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Use AtomPair for LINCS indexing
2018-12-27
B
e
r
k
Hess
Use AtomPair for LINCS in
d
exing
commit
|
commitdiff
|
tree
2018-12-27
Berk
H
ess
Use arrayref in LIN
C
S
commit
|
commitdiff
|
tree
2018-12-21
Berk
H
ess
Improve nbn
x
n cjFrom
C
i()
f
unction
commit
|
commitdiff
|
tree
2018-12-18
Berk
Hes
s
Use std::vector in
L
I
N
C
S
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
Fi
x
ed
n
ullpt
r
de
r
efence in LI
N
CS error
commit
|
commitdiff
|
tree
2018-12-14
Berk
Hes
s
F
i
x LINCS triangle
c
onst
r
aining with OpenMP
commit
|
commitdiff
|
tree
2018-12-12
Berk H
e
ss
Tempor
a
ry fix for O
p
enCL PM
E
gath
e
r
commit
|
commitdiff
|
tree
2018-12-11
B
erk Hess
Fix update grou
p
s wi
t
h 2D/3D DLB
commit
|
commitdiff
|
tree
2018-12-11
Berk
He
s
s
Make l
a
rge PME grids work on GPU
commit
|
commitdiff
|
tree
2018-12-11
Ber
k
H
e
s
s
Document mdrun mdp op
t
ion modification
commit
|
commitdiff
|
tree
2018-12-05
B
e
rk Hess
Add update
g
roups t
o
par
a
l
lelization
docs
commit
|
commitdiff
|
tree
2018-11-26
B
e
rk
H
ess
Fix FP ex
c
eption
i
n pull code
commit
|
commitdiff
|
tree
2018-11-16
Berk Hess
grom
p
p
n
o
w c
h
ecks tau-p>=2*tau-t with NH+PR
commit
|
commitdiff
|
tree
2018-11-08
Berk H
e
ss
Fix bug with DD for dims without PBC
commit
|
commitdiff
|
tree
2018-11-01
Berk Hes
s
Fi
x
broken update groups
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Li
m
it
auto assignment of bondeds to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Pin important buffers in
CUDA b
o
n
d
e
d
s
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
H
e
ss
Work around expa
n
d
ed e
n
s
emble
i
ssues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Fix FP e
x
c
e
ption in
energy redu
c
t
i
on
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
Hess
Correct
V
V
integrator ns
t
calcener
g
y use
commit
|
commitdiff
|
tree
2018-10-31
B
e
r
k
Hess
Correct
grom
p
p ns
t
expanded/nst
c
alcenergy check
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
A
dd
missing mass term to del
t
aH
commit
|
commitdiff
|
tree
2018-10-23
B
e
rk Hess
A
d
d missin
g
const
r
aint
t
er
m
to
deltaH
commit
|
commitdiff
|
tree
2018-10-21
B
e
r
k Hess
Fix m
d
run start/
e
nd
time print
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add
env
.
var
.
to disable u
p
dat
e
groups
commit
|
commitdiff
|
tree
2018-10-12
Be
r
k Hess
Implement ass
i
gni
n
g bond
e
ds to the GPU
commit
|
commitdiff
|
tree
2018-10-10
Be
r
k
H
e
s
s
M
ove pull output functions to
o
utput
.
cp
p
commit
|
commitdiff
|
tree
2018-10-10
B
e
rk Hess
M
inor refactoring in bon
d
ed threadi
n
g
commit
|
commitdiff
|
tree
2018-10-09
Berk Hess
Fix compiler warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
En
a
ble update groups
commit
|
commitdiff
|
tree
2018-10-05
Berk
H
ess
Add update groups to DD
a
tom displacement
commit
|
commitdiff
|
tree
2018-10-04
B
erk Hess
Make AVX
2
p
a
s
s TSAN
commit
|
commitdiff
|
tree
2018-10-04
B
e
rk Hess
Add note to avoi
d
constraints=a
l
l
-
bonds
commit
|
commitdiff
|
tree
2018-10-03
Berk Hes
s
Remove unnecessary clearing in gmxcpp
commit
|
commitdiff
|
tree
2018-10-03
Berk He
s
s
Convert gmx_cpp to
C
+
+
commit
|
commitdiff
|
tree
2018-10-02
Ber
k
H
e
s
s
U
pda
t
e DD cutoffs
f
o
r
u
p
date groups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hes
s
Correc
t
update group angle param type
commit
|
commitdiff
|
tree
2018-09-29
B
erk Hess
Ref
a
ctoring i
n
c
a
lc_ve
r
letbuf
.
cpp
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add UpdateGrou
p
sCog to DD
commit
|
commitdiff
|
tree
2018-09-27
Berk
H
ess
Move max
R
eferenceTemperature() to inputrec
commit
|
commitdiff
|
tree
2018-09-27
Be
r
k H
e
ss
I
m
p
rove upd
a
te group ra
d
ii
commit
|
commitdiff
|
tree
2018-09-27
B
erk Hess
Re
o
rganize RVec scaling functions
commit
|
commitdiff
|
tree
2018-09-26
B
erk H
e
ss
Extract settle
t
est wa
t
er
coord
i
nate
s
commit
|
commitdiff
|
tree
2018-09-26
Berk H
e
ss
Suppor
t
atom groups i
n
n
b
nxn_search
commit
|
commitdiff
|
tree
2018-09-25
Ber
k
He
s
s
Ad
d
UpdateGroupsCog class
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix p
e
rformance repo
r
t
w
h
en ini
t
_
step!
