointer :: identPtrList => null() |
| 49 |
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#endif |
| 50 |
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| 51 |
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| 64 |
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| 65 |
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contains |
| 66 |
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| 67 |
+ |
!! Adds a new lj_atype to the list. |
| 68 |
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subroutine new_lj_atype(ident,mass,epsilon,sigma,status) |
| 69 |
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real( kind = dp ), intent(in) :: mass |
| 70 |
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real( kind = dp ), intent(in) :: epsilon |
| 72 |
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integer, intent(in) :: ident |
| 73 |
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integer, intent(out) :: status |
| 74 |
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|
| 75 |
< |
type (lj_atype), pointer :: this_lj_atype |
| 116 |
< |
type (lj_atype), pointer :: lj_atype_ptr |
| 117 |
< |
|
| 118 |
< |
type (lj_atype), dimension(:,:), pointer :: thisMix |
| 119 |
< |
type (lj_atype), dimension(:,:), pointer :: oldMix |
| 75 |
> |
type (lj_atype), pointer :: newLJ_atype |
| 76 |
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integer :: alloc_error |
| 77 |
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integer :: atype_counter = 0 |
| 78 |
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integer :: alloc_size |
| 79 |
< |
|
| 79 |
> |
integer :: err_stat |
| 80 |
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status = 0 |
| 81 |
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| 82 |
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| 83 |
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|
| 84 |
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! allocate a new atype |
| 85 |
< |
allocate(this_lj_atype,stat=alloc_error) |
| 85 |
> |
allocate(newLJ_atype,stat=alloc_error) |
| 86 |
|
if (alloc_error /= 0 ) then |
| 87 |
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status = -1 |
| 88 |
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return |
| 89 |
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end if |
| 90 |
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|
| 91 |
|
! assign our new lj_atype information |
| 92 |
< |
this_lj_atype%mass = mass |
| 93 |
< |
this_lj_atype%epsilon = epsilon |
| 94 |
< |
this_lj_atype%sigma = sigma |
| 95 |
< |
this_lj_atype%sigma2 = sigma * sigma |
| 96 |
< |
this_lj_atype%sigma6 = this_lj_atype%sigma2 * this_lj_atype%sigma2 & |
| 97 |
< |
* this_lj_atype%sigma2 |
| 92 |
> |
newLJ_atype%mass = mass |
| 93 |
> |
newLJ_atype%epsilon = epsilon |
| 94 |
> |
newLJ_atype%sigma = sigma |
| 95 |
> |
newLJ_atype%sigma2 = sigma * sigma |
| 96 |
> |
newLJ_atype%sigma6 = newLJ_atype%sigma2 * newLJ_atype%sigma2 & |
| 97 |
> |
* newLJ_atype%sigma2 |
| 98 |
|
! assume that this atype will be successfully added |
| 99 |
< |
this_lj_atype%atype_ident = ident |
| 100 |
< |
this_lj_atype%atype_number = n_lj_atypes + 1 |
| 99 |
> |
newLJ_atype%atype_ident = ident |
| 100 |
> |
newLJ_atype%atype_number = n_lj_atypes + 1 |
| 101 |
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|
| 102 |
< |
|
| 103 |
< |
! First time through allocate a array of size ljMixed_blocksize |
| 104 |
< |
if(.not. associated(ljMixed)) then |
| 105 |
< |
allocate(thisMix(ljMixed_blocksize,ljMixed_blocksize)) |
| 150 |
< |
if (alloc_error /= 0 ) then |
| 151 |
< |
status = -1 |
| 152 |
