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Avoid numerical overflow with overlapping atoms
2016-05-31
Ber
k
Hess
Avoid nu
m
erical over
f
low with overlappi
n
g atoms
commit
|
commitdiff
|
tree
2016-05-31
B
erk H
e
s
s
Add
check for finit
e
ene
r
gies
commit
|
commitdiff
|
tree
2016-05-28
Roland
Schul
z
Fix build wit
h
clang 3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-26
Mar
k
Abraham
New quote
commit
|
commitdiff
|
tree
2016-05-21
Erik Lindahl
Disab
l
e
automa
t
ed FFTW3 b
u
ilds on
W
indows
commit
|
commitdiff
|
tree
2016-05-17
Ro
l
and Schulz
Add reference to TopoTools 1
.
6
commit
|
commitdiff
|
tree
2016-05-17
T
e
em
u
M
u
r
t
ola
Fix some th
r
ead affinit
y
cases
commit
|
commitdiff
|
tree
2016-05-13
Roland
S
chulz
D
on't use abo
r
t for fata
l
errors
commit
|
commitdiff
|
tree
2016-05-12
Mark Abr
a
ham
Merg
e
branc
h
re
l
e
a
s
e
-5-1 into release
-
201
6
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraha
m
GROMACS 2016
b
eta1 release
commit
|
commitdiff
|
tree
2016-05-12
Vedran M
i
let
i
ć
Re
m
o
v
e
static functi
o
n qualifier in
OpenCL kernel utils
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu M
u
r
tola
A
d
d
itional Jenkins
d
ocument
a
tion
commit
|
commitdiff
|
tree
2016-05-10
Mark Ab
r
a
h
am
Bum
p
clang
s
tatic analy
z
er to ve
r
sion
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Minor update to sphi
n
x dep
e
n
d
ency
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
urtola
Includ
e
releng d
o
cumentation to d
e
velop
e
r guide
commit
|
commitdiff
|
tree
2016-05-10
Eri
k
Lindahl
Fi
x
precisi
o
n loss in tabulated no
r
mal dis
t
r
i
bution
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Facilit
a
te
l
inki
n
g
with libcxx
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
Flush streams when
n
o
t writing n
e
wline ch
a
racter
commit
|
commitdiff
|
tree
2016-05-10
Be
r
k Hess
Optimized
t
he
v
s
ite threading
commit
|
commitdiff
|
tree
2016-05-10
Roland Schulz
Ad
d
OpenMP f
o
r functions li
m
iting sca
l
ing
commit
|
commitdiff
|
tree
2016-05-08
Mar
k
Ab
r
aham
Fixes for clang 3
.
7 o
n
P
o
w
erPC
commit
|
commitdiff
|
tree
2016-05-08
James W
.
Barnett
Correct
a
nd clarify
o
u
t
put units
f
or fluct_p
r
ops
commit
|
commitdiff
|
tree
2016-05-08
E
rik Lin
d
ahl
Fix
Luzar
/
C
hander literatur
e
refe
r
en
c
e
in g_hbond
commit
|
commitdiff
|
tree
2016-05-08
Davi
d
van der
Spoel
Modif
y
lmfi
t
library
t
o
avo
i
d cla
s
hes wit
h
other
v
e
rsions
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu Mur
t
o
l
a
Use HardwareTopology
t
o set nt
h
read
s
_hw_a
v
ail
commit
|
commitdiff
|
tree
2016-04-28
Te
e
m
u
Murtola
Remove gmx_hw_i
n
fo_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
S
z
i
l
árd Páll
W
orkaround for gcc false positive wa
r
n
ing
commit
|
commitdiff
|
tree
2016-04-27
Teemu
Murt
o
la
Im
p
r
ove r
e
lease workf
l
ow testing
commit
|
commitdiff
|
tree
2016-04-27
T
e
emu Murtola
Disable multiple
ranks for non-MPI uni
t
tes
t
s
commit
|
commitdiff
|
tree
2016-04-27
Mark Abrah
a
m
M
e
rge br
a
