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GROMACS 2016 beta1 release
2016-05-12
Mark Abra
h
am
G
R
OMACS 2016 be
t
a1 re
l
ease
commit
|
commitdiff
|
tree
2016-05-12
Vedran Mile
t
i
ć
Remove
s
tatic function qualifier
in
O
p
enCL kernel uti
l
s
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Addi
t
ion
a
l
Jenki
n
s docum
e
n
t
at
i
on
commit
|
commitdiff
|
tree
2016-05-10
Mark
Abraham
Bump clang s
t
atic analyzer to
v
er
s
ion 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Teemu M
u
rtola
In
c
lude re
l
eng do
c
umentation to de
v
eloper guide
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Fix precision loss in tabulated n
o
rmal
distribution
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Facilitate link
i
ng with
l
ib
c
xx
commit
|
commitdiff
|
tree
2016-05-10
Erik Li
n
dahl
Flus
h
s
t
reams w
h
en not
w
rit
i
ng newline
characte
r
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk Hess
Optimized the vsite thre
a
din
g
commit
|
commitdiff
|
tree
2016-05-10
R
o
land Schulz
Add
O
penMP
for functions limiting
s
caling
commit
|
commitdiff
|
tree
2016-05-08
Mark Abr
a
ham
Fixes for clang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
J
a
m
e
s
W
.
Barnett
Correct a
n
d
c
l
arify outpu
t
units for fluct_props
commit
|
commitdiff
|
tree
2016-05-08
Erik L
i
ndahl
Fix Luz
a
r/Ch
a
n
d
er literatu
r
e refe
r
enc
e
in g_hbond
commit
|
commitdiff
|
tree
2016-05-08
David
v
an d
e
r Spoel
Modify lmfit
l
ibrary
to avoid clashes
with other
v
ersions
.
commit
|
commitdiff
|
tree
2016-04-28
Te
e
m
u
Murtola
Use H
a
rdwareTopology to set nth
r
eads_h
w
_
avail
commit
|
commitdiff
|
tree
2016-04-28
Teem
u
Mu
r
to
l
a
R
emove
g
m
x_hw_info_t::n
c
o
re
commit
|
commitdiff
|
tree
2016-04-28
Szilárd Páll
Workarou
n
d for gcc
f
alse positive warning
commit
|
commitdiff
|
tree
2016-04-27
Teemu
M
u
r
tola
Impr
o
v
e
releas
e
workf
l
ow testing
commit
|
commitdiff
|
tree
2016-04-27
Tee
m
u Murtola
Disable
multiple ranks for
n
on-MPI unit tests
commit
|
commitdiff
|
tree
2016-04-27
M
a
rk
A
braham
Merge
b
ra
n
ch release-5-1
commit
|
commitdiff
|
tree
2016-04-27
Szi
l
árd
P
ál
l
Fix multiple
MPI ranks per node wit
h
OpenCL
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix issues with failing
t
h
re
a
d
affinity setting
commit
|
commitdiff
|
tree
2016-04-19
Roland
Schul
z
Fix numerically unstab
l
e
selecti
o
n test
commit
|
commitdiff
|
tree
2016-04-19
Szi
l
ár
d
Páll
Move out C
U
D
A
profiler triggers f
r
o
m
NBNXN
commit
|
commitdiff
|
tree
2016-04-19
B
erk Hess
Allo
w
rcoulomb>r
v
dw with PME
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Re
p
l
a
ce libxml2 with ti
n
yxml2 for use in te
s
t code
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
T
u
ne
n
stli
s
t increase
f
o
r KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark
A
braham
Fix parse_digits_from_strin
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
B
road
c
ast
pull external p
o
t
e
n
t
ial provider strin
g
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix mdp la
b
el generation
commit
|
commitdiff
|
tree
2016-04-19
Be
r
k Hess
Fix gmx hb
o
nd
gr
o
up over
l
ap check
commit
|
commitdiff
|
tree
2016-04-14
M
a
rk Abraha
m
Merge
branch release-5-1
commit
|
commitdiff
|
tree
2016-04-14
Carsten K
u
tzner
Corr
e
cted value of electr
i
c conversion
factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland Schulz
AVX512 tra
n
sposeS
c
atterIncr/DecrU with load/
s
tore
commit
|
commitdiff
|
tree
2016-04-04
Erik
Li
n
dahl
Fix c
o
mpile error for IBM VMX
on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik
L
i
ndahl
Fix SIMD detection
o
n new AMD
A
VX C
P
Us
w
/o fm
a
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix
u
n
it
tes
t
segf
a
ults w
i
th gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik L
i
ndahl
Fix incorr
e
ct
r
eturn type f
o
r scalar version of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen Yesy
l
ev
s
k
yy
Ad
d
ed
r
e
ferences to ProtSqu
e
eze an
d
g_membed t
o
the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
R
o
la
n
d
S
chulz
F
i
x coolquotes
commit
|
commitdiff
|
tree
2016-04-01
Mark Abraham
Revert to treating
-1
a
s "gen
e
rate a seed"
i
n
.