< |
return |
| 153 |
< |
end if |
| 154 |
< |
ljMixed => thisMix |
| 155 |
< |
! If we have outgrown ljMixed_blocksize, allocate a new matrix twice the size and |
| 156 |
< |
! point ljMix at the new matrix. |
| 157 |
< |
else if( (n_lj_atypes + 1) > size(ljMixed)) then |
| 158 |
< |
alloc_size = 2*size(ljMixed) |
| 159 |
< |
allocate(thisMix(alloc_size,alloc_size)) |
| 160 |
< |
if (alloc_error /= 0 ) then |
| 161 |
< |
status = -1 |
| 162 |
< |
return |
| 163 |
< |
end if |
| 164 |
< |
! point oldMix at old ljMixed array |
| 165 |
< |
oldMix => ljMixed |
| 166 |
< |
! Copy oldMix into new Mixed array |
| 167 |
< |
thisMix = oldMix |
| 168 |
< |
! Point ljMixed at new array |
| 169 |
< |
ljMixed => thisMix |
| 170 |
< |
! Free old array so we don't have a memory leak |
| 171 |
< |
deallocate(oldMix) |
| 102 |
> |
call add_atype(newLJ_atype,ljListHead,ljListTail,err_stat) |
| 103 |
> |
if (err_stat /= 0 ) then |
| 104 |
> |
status = -1 |
| 105 |
> |
return |
| 106 |
|
endif |
| 107 |
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|
| 174 |
– |
|
| 175 |
– |
|
| 176 |
– |
|
| 177 |
– |
|
| 178 |
– |
! Find bottom of atype master list |
| 179 |
– |
! if lj_atype_list is null then we are at the top of the list. |
| 180 |
– |
if (.not. associated(lj_atype_list)) then |
| 181 |
– |
|
| 182 |
– |
write(*,*) "Associating lists for first time" |
| 183 |
– |
|
| 184 |
– |
|
| 185 |
– |
this_lj_atype%atype_number = 1 |
| 186 |
– |
|
| 187 |
– |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
| 188 |
– |
|
| 189 |
– |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma & |
| 190 |
– |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma |
| 191 |
– |
|
| 192 |
– |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma6 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 193 |
– |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 194 |
– |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 |
| 195 |
– |
|
| 196 |
– |
ljMixed(n_lj_atypes,n_lj_atypes)%epsilon = this_lj_atype%epsilon |
| 197 |
– |
|
| 198 |
– |
lj_atype_list => this_lj_atype |
| 199 |
– |
|
| 200 |
– |
write(*,*) "lj_atype_list first time through -- ident", lj_atype_list%atype_ident |
| 201 |
– |
else ! we need to find the bottom of the list to insert new atype |
| 202 |
– |
write(*,*) "Second time through" |
| 203 |
– |
lj_atype_ptr => lj_atype_list |
| 204 |
– |
write(*,*) "lj_atype_ptr to next" |
| 205 |
– |
atype_counter = 1 |
| 206 |
– |
find_end: do |
| 207 |
– |
if (.not. associated(lj_atype_ptr)) exit find_end |
| 208 |
– |
|
| 209 |
– |
write(*,*) "Inside find_end-this ident", lj_atype_ptr%atype_ident |
| 210 |
– |
! Set up mixing for new atype and current atype in list |
| 211 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
| 212 |
– |
calcLJMix("sigma",this_lj_atype%sigma, & |
| 213 |
– |
lj_atype_ptr%sigma) |
| 214 |
– |
|
| 215 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
| 216 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
| 217 |
– |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
| 218 |
– |
|
| 219 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
| 220 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 221 |
– |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 222 |
– |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
| 223 |
– |
|
| 224 |
– |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epsilon = & |
| 225 |
– |
calcLJMix("epsilon",this_lj_atype%epsilon, & |
| 226 |
– |
lj_atype_ptr%epsilon) |
| 227 |
– |
|
| 228 |
– |
! Advance to next pointer |
| 229 |
– |
lj_atype_ptr => lj_atype_ptr%next |
| 230 |
– |
atype_counter = atype_counter + 1 |
