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Change nbnxn grid reallocation
2018-05-22
Berk Hess
Change nbnx
n
grid r
e
alloca
t
ion
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vector
i
n
n
bnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
U
se std::vector in nbnxn_gri
d
_t
commit
|
commitdiff
|
tree
2018-05-22
Kevi
n
B
oyd
Cosmetic documentation cha
n
ges
commit
|
commitdiff
|
tree
2018-05-22
Kevin B
o
y
d
Min
o
r
f
ixes to m
d
ru
n
p
e
rform
a
nce documen
t
at
i
on
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iup
i
nov
prep
a
reGpu
K
e
r
n
e
lArgumen
t
s() and launchGp
u
Ke
r
n
e
l
(
) are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk
H
ess
S
p
lit off
d
o
m
dec distri
b
ution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk He
s
s
Split atom redis
t
ribution off from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
Rem
o
v
e
c
o
mm
r
ec from
s
e
t_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Rol
a
nd
Schulz
Use same
OpenC
L
kernel for differ
e
n
t V
e
ndor
s
commit
|
commitdiff
|
tree
2018-05-10
Cars
t
en K
u
tzner
Introduce helper
classes f
o
r forc
e
pr
o
vider i
n
put and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Ba
u
er
Fix md -cpi -noappend
commit
|
commitdiff
|
tree
2018-05-04
Mark Abr
a
ham
Merge "Merge branch relea
s
e
-
2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark Ab
r
ah
a
m
More const correctness
commit
|
commitdiff
|
tree
2018-05-03
Mark Abraham
Merge
b
r
a
nch r
e
l
ease-2018
commit
|
commitdiff
|
tree
2018-05-02
Ro
l
and Schulz
Ena
b
le u
n
crustify for OpenCL
commit
|
commitdiff
|
tree
2018-05-02
Roland Schulz
Support 4 si
z
ed clu
s
t
e
r
fo
r
GP
U
NBL search
commit
|
commitdiff
|
tree
2018-04-27
B
erk Hess
Remove pull MPI
code duplicati
o
n
commit
|
commitdiff
|
tree
2018-04-26
Paul Baue
r
Reorganize files for reference manual
commit
|
commitdiff
|
tree
2018-04-26
P
a
ul Bauer
S
p
lit up
analysis
c
hap
t
e
r in reference manual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
S
pl
i
t up
special topics sectio
n
in man
u
al
commit
|
commitdiff
|
tree
2018-04-25
P
aul Bauer
Add page breaks in
r
eferen
c
e m
a
nual
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
auer
Split up Interaction functions manual page
commit
|
commitdiff
|
tree
2018-04-25
Mark Abraham
Refact
o
r
SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul B
a
uer
C
hange image conversion to only
b
e build once
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
D
eviceBuffer h
e
ade
r
s
a
r
e
added
commit
|
commitdiff
|
tree
2018-04-23
Szilár
d
Páll
Fi
x
icc warnin
g
in po
s
t-s
u
bm
i
t
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Add post-submit with ARM H
P
C
Toolcha
i
n
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Pá
l
l
Tweak PME run mode checks
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Convert manual from
L
a
TeX t
o
Ma
r
kup
commit
|
commitdiff
|
tree
2018-04-21
Paul Baue
r
Second change trackin
g
com
m
it
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul Bauer
Intermed
i
ate
c
ommit to track changes to manual
commit
|
commitdiff
|
tree
2018-04-17
Vivec
a
Lindahl
Disallow -skip
values <= 0 f
o
r gmx trjconv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
Ba
u
er
Fix
l
e
g
acy topology mem
o
ry error
commit
|
commitdiff
|
tree
2018-04-17
Mark Abrah
a
m
Shift p
e
r-step con
t
ro
l
logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark
Ab
r
aha
m
Break apart update_con
s
t
r
a
ints
commit
|
commitdiff
|
tree
2018-04-16
Sz
i
lá
r
d Páll
Add
post-submit
te
s
t wi
t
h
h
wlo
c
off
commit
|
commitdiff
|
tree
2018-04-16
Ber
k
Hess
Mov
e
na
t
oms_mol out of gmx_mol
b
lock_t
commit
|
commitdiff
|
tree
2018-04-16
Ma
r
k Abraha
m
Updated md
r
un com
p
arison
i
nfrastructure
commit
|
commitdiff
|
tree
2018-04-13
Mark Abraham
Clean up cons
t
raints code
commit
|
commitdiff
|
tree
2018-04-12
Mark A
b
raham
Remove u
s
e of where(
)
, if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reorgan
i
ze energy e
v
aluation for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iup
i
nov
Prevent
Op
e
nCL
t
imi
n
g memory
l
eak
commit
|
commitdiff
|
tree
2018-04-09
Berk
Hess
C
o
nv
e
rt gmx
_
molblock
_
t
t
o
C
++
commit
|
commitdiff
|
tree
2018-04-05
Mar
k
Abr
a
ham
Sim
p
lified
h
a
ndling of simulat
i
on r
u
nners
commit
|
commitdiff
|
tree
2018-04-05
Mark
A
b
raham
Create
g
r
omacs/md
r
un module
a
nd mov
e
c
o
de there
commit
|
commitdiff
|
tree
2018-04-05
Szilá
r
d Páll
Refactor
cj
preload in the nonb
o
nded Open
C
L kernels
commit
|
commitdiff
|
tree
2018-04-04
Mark A
b
r
a
ham
Quiet checkpo
i
nt
r
eadin
g
commit
|
commitdiff
|
tree
2018-04-04
Pascal Me
r
z
Mov
e
checkNumberOfBondedInte
r
actions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
o
nvert gmx
_
mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
R
e
move lef
t
over mention of twin-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
M
e
rge "Merge branch release-201
8
"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move file opening out
o
f init_pull()
commit
|
commitdiff
|
tree
2018-03-29
Sz
i
lárd Páll
Tweak
/
enab
l
e icc 18 post-
s
ub
m
i
t tests
commit
|
commitdiff
|
tree
2018-03-29
Magn
u
s Lundb
o
rg
Improved
c
h
eck of if only forces are computed in do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
Paul
B
a
u
er
F
ix cm
a
ke Sphi
n
x de
t
ection
f
or versions >
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd
Páll
S
witch CUD
A
9
.