m
dp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add option for ex
t
er
n
a
l
pull pote
n
tial
commit
|
commitdiff
|
tree
2016-03-31
J
a
mes W
.
Barnett
Reve
r
t
behavior for han
d
l
i
ng SETT
L
E errors
commit
|
commitdiff
|
tree
2016-03-31
Szil
á
r
d
Páll
refactor CUDA te
x
ture
-
based table initialization
commit
|
commitdiff
|
tree
2016-03-31
Szilard Pall
avoid CPU oversubscription w
i
th GP
U
s
commit
|
commitdiff
|
tree
2016-03-30
S
z
ilárd Páll
LJ combin
a
tion ru
l
e
ke
r
ne
l
s for OpenCL
commit
|
commitdiff
|
tree
2016-03-30
S
z
ilárd Páll
R
e-e
n
able i-a
t
om
t
ype l
o
cal
mem prefetc
h
in
O
penCL
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct mdrun tMP
I
(non-)paralle
l
error message
commit
|
commitdiff
|
tree
2016-03-30
Teemu M
u
rtola
Make
in
c
ludes
o
rter
.
py work with D
o
xyg
e
n 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
S
zilárd Páll
Descr
i
be AMD APPSD
K
3
.
0
issues in
the gu
i
d
e
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
F
ix err
o
r re
p
orting fo
r
documentation buil
d
commit
|
commitdiff
|
tree
2016-03-30
Mar
k
Abraham
C
l
ean up vsite c
o
de
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzne
r
Clean-up code for sw
a
p
c
oords
.
commit
|
commitdiff
|
tree
2016-03-22
Be
r
k Hess
LJ com
b
inat
i
o
n rule ke
r
nels for CUDA
commit
|
commitdiff
|
tree
2016-03-19
Mark
A
b
raham
Ad
d
more cons
t
c
o
r
r
e
ctne
s
s
commit
|
commitdiff
|
tree
2016-03-19
Mar
k
Abra
h
am
Impro
v
ed
some m
d
run
integrat
i
on tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Warn about
O
p
enMPI
1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
B
erk Hess
Fi
x
non-normalization of FFT aut
o
corr
commit
|
commitdiff
|
tree
2016-03-18
Mar
k
Abraham
Fix typo in Fourier dihedral equation
commit
|
commitdiff
|
tree
2016-03-18
V
i
v
eca Lindahl
Added
p
ull coor
d
inat
e
g
e
ometr
y
angle
.
commit
|
commitdiff
|
tree
2016-03-18
David van der
Spoel
Fixe
d
div
i
s
i
on
b
y ze
r
o in polarize
.