| 231 |
– |
end do find_end |
| 232 |
– |
|
| 233 |
– |
lj_atype_ptr => this_lj_atype |
| 234 |
– |
write(*,*) "just added: ", lj_atype_ptr%atype_ident |
| 235 |
– |
end if |
| 236 |
– |
|
| 237 |
– |
write(*,*) "lj_atype_list now contains.." |
| 238 |
– |
|
| 239 |
– |
lj_atype_ptr => lj_atype_list |
| 240 |
– |
do while (associated(lj_atype_ptr)) |
| 241 |
– |
write(*,*) "lj_atype_list contains ident", lj_atype_ptr%atype_ident |
| 242 |
– |
lj_atype_ptr => lj_atype_ptr%next |
| 243 |
– |
end do |
| 244 |
– |
|
| 245 |
– |
! Insert new atype at end of list |
| 246 |
– |
|
| 247 |
– |
! Increment number of atypes |
| 248 |
– |
|
| 108 |
|
n_lj_atypes = n_lj_atypes + 1 |
| 109 |
|
|
| 251 |
– |
! Set up self mixing |
| 110 |
|
|
| 111 |
|
end subroutine new_lj_atype |
| 112 |
|
|
| 124 |
|
|
| 125 |
|
integer :: thisStat |
| 126 |
|
integer :: i |
| 127 |
+ |
|
| 128 |
+ |
integer :: myNode |
| 129 |
|
#ifdef IS_MPI |
| 130 |
|
integer, allocatable, dimension(:) :: identRow |
| 131 |
|
integer, allocatable, dimension(:) :: identCol |
| 132 |
|
integer :: nrow |
| 133 |
|
integer :: ncol |
| 274 |
– |
integer :: alloc_stat |
| 134 |
|
#endif |
| 135 |
|
status = 0 |
| 136 |
+ |
|
| 137 |
|
|
| 138 |
< |
write(*,*) "Initializing ljFF" |
| 138 |
> |
|
| 139 |
> |
|
| 140 |
|
!! if were're not in MPI, we just update ljatypePtrList |
| 141 |
|
#ifndef IS_MPI |
| 142 |
< |
call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat) |
| 142 |
> |
call create_IdentPtrlst(ident,ljListHead,identPtrList,thisStat) |
| 143 |
|
if ( thisStat /= 0 ) then |
| 144 |
|
status = -1 |
| 145 |
|
return |
| 146 |
|
endif |
| 147 |
< |
write(*,*) "component pointer list initialized" |
| 147 |
> |
|
| 148 |
|
!! Allocate pointer lists |
| 149 |
|
allocate(point(nComponents),stat=alloc_stat) |
| 150 |
|
if (alloc_stat /=0) then |
| 160 |
|
|
| 161 |
|
! if were're in MPI, we also have to worry about row and col lists |
| 162 |
|
#else |
| 163 |
+ |
|
| 164 |
|
! We can only set up forces if mpiSimulation has been setup. |
| 165 |
|
if (.not. isMPISimSet()) then |
| 166 |
+ |
write(default_error,*) "MPI is not set" |
| 167 |
|
status = -1 |
| 168 |
|
return |
| 169 |
|
endif |
| 170 |
< |
nrow = getNrow() |
| 171 |
< |
ncol = getNcol() |
| 170 |
> |
nrow = getNrow(plan_row) |
| 171 |
> |
ncol = getNcol(plan_col) |
| 172 |
> |
mynode = getMyNode() |
| 173 |
|
!! Allocate temperary arrays to hold gather information |
| 174 |
|
allocate(identRow(nrow),stat=alloc_stat) |
| 175 |
|
if (alloc_stat /= 0 ) then |
| 182 |
|
status = -1 |
| 183 |
|
return |
| 184 |
|
endif |
| 185 |
+ |
|
| 186 |
|
!! Gather idents into row and column idents |
| 187 |
+ |
|
| 188 |
|
call gather(ident,identRow,plan_row) |
| 189 |
|
call gather(ident,identCol,plan_col) |
| 190 |
< |
|
| 190 |
> |
|
| 191 |
> |
|
| 192 |
|
!! Create row and col pointer lists |
| 193 |
< |
call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat) |
| 193 |
> |
|
| 194 |
> |
call create_IdentPtrlst(identRow,ljListHead,identPtrListRow,thisStat) |
| 195 |
|
if (thisStat /= 0 ) then |
| 196 |
|
status = -1 |
| 197 |
|
return |
| 198 |
|
endif |
| 199 |
< |
|
| 200 |
< |
call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat) |
| 199 |
> |
|
| 200 |
> |
call create_IdentPtrlst(identCol,ljListHead,identPtrListColumn,thisStat) |
| 201 |
|
if (thisStat /= 0 ) then |
| 202 |
|
status = -1 |
| 203 |
|
return |
| 204 |
|
endif |
| 205 |
|
|
| 206 |
|
!! free temporary ident arrays |
| 207 |
< |
deallocate(identCol) |
| 208 |
< |
deallocate(identRow) |
| 209 |
< |
|
| 210 |
< |
!! Allocate Simulation arrays |
| 211 |
< |