nch rele
a
se-5-
1
commit
|
commitdiff
|
tree
2016-04-27
Szilárd
P
áll
F
ix multi
p
le MPI ranks p
e
r n
o
de with OpenCL
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fi
x
issues with failing th
r
e
ad affinity set
t
i
ng
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
Fix n
u
meri
c
a
l
l
y
u
nstable sel
e
c
t
ion test
commit
|
commitdiff
|
tree
2016-04-19
Szil
á
rd P
á
l
l
Move
out CUDA pro
f
i
ler
trigger
s
from NBNXN
commit
|
commitdiff
|
tree
2016-04-19
Be
r
k
Hess
Allow rcoulomb>rvdw with
P
M
E
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Replace libxm
l
2 with tinyxml2
for use in te
s
t
c
ode
commit
|
commitdiff
|
tree
2016-04-19
Rol
a
nd Sch
u
lz
Tu
n
e nst
l
ist
inc
r
ea
s
e for KNL
commit
|
commitdiff
|
tree
2016-04-19
Mark A
b
raham
Fix parse_digi
t
s_from_stri
n
g
commit
|
commitdiff
|
tree
2016-04-19
B
e
r
k Hess
Broadcast pull exter
n
al potential provider string
commit
|
commitdiff
|
tree
2016-04-19
Mar
k
Abraham
Fix md
p
labe
l
g
ene
r
a
t
ion
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Fix gmx hbond grou
p
overlap check
commit
|
commitdiff
|
tree
2016-04-14
Mark Abr
a
ham
M
e
rge bra
n
ch release-5-1
commit
|
commitdiff
|
tree
2016-04-14
Car
s
t
e
n Kut
z
ner
Cor
r
ected value of electric
conversion
f
actor f i
n
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Rol
a
nd Schulz
AVX512
t
r
a
n
sposeScatterIncr/D
e
crU with load/sto
r
e
commit
|
commitdiff
|
tree
2016-04-04
E
rik Lindahl
Fix compile
e
rror for IBM VMX
on ppc64
commit
|
commitdiff
|
tree
2016-04-04
E
rik
L
inda
h
l
Fix SIMD detection on new AMD AVX CPUs w/o fma
commit
|
commitdiff
|
tree
2016-04-03
E
r
ik Li
n
dahl
Fix unit test segfaults with gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
E
r
ik Lindahl
F
i
x incorr
e
ct retur
n
ty
p
e for s
c
a
l
ar version of
simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Semen Yesyl
e
vskyy
Add
e
d references t
o
ProtSque
e
ze and g_membed to the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Ro
l
and Schulz
Fix co
o
lquote
s
commit
|
commitdiff
|
tree
2016-04-01
M
a
rk Abrah
a
m
R
evert to treating -1
as
"
genera
t
e a seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Berk
Hess
Ad
d
option for external pull
potential
commit
|
commitdiff
|
tree
2016-03-31
James W
.
Ba
r
nett
Revert behavior
for handling SETTLE errors
commit
|
commitdiff
|
tree
2016-03-31
Szilárd
P
áll
refactor
CUDA texture-ba
s
ed
t
able in
i
tializa
t
ion
commit
|
commitdiff
|
tree
2016-03-31
Szila
r
d Pall
avoid CPU
o
v
ersubscription with GPUs
commit
|
commitdiff
|
tree
2016-03-30
Szil
á
rd Pál
l
L
J
combina
t
i
on rule kernels for OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Re
-
en
a
ble i-at
o
m
t
ype lo
c
al
m
em pr
e
fetch in
O
penCL
commit
|
commitdiff
|
tree
2016-03-30
Berk Hes
s
Correct mdrun tMPI
(
non-
)
para
l
lel error message
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtol
a
Make includesor
t
er
.
py wor
k
w
i
th
D
oxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Desc
r
ibe A
M
D APP
S
DK 3
.
