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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-05-09
Roland Schul
z
Merge "Merge
b
ranch release-4-6 into release-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-05-09
Roland
Schulz
F
i
x OpenMP scope error
commit
|
commitdiff
|
tree
2014-04-29
Berk Hess
Removed
trun
c
atio
n
of nrdf in v-res
c
ale thermostat
commit
|
commitdiff
|
tree
2014-04-24
Magnus Lundbo
r
g
More
e
f
fi
c
ient TNG selection grou
p
creation
commit
|
commitdiff
|
tree
2014-04-23
Berk H
e
ss
F
i
xed nbnxn FE list alloc
a
tion
iss
u
e
commit
|
commitdiff
|
tree
2014-04-21
Michael Shirts
Issu
e
warnings fo
r
potentia
l
switch
w
/o defi
n
i
n
g s
w
itch
.
.
.
commit
|
commitdiff
|
tree
2014-04-16
Magnu
s
Lundborg
Fix
e
d
b
ug inverting com
p
ressi
o
n
precision
.
commit
|
commitdiff
|
tree
2014-04-16
Mark
Abraham
Fix
and
simplify
ve
r
s
ion
m
a
t
ching for r
u
n
n
in
g
tests
commit
|
commitdiff
|
tree
2014-04-07
Mark Abraham
Fix inva
l
id dereference in g_
t
une_pme
commit
|
commitdiff
|
tree
2014-04-07
Erik Lindahl
Make sure wa
t
er optimization is disabl
e
d
for esoteric
.
.
.
commit
|
commitdiff
|
tree
2014-04-07
Teemu Murtola
Do
x
ygen
doc
u
mentation f
o
r version
.
h
commit
|
commitdiff
|
tree
2014-04-03
Mar
k
Abraham
M
ov
e
string
-
pars
i
ng code to where
i
t can b
e
reused
commit
|
commitdiff
|
tree
2014-04-02
R
oland S
c
hu
l
z
Add doc
f
or spec
.
va
l
ues
o
f
GMX_MAXB
A
C
K
UP
commit
|
commitdiff
|
tree
2014-04-02
David van
d
er Spoel
Removed pos
s
ibi
l
ity of
c
ompi
l
ing w
i
th GSL
.
commit
|
commitdiff
|
tree
2014-04-02
T
e
em
u
Mur
t
ola
Move
s
t
r
i
n
g2
.
*
to util
i
ty/cstringutil
.
*
commit
|
commitdiff
|
tree
2014-04-02
Mark Abr
a
ham
Fixe
s
for g_tune_pm
e
for 5
.
0
commit
|
commitdiff
|
tree
2014-04-02
M
ar
k
Ab
r
ah
a
m
Fix bug accu
m
ula
t
ing nrank_pp_intranod
e
on PME
r
anks
commit
|
commitdiff
|
tree
2014-04-02
Berk Hess
Added L
J
-
P
ME and LJ
P
ot-swit
c
h
t
o
P
ME load es
t
imate
commit
|
commitdiff
|
tree
2014-04-02
Ma
r
k
A
b
raham
Re-
u
s
e
gm
x
_
g
reatest_common_diviso
r
()
commit
|
commitdiff
|
tree
2014-04-01
Teemu Murtola
M
ove smalloc
.
h to u
t
i
l
ity/
commit
|
commitdiff
|
tree
2014-03-31
David van der
Sp
o
el
F
i
xed co
m
pilation issue in fgr
i
d
.
cp
p
d
u
e to int/enum
commit
|
commitdiff
|
tree
2014-03-31
Mark Abra
h
a
m
Remo
v
e quot
e
commit
|
commitdiff
|
tree
2014-03-31
Rossen Apostol
o
v
Added C
M
ake support for
Extr
a
e
.
commit
|
commitdiff
|
tree
2014-03-31
Teemu Murt
o
la
Cl
e
a
n up
s
ma
l
loc
.
