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Prepare for beta 2
2018-10-21
B
e
r
k
H
ess
Fix
mdrun
s
tar
t
/e
n
d time print
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add env
.
var
.
to
di
s
able upd
a
te gr
o
ups
commit
|
commitdiff
|
tree
2018-10-12
Berk H
e
ss
Implement
assi
g
ni
n
g bondeds to the
GP
U
commit
|
commitdiff
|
tree
2018-10-10
B
erk Hess
Move
pu
l
l
o
u
t
p
u
t fun
c
tions to output
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Ber
k
Hess
Minor
r
e
factoring
i
n bonded threading
commit
|
commitdiff
|
tree
2018-10-09
Be
r
k H
e
s
s
Fix compiler warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update groups
commit
|
commitdiff
|
tree
2018-10-05
Berk Hess
Add upda
t
e
g
roups to DD atom dis
p
la
c
ement
commit
|
commitdiff
|
tree
2018-10-04
B
erk
H
ess
Make AVX2 pas
s
TSAN
commit
|
commitdiff
|
tree
2018-10-04
Berk H
e
ss
Add note to avoid constraints=all
-
bond
s
commit
|
commitdiff
|
tree
2018-10-03
B
erk Hess
Remove unnecessary clear
i
ng
i
n
gmxcpp
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
Convert gmx_cpp t
o
C++
commit
|
commitdiff
|
tree
2018-10-02
Ber
k
H
ess
U
p
date DD cutoffs for update groups
commit
|
commitdiff
|
tree
2018-09-30
Be
r
k
H
ess
Co
r
rect update g
r
oup angle param type
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Ref
a
cto
r
in
g
i
n calc_ver
l
etbu
f
.
cpp
commit
|
commitdiff
|
tree
2018-09-29
Berk He
s
s
Add UpdateGroupsCog to DD
commit
|
commitdiff
|
tree
2018-09-27
B
e
rk Hess
Move m
a
x
R
efe
r
enceTemperatu
r
e()
to inputrec
commit
|
commitdiff
|
tree
2018-09-27
Ber
k
Hess
Improve update
group r
a
dii
commit
|
commitdiff
|
tree
2018-09-27
Be
r
k
H
ess
Reor
g
a
nize RVec scaling fu
n
ctions
commit
|
commitdiff
|
tree
2018-09-26
Berk Hes
s
Extr
a
ct se
t
tle test
w
a
t
er coordinate
s
commit
|
commitdiff
|
tree
2018-09-26
Be
r
k Hess
Su
p
port atom groups in nbnxn_search
commit
|
commitdiff
|
tree
2018-09-25
Berk Hess
Add UpdateG
r
oupsCog class
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix performa
n
ce report
w
hen init_step!=0
commit
|
commitdiff
|
tree
2018-09-22
Berk H
e
ss
Add update
grou
p
s boolean to DD
commit
|
commitdiff
|
tree
2018-09-22
B
e
r
k
H
ess
Rena
m
e
D
D
c
o
n
strai
n
t b
o
o
l
eans
commit
|
commitdiff
|
tree
2018-09-22
Be
r
k Hess
Add u
p
d
a
t
e
g
r
oups
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Change pull buffers to s
t
d::
v
ector
commit
|
commitdiff
|
tree
2018-09-20
Berk Hes
s
Fix type bug in trilinic D
D
code
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert gmx
_
cmap_t to C+
+
commit
|
commitdiff
|
tree
2018-09-19
B
e
rk He
s
s
Conver
t
g
mx_ffparams_t to C++
commit
|
commitdiff
|
tree
2018-09-18
B
e
r
k
Hess
Introduce ext
r
actILi
s
t
s helpe
r
fun
c
t
io
n
commit
|
commitdiff
|
tree
2018-09-18
B
erk Hes
s
Refactor ddbox handling
commit
|
commitdiff
|
tree
2018-09-17
B
e
rk Hess
M
o
ve ifun
c
stuff fr
o
m i
d
ef
.
h t
o
ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Change p
o
inter
s
to
I
nteractionLis
t
to refe
r
ences
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
Refac
t
o
ring in D
D
redistri
b
ute
commit
|
commitdiff
|
tree
2018-09-14
Ber
k
Hess
Refa
c
t
or g
e
t
A
t
o
mGroupDi
s
tribution()
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
C
h
a
nge gmx_molty
p
e
_t
.