0 issu
e
s in
the guid
e
commit
|
commitdiff
|
tree
2016-03-30
Teemu Mur
t
o
la
Fix
e
rror repor
t
ing for documentat
i
on build
commit
|
commitdiff
|
tree
2016-03-30
M
a
r
k A
b
raham
Clean up vsite c
o
de
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
Cle
a
n-up code fo
r
swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combi
n
a
ti
o
n rule ker
n
e
l
s for
CUDA
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Add more const c
o
rrectne
s
s
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Improved
some mdrun integration tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abr
a
ham
Warn
a
bou
t
O
p
e
n
M
P
I 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix non
-
norma
l
ization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-18
Mark A
b
raham
Fix
t
y
p
o in Fou
r
ier dihedral equ
a
tion
commit
|
commitdiff
|
tree
2016-03-18
Vi
v
eca Lin
d
ahl
Added pull coordinate ge
o
m
etry
angl
e
.
commit
|
commitdiff
|
tree
2016-03-18
David v
a
n der Sp
o
el
Fi
x
ed division by zero i
n
polarize
.
commit
|
commitdiff
|
tree
2016-03-18
Nicholas Breen
Var
i
ous minor spelling fixes -
m
es
s
age
s
and code
commen
t
s
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Carst
e
n
K
utzner
F
i
x
me
m
bed initiali
z
ation
commit
|
commitdiff
|
tree
2016-03-15
Mark Abra
h
am
M
erge branch release-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-03-11
Mar
k
Abra
h
a
m
Merge bran
c
h release-5-0 into re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-03-10
Mark
Abrah
a
m
Requir
e
2
0
15 version for MSVC
commit
|
commitdiff
|
tree
2016-02-27
Be
r
k Hess
Remove epsfac from
G
PU ker
n
e
l
inne
r
-loops
commit
|
commitdiff
|
tree
2016-02-23
Mar
k
Abra
h
am
Re
p
lace cppche
c
k suppression in checkp
o
int code
commit
|
commitdiff
|
tree
2016-02-16
Ma
r
k
Abraha
m
Merge br
a
nch
r
e
lease-5-0
in
t
o re
l
e
a
se-5-1
commit
|
commitdiff
|
tree
2016-02-14
Mark Abr
a
ham
Re-ge
n
er
a
ted eps for
f
igure
4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraha
m
Re
-
remove *_
s
tochd
_
sta
t
e function declarations
commit
|
commitdiff
|
tree
2016-02-10
Eri
k
Lindahl
S
c
a
l
ar fu
n
ctions mimicking the
S
IMD
i
nterface
commit
|
commitdiff
|
tree
2016-02-08
M
ark Abraham
M
erge branch
release-5-0 int
o
release-5-
1
commit
|
commitdiff
|
tree
2016-02-06
Mark
Ab
r
aham
Me
r
ge b
r
anch
relea
s
e
-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
br
a
ham
Bumpe
d
patch number to prep
a
re for future 5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
M
ark Abraham
Ver
s
i
on 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
M
erge
r
elease-5-
0
into re
l
ease
-
5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Merge branch rel
e
ase-5-
1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Avo
i
d
FP excep
t
ion
commit
|
commitdiff
|
tree
2016-01-27
Mark A
b
ra
h
am
M
e
rge
b
ra
n
ch rel
e
ase-5-
1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Remove bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-26
M
a
rk Abraham
F
i
x default
f
o
r GMX_USE_NVML
commit
|
commitdiff
|
tree
2016-01-25
Mark
Abraham
M
e
rge
b
ranch
r
eleas
e
-5-
1
commit
|
commitdiff
|
tree
2016-01-12
Ma
r
k Abraha
m
Merg
e
branch rele
a
se-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-01-08
Mark Ab
r
a
ham
M
e
rge branch releas
e
-5-1
commit
|
commitdiff
|
tree
2016-01-07
Mark
Abraham
Fix some
mdrun header depe
n
dencies
commit
|
commitdiff
|
tree
2016-01-07
Mark
Abraham
Avoid
m
o
re C++
b
indings for MP
I
commit
|
commitdiff
|
tree
2016-01-07
Mark Abr
a
ha
m
S
t
o
p
using
UND
E
F
I
N
ED as nam
e
of a symbol
commit
|
commitdiff
|
tree
2016-01-07
M
ar
k
Abraham
Remove fields used only for SD2
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Backpo
r
t md-vv
fixes
commit
|
commitdiff
|
tree
next