h
commit
|
commitdiff
|
tree
2014-03-31
Car
s
ten Kutzn
e
r
Fix documentati
o
n o
f
s
w
ap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-31
R
o
land S
c
hulz
Disabl
e
shared li
b
rari
e
s by defa
u
lt for md
r
un-only
commit
|
commitdiff
|
tree
2014-03-31
T
eemu Murtola
Re
m
ove d
e
pe
n
dency
o
n commandline/
f
rom oenv
.
cpp
commit
|
commitdiff
|
tree
2014-03-29
Chris
t
ian Wennb
e
rg
F
r
ee-e
n
ergy suppo
r
t for LJ-PME
commit
|
commitdiff
|
tree
2014-03-29
T
e
emu
Murtola
Optimize inte
r
module depend
e
ncies
commit
|
commitdiff
|
tree
2014-03-29
Teemu Mur
t
ola
Improve vers
i
on i
n
formation han
d
ling
commit
|
commitdiff
|
tree
2014-03-29
Te
e
mu Murtol
a
Better i
n
clude depende
n
cy graph gene
r
ator
commit
|
commitdiff
|
tree
2014-03-28
C
a
rsten
Ku
t
z
n
er
Fix do
c
ume
n
tation
issu
e
s
f
or inte
r
active M
D
module
.
commit
|
commitdiff
|
tree
2014-03-28
Christian Wennberg
N
e
w VDW
kernel
f
lavour for LJ-PME and
u
pdated group
.
.
.
commit
|
commitdiff
|
tree
2014-03-26
Daniel Landau
Add Cray c
o
mpiler suppor
t
commit
|
commitdiff
|
tree
2014-03-26
Carsten Kutzner
Doc
u
ment
a
tion house-keeping in
file s
w
apcoords
.
c
commit
|
commitdiff
|
tree
2014-03-26
Ma
r
ti
n
Hoefl
i
n
g
Interactive Mo
l
e
cula
r
Dynami
c
s (IMD
)
commit
|
commitdiff
|
tree
2014-03-23
M
a
r
k
Abraham
K
e
ep CMak
e
quiet a
b
out non-detectio
n
of op
t
iona
l
s
t
uf
f
commit
|
commitdiff
|
tree
2014-03-23
B
e
r
k Hess
Fixed bu
g
in parallel
v/
f
constraining
commit
|
commitdiff
|
tree
2014-03-23
B
e
rk
He
s
s
CUDA c
u
t-off
k
e
r
ne
l
s now shif
t
exc
l
usion energies
commit
|
commitdiff
|
tree
2014-03-23
Mark Abraha
m
F
ix print_date_and_time
commit
|
commitdiff
|
tree
2014-03-18
Roland Schul
z
Fix dependencies on
c
onfig
.
h for typedefs
.
h
commit
|
commitdiff
|
tree
2014-03-18
C
h
ristian Wenn
b
erg
Bugf
i
x in LJ
-
P
M
E
without electrostatics
commit
|
commitdiff
|
tree
2014-03-18
Mark A
b
ra
h
am
Rem
o
ved more stuff related to gmx
.
ff and gmx2
.
ff
commit
|
commitdiff
|
tree
2014-03-18
Te
e
mu
Mu
r
tola
Rem
o
ve i
n
teractive
he
l
p f
r
om co
r
e selection pars
e
r
commit
|
commitdiff
|
tree
2014-03-18
Teemu Murtola
Impr
o
ve
interactive selection input
commit
|
commitdiff
|
tree
2014-03-17
Ros
s
e
n
A
post
o
lov
Cle
a
ned up endif/else
-
s in CMakeLists
.
txt
a
nd *
.
cmake
.
.
.
commit
|
commitdiff
|
tree
2014-03-17
M
a
rk Abraham
Merge "M
e
rge branch
relea
s
e-4-6"
commit
|
commitdiff
|
tree
2014-03-17
Ma
r
k
Abraham
Fix perturbati
o
n to Ve
r
let sc
h
e
m
e when not pertur
b
ing
commit
|
commitdiff
|
tree
2014-03-14
Carsten
K
utzner
Avoid cros
s
product with
z
ero vector
i
n
r
otational
.
.
