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Merge branch release-2016
2017-04-17
Mar
k
Abra
h
am
M
inor
change
to G
P
U compat
i
b
il
i
ty re
p
orting handling
commit
|
commitdiff
|
tree
2017-04-17
Mark
A
b
r
aham
Propose a
p
o
s
t
-su
b
mit matrix
commit
|
commitdiff
|
tree
2017-04-17
Teemu Murtola
Consistent
a
p
p
roach for whol
e
-
p
r
ogram tests
commit
|
commitdiff
|
tree
2017-03-31
M
a
rk Abra
h
am
Merge
b
ra
n
ch rele
a
se-2016
commit
|
commitdiff
|
tree
2017-03-22
M
ark Abraham
Ad
d
sectio
n
to user guide for ma
n
aging simulation
s
commit
|
commitdiff
|
tree
2017-03-17
M
.
E
r
ic Irrgang
Ad
d
an extra
verbose tar
g
et for
d
o
cs
commit
|
commitdiff
|
tree
2017-03-16
Szilárd
Páll
Pr
i
nt
c
ode of unknown
OpenC
L
error
commit
|
commitdiff
|
tree
2017-03-14
Mark Abraham
M
erge br
a
nch
release-2
0
16
commit
|
commitdiff
|
tree
2017-03-14
Mark Abraham
B
u
m
p
ed
versio
n
to
p
repare f
o
r
n
ext patch rele
a
se
commit
|
commitdiff
|
tree
2017-03-13
Mark Abraha
m
Version 20
1
6
.
3
commit
|
commitdiff
|
tree
2017-03-13
Mark Abrah
a
m
Mod
e
rnize write_inpfile
commit
|
commitdiff
|
tree
2017-03-13
Mark Abr
a
h
a
m
Moder
n
i
ze read_inpfile
commit
|
commitdiff
|
tree
2017-03-13
Ake S
a
ndgren
Fix tune_p
m
e detection of
GPU su
p
port
commit
|
commitdiff
|
tree
2017-03-13
Ake Sa
n
dgren
Fi
x
sp
a
ci
n
g in tune_
p
me call
t
o
th
r
e
a
d
-
mpi m
d
run
commit
|
commitdiff
|
tree
2017-03-09
S
zi
l
árd
Páll
F
i
x
mdrun hanging u
p
on
ex
i
t wi
t
h s
e
p PME ranks
commit
|
commitdiff
|
tree
2017-03-07
M
ar
k
Abra
h
am
Fix
m
inor iss
u
e
s in gm
x
traj -av -af
commit
|
commitdiff
|
tree
2017-03-04
Teemu
Murto
l
a
Remove M
D
Modul
e
s
u
s
e
from md
l
i
b
commit
|
commitdiff
|
tree
2017-03-04
David van der
Spoel
R
e
moves rog
u
e printi
n
g to xvg file in gm
x
mindist
commit
|
commitdiff
|
tree
2017-03-04
Teemu M
u
rtola
Split md module face
t
s to different interfaces
commit
|
commitdiff
|
tree
2017-03-04
Ma
r
k Abra
h
am
Fixes for
xl compil
e
rs 13
.
1
.
5 on
P
o
w
e
r8
commit
|
commitdiff
|
tree
2017-02-20
Mar
k
A
b
raham
Add tests for ol
d
gmx energ
y
f
unctionality
commit
|
commitdiff
|
tree
2017-02-17
Mark Abr
a
h
am
U
se gmx::Mu
t
ex and gmx::lock_guard to
fix some iss
u
es
commit
|
commitdiff
|
tree
2017-02-15
Mark Abraham
Merge branch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2017-02-14
Mark Abraham
Reduce com
p
ila
t
ion
c
oup
l
ing
commit
|
commitdiff
|
tree
2017-02-10
Mark Abraha
m
Corrected
output of gmx do_dssp -sc
commit
|
commitdiff
|
tree
2017-02-09
Teemu Mu
r
tola
M
ulti
-
r
ank thread affinity te
s
ts
commit
|
commitdiff
|
tree
2017-02-09
M
ark
A
braham
C
o
mplete the removal of stateful RN
G
commit
|
commitdiff
|
tree
2017-02-09
M
ark Abraham
Im
p
roved stat
e
_change_natoms
an
d
used it more
commit
|
commitdiff
|
tree
2017-02-09
Teemu
Murtola
Doc
u
m
e
nt key-val
u
e tree transforms
a
nd imp
r
ove c
h
ecks
commit
|
commitdiff
|
tree
2017-02-08
Mark Abra
h
am
E
xtend ser
i
a
l
i
zatio
n
to gmx_int64_t
commit
|
commitdiff
|
tree
2017-02-08
Te
e
mu
M
urtola
Generic Key
V
a
lueTree broadcast
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murt
o
la
G
e
ne
r
i
c
gmx che
c
k impl
e
mentation wi
t
h K
e
yVa
l
ue
T
ree
commit
|
commitdiff
|
tree
2017-02-08
Tee
m
u Murtola
Generic gmx dump im
p
lementation for
K
e
yVa
l
ueT
r
ee
commit
|
commitdiff
|
tree
2017-02-08
Te
e
mu Murtola
Generic tpr ha
n
d
l
ing for elec
t
ric field
commit
|
commitdiff
|
tree
2017-02-08
Aleksei Iupino
v
PME
force
g
ath
e
ri
n
g tests
commit
|
commitdiff
|
tree
2017-02-08
Aleksei Iupinov
Fix
in
v
alid tricli
n
ic box
i
n the PME test d
a
ta
commit
|
commitdiff
|
tree
2017-02-08
Mark Abr
a
ham
G
i
ve MDModu
l
es responsibi
l
ity
f
or
o
ption handling
commit
|
commitdiff
|
tree
2017-02-07
Vedran Miletić
Document
running C
l
ang static a
n
alyzer m
a
nually
commit
|
commitdiff
|
tree
2017-02-07
Ma
r
k
Abraham
M
e
r
ge branch release-2016
commit
|
commitdiff
|
tree
2017-02-07
Mark Ab
r
aham
Bumped
vers
i
on
t
o prep
a
re for next
patch release
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraham
Vers
i
on 2016
.
