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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-09-01
Mark Abraham
M
e
rge "M
e
rge branc
h
re
l
e
ase-4-6 i
n
to release-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-09-01
M
a
rk
Abraham
Fixes and upd
a
tes
to BlueGene/Q
s
upport
commit
|
commitdiff
|
tree
2014-09-01
Mark Abr
a
ham
M
erge "Merge bra
n
c
h
release-
4
-6 into relea
s
e-5-0"
into
.
.
.
commit
|
commitdiff
|
tree
2014-08-31
Erik Li
n
dahl
Ad
d
ed negative zero preproces
s
or constants
commit
|
commitdiff
|
tree
2014-08-28
Ber
k
Hess
F
ixed two PME is
s
ues wi
t
h MPI+
O
penMP
commit
|
commitdiff
|
tree
2014-08-24
Berk
Hess
Initialize unused velocity const
r
aint
co
m
ponents
commit
|
commitdiff
|
tree
2014-08-23
Mar
k
Abraham
Unify documentation for
webpa
g
e build
commit
|
commitdiff
|
tree
2014-08-22
M
ark Ab
r
aham
Fix z
l
i
b usage with T
N
G
commit
|
commitdiff
|
tree
2014-08-21
Magnu
s
L
u
n
dborg
Fixed TNG memo
r
y a
l
ign
m
en
t
pr
o
blem and reset
p
o
i
n
ters
.
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Add _GNU_SOURC
E
=1
t
o find c
l
o
n
e
(
) with PGI
commit
|
commitdiff
|
tree
2014-08-20
Roland Schul
z
Chang
e
e
r
ro
r
to
w
arning
for
m
issing OMP_NU
M
_THREADS
commit
|
commitdiff
|
tree
2014-08-20
Erik Linda
h
l
Fix matrix po
i
nter
dere
f
erence
bug in update
.
c
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik L
i
ndahl
E
nable SIMD regist
e
r c
a
lling conv
e
ntion with gmx_simdca
l
l
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Add cycle c
o
unters
for 64-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
S
horte
n
plu
g
in configuration message
commit
|
commitdiff
|
tree
2014-08-17
Eri
k
Lindahl
Fix Portland c
o
mpiler w
a
r
n
ings
commit
|
commitdiff
|
tree
2014-08-17
Berk He
s
s
Halved the cost of the pull communic
a
tion
commit
|
commitdiff
|
tree
2014-08-17
Roland Schulz
Do
n
't build tests until they
are run
commit
|
commitdiff
|
tree
2014-08-16
M
ark Abraham
Fix gm
x
t
u
ne
_
pme
with
L
J-PME
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraham
Fi
x
w
a
l
lcycle counti
n
g wit
h
md
-
vv, sd and sd2
commit
|
commitdiff
|
tree
2014-08-16
Te
e
m
u
Mu
r
tola
Di
s
able an
a
lys
i
sdata
g
eneri
c
tests i
f
not
c
omp
i
labl
e
commit
|
commitdiff
|
tree
2014-08-14
Berk
Hess
Correcte
d
SIMD m
a
th over
f
low doc
u
mentatio
n
commit
|
commitdiff
|
tree
2014-08-11
St
e
fan
F
l
e
isc
h
mann
Avoid stack ov
e
rflow on Windows
w
ith CMake > 2
.
8
.
10
.
