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Fix small leaks in do_md cleanup
2018-12-21
Berk Hess
Imp
r
ove nbn
x
n
c
j
FromCi() func
t
ion
commit
|
commitdiff
|
tree
2018-12-18
Berk H
e
ss
U
s
e
std::vector
i
n L
I
N
C
S
commit
|
commitdiff
|
tree
2018-12-14
Berk H
e
s
s
Fixed nullptr derefence in LI
N
CS
error
commit
|
commitdiff
|
tree
2018-12-14
B
erk Hess
Fix
LINCS tria
n
gl
e
cons
t
raining with
OpenMP
commit
|
commitdiff
|
tree
2018-12-12
Berk Hess
T
e
mporary fix for OpenCL PME
g
ather
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Fix update
g
r
o
ups with 2D/3D D
L
B
commit
|
commitdiff
|
tree
2018-12-11
B
e
r
k Hess
Make large
P
ME grids work on GPU
commit
|
commitdiff
|
tree
2018-12-11
Berk
H
ess
Documen
t
mdrun
m
dp op
t
ion modificati
o
n
commit
|
commitdiff
|
tree
2018-12-05
Berk Hess
A
d
d update
gro
u
ps t
o
paralle
l
izat
i
on docs
commit
|
commitdiff
|
tree
2018-11-26
Berk Hess
F
i
x
F
P exception in pull cod
e
commit
|
commitdiff
|
tree
2018-11-16
Berk H
e
s
s
grompp no
w
checks tau-p
>
=2*tau-t with NH+P
R
commit
|
commitdiff
|
tree
2018-11-08
Berk
H
ess
Fix bug wit
h
D
D
for
dims without
P
BC
commit
|
commitdiff
|
tree
2018-11-01
Berk Hess
Fix broken upda
t
e g
r
o
ups
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Limit
auto a
s
signment of bondeds to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk He
s
s
Pin
i
m
p
o
rtan
t
buffer
s
in CUD
A
bonde
d
s
commit
|
commitdiff
|
tree
2018-10-31
Berk H
e
s
s
Work around
expa
n
ded ensemble issu
e
s
commit
|
commitdiff
|
tree
2018-10-31
Berk
H
es
s
Fi
x
FP except
i
on
i
n energy
r
ed
u
ction
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
Hess
C
orrect VV in
t
egrato
r
nstcalcenergy use
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Correct g
r
ompp nstexpanded/nstcal
c
e
nergy che
c
k
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Ad
d
missing mass t
e
rm to
deltaH
commit
|
commitdiff
|
tree
2018-10-23
B
erk
H
ess
Add m
i
ssing con
s
traint term to deltaH
commit
|
commitdiff
|
tree
2018-10-21
B
e
rk Hess
Fix mdrun start/end time pr
i
nt
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add
env
.
var
.
to disable up
d
a
te gro
u
ps
commit
|
commitdiff
|
tree
2018-10-12
Berk
H
ess
Implement assi
g
ni
n
g bondeds
t
o
the GPU
commit
|
commitdiff
|
tree
2018-10-10
Berk H
e
ss
M
o
ve pu
l
l o
u
tpu
t
functions
t
o o
u
tput
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk
H
ess
Minor refact
o
ri
n
g
i
n bonded
t
hreading
commit
|
commitdiff
|
tree
2018-10-09
Ber
k
Hess
Fi
x
compiler warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
E
n
a
ble update
g
roups
commit
|
commitdiff
|
tree
2018-10-05
Berk
Hess
Add upd
a
te
g
r
o
ups to
D
D a
t
om displaceme
n
t
commit
|
commitdiff
|
tree
2018-10-04
Ber
k
Hess
Make AV
X
2 pass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Add
n
o
t
e to
avoid constr
a
ints=all-bonds
commit
|
commitdiff
|
tree
2018-10-03
Berk
Hes
s
Remove un
n
ecessary clea
r
ing in gmxc
p
p
commit
|
commitdiff
|
tree
2018-10-03
B
e
rk Hess
Convert gmx_cpp to C++
commit
|
commitdiff
|
tree
2018-10-02
Berk Hess
Update DD c
u
toffs for update groups
commit
|
commitdiff
|
tree
2018-09-30
B
e
rk Hess
C
o
r
r
ect update group an
g
le pa
r
am type
commit
|
commitdiff
|
tree
2018-09-29
Be
r
k Hess
Refactor
i
ng in calc_v
e
rle
t
buf
.
c
p
p
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add Update
G
roupsCog
t
o DD
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
Mov
e
maxReferenceTemp
e
rature() to
inputrec
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
Imp
r
ove update
g
roup radii
commit
|
commitdiff
|
tree
2018-09-27
B
e
rk Hess
Reorganize RVec scaling functions
commit
|
commitdiff
|
tree
2018-09-26
Be
r
k Hess
E
x
tract set
t
le te
s
t
water coo
r
din
a
tes
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Support atom
gro
u
ps in nbnxn_search
commit
|
commitdiff
|
tree
2018-09-25
Berk He
s
s
Add
U
pdateGroupsCo
g
class
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix per
f
ormance report when init_step!=0
commit
|
commitdiff
|
tree
2018-09-22
Ber
k
He
s
s
Add
u
p
date groups boolea
n
to D
D
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Rename DD constrai
n
t
b
ooleans
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Ad
d
upda
t
e gr
o
ups
commit
|
commitdiff
|
tree
2018-09-20
Berk Hes
s
Change pu
l
l buffers
to st
d
::vector
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Fix type bug in trilinic DD c
o
de
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert gmx_cmap
_
t to C++
commit
|
commitdiff
|
tree
2018-09-19
Berk He
s
s
Co
n
ver
t
gmx_ff
p
arams_t to C++
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
Intr
o
duce ext
r
actILi
s
ts helper
functio
n
commit
|
commitdiff
|
tree
2018-09-18
Be
r
k Hess
Refactor ddb
o
x
hand
l
ing
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Move ifunc stuff from
i
def
.