commit
|
commitdiff
|
tree
2016-03-18
Nichola
s
B
r
een
Various mino
r
spelling fixes - mes
s
a
ges
a
n
d code comments
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Carsten K
u
tzner
F
i
x membed
i
niti
a
lizati
o
n
commit
|
commitdiff
|
tree
2016-03-15
Mark Abraham
Merge br
a
nch rel
e
a
s
e-5-
0
into releas
e
-5-1
commit
|
commitdiff
|
tree
2016-03-11
M
a
rk Abraham
Merge branch relea
s
e-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mark
A
braham
Require 2015 versio
n
for MSVC
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remove ep
s
fac from
GPU k
e
rnel inner-loo
p
s
commit
|
commitdiff
|
tree
2016-02-23
Mark Abraham
Replace cpp
c
heck suppression
i
n
checkpoint code
commit
|
commitdiff
|
tree
2016-02-16
M
a
rk Abraham
Merge bran
c
h release-5-
0
into re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-02-14
Mark Abraham
Re-generated
e
ps for figure
4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Re-r
e
m
ove
*
_
stochd_sta
t
e func
t
ion decla
r
atio
n
s
commit
|
commitdiff
|
tree
2016-02-10
Er
i
k Lindahl
Scalar functions mimicking th
e
SIMD in
t
e
r
fac
e
commit
|
commitdiff
|
tree
2016-02-08
Mark Abraham
Merge
b
r
a
nch rele
a
s
e
-5-0
i
nto release-5-1
commit
|
commitdiff
|
tree
2016-02-06
M
a
rk Abraham
Merge branch re
l
ease-
5
-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
Abraha
m
Bumped patch number to prepare
f
or
f
uture 5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk Abr
a
ham
Versio
n
5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
M
erge rele
a
se-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Me
r
ge
branch release-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark A
b
r
aha
m
Avoid FP exc
e
p
t
ion
commit
|
commitdiff
|
tree
2016-01-27
M
a
rk Abraham
Merge branch releas
e
-
5
-1
commit
|
commitdiff
|
tree
2016-01-27
Mark
Abraham
Remove bNotLastFram
e
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fix default for GMX_
U
SE
_
N
VML
commit
|
commitdiff
|
tree
2016-01-25
Mark A
b
raham
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-12
Mark Abraham
Merge
branch release-
5
-0 into
release-5-1
commit
|
commitdiff
|
tree
2016-01-08
Mark
Abraham
Merge b
r
anch release-5-1
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Fix some mdrun header dependencies
commit
|
commitdiff
|
tree
2016-01-07
Mark Ab
r
aham
Avoid mo
r
e
C
++ bindi
n
gs for M
P
I
commit
|
commitdiff
|
tree
2016-01-07
Mark
Abraham
Stop u
s
ing UND
E
FINED
a
s name of a sym
b
ol
commit
|
commitdiff
|
tree
2016-01-07
M
a
rk Abraham
Remo
v
e f
i
elds used only for
SD2
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Backpo
r
t md-vv
fixes
commit
|
commitdiff
|
tree
2016-01-06
Mar
k
A
b
raham
Fix spurious gcc
warning
commit
|
commitdiff
|
tree
2015-12-29
Berk
H
es
s
Corr
e
c
t
vect
o
r
che
c
k of gmx check
commit
|
commitdiff
|
tree
2015-12-29
Teemu
Murto
l
a
Packaging buil
d
s
cr
i
pt for web sit
e
commit
|
commitdiff
|
tree
2015-12-28
Mark Ab
r
aham
M
e
r
g
e branch relea
s
e-5-1
commit
|
commitdiff
|
tree
2015-12-27
Mark
A
braham
Fix
s
o
me OpenC
L
issues
commit
|
commitdiff
|
tree
2015-12-27
B
erk
H
ess
R
eor
g
anized domdec initializa
t
ion
commit
|
commitdiff
|
tree
2015-12-24
M
a
rk Abraham
Shell code cleanup
commit
|
commitdiff
|
tree
2015-12-24
Er
i
k Lindahl
IBM P
o
w
er6 VMX extended SIMD
commit
|
commitdiff
|
tree
2015-12-17
Mark
Abraham
Simplified ene
r
gy-summa
t
i
on
c
o
d
e
commit
|
commitdiff
|
tree
2015-12-16
Berk Hes
s
A
d
d
one element to state
rvec a
r
rays
commit
|
commitdiff
|
tree
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