.
commit
|
commitdiff
|
tree
2014-03-11
Mark Abraham
Fix MKL
linking
commit
|
commitdiff
|
tree
2014-03-11
Mark Ab
r
aham
Avo
i
d a
r
r
ay-boun
d
s warnings
w
ith gcc 4
.
8
.
2
commit
|
commitdiff
|
tree
2014-03-11
Roland Schulz
S
i
mplify gm
x
TestLibXml2
commit
|
commitdiff
|
tree
2014-03-11
Berk Hess
PME
l
o
ad balanci
n
g
now works with LJ-PME
commit
|
commitdiff
|
tree
2014-03-11
Teemu
M
urto
l
a
Fi
x
misc
.
Dox
y
gen i
s
s
u
es
commit
|
commitdiff
|
tree
2014-03-11
R
o
land Schu
l
z
Fix Che
c
kCXX
C
ompilerFlag
commit
|
commitdiff
|
tree
2014-03-11
Sz
i
lárd Páll
Bump
r
eq
u
ired CUDA
v
er
s
io
n
to
4
.
0
commit
|
commitdiff
|
tree
2014-03-11
Roland Schulz
R
e
p
l
a
c
e
in
l
ine with
g
mx_i
n
l
i
ne
commit
|
commitdiff
|
tree
2014-03-10
Mark Abra
h
am
Fix
d
epe
n
d
e
ncy on swapcoords enums
commit
|
commitdiff
|
tree
2014-03-06
R
oland S
c
h
u
l
z
Remove KERNEL_WID
T
H
commit
|
commitdiff
|
tree
2014-03-06
Rossen
A
p
o
s
t
olov
R
e
mov
e
d the depr
e
cated gmx
.
ff and gmx2
.
f
f
.
commit
|
commitdiff
|
tree
2014-03-06
Roland
S
c
hul
z
U
s
e
gmx_
i
nt64_t
f
o
r gmx_off_t
commit
|
commitdiff
|
tree
2014-03-06
Be
r
k Hess
F
i
xed exit
wi
t
h FEP with PME n
o
d
e
s without
L
J-PME
commit
|
commitdiff
|
tree
2014-03-06
ngoga
M
artini CG - Combined ang
l
e
-tors
i
on potentials
commit
|
commitdiff
|
tree
2014-03-06
Davi
d
van der Spoel
S
ix new quotes from class
i
c literature
.
commit
|
commitdiff
|
tree
2014-03-05
Roland Schulz
Remov
e
dependency on T
N
G
in
trxio
.
h
commit
|
commitdiff
|
tree
2014-03-05
R
ol
a
nd Schulz
Report
MIC
S
IMD correctly
commit
|
commitdiff
|
tree
2014-03-05
Mark Ab
r
aham
M
e
rg
e
"M
e
rge rele
a
s
e
-4-6 into master"
commit
|
commitdiff
|
tree
2014-03-05
Ber
k
Hess
Bu
f
fer estim
a
te now work
s
wi
t
h rvd-switch
=
0
commit
|
commitdiff
|
tree
2014-03-05
Roland Schulz
Check zli
b
can
a
ct
u
ally
be lin
k
ed
commit
|
commitdiff
|
tree
2014-03-05
Roland Schulz
Av
o
id segfault when c
o
m
p
aring
t
p
r
commit
|
commitdiff
|
tree
2014-03-04
Mark Abraham
Add enum and docs for us
i
ng tpx_version
commit
|
commitdiff
|
tree
2014-03-02
Te
e
mu M
u
rtola
Fix inco
r
rect grid cell size in g_sas -nopbc
commit
|
commitdiff
|
tree
2014-03-01
Tee
m
u M
u
r
t
ola
Move de
f
ault library path searc
h
to progr
a
m context
commit
|
commitdiff
|
tree
2014-03-01
Mark Abraham
A
dd f
a
tal error fo
r
Anders
e
n
+constra
i
nt
s
+DD
commit
|
commitdiff
|
tree
2014-03-01
Christoph Junghans
s
w
itch ld_seed
from int t
o
gmx_int64_t
commit
|
commitdiff
|
tree
2014-03-01
Szil
a
rd P
a
ll
Added CUD
A
LJ-P
M
E nbnxn ke
r
nels
commit
|
commitdiff
|
tree
2014-02-27
T
e
emu Murt
o
la
Improve
support
f
o
r
d
ata sets
in C++ t
o
o
l
s
commit
|
commitdiff
|
tree
2014-02-27
Szilard Pa
l
l
CUDA ke
r
nels for switched LJ
commit
|
commitdiff
|
tree
2014-02-27
T
e
em
u
Murtola
Improve floating poin
t
c
o
mparisons in unit
tests
commit
|
commitdiff
|
tree
2014-02-26
B
e
rk Hess
Free-e
n
ergy now works wi
t
h t
h
e Ver
l
et scheme
commit
|
commitdiff
|
tree
2014-02-26
Alexey Shv
e
tsov
F
i
x
-Wmaybe-uninitia
l
ized warnings in some f
i
les
commit
|
commitdiff
|
tree
2014-02-26
Teemu Murtola
M
isc
.