2
commit
|
commitdiff
|
tree
2017-02-07
B
erk Hess
A
dd mdp option
che
c
k with deco
u
p
led modes
commit
|
commitdiff
|
tree
2017-02-05
M
ark
Ab
r
aham
Merge branch release-5-1 int
o
release-2016
commit
|
commitdiff
|
tree
2017-02-03
Mark Abra
h
am
Remove type
d
ef s
t
ru
c
t in
s
ome mdtypes files
commit
|
commitdiff
|
tree
2017-01-31
Mark Abraham
Merge b
r
anch release-5-1 into
release-201
6
commit
|
commitdiff
|
tree
2017-01-24
Aleksei
Iupin
o
v
PME spline computation and charge sprea
d
ing tests
commit
|
commitdiff
|
tree
2017-01-24
Szilárd Pál
l
Re
m
ove unused a
r
gument in G
P
U
k
e
r
nels
commit
|
commitdiff
|
tree
2017-01-24
Al
e
ksei I
u
pinov
Add const q
u
a
lifie
r
to some PME
s
p
r
e
ad arg
u
ment
s
commit
|
commitdiff
|
tree
2017-01-23
M
ark Abrah
a
m
Stoppe
d
h
e
ader f
i
le
s
including state
.
h
commit
|
commitdiff
|
tree
2017-01-23
David
van der Spoel
Added refer
e
n
ce for dihedral function in OPLS
.
commit
|
commitdiff
|
tree
2017-01-22
Mark Ab
r
ah
a
m
Fixed gmx r
m
sf -q -oq
.
commit
|
commitdiff
|
tree
2017-01-21
Mark Abraham
Re
m
oved init_st
a
te
commit
|
commitdiff
|
tree
2017-01-20
Berk Hess
D
i
sa
l
lo
w
overwriting o
f
dihed
r
al t
y
pe
9
commit
|
commitdiff
|
tree
2017-01-19
Aleksei Iu
p
i
n
ov
P
ME B-
S
p
line mo
d
uli co
m
putati
o
n unit test
commit
|
commitdiff
|
tree
2017-01-19
Berk Hess
Fix PME
o
rder and
grid
s
ize checks
commit
|
commitdiff
|
tree
2017-01-18
Rola
n
d
S
chulz
Add AlignedArray
commit
|
commitdiff
|
tree
2017-01-14
Ma
r
k Abraha
m
Merge branch
rele
a
se-201
6
commit
|
commitdiff
|
tree
2017-01-06
Mark Abrah
a
m
Docum
e
n
t
ISeriali
z
er class
commit
|
commitdiff
|
tree
2017-01-05
Roland Schulz
Fix uni
t
ialized memory
a
cces
s
commit
|
commitdiff
|
tree
2017-01-04
Mark Ab
r
aham
St
o
p
t
rying to use
obj
d
ump
-
-rel
o
c
on Mac
commit
|
commitdiff
|
tree
2017-01-04
Mark A
b
raham
Fi
x
docu
m
entation of OptionsVis
i
t
or
commit
|
commitdiff
|
tree
2017-01-03
Mark Abraham
Merge branch release
-
5
-1 in
t
o releas
e
-2016
commit
|
commitdiff
|
tree
2016-12-20
Mark Abraham
Corrected documentatio
n
about eigenval
u
e
h
andl
i
ng
commit
|
commitdiff
|
tree
2016-12-20
Mark Ab
r
a
h
a
m
Sanitize so
m
e include headers
commit
|
commitdiff
|
tree
2016-12-20
Mark
A
braham
Merg
e
branch
r
e
l
ease-2016
commit
|
commitdiff
|
tree
2016-12-10
T
eemu Mu
r
to
l
a
Build scripts for i
m
proved release workflo
w
commit
|
commitdiff
|
tree
2016-12-09
Mark Abraham
Re
m
ove nxframe fro
m
t_trxstat
u
s
commit
|
commitdiff
|
tree
2016-12-09
S
zilá
r
d Páll
Tur
n
off hwloc support whe
n
static lib fou
n
d
commit
|
commitdiff
|
tree
2016-12-08
Berk Hess
Made mdrun -pf
o
rce terminate w
i
t
h non-fi
n
ite forces
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtola
Fi
x
p
ossible
m
e
mory err
o
r with long selections
commit
|
commitdiff
|
tree
2016-12-08