!! NOTE: This bit of code should be fixed, it can cause large |
| 344 |
< |
!! memory fragmentation if call repeatedly |
| 345 |
< |
|
| 346 |
< |
if (.not.allocated(qRow)) then |
| 347 |
< |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 348 |
< |
if (alloc_stat /= 0 ) then |
| 349 |
< |
status = -1 |
| 350 |
< |
return |
| 351 |
< |
endif |
| 352 |
< |
else |
| 353 |
< |
deallocate(qrow) |
| 354 |
< |
allocate(qRow(3,nrow),stat=alloc_stat) |
| 355 |
< |
if (alloc_stat /= 0 ) then |
| 356 |
< |
status = -1 |
| 357 |
< |
return |
| 358 |
< |
endif |
| 359 |
< |
endif |
| 360 |
< |
|
| 361 |
< |
if (.not.allocated(3,qCol)) then |
| 362 |
< |
allocate(qCol(ncol),stat=alloc_stat) |
| 363 |
< |
if (alloc_stat /= 0 ) then |
| 364 |
< |
status = -1 |
| 365 |
< |
return |
| 366 |
< |
endif |
| 367 |
< |
else |
| 368 |
< |
deallocate(qCol) |
| 369 |
< |
allocate(qCol(3,ncol),stat=alloc_stat) |
| 370 |
< |
if (alloc_stat /= 0 ) then |
| 371 |
< |
status = -1 |
| 372 |
< |
return |
| 373 |
< |
endif |
| 374 |
< |
endif |
| 375 |
< |
|
| 376 |
< |
if (.not.allocated(fRow)) then |
| 377 |
< |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 378 |
< |
if (alloc_stat /= 0 ) then |
| 379 |
< |
status = -1 |
| 380 |
< |
return |
| 381 |
< |
endif |
| 382 |
< |
else |
| 383 |
< |
deallocate(fRow) |
| 384 |
< |
allocate(fRow(3,nrow),stat=alloc_stat) |
| 385 |
< |
if (alloc_stat /= 0 ) then |
| 386 |
< |
status = -1 |
| 387 |
< |
return |
| 388 |
< |
endif |
| 389 |
< |
endif |
| 390 |
< |
|
| 391 |
< |
if (.not.allocated(fCol)) then |
| 392 |
< |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 393 |
< |
if (alloc_stat /= 0 ) then |
| 394 |
< |
status = -1 |
| 395 |
< |
return |
| 396 |
< |
endif |
| 397 |
< |
else |
| 398 |
< |
deallocate(fCol) |
| 399 |
< |
allocate(fCol(3,ncol),stat=alloc_stat) |
| 400 |
< |
if (alloc_stat /= 0 ) then |
| 401 |
< |
status = -1 |
| 402 |
< |
return |
| 403 |
< |
endif |
| 404 |
< |
endif |
| 405 |
< |
|
| 406 |
< |
if (.not.allocated(eRow)) then |
| 407 |
< |
allocate(eRow(nrow),stat=alloc_stat) |
| 408 |
< |
if (alloc_stat /= 0 ) then |
| 409 |
< |
status = -1 |
| 410 |
< |
return |
| 411 |
< |
endif |
| 412 |
< |
else |
| 413 |
< |
deallocate(eRow) |
| 414 |
< |
allocate(eRow(nrow),stat=alloc_stat) |
| 415 |
< |
if (alloc_stat /= 0 ) then |
| 416 |
< |
status = -1 |
| 417 |
< |
return |
| 418 |
< |
endif |
| 207 |
> |
if (allocated(identCol)) then |
| 208 |
> |
deallocate(identCol) |
| 209 |
> |
end if |
| 210 |
> |
if (allocated(identCol)) then |
| 211 |
> |
deallocate(identRow) |
| 212 |
|
endif |
| 213 |
|
|
| 421 |
– |
if (.not.allocated(eCol)) then |
| 422 |
– |
allocate(eCol(ncol),stat=alloc_stat) |
| 423 |
– |
if (alloc_stat /= 0 ) then |
| 424 |
– |
status = -1 |
| 425 |
– |
return |
| 426 |
– |
endif |
| 427 |
– |
else |
| 428 |
– |
deallocate(eCol) |
| 429 |
– |
allocate(eCol(ncol),stat=alloc_stat) |
| 430 |
– |
if (alloc_stat /= 0 ) then |
| 431 |
– |
status = -1 |
| 432 |
– |
return |
| 433 |
– |
endif |
| 434 |
– |
endif |
| 435 |
– |
|
| 436 |
– |
if (.not.allocated(eTemp)) then |
| 437 |
– |
allocate(eTemp(nComponents),stat=alloc_stat) |
| 438 |
– |
if (alloc_stat /= 0 ) then |
| 439 |
– |
status = -1 |
| 440 |
– |
return |
| 441 |
– |
endif |
| 442 |
– |
else |
| 443 |
– |
deallocate(eTemp) |
| 444 |
– |
allocate(eTemp(nComponets),stat=alloc_stat) |
| 445 |
– |
if (alloc_stat /= 0 ) then |
| 446 |
– |
status = -1 |
| 447 |
– |
return |
| 448 |
– |
endif |
| 449 |
– |
endif |
| 450 |
– |
|
| 451 |
– |
|
| 214 |
|
!! Allocate neighbor lists for mpi simulations. |
| 215 |
|
if (.not. allocated(point)) then |
| 216 |
|
allocate(point(nrow),stat=alloc_stat) |