h
to
i
func
.
h
commit
|
commitdiff
|
tree
2018-09-17
B
erk Hess
Chan
g
e
po
i
nters to Inter
a
ctionList to references
commit
|
commitdiff
|
tree
2018-09-16
Berk
He
s
s
Refactoring in DD r
e
d
ist
r
ibu
t
e
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
Refactor getAtomGroupDistribu
t
ion()
commit
|
commitdiff
|
tree
2018-09-14
Berk H
e
ss
C
hange gmx_moltype_t
.
ilist
to Int
e
r
actionLists
commit
|
commitdiff
|
tree
2018-09-13
Berk
H
ess
A
d
d
C++ vers
i
on of t_ilist
commit
|
commitdiff
|
tree
2018-09-12
B
e
rk Hess
Conve
r
t
vsite structs to C++
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
C
o
nve
r
t
DD gmx_
r
e
verse_top_t to C++
commit
|
commitdiff
|
tree
2018-09-10
Berk
H
e
ss
Fix PM
E
fo
r
ces with FE
w
ithout perturb
e
d
q/
L
J
commit
|
commitdiff
|
tree
2018-08-29
B
erk Hess
Refa
c
t
o
r
w
a
ll potential
calculation
commit
|
commitdiff
|
tree
2018-08-24
Berk H
e
ss
Repla
c
e gmx_hash_t by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk Hess
M
e
rge
"Merge bra
n
c
h relea
s
e-2
0
18
"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add si
z
e optimizatio
n
to HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add test
s
for Has
h
edMap
commit
|
commitdiff
|
tree
2018-08-22
Ber
k
Hess
Fix miss
i
ng
interactions with GPU and DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
En
s
ur
e
domai
n
s
a
re la
r
ge enough for atom motion
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
F
i
xed mdrun segv with QM/MM ONIOM s
c
h
e
me
commit
|
commitdiff
|
tree
2018-08-20
Ber
k
Hess
Refa
c
tor calc_verlet_buffer_size()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Re
m
ove compacting from DD redistrib
u
te
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fi
x
Verlet
b
uffer es
t
i
m
ate with BD
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k Hess
Fix clang namespace com
m
en
t
warning
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k Hess
Fix a
s
s
ertion failur
e
in CG
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk Hess
Really f
i
x CG with multiple
d
om
a
ins
commit
|
commitdiff
|
tree
2018-08-20
Berk He
s
s
Make g
m
x
_ga2la_t a proper class
commit
|
commitdiff
|
tree
2018-08-18
Berk
He
s
s
Add check f
o
r
p
ull group PB
C
to gro
m
pp
commit
|
commitdiff
|
tree
2018-08-17
B
erk Hess
Make p
u
ll pbc
a
t
om use LocalAtomSet
commit
|
commitdiff
|
tree
2018-07-18
Ber
k
Hess
Apply lo
c
a
l atom sets in pull
c
ode
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
C
o
n
vert gmx_hash_t to
C
++
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
Localize vari
a
bles in d
d
_redistribute_cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
Convert D
D
DL
B
cell size
handling
t
o C++
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
Fix recent bug w
i
th 2D/3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Be
r
k
Hess
Removed smalloc
.
h from many DD files
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Convert
g
mx_dom
d
ec_co
n
straint
s
_t to C++
commit
|
commitdiff
|
tree
2018-06-29
B
erk
H
ess
Convert gmx_do
m
dec_specat
_
c
omm_t to C
+
+
commit
|
commitdiff
|
tree
2018-06-29
Berk Hes
s
Initialize DD DLB variable
commit
|
commitdiff
|
tree
2018-06-29
Berk H
e
s
s
New quo
t
e f
r
om a referee
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Rename
a
tomGroups in
gmx
_
domdec_t to atomGrouping
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Clean up d
d
_mov
e
_cellx()
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Convert gm
x
_domd
e
c_sort_
t
to C++
commit
|
commitdiff
|
tree
2018-06-28
Berk Hes
s
Change
B
lo
c
kRanges to
class RangePartitioni
n
g
commit
|
commitdiff
|
tree
2018-06-27
B
erk He
s
s
Fix bug with 2D/3D tri
c
linic DD
commit
|
commitdiff
|
tree
2018-06-27
Ber
k
Hess
Base
v
acuum DD on
a
t
om coor
d
in
a
t
e
s
commit
|
commitdiff
|
tree
2018-06-27
Berk He
s
s
Ad
d
con
s
istency che
c
k
to DDAtomR
a
nges
commit
|
commitdiff
|
tree
2018-06-27
Berk
H
ess
Partia
l
conversion o
f
gmx_do
m
dec_comm_t to C++
commit
|
commitdiff
|
tree
2018-06-27
Berk He
s
s
Templat
e
and ov
e
rload dd_sendrecv functions
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Correct DD
zone si
z
e loop bound
commit
|
commitdiff
|
tree
2018-06-14
Berk Hess
Min
i
mizati
o
n no
w
detects
in
f
inite f
o
rces
commit
|
commitdiff
|
tree
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