D
o
x
y
gen build
sys
t
e
m
impr
o
vemen
t
s
commit
|
commitdiff
|
tree
2014-02-26
Er
i
k
Lindahl
Added message to warn that group kernels a
r
e dep
r
ecated
.
commit
|
commitdiff
|
tree
2014-02-26
Mic
h
ael Shirts
Updating and improving And
e
rsen th
e
rmostat
d
ocumentat
i
on
commit
|
commitdiff
|
tree
2014-02-26
Rolan
d
Schulz
ICC
a
l
i
asing op
t
imization flags
commit
|
commitdiff
|
tree
2014-02-26
R
o
land
Schulz
Replace al
l
m
d
r
un r
n
g
s with cycle based rng
commit
|
commitdiff
|
tree
2014-02-26
M
a
rk Abraham
Add
T
h
re
a
dSan
i
tizer bui
l
d type
commit
|
commitdiff
|
tree
2014-02-25
Berk Hess
Fixes se
p
erate PME nodes withou
t
LJ-PME
commit
|
commitdiff
|
tree
2014-02-24
Berk Hess
Fixe
d
bug
with
L
J pot-sw
i
t
ch in
4
xN kernel
s
commit
|
commitdiff
|
tree
2014-02-24
Mark Ab
r
a
ham
Permit warning-free use o
f
A
n
dersen the
r
mostat
commit
|
commitdiff
|
tree
2014-02-24
Mark Abrah
a
m
S
u
ppress ic
c
warning for Boost 1
.
55 use o
f
#pra
g
ma
.
.
.
commit
|
commitdiff
|
tree
2014-02-23
Rossen Apos
t
o
l
ov
Rem
o
ved depre
c
ated Encad FF
.
commit
|
commitdiff
|
tree
2014-02-21
Roland Schulz
Fix load_
l
j
_
pair_par
a
ms2 for MIC
commit
|
commitdiff
|
tree
2014-02-21
Roland Schulz
Updat
e
d
Boost to latest 1
.
55
.
0
commit
|
commitdiff
|
tree
2014-02-21
Roland
S
c
h
u
l
z
M
e
rge "Merge
release-4-6
i
n
t
o m
a
ster
"
commit
|
commitdiff
|
tree
2014-02-20
Mark
Abraham
Remove
p
a
r
ticle decomposition
commit
|
commitdiff
|
tree
2014-02-20
C
hri
s
toph Junghans
add
e
d g
m
x_is_
{
sin
g
le
,
double}_precision
commit
|
commitdiff
|
tree
2014-02-20
Roland Schulz
Fix aligned s
t
o
re to unaligned m
e
mory
commit
|
commitdiff
|
tree
2014-02-20
Mark
Abrah
a
m
avoid
mdrun crash whe
n
rdts
c
p is not su
p
porte
d
commit
|
commitdiff
|
tree
2014-02-20
Mark Abr
a
ham
Ad
d
integration t
e
sts for repli
c
a exchange
commit
|
commitdiff
|
tree
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