=
0
commit
|
commitdiff
|
tree
2018-09-22
B
erk
H
ess
A
d
d u
p
d
ate groups boolean t
o
DD
commit
|
commitdiff
|
tree
2018-09-22
B
erk Hes
s
Re
n
ame DD constraint booleans
commit
|
commitdiff
|
tree
2018-09-22
Berk He
s
s
Add updat
e
groups
commit
|
commitdiff
|
tree
2018-09-20
Be
r
k Hes
s
Change pull
b
uf
f
e
r
s to std:
:
ve
c
t
o
r
commit
|
commitdiff
|
tree
2018-09-20
B
erk Hess
Fix type
b
ug in trilinic DD code
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
C
onvert gmx_cmap_t to C++
commit
|
commitdiff
|
tree
2018-09-19
Berk
H
ess
Convert gmx
_
f
f
p
ara
m
s_t
to C+
+
commit
|
commitdiff
|
tree
2018-09-18
Berk H
e
ss
Intr
o
d
uce ex
t
r
a
ctI
L
ists helper fun
c
tion
commit
|
commitdiff
|
tree
2018-09-18
Berk H
e
ss
Refa
c
t
o
r ddbox
h
andling
commit
|
commitdiff
|
tree
2018-09-17
Berk
H
ess
Move
ifunc stuff from
i
def
.
h to i
f
u
n
c
.
h
commit
|
commitdiff
|
tree
2018-09-17
B
er
k
Hess
C
hange pointer
s
to InteractionList t
o
references
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
Refac
t
o
ring
i
n DD redistr
i
bute
commit
|
commitdiff
|
tree
2018-09-14
Berk
H
ess
Ref
a
ctor
g
etAtomGroupDistribution()
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
Change gm
x
_
moltype_t
.
ilis
t
to
I
n
ter
a
ctionLists
commit
|
commitdiff
|
tree
2018-09-13
Berk H
e
ss
Add
C++ version of t_ilis
t
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Co
n
vert vs
i
te
s
tructs to
C
++
commit
|
commitdiff
|
tree
2018-09-12
Berk
He
s
s
Convert
D
D gm
x
_
r
everse_top_t t
o
C
+
+
commit
|
commitdiff
|
tree
2018-09-10
Be
r
k Hess
Fix PME force
s
with FE without pertur
b
ed
q
/LJ
commit
|
commitdiff
|
tree
2018-08-29
B
e
rk He
s
s
R
e
fa
c
t
o
r
wal
l
poten
t
ial calculation
commit
|
commitdiff
|
tree
2018-08-24
B
erk He
s
s
R
e
pla
c
e gmx_has
h
_t by HashedM
a
p
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Merge
"
M
erge branch release-2018"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add
s
ize optimization to Hashe
d
Map
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk
H
ess
Add tests for HashedMap
commit
|
commitdiff
|
tree
2018-08-22
Berk Hess
Fix
m
issing interactions wit
h
GPU and D
D
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Ensu
r
e
d
omains are la
r
ge enough for a
t
om motion
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Fixe
d
mdru
n
se
g
v with QM/MM ONIO
M
scheme
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk Hess
Refactor calc_verl
e
t
_
buffer
_
size()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
R
e
move
compac
t
ing
f
rom DD redistribute
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Fix Verlet buffer estim
a
te
with B
D
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Fix clang
name
s
pace comme
n
t warning
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix as
s
ertion failure in CG
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Real
l
y fix CG wit
h
mu
l
t
i
ple do
m
ains
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Make g
m
x_g
a
2la_
t
a
proper class
commit
|
commitdiff
|
tree
2018-08-18
Berk Hess
Add chec
k
for pull
g
ro
u
p PB
C
to
g
rompp
commit
|
commitdiff
|
tree
2018-08-17
B
e
rk Hess
Make pull pb
c
at
o
m use
L
o
c
alA
t
omSet
commit
|
commitdiff
|
tree
2018-07-18
Ber
k
Hess
Appl
y
loc
a
l atom sets in pull c
o
de
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
Conver
t
g
m
x
_hash
_
t to C
+
+
commit
|
commitdiff
|
tree
2018-07-03
Berk H
e
ss
Localize
v
aria
b
les i
n
d
d_redistr
i
b
u
t
e_
c
g()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
C
o
nvert DD DLB cell size han
d
l
i
ng to
C
+
+
commit
|
commitdiff
|
tree
2018-07-02
Be
r
k Hes
s
Fi
x
recent
bug with 2D/3
D
DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
R
e
moved sm
a
ll
o
c
.
h from many DD files
commit
|
commitdiff
|
tree
2018-06-29
B
erk
H
e
s
s
Convert gmx_domdec_constrain
t
s_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Con
v
e
rt
gmx_domdec_specat_c
o
mm_t
t
o C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hes
s
Ini
t
ial
i
z
e DD DLB variable
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
New quote from a referee
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Rename atom
G
roups in
gmx_d
o
mdec
_
t to atomGrouping
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Clean
up
d
d_move_cellx()
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Convert gmx
_
domdec_s
o
rt_
t
to C++
commit
|
commitdiff
|
tree
2018-06-28
B
e
rk Hess
C
hange B
l
o
c
kRanges to
c
lass RangePar
t
itionin
g
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Fix bug
w
it
h
2
D
/3D
t
riclinic DD
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
B
ase
vacuum DD on
a
tom
c
o
ordi
n
ates
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Add con
s
i
stency check
to DDAtomRang
e
s
commit
|
commitdiff
|
tree
2018-06-27
B
e
rk Hess
Partial conversion o
f
gmx
_
domdec_c
o
m
m
_t to C++
commit
|
commitdiff
|
tree
2018-06-27
Berk
Hess
Template and overload dd_s
e
ndrecv fu
n
c
ti
o
ns
commit
|
commitdiff
|
tree
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