| 242 |
|
|
| 243 |
|
#endif |
| 244 |
|
|
| 245 |
< |
|
| 246 |
< |
do i = 1, nComponents |
| 247 |
< |
write(*,*) "Ident pointer list ident: ", identPtrList(i)%this%atype_ident |
| 248 |
< |
end do |
| 249 |
< |
|
| 245 |
> |
call createMixingList(thisStat) |
| 246 |
> |
if (thisStat /= 0) then |
| 247 |
> |
status = -1 |
| 248 |
> |
return |
| 249 |
> |
endif |
| 250 |
|
isljFFinit = .true. |
| 251 |
|
|
| 252 |
+ |
|
| 253 |
|
end subroutine init_ljFF |
| 254 |
|
|
| 255 |
|
|
| 256 |
|
|
| 257 |
|
|
| 258 |
|
|
| 496 |
– |
!! Takes an ident array and creates an atype pointer list |
| 497 |
– |
!! based on those identities |
| 498 |
– |
subroutine new_ljatypePtrList(mysize,ident,PtrList,status) |
| 499 |
– |
integer, intent(in) :: mysize |
| 500 |
– |
integer,dimension(:), intent(in) :: ident |
| 501 |
– |
integer, optional :: status |
| 502 |
– |
type(lj_atypePtr), dimension(:), pointer :: PtrList |
| 259 |
|
|
| 260 |
< |
integer :: thisIdent |
| 260 |
> |
subroutine createMixingList(status) |
| 261 |
> |
integer :: listSize |
| 262 |
> |
integer :: status |
| 263 |
|
integer :: i |
| 264 |
< |
integer :: alloc_error |
| 507 |
< |
type (lj_atype), pointer :: tmpPtr |
| 264 |
> |
integer :: j |
| 265 |
|
|
| 266 |
< |
if (present(status)) status = 0 |
| 266 |
> |
integer :: outerCounter = 0 |
| 267 |
> |
integer :: innerCounter = 0 |
| 268 |
> |
type (lj_atype), pointer :: tmpPtrOuter => null() |
| 269 |
> |
type (lj_atype), pointer :: tmpPtrInner => null() |
| 270 |
> |
status = 0 |
| 271 |
|
|
| 272 |
< |
write(*,*) "Creating new ljatypePtrList...." |
| 273 |
< |
! First time through, allocate list |
| 274 |
< |
if (.not.associated(PtrList)) then |
| 275 |
< |
write(*,*) "allocating pointer list...." |
| 276 |
< |
allocate(PtrList(mysize)) |
| 272 |
> |
listSize = getListLen(ljListHead) |
| 273 |
> |
if (listSize == 0) then |
| 274 |
> |
status = -1 |
| 275 |
> |
return |
| 276 |
> |
end if |
| 277 |
> |
|
| 278 |
> |
|
| 279 |
> |
if (.not. associated(ljMixed)) then |
| 280 |
> |
allocate(ljMixed(listSize,listSize)) |
| 281 |
|
else |
| 282 |
< |
! We want to creat a new ident list so free old list |
| 283 |
< |
deallocate(PtrList) |
| 284 |
< |
allocate(PtrList(mysize)) |
| 520 |
< |
endif |
| 282 |
> |
status = -1 |
| 283 |
> |
return |
| 284 |
> |
end if |
| 285 |
|
|
| 286 |
< |
! Match pointer list |
| 287 |
< |
write(*,*) "Doing ident search" |
| 288 |
< |
do i = 1, mysize |
| 289 |
< |
thisIdent = ident(i) |
| 290 |
< |
write(*,*) "Calling getLJatype for ident ", thisIdent |
| 291 |
< |
call getLJatype(thisIdent,tmpPtr) |
| 292 |
< |
|
| 293 |
< |
if (.not. associated(tmpPtr)) then |
| 294 |
< |
write(*,*) "tmpptr was not associated" |
| 295 |
< |
status = -1 |
| 296 |
< |
return |
| 286 |
> |
|
| 287 |
> |
|
| 288 |
> |
tmpPtrOuter => ljListHead |
| 289 |
> |
tmpPtrInner => tmpPtrOuter%next |
| 290 |
> |
do while (associated(tmpPtrOuter)) |
| 291 |
> |
outerCounter = outerCounter + 1 |
| 292 |
> |
! do self mixing rule |
| 293 |
> |
ljMixed(outerCounter,outerCounter)%sigma = tmpPtrOuter%sigma |
| 294 |
> |
|
| 295 |
> |
ljMixed(outerCounter,outerCounter)%sigma2 = ljMixed(outerCounter,outerCounter)%sigma & |
| 296 |
> |
* ljMixed(outerCounter,outerCounter)%sigma |
| 297 |
> |
|
| 298 |
> |
ljMixed(outerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,outerCounter)%sigma2 & |
| 299 |
> |
* ljMixed(outerCounter,outerCounter)%sigma2 & |
| 300 |
> |
* ljMixed(outerCounter,outerCounter)%sigma2 |
| 301 |
> |
|
| 302 |
> |
ljMixed(outerCounter,outerCounter)%epsilon = tmpPtrOuter%epsilon |
| 303 |
> |
|
| 304 |
> |
innerCounter = outerCounter + 1 |