2
commit
|
commitdiff
|
tree
2014-08-10
E
rik Lindahl
Improve Gromacs portability
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Replace __LP64__ with chec
k
for
p
ointer size
commit
|
commitdiff
|
tree
2014-08-10
Berk Hess
A
d
d
ed checks for TPI + Verlet scheme
commit
|
commitdiff
|
tree
2014-08-10
R
o
land
S
ch
u
lz
Check MD5
s
u
m f
o
r re
g
ressiontest
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
Fix portabili
t
y
i
ssue with ArrayRef initializer overloading
commit
|
commitdiff
|
tree
2014-08-07
Erik
L
indahl
Cha
n
g
e
d n
a
mes of te
s
t files to avoid Fujitsu compil
e
r
bu
g
commit
|
commitdiff
|
tree
2014-08-05
Berk
H
ess
Fi
x
h
ang with LJ-PME a
n
d empt
y
domains
commit
|
commitdiff
|
tree
2014-08-05
R
ola
n
d
Sc
h
ulz
Workaro
u
nd for ICC 14
commit
|
commitdiff
|
tree
2014-08-01
Eri
k
Lindahl
Added tests for de
n
ormal
a
nd underflow for simd exp(
)
commit
|
commitdiff
|
tree
2014-07-28
Roland Schulz
Fix bui
l
d
of binary p
a
cka
g
e
commit
|
commitdiff
|
tree
2014-07-28
R
o
land Schulz
Re
m
ove
R
andom123
/
features
commit
|
commitdiff
|
tree
2014-07-25
R
o
land Sch
u
l
z
W
o
rkaround for
IC
C
14 bug
commit
|
commitdiff
|
tree
2014-07-24
Rolan
d
Sch
u
l
z
Fix Cygwi
n
+
S
hared-Libs+FFTW
commit
|
commitdiff
|
tree
2014-07-21
R
o
l
a
nd Schulz
Fix GMX_NONBONDED_NUM_THREAD
S
!=GMX_PAIRSEARCH
_
NUM_
T
HREADS
commit
|
commitdiff
|
tree
2014-07-16
T
ee
m
u M
u
rtola
Fix HTML help and ma
n
p
age
s
for comman
d
s with da
s
hes
commit
|
commitdiff
|
tree
2014-07-13
Erik Lindahl
Avoid
c
lang/32 optim
i
zation affecti
n
g IEEE
e
ndian detect
i
on
commit
|
commitdiff
|
tree
2014-07-11
Teemu Mu
r
tola
Fix HTML
links
t
hat contain file extensions
commit
|
commitdiff
|
tree
2014-07-09
M
a
rk A
b
raham
Quie
t
e
n
r
epeated
cma
k
e
r
u
n
s
commit
|
commitdiff
|
tree
2014-07-09
Rola
n
d Schulz
Fix Cygwin
build
commit
|
commitdiff
|
tree
2014-07-08
Erik Lindahl
Make I
E
EE7
5
4 c
h
e
ck mo
r
e ro
b
ust
commit
|
commitdiff
|
tree
2014-07-08
T
e
e
mu M
u
rtola
Make select
i
ons
i
gnore \r in input
commit
|
commitdiff
|
tree
2014-07-07
Mark A
b
raha
m
Fix tarball and install, particu
l
ar
l
y
for INSTALL
commit
|
commitdiff
|
tree
2014-07-05
Magn
u
s Lundborg
F
i
x bug causing reading n
e
xt frame no
t
to stop
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lundborg
Fix tng_num_frame_sets_get() with no frame
s
ets
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu Murt
o
la
Rein
s
tantiate un
s
orte
d
i
n
dex gr
o
up che
c
k
commit
|
commitdiff
|
tree
2014-07-05
R
oland Schulz
A
d
d r
u
n
ning te
s
t
s to install
-
guide
commit
|
commitdiff
|
tree
2014-07-05
Teemu Murtola
Update some
in
s
tallation-rel
a
t
e
d docs
commit
|
commitdiff
|
tree
2014-07-01
Mark Abraham
Fix G
M
o
c
k to work on MSVC
commit
|
commitdiff
|
tree
2014-06-29
Mark Abrah
a
m
Refer to "mixed" pre
c
ision
in user-facing document
a
tion
commit
|
commitdiff
|
tree
2014-06-29
B
e
rk Hess
Tak
e
LJ-PME into account for table spaci
n
g
commit
|
commitdiff
|
tree
2014-06-29
Erik
L
in
d
ahl
Fixe
d
fre
e
energy
w
i
t
h
LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Convert in
s
tall g
u
i
de
t
o
mar
k
down
commit
|
commitdiff
|
tree
2014-06-29
Mark A
b
raha
m
Merge
"
Merge release-
4
-6 into release-5-
0
" into release
-
5-0
commit
|
commitdiff
|
tree
2014-06-29
Berk H
e
ss
Updated LJ
-
PME documentat
i
on
commit
|
commitdiff
|
tree
2014-06-29
Ro
s
sen
Apo
s
tolov
Use cosi
s
tent
s
tyle when
r
eferr
i
ng to
force f
i
e
ld
s
.
commit
|
commitdiff
|
tree
2014-06-29
Teemu Murtola
Rem
o
ve some har
d
coded selec
t
ion
s
t
ring b
u
ffers
commit
|
commitdiff
|
tree
2014-06-29
R
o
l
and Sch
u
lz
F
i
x d
e
t
e
c
t
ion of i386 in tmpi
commit
|
commitdiff
|
tree
2014-06-29
Eri
k
Lindahl
Enable rtp angle/dihedral ent
r
i
es not connecte
d
by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Mi
c
h
a
el
S
hirts
Allow printi
n
g
p
otential energ
i
es
t
o dhdl
.