0
/gcc 5 test to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
B
erk
H
ess
Mo
d
ularize pull_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark A
b
r
a
h
a
m
Free more me
m
ory in grom
p
p a
n
d mdr
u
n
commit
|
commitdiff
|
tree
2018-03-28
Be
r
k Hess
R
e
m
ove mol
s
from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Merge branch release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mar
k
Abrah
a
m
Clarified
md
p
options rela
t
ing to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
More
gcc-8 fixes f
o
r
P
O
WER
commit
|
commitdiff
|
tree
2018-03-21
D
avid van der Spoel
Rename
d
entropy
.
* to thermochem
i
stry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Versio
n
201
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
M
a
r
k
Abraham
Merg
e
"Merg
e
branch release-2016 into releas
e
-2
0
1
8
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
U
pdate release notes fo
r
20
1
8
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Merg
e
bra
n
ch release-2016 into r
e
leas
e
-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
U
p
date
use
of gp
u
_id in J
e
nk
i
ns
commit
|
commitdiff
|
tree
2018-03-20
Ber
k
Hes
s
Disallow single simulat
i
on with
m
ultisim
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
Upda
t
e use
of gpu_id in
J
e
nkins
commit
|
commitdiff
|
tree
2018-03-20
M
ar
k
Abrah
a
m
Update use
o
f
g
p
u_i
d
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abr
a
ham
Add helper fu
n
ction to make a
vecto
r
from an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
M
ark
A
braham
Fi
x
VSX S
I
MD with
gc
c
8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free topology when allocated
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Cor
r
ec
t
PMF sign e
r
ror in AWH b
i
a
s
s
haring
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k Hess
Imp
r
ove inte
r
-simulation
signali
n
g
commit
|
commitdiff
|
tree
2018-03-14
Mark Abrah
a
m
M
a
ke a persiste
n
t physical n
o
d
e comm
u
n
i
cator
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fix
mdrun signa
l
ling w
i
th
AW
H
bias s
h
aring
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk H
e
ss
Add A
W
H
fixes to
relea
s
e
n
o
t
es
commit
|
commitdiff
|
tree
2018-03-13
S
z
ilárd Pá
l
l
Requ
i
re
OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble checkpoint
i
ng
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH dec
o
n
v
o
lution wh
e
n sharing
a bi
a
s
commit
|
commitdiff
|
tree
2018-03-13
Mark A
b
raha
m
Introduce
c
o
n
stra
i
n_shak
e
commit
|
commitdiff
|
tree
2018-03-13
Sz
i
l
árd
Pál
l
Fix cla
n
g
6
.
0 with
C
UDA
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
M
a
rk Abraham
Mer
g
e "Me
r
g
e
branch release-2018"
commit
|
commitdiff
|
tree
2018-03-09
Berk Hes
s
Correc
t
pdb2gm
x
-missing optio
n
commit
|
commitdiff
|
tree
2018-03-06
Berk H
e
s
s
Convert t_filenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Merge
bran
c
h
r
elease-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Fixed dvdlambda
f
or SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilár
d
Páll
Add
to the contributor
s
ection
commit
|
commitdiff
|
tree
2018-03-01
B
erk Hess
Detect AMD
S
M
T to
p
ol
o
gy
commit
|
commitdiff
|
tree
2018-02-28
M
a
rk Abraham
Moved and remove
d
constraint code
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
Reorg
a
nize
d
c
o
nstraint
code
commit
|
commitdiff
|
tree
2018-02-27
Mark Abra
h
am
Fix GPU utils
t
es
t
commit
|
commitdiff
|
tree
2018-02-26
Pau
l
B
a
ue
r
Change
T
NG file opening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit defin
e
.
mdp
f
ield to assign values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei
I
u
p
ino
v
Advice users on infin
i
te output of TPI
commit
|
commitdiff
|
tree
2018-02-26
M
a
r
k
Abraham
Organize for recording
2
016-era release not
e
s
and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Ber
k
Hess
F
i
x md
inte
g
rator with Nose-Hoove
r
coupli
n
g
commit
|
commitdiff
|
tree
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