| 305 |
> |
do while (associated(tmpPtrInner)) |
| 306 |
> |
|
| 307 |
> |
ljMixed(outerCounter,innerCounter)%sigma = & |
| 308 |
> |
calcLJMix("sigma",tmpPtrOuter%sigma, & |
| 309 |
> |
tmpPtrInner%sigma) |
| 310 |
> |
|
| 311 |
> |
ljMixed(outerCounter,innerCounter)%sigma2 = & |
| 312 |
> |
ljMixed(outerCounter,innerCounter)%sigma & |
| 313 |
> |
* ljMixed(outerCounter,innerCounter)%sigma |
| 314 |
> |
|
| 315 |
> |
ljMixed(outerCounter,innerCounter)%sigma6 = & |
| 316 |
> |
ljMixed(outerCounter,innerCounter)%sigma2 & |
| 317 |
> |
* ljMixed(outerCounter,innerCounter)%sigma2 & |
| 318 |
> |
* ljMixed(outerCounter,innerCounter)%sigma2 |
| 319 |
> |
|
| 320 |
> |
ljMixed(outerCounter,innerCounter)%epsilon = & |
| 321 |
> |
calcLJMix("epsilon",tmpPtrOuter%epsilon, & |
| 322 |
> |
tmpPtrInner%epsilon) |
| 323 |
> |
ljMixed(innerCounter,outerCounter)%sigma = ljMixed(outerCounter,innerCounter)%sigma |
| 324 |
> |
ljMixed(innerCounter,outerCounter)%sigma2 = ljMixed(outerCounter,innerCounter)%sigma2 |
| 325 |
> |
ljMixed(innerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,innerCounter)%sigma6 |
| 326 |
> |
ljMixed(innerCounter,outerCounter)%epsilon = ljMixed(outerCounter,innerCounter)%epsilon |
| 327 |
> |
|
| 328 |
> |
|
| 329 |
> |
tmpPtrInner => tmpPtrInner%next |
| 330 |
> |
innerCounter = innerCounter + 1 |
| 331 |
> |
end do |
| 332 |
> |
! advance pointers |
| 333 |
> |
tmpPtrOuter => tmpPtrOuter%next |
| 334 |
> |
if (associated(tmpPtrOuter)) then |
| 335 |
> |
tmpPtrInner => tmpPtrOuter%next |
| 336 |
|
endif |
| 337 |
|
|
| 535 |
– |
PtrList(i)%this => tmpPtr |
| 338 |
|
end do |
| 339 |
|
|
| 340 |
< |
end subroutine new_ljatypePtrList |
| 340 |
> |
end subroutine createMixingList |
| 341 |
|
|
| 540 |
– |
!! Finds a lj_atype based upon numerical ident |
| 541 |
– |
!! returns a null pointer if error |
| 542 |
– |
subroutine getLJatype(ident,ljAtypePtr) |
| 543 |
– |
integer, intent(in) :: ident |
| 544 |
– |
type (lj_atype), pointer :: ljAtypePtr |
| 545 |
– |
type (lj_atype), pointer :: tmplj_atype_ptr => null() |
| 342 |
|
|
| 547 |
– |
write(*,*) "Finding ljAtype for ident ", ident |
| 548 |
– |
ljAtypePtr => null() |
| 343 |
|
|
| 550 |
– |
if(.not. associated(lj_atype_list)) return |
| 344 |
|
|
| 552 |
– |
! Point at head of list. |
| 553 |
– |
write(*,*) "Searching at head of list" |
| 554 |
– |
tmplj_atype_ptr => lj_atype_list |
| 555 |
– |
find_ident: do |
| 556 |
– |
if (.not.associated(tmplj_atype_ptr)) then |
| 557 |
– |
write(*,*) "Find_ident, pointer not associated" |
| 558 |
– |
exit find_ident |
| 559 |
– |
else if( tmplj_atype_ptr%atype_ident == ident) then |
| 560 |
– |
ljAtypePtr => tmplj_atype_ptr |
| 561 |
– |
exit find_ident |
| 562 |
– |
endif |
| 563 |
– |
tmplj_atype_ptr => tmplj_atype_ptr%next |
| 564 |
– |
end do find_ident |
| 345 |
|
|
| 346 |
|
|
| 347 |
|
|
| 348 |
|
|
| 569 |
– |
end subroutine getLJatype |
| 570 |
– |
|
| 571 |
– |
|
| 349 |
|
!! FORCE routine Calculates Lennard Jones forces. |
| 350 |
|
!-------------------------------------------------------------> |
| 351 |
|
subroutine do_lj_ff(q,f,potE,do_pot) |
| 359 |
|
type(lj_atype), pointer :: ljAtype_i |
| 360 |
|
type(lj_atype), pointer :: ljAtype_j |
| 361 |
|
|
| 362 |
< |
#ifdef MPI |
| 363 |
< |
real( kind = DP ), dimension(3,getNcol()) :: efr |
| 362 |
> |
#ifdef IS_MPI |
| 363 |
> |
real( kind = DP ), dimension(3,getNcol(plan_col)) :: efr |
| 364 |
|
real( kind = DP ) :: pot_local |
| 365 |
|
#else |
| 366 |
|
real( kind = DP ), dimension(3,getNlocal()) :: efr |
| 367 |
|
#endif |
| 368 |
|
|
| 369 |
+ |
!! Local arrays needed for MPI |
| 370 |
+ |
#ifdef IS_MPI |
