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GROMACS 2016 beta1 release
2016-05-12
Ma
r
k
Abraham
GROMACS 2016 beta1 relea
s
e
commit
|
commitdiff
|
tree
2016-05-12
Vedran Mi
l
etić
Remove static fun
c
tion qua
l
ifier i
n
OpenCL kernel util
s
commit
|
commitdiff
|
tree
2016-05-10
Teemu M
u
rt
o
l
a
Additional Jenkins docum
e
ntation
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Bump clang
s
ta
t
ic analy
z
er to ver
s
i
o
n
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu Murtola
Include releng docu
m
e
ntation to d
e
velope
r
guide
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Fix pr
e
cision loss in tabulated normal distribu
t
i
on
commit
|
commitdiff
|
tree
2016-05-10
Mark Ab
r
aham
Facilit
a
te li
n
king with
libcxx
commit
|
commitdiff
|
tree
2016-05-10
E
r
ik Lindahl
F
l
ush streams when not writing newline c
h
a
racter
commit
|
commitdiff
|
tree
2016-05-10
B
erk Hess
Optimized
th
e
v
si
t
e threading
commit
|
commitdiff
|
tree
2016-05-10
Roland Schulz
Add OpenMP for functions
l
imiting scalin
g
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fixes for clang 3
.
7 on Powe
r
P
C
commit
|
commitdiff
|
tree
2016-05-08
James W
.
Barn
e
tt
C
orrec
t
an
d
clarify output
uni
t
s for fluct_props
commit
|
commitdiff
|
tree
2016-05-08
Erik
L
ind
a
hl
Fix Luzar/Chande
r
li
t
erature referen
c
e in
g_hbo
n
d
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Mo
d
ify lmfit librar
y
to avo
i
d clashes w
i
th o
t
her v
e
rsio
n
s
.
commit
|
commitdiff
|
tree
2016-04-28
Te
e
mu Murtola
Us
e
HardwareTop
o
logy to
set nthre
a
ds_hw_a
v
ail
commit
|
commitdiff
|
tree
2016-04-28
Teemu
M
urtola
R
e
move gmx_hw_i
n
f
o_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
Szilárd Páll
W
o
rkaround for g
c
c f
a
lse positiv
e
warning
commit
|
commitdiff
|
tree
2016-04-27
Teemu
M
urtola
Improve release
w
o
r
k
flow testin
g
commit
|
commitdiff
|
tree
2016-04-27
Teemu Mur
t
ola
Disable m
u
ltiple ranks f
o
r no
n
-MPI
u
nit tests
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
Merg
e
b
r
anch release-5-1
commit
|
commitdiff
|
tree
2016-04-27
S
zilárd P
á
ll
F
ix multiple M
P
I
r
anks
per n
o
de with
Op
e
nCL
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix issu
e
s with failing thread a
f
fin
i
t
y setting
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Fix numerically unstable selec
t
ion tes
t
commit
|
commitdiff
|
tree
2016-04-19
Szilárd Páll
Move ou
t
CUDA pro
f
i
l
er triggers fr
o
m NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>rvdw wi
t
h PME
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraha
m
Replace libxml2 with t
i
nyx
m
l
2
for
u
se in test cod
e
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Tun
e
n
stlist in
c
r
e
a
se for KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraha
m
Fix p
a
rse_digits_from_stri
n
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcast pu
l
l externa
l
potential provider string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Fix mdp label generatio
n
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix gmx hbon
d
group overlap check
commit
|
commitdiff
|
tree
2016-04-14
Mark Abrah
a
m
Merge b
r
anch r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-04-14
Carsten
Kutz
n
er
Correc
t
ed v
a
lue of electric conversion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Roland S
c
h
ul
z
AV
X
512 transposeS
c
a
t
terIn
c
r
/DecrU with load/
s
to
r
e
commit
|
commitdiff
|
tree
2016-04-04
Erik Li
n
dahl
Fix
c
ompile error
for IBM VMX on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik
L
in
d
ahl
Fix
S
IMD detection on new AMD AV
X
CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
Eri
k
Lindahl
Fix unit test seg
f
aul
t
s wit
h
gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindah
l
Fix inc
o
rrect return type for scalar version of simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen
Y
e
sylev
s
ky
y
Added ref
e
re
n
ces to ProtSqueeze an
d
g_membed
t
o
t
he
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Roland
S
chu
l
z
Fix coolquotes
commit
|
commitdiff
|
tree
2016-04-01
M
a
rk Abraham
Reve
r
t to treating -1 as
"
generate a see
d
" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
A
dd
option for external
pull
poten
t
ial
commit
|
commitdiff
|
tree
2016-03-31
James W
.
Barnett
Revert beh
a
vior for han
d
ling SETTLE
e
rror
s
commit
|
commitdiff
|
tree
2016-03-31
Szilár
d
P
á
ll
r
ef
a
c
t
or CUDA
te
x
ture-based
table init
i
a
l
iza
t
ion
commit
|
commitdiff
|
tree
2016-03-31
Szilard Pal
l
avo
i
d
C
PU oversubscription
wit
h
GPUs
commit
|
commitdiff
|
tree
2016-03-30
S
z
ilárd Páll
LJ
combi
n
ation rule kernels for OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Szi
l
árd Páll
Re
-
enable i-atom type local mem pre
f
etch in
O
penCL
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct mdrun tMPI (non-)parallel er
r
or message
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Mak
e
incl
u
desorter
.
py work
with Doxygen 1
.
8
.
1
0+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Descri
b
e AMD
A
PPS
D
K 3
.