Mar
k
Abra
h
am
Co
n
solida
t
e files supporting TNG file I/O
commit
|
commitdiff
|
tree
2016-12-07
Mark Ab
r
a
ham
Merge branch release-20
1
6
commit
|
commitdiff
|
tree
2016-12-07
David
van der Spoel
Couple of
n
ew
q
uotes
commit
|
commitdiff
|
tree
2016-12-07
Teemu
Murtola
Fix u
s
e of position
v
a
r
iables with plus/merge
commit
|
commitdiff
|
tree
2016-12-07
Mark Abraham
F
i
x mem
o
ry ha
n
dling i
n
g
m
x d
u
m
p
of TNG files
commit
|
commitdiff
|
tree
2016-12-05
Mark Abraha
m
Remove undu
e
narrow
i
ng of int
e
ger in TNG read
i
ng
commit
|
commitdiff
|
tree
2016-12-01
Ma
r
k
Abraham
Fix
min
o
r
t
r
j
conv bug
commit
|
commitdiff
|
tree
2016-11-24
Berk Hess
Change spli
n
e mod
u
li calcula
t
i
o
n to
double
commit
|
commitdiff
|
tree
2016-11-16
Carsten Kutzn
e
r
I
n
creas
e
d the def
a
ult res
e
t st
e
p to 1500 in gmx tune_
p
me
commit
|
commitdiff
|
tree
2016-11-16
Mark Abraha
m
Remo
v
e unimplemented gmx trjcat -vel
commit
|
commitdiff
|
tree
2016-11-08
D
a
n
H
orák
F
i
x
x86
conditional
commit
|
commitdiff
|
tree
2016-11-01
Al
e
k
s
e
i Iupinov
Rem
o
ve imatrix type and related unused/erroneous c
o
de
commit
|
commitdiff
|
tree
2016-10-31
Mark Abr
a
ham
Merge branch re
l
e
a
se
-
2016
commit
|
commitdiff
|
tree
2016-10-31
Mark Ab
r
a
h
a
m
M
er
g
e bran
c
h
r
e
l
ease-20
1
6
commit
|
commitdiff
|
tree
2016-10-28
Mark Abraham
Bum
p
ed version to prepare for n
e
xt pa
t
ch
release
commit
|
commitdiff
|
tree
2016-10-28
Mark Abraham
Vers
i
o
n
2
016
.
1
commit
|
commitdiff
|
tree
2016-10-28
B
e
rk Hes
s
DLB can now turn off, when
s
lower
commit
|
commitdiff
|
tree
2016-10-28
Sz
i
lárd Páll
GPU-related add
i
ti
o
ns
t
o the
i
nst
a
ll/
u
ser guid
e
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
Fix DLB timing with CUDA and OpenCL
commit
|
commitdiff
|
tree
2016-10-27
Szilár
d
Páll
Make -cl-fast
-
relaxed-math defaul
t
commit
|
commitdiff
|
tree
2016-10-21
Mark Abrah
a
m
Update i
n
stall
guide
commit
|
commitdiff
|
tree
2016-10-21
M
ark Abraham
Up
d
ate
cppc
h
eck support to 1
.
76
.
1
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murtola
Serializ
a
tion s
u
pp
o
rt for KeyValu
e
Tr
e
e
commit
|
commitdiff
|
tree
2016-10-19
Mar
k
Abrah
a
m
Upgrade cov
e
rage matrix
.
commit
|
commitdiff
|
tree
2016-10-18
Mark Abraham
Fix SIMD suggesti
o
n
fo
r
VMX
commit
|
commitdiff
|
tree
2016-10-17
E
rik
Li
n
dah
l
New cla
s
ses f
o
r spline
i
nterpolation tables
commit
|
commitdiff
|
tree
2016-10-16
T
e
e
m
u Murtol
a
Imp
r
oved er
r
or handling for KeyValue
T
ree
o
perat
i
ons
commit
|
commitdiff
|
tree
2016-10-14
Teemu Mu
r
tola
Use
gmx_m
t
o
p_t in selection
s
, part 2
commit
|
commitdiff
|
tree
2016-10-13
T
e
emu Murtola
A
dd bac
k
-mappin
g
t
o KeyValueTreeTransf
o
r
m
commit
|
commitdiff
|
tree
2016-10-13
T
eemu
M
u
rtola
Update bundled TNG
commit
|
commitdiff
|
tree
next