| 371 |
+ |
real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow |
| 372 |
+ |
real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol |
| 373 |
+ |
|
| 374 |
+ |
real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow |
| 375 |
+ |
real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol |
| 376 |
+ |
real(kind = dp), dimension(3,getNlocal()) :: fMPITemp |
| 377 |
+ |
|
| 378 |
+ |
real(kind = dp), dimension(getNrow(plan_row)) :: eRow |
| 379 |
+ |
real(kind = dp), dimension(getNcol(plan_col)) :: eCol |
| 380 |
+ |
|
| 381 |
+ |
real(kind = dp), dimension(getNlocal()) :: eTemp |
| 382 |
+ |
#endif |
| 383 |
+ |
|
| 384 |
+ |
|
| 385 |
+ |
|
| 386 |
|
real( kind = DP ) :: pe |
| 387 |
|
logical :: update_nlist |
| 388 |
|
|
| 405 |
|
integer :: ncol |
| 406 |
|
integer :: natoms |
| 407 |
|
|
| 408 |
+ |
|
| 409 |
+ |
|
| 410 |
+ |
|
| 411 |
|
! Make sure we are properly initialized. |
| 412 |
|
if (.not. isljFFInit) then |
| 413 |
|
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
| 424 |
|
natoms = getNlocal() |
| 425 |
|
call getRcut(rcut,rcut2=rcutsq) |
| 426 |
|
call getRlist(rlist,rlistsq) |
| 427 |
+ |
|
| 428 |
|
#ifndef IS_MPI |
| 429 |
|
nrow = natoms - 1 |
| 430 |
|
ncol = natoms |
| 438 |
|
|
| 439 |
|
!! See if we need to update neighbor lists |
| 440 |
|
call check(q,update_nlist) |
| 441 |
+ |
if (firstTime) then |
| 442 |
+ |
update_nlist = .true. |
| 443 |
+ |
firstTime = .false. |
| 444 |
+ |
endif |
| 445 |
|
|
| 446 |
|
!--------------WARNING........................... |
| 447 |
|
! Zero variables, NOTE:::: Forces are zeroed in C |
| 453 |
|
pe = 0.0E0_DP |
| 454 |
|
|
| 455 |
|
#else |
| 456 |
< |
f_row = 0.0E0_DP |
| 457 |
< |
f_col = 0.0E0_DP |
| 456 |
> |
fRow = 0.0E0_DP |
| 457 |
> |
fCol = 0.0E0_DP |
| 458 |
|
|
| 459 |
|
pe_local = 0.0E0_DP |
| 460 |
|
|
| 465 |
|
efr = 0.0E0_DP |
| 466 |
|
|
| 467 |
|
! communicate MPI positions |
| 468 |
< |
#ifdef MPI |
| 469 |
< |
call gather(q,qRow,plan_row3) |
| 470 |
< |
call gather(q,qCol,plan_col3) |
| 468 |
> |
#ifdef IS_MPI |
| 469 |
> |
call gather(q,qRow,plan_row3d) |
| 470 |
> |
call gather(q,qCol,plan_col3d) |
| 471 |
|
#endif |
| 472 |
|
|
| 473 |
|
|
| 479 |
|
|
| 480 |
|
nlist = 0 |
| 481 |
|
|
| 482 |
< |
|
| 482 |
> |
|
| 483 |
|
|
| 484 |
|
do i = 1, nrow |
| 485 |
|
point(i) = nlist + 1 |
| 486 |
< |
#ifdef MPI |
| 486 |
> |
#ifdef IS_MPI |
| 487 |
|
ljAtype_i => identPtrListRow(i)%this |
| 488 |
|
tag_i = tagRow(i) |
| 489 |
|
rxi = qRow(1,i) |
| 498 |
|
#endif |
| 499 |
|
|
| 500 |
|
inner: do j = j_start, ncol |
| 501 |
< |
#ifdef MPI |
| 501 |
> |
#ifdef IS_MPI |
| 502 |
|
! Assign identity pointers and tags |
| 503 |
|
ljAtype_j => identPtrListColumn(j)%this |
| 504 |
< |
tag_j = tagCol(j) |
| 504 |
> |
tag_j = tagColumn(j) |
| 505 |
|
if (newtons_thrd) then |
| 506 |
|
if (tag_i <= tag_j) then |
| 507 |
|
if (mod(tag_i + tag_j,2) == 0) cycle inner |
| 522 |
|
#endif |
| 523 |
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 524 |
|
|
| 525 |
< |
#ifdef MPI |
| 525 |
> |
#ifdef IS_MPI |
| 526 |
|
if (rijsq <= rlistsq .AND. & |
| 527 |
|
tag_j /= tag_i) then |
| 528 |
|
#else |
| 529 |
+ |
|
| 530 |
|
if (rijsq < rlistsq) then |
| 531 |
|
#endif |
| 532 |
|
|
| 537 |
|
endif |
| 538 |
|
list(nlist) = j |
| 539 |
|
|
| 540 |
< |
|
| 540 |
> |
|
| 541 |
|
if (rijsq < rcutsq) then |
| 542 |
|
|
| 543 |
|
r = dsqrt(rijsq) |
| 544 |
|
|
| 545 |
|
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 546 |
|
|
| 547 |
< |
#ifdef MPI |
| 547 |
> |
#ifdef IS_MPI |
| 548 |
|
eRow(i) = eRow(i) + pot*0.5 |
| 549 |
|
eCol(i) = eCol(i) + pot*0.5 |
| 550 |
|
#else |
| 551 |