0
issues in the guide
commit
|
commitdiff
|
tree
2016-03-30
Teemu
Murtola
Fix error repo
r
t
i
ng for documentation b
u
ild
commit
|
commitdiff
|
tree
2016-03-30
Mark
Abraham
C
l
ean up vsite code
commit
|
commitdiff
|
tree
2016-03-22
C
a
r
sten Ku
t
zner
Clea
n
-up code for swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
B
e
rk Hes
s
LJ combination rule kernels fo
r
C
U
D
A
commit
|
commitdiff
|
tree
2016-03-19
Mark Ab
r
aham
Add
more const c
o
rrectness
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Im
p
roved some mdrun integration
tests
commit
|
commitdiff
|
tree
2016-03-18
Mark
Abraham
Warn
a
bou
t
Op
e
n
MPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk He
s
s
Fix non-normal
i
zation
o
f FFT
a
u
tocorr
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
F
i
x typo
i
n Fourier dihedral equa
t
ion
commit
|
commitdiff
|
tree
2016-03-18
V
i
veca Lindahl
Added
pull coordinate
geometry angle
.
commit
|
commitdiff
|
tree
2016-03-18
David van de
r
Spoel
F
i
x
e
d
division by zero in polarize
.
commit
|
commitdiff
|
tree
2016-03-18
Nich
o
las Breen
Various m
i
no
r
spelling fixes - messages and code comments
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Carst
e
n Kutz
n
er
Fix membed in
i
tializ
a
tion
commit
|
commitdiff
|
tree
2016-03-15
Mark Ab
r
aham
Merge bran
c
h
release-5-0 in
t
o re
l
ease-5
-
1
commit
|
commitdiff
|
tree
2016-03-11
Mark
Abraham
Merge branch release-5-0 in
t
o release-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mark Abraham
Require 2015 ver
s
i
o
n
for MSVC
commit
|
commitdiff
|
tree
2016-02-27
B
e
rk Hess
Remove epsfac from GPU
ker
n
el i
n
ner-loops
commit
|
commitdiff
|
tree
2016-02-23
Mark Abraha
m
Replac
e
cppche
c
k supp
r
e
s
sion in ch
e
ckpoint
c
ode
commit
|
commitdiff
|
tree
2016-02-16
Mark Abr
a
h
a
m
M
e
r
g
e bra
n
ch release-5-0 into r
e
leas
e
-5-1
commit
|
commitdiff
|
tree
2016-02-14
Ma
r
k Abraham
Re-generated
e
ps for figure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark
Abraham
Re
-
remove
*
_stochd_state function dec
l
ara
t
ions
commit
|
commitdiff
|
tree
2016-02-10
Erik Lindahl
Scal
a
r functions mimicking the SIMD interface
commit
|
commitdiff
|
tree
2016-02-08
Mark Ab
r
aham
Me
r
g
e branch rel
e
a
se-5
-
0 into rele
a
se-
5
-1
commit
|
commitdiff
|
tree
2016-02-06
Mark Abraham
M
e
rge
b
r
a
nch
release-
5
-1
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Bump
e
d
p
atch nu
m
b
er
to prepare
f
or fut
u
re 5
.
1
.
3
re
l
ease
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk Abraham
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraha
m
Merge
r
e
l
ease-5-0
i
nto re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark
A
br
a
ham
Merge
branch relea
s
e-5
-
1
commit
|
commitdiff
|
tree
2016-01-28
M
a
r
k Abrah
a
m
A
void FP ex
c
e
ption
commit
|
commitdiff
|
tree
2016-01-27
Mar
k
Ab
r
aham
Merge br
a
nch release-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mar
k
Abraham
Re
m
o
v
e bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fi
x
default for GMX_USE_N
V
M
L
commit
|
commitdiff
|
tree
2016-01-25
Mark Abraham
Merge branch release-5-
1
commit
|
commitdiff
|
tree
2016-01-12
Mark Abra
h
am
Merge branch release
-
5-0
into release-5-1
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Merge branch r
e
lea
s
e-
5
-
1
commit
|
commitdiff
|
tree
2016-01-07
Mar
k
Abraham
Fix some mdr
u
n header dep
e
ndencies
commit
|
commitdiff
|
tree
2016-01-07
M
ark Abraham
Avoi
d
more C++ bindings
for
MPI
commit
|
commitdiff
|
tree
2016-01-07
M
ark Abrah
a
m
S
t
op
u
sing UND
E
FINED as name of
a symbol
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
R
emo
v
e fields us
e
d
o
nly for SD2
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Backpor
t
md-vv fixes
commit
|
commitdiff
|
tree
2016-01-06
Mark Abraham
Fix spurious gcc
warn
i
ng
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Corre
c
t vector check of
g
mx check
commit
|
commitdiff
|
tree
2015-12-29
Teemu Mur
t
ola
Packaging bui
l
d scri
p
t for web
s
ite
commit
|
commitdiff
|
tree
2015-12-28
Mark Ab
r
aha
m
Merge
branch
r
eleas
e
-5-
1
commit
|
commitdiff
|
tree
2015-12-27
Mark Abraham
Fix so
m
e OpenCL is
s
ues
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reor
g
anized d
o
mdec i
n
iti
a
lization
commit
|
commitdiff
|
tree
2015-12-24
Ma
r
k Abrah
a
m
Shell code cleanup
commit
|
commitdiff
|
tree
2015-12-24
Erik Lindahl
IBM Pow
e
r6 V
M
X extended S
I
MD
commit
|
commitdiff
|
tree
2015-12-17
Mark
Abraham
S
i
mplified ener
g
y-summation
c
ode
commit
|
commitdiff
|
tree
2015-12-16
Berk Hess
Add on
e
e
l
ement to
s
tate rvec arrays
commit
|
commitdiff
|
tree
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