i
l
ist
to
InteractionL
i
sts
commit
|
commitdiff
|
tree
2018-09-13
Berk Hess
Ad
d
C
+
+
v
ersion of t_ilis
t
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Convert vsit
e
structs to C+
+
commit
|
commitdiff
|
tree
2018-09-12
Berk H
e
ss
Con
v
ert
D
D
g
m
x
_
r
everse_top_t to C+
+
commit
|
commitdiff
|
tree
2018-08-29
B
e
rk Hes
s
Refactor wall potent
i
al calculation
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk Hess
Replace gmx_hash
_
t by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Ber
k
Hess
Merge
"Me
r
ge branch releas
e
-20
1
8"
commit
|
commitdiff
|
tree
2018-08-24
Berk He
s
s
Add
s
ize opti
m
ization
to HashedMap
commit
|
commitdiff
|
tree
2018-08-24
B
e
r
k
He
s
s
Ad
d
tes
t
s f
o
r Hash
e
dMap
commit
|
commitdiff
|
tree
2018-08-22
Berk He
s
s
Fix m
i
ssing i
n
t
e
ractions
w
ith
G
PU and DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Ensure doma
i
n
s
are large enoug
h
for atom motion
commit
|
commitdiff
|
tree
2018-08-21
Berk He
s
s
Fix
e
d mdrun segv
wit
h
Q
M/MM
ONIOM schem
e
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Refactor calc_
v
erlet_buf
f
er
_
size()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hes
s
Remove compacting f
r
om
DD redistr
i
bute
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk Hess
Fix Ver
l
e
t buffer
estim
a
te with BD
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix clang namespace
c
ommen
t
warning
commit
|
commitdiff
|
tree
2018-08-20
Berk H
e
ss
Fix assert
i
on f
a
ilur
e
i
n CG
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk
H
ess
R
eally fix
C
G with multip
l
e domains
commit
|
commitdiff
|
tree
2018-08-20
B
erk Hes
s
M
a
k
e
g
mx_g
a
2
la_t
a
proper
c
la
s
s
commit
|
commitdiff
|
tree
2018-08-18
Berk Hess
Add check
f
or pu
l
l group
PBC to gro
m
pp
commit
|
commitdiff
|
tree
2018-08-17
Be
r
k He
s
s
Mak
e
pu
l
l
p
bc atom use Lo
c
alAt
o
mSet
commit
|
commitdiff
|
tree
2018-07-18
Be
r
k Hess
Apply local at
o
m
s
ets in pull c
o
de
commit
|
commitdiff
|
tree
2018-07-03
Berk He
s
s
Convert gmx
_
hash_t to C++
commit
|
commitdiff
|
tree
2018-07-03
Be
r
k
Hess
Loca
l
i
z
e variables in dd_re
d
i
s
tri
b
u
te
_
cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
Convert DD DL
B
cell size handl
i
n
g to C++
commit
|
commitdiff
|
tree
2018-07-02
Ber
k
H
e
s
s
Fix
r
e
c
e
n
t
b
u
g
w
i
th 2D
/
3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
Removed
smal
l
oc
.
h from many DD
f
iles
commit
|
commitdiff
|
tree
2018-06-29
Berk He
s
s
Con
v
ert gmx_domdec_constra
i
nts_t
to C
+
+
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Convert g
m
x_dom
d
ec
_
s
p
ecat_com
m
_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Initialize DD D
L
B varia
b
l
e
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
New quote f
r
o
m a referee
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Rename atomGroups in
g
m
x
_domdec_t to
atom
G
r
o
uping
commit
|
commitdiff
|
tree
2018-06-28
B
e
r
k Hess
Clean up dd_move_cellx()
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Convert gmx_domd
e
c_sort_t
t
o C++
commit
|
commitdiff
|
tree
2018-06-28
Berk Hess
Change BlockRanges t
o
class RangePartitioning
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Fix
bug with 2D/3D tric
l
ini
c
DD
commit
|
commitdiff
|
tree
2018-06-27
B
erk Hess
Base va
c
uum DD on atom coordin
a
tes
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Add co
n
sistency check to DDAtomRange
s
commit
|
commitdiff
|
tree
2018-06-27
Berk
Hess
Partial con
v
ersion of
g
mx_do
m
dec_comm_t to C++
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
Template a
n
d overlo
a
d dd_sen
d
recv
functions
commit
|
commitdiff
|
tree
2018-06-27
Berk Hess
C
orrect DD zone
size loop bound
commit
|
commitdiff
|
tree
2018-06-14
B
e
r
k Hes
s
Minimization n
o
w
d
etec
t
s infini
t
e forces
commit
|
commitdiff
|
tree
2018-06-14
Be
r
k
H
ess
Introduced
D
D
A
tomRanges class
commit
|
commitdiff
|
tree
2018-06-13
B
erk
H
e
s
s
Remove L
I
NCS pr
i
nts to log
f
ile
commit
|
commitdiff
|
tree
2018-06-13
Berk
H
ess
Partial conver
s
ion o
f
gmx_
d
om
d
ec_t to C++
commit
|
commitdiff
|
tree
2018-06-12
Ber
k
Hess
Add AWH continuat
i
on consisten
c
y checking
commit
|
commitdiff
|
tree
2018-06-12
B
erk Hess
Add f
a
tal error
for inconsistent graph
commit
|
commitdiff
|
tree
2018-06-12
Ber
k
Hess
Avo
i
d
C
OM removal moving
froz
e
n at
o
ms
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Remo
v
e
c
onstraint v
correcti
o
n for frozen atoms
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Clean up make
_
at2con
commit
|
commitdiff
|
tree
2018-06-06
Be
r
k Hess
Fix M
P
I
i
n
consis
t
ency in EM after constraint failure
commit
|
commitdiff
|
tree
2018-06-05
B
e
rk H
e
ss
Make nbnxn_g
r
id_t counts and si
z
es arrays
commit
|
commitdiff
|
tree
2018-06-04
Be
r
k Hess
Fix segv in
A
W
H error message
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
F
ix grompp bu
g
with
blocks of sa
m
e
mol
e
cul
e
s
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
S
i
mplify idef_
f
e in calc_listed
_
lambda
commit
|
commitdiff
|
tree
2018-05-24
Ber
k
H
ess
C
hange
nbs in nbv to std::un
i
q
u
e
commit
|
commitdiff
|
tree
2018-05-24
Berk He
s
s
Conve
r
t gmx
_
domdec_master_t
to C+
+
commit
|
commitdiff
|
tree
2018-05-23
Berk Hes
s
Spl
i
t off co
l
le
c
t
.
c
p
p
from dom
d
e
c
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert
n
bn
x
n_search to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Chan
g
e
nbnxn grid reallocation
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std::vector in nbnxn_
s
earch_t
commit
|
commitdiff
|
tree
2018-05-22
Berk
H
ess
U
se st
d
::vector in nbnxn_grid_t
commit
|
commitdiff
|
tree
2018-05-18
Berk Hess
C
l
ean up in nbnxn_
g
rid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk Hes
s
Split
o
ff d
o
mdec distr
i
bution and cellsizes
commit
|
commitdiff
|
tree
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