< |
pe = pe + pot |
| 551 |
> |
pe = pe + pot |
| 552 |
|
#endif |
| 553 |
|
|
| 554 |
|
efr(1,j) = -rxij |
| 562 |
|
ftmp = dudr * drdx1 |
| 563 |
|
|
| 564 |
|
|
| 565 |
< |
#ifdef MPI |
| 565 |
> |
#ifdef IS_MPI |
| 566 |
|
fCol(dim,j) = fCol(dim,j) - ftmp |
| 567 |
|
fRow(dim,i) = fRow(dim,i) + ftmp |
| 568 |
|
#else |
| 577 |
|
enddo inner |
| 578 |
|
enddo |
| 579 |
|
|
| 580 |
< |
#ifdef MPI |
| 580 |
> |
#ifdef IS_MPI |
| 581 |
|
point(nrow + 1) = nlist + 1 |
| 582 |
|
#else |
| 583 |
|
point(natoms) = nlist + 1 |
| 591 |
|
JEND = POINT(i+1) - 1 |
| 592 |
|
! check thiat molecule i has neighbors |
| 593 |
|
if (jbeg .le. jend) then |
| 594 |
< |
#ifdef MPI |
| 594 |
> |
#ifdef IS_MPI |
| 595 |
|
ljAtype_i => identPtrListRow(i)%this |
| 596 |
|
rxi = qRow(1,i) |
| 597 |
|
ryi = qRow(2,i) |
| 604 |
|
#endif |
| 605 |
|
do jnab = jbeg, jend |
| 606 |
|
j = list(jnab) |
| 607 |
< |
#ifdef MPI |
| 607 |
> |
#ifdef IS_MPI |
| 608 |
|
ljAtype_j = identPtrListColumn(j)%this |
| 609 |
< |
rxij = wrap(rxi - q_col(1,j), 1) |
| 610 |
< |
ryij = wrap(ryi - q_col(2,j), 2) |
| 611 |
< |
rzij = wrap(rzi - q_col(3,j), 3) |
| 609 |
> |
rxij = wrap(rxi - qCol(1,j), 1) |
| 610 |
> |
ryij = wrap(ryi - qCol(2,j), 2) |
| 611 |
> |
rzij = wrap(rzi - qCol(3,j), 3) |
| 612 |
|
#else |
| 613 |
|
ljAtype_j = identPtrList(j)%this |
| 614 |
|
rxij = wrap(rxi - q(1,j), 1) |
| 622 |
|
r = dsqrt(rijsq) |
| 623 |
|
|
| 624 |
|
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
| 625 |
< |
#ifdef MPI |
| 625 |
> |
#ifdef IS_MPI |
| 626 |
|
eRow(i) = eRow(i) + pot*0.5 |
| 627 |
|
eCol(i) = eCol(i) + pot*0.5 |
| 628 |
|
#else |
| 638 |
|
|
| 639 |
|
drdx1 = efr(dim,j) / r |
| 640 |
|
ftmp = dudr * drdx1 |
| 641 |
< |
#ifdef MPI |
| 641 |
> |
#ifdef IS_MPI |
| 642 |
|
fCol(dim,j) = fCol(dim,j) - ftmp |
| 643 |
|
fRow(dim,i) = fRow(dim,i) + ftmp |
| 644 |
|
#else |
| 654 |
|
|
| 655 |
|
|
| 656 |
|
|
| 657 |
< |
#ifdef MPI |
| 657 |
> |
#ifdef IS_MPI |
| 658 |
|
!!distribute forces |
| 856 |
– |
call scatter(fRow,f,plan_row3) |
| 659 |
|
|
| 660 |
< |
call scatter(fCol,f_tmp,plan_col3) |
| 660 |
> |
call scatter(fRow,f,plan_row3d) |
| 661 |
|
|
| 662 |
+ |
call scatter(fCol,fMPITemp,plan_col3d) |
| 663 |
+ |
|
| 664 |
|
do i = 1,nlocal |
| 665 |
< |
f(1:3,i) = f(1:3,i) + f_tmp(1:3,i) |
| 665 |
> |
f(1:3,i) = f(1:3,i) + fMPITemp(1:3,i) |
| 666 |
|
end do |
| 667 |
|
|
| 668 |
|
|
| 669 |
|
|
| 670 |
|
if (do_pot) then |
| 671 |
|
! scatter/gather pot_row into the members of my column |
| 672 |
< |
call scatter(e_row,e_tmp,plan_row) |
| 672 |
> |
call scatter(eRow,eTemp,plan_row) |
| 673 |
|
|
| 674 |
|
! scatter/gather pot_local into all other procs |
| 675 |
|
! add resultant to get total pot |
| 676 |
|
do i = 1, nlocal |
| 677 |
< |
pe_local = pe_local + e_tmp(i) |
| 677 |
> |
pe_local = pe_local + eTemp(i) |
| 678 |
|
enddo |
| 679 |
|
if (newtons_thrd) then |
| 680 |
< |
e_tmp = 0.0E0_DP |
| 681 |
< |
call scatter(e_col,e_tmp,plan_col) |
| 680 |
> |
eTemp = 0.0E0_DP |
| 681 |
> |
call scatter(eCol,eTemp,plan_col) |
| 682 |
|
do i = 1, nlocal |
| 683 |
< |
pe_local = pe_local + e_tmp(i) |
| 683 |
> |
pe_local = pe_local + eTemp(i) |
| 684 |
|
enddo |
| 685 |
|
endif |
| 686 |
|
endif |
| 689 |
|
|
| 690 |
|
potE = pe |
| 691 |
|
|
| 888 |
– |
|
| 692 |
|
end subroutine do_lj_ff |
| 693 |
|
|
| 694 |
|
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
| 744 |
|
epsilon = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon |
| 745 |
|
|
| 746 |
|
|
| 747 |
< |
|
| 747 |
> |
|
| 748 |
> |
|
| 749 |
|
call getRcut(rcut,rcut2=rcut2,rcut6=rcut6,status=errorStat) |
| 750 |
|
|
| 751 |
|
r2 = r * r |