x
v
g
f
il
e
commit
|
commitdiff
|
tree
2014-06-29
Da
v
id van der
S
p
oel
Fixes #1532, SEGV in
g
_current
.
commit
|
commitdiff
|
tree
2014-06-29
Ro
l
an
d
Schulz
Merge "Merge br
a
n
c
h
'release-4-6'
into release-5
-
0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Roland Schulz
Fix
error for no 64
b
it file support
commit
|
commitdiff
|
tree
2014-06-28
Erik
Lindahl
Fixed CMAP
g
eneration for ala
n
ine
dipeptide special
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Magnus Lundborg
Update TN
G
build s
y
s
t
e
m
commit
|
commitdiff
|
tree
2014-06-28
M
ar
k
Abraha
m
U
se
p
a
rallel te
r
minology more consistently
commit
|
commitdiff
|
tree
2014-06-28
ngoga
D
ef
a
ult SD integrator is now sd
1
by Nicu Gog
a
commit
|
commitdiff
|
tree
2014-06-27
Erik Linda
h
l
Always
set b-stat
e
posres, even
i
f i
d
e
n
t
ical to a-
s
tat
e
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Upd
a
te g_density to handle
bilayers b
e
tter
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Fix LJPME Lorentz
-
Berth
e
lot combinat
i
on
r
ules
commit
|
commitdiff
|
tree
2014-06-27
R
ossen Apo
s
tolov
Changed linkin
g
order
t
o make
Extrae wo
r
k
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Li
n
dahl
Improve
PDB I/O (keep occupancy,
b-
f
act
o
r, element)
commit
|
commitdiff
|
tree
2014-06-27
Ca
r
sten Kutzner
Remove o
b
solete pull-geome
t
ry o
p
tio
n
'position' from
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Ro
l
and Schulz
Fix Ph
i
P
latform file for MPI
commit
|
commitdiff
|
tree
2014-06-27
E
rik L
i
ndah
l
Avoid warnings
a
bout coupling whe
n
free_energy
=
no
commit
|
commitdiff
|
tree
2014-06-27
R
oss
e
n Apostolov
Ad
d
ed info
r
matio
n
a
b
out dihedral restrain
t
s
.
commit
|
commitdiff
|
tree
2014-06-27
R
o
s
sen Aposto
l
ov
Remove install_
m
a
n
ifest
.
tx
t
during make cle
a
n
.
commit
|
commitdiff
|
tree
2014-06-26
Mar
k
Ab
r
aham
Merge
"Merge rele
a
se-4-
6
int
o
rele
a
se-5-0" into rel
e
as
e
-5-0
commit
|
commitdiff
|
tree
2014-06-25
Erik
Lindahl
Updated A
m
ber GBSA pa
r
amet
e
rs
commit
|
commitdiff
|
tree
2014-06-25
E
rik Lindahl
Make source compile u
n
der Linux X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
M
a
ke i
t
h
arder for comp
i
ler t
o
opt
i
mize
a
way
S
I
M
D CMake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Abra
h
am
Ma
n
ual f
i
xes
commit
|
commitdiff
|
tree
2014-06-24
Ma
g
n
us Lundborg
I
m
proved che
c
k to
decide if
to
add ch
a
in/r
e
sidu
e
.
commit
|
commitdiff
|
tree
2014-06-24
David van de
r
Spoel
Added check in grompp
for shells
and in
p
utr
e
c
i
s
sues
.
commit
|
commitdiff
|
tree
2014-06-24
Erik
Lin
d
ahl
Fixed G
R
OMOS
assignment o
f
P
RO-NH terminus torsions
commit
|
commitdiff
|
tree
2014-06-24
Erik Lind
a
h
l
Make s
u
r
e duplicates bondeds are s
e
t
f
rom h
a
ckblock
s
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Clean up CMAP placeme
n
t in
paramet
e
r
list
commit
|
commitdiff
|
tree
2014-06-24
Erik L
i
ndahl
Added multisimula
t
ion info to log/output
commit
|
commitdiff
|
tree
2014-06-24
Rossen
A
postolov
Extend ver
s
ion checking/warnings for chec
k
po
i
n
t
continuatio
n
commit
|
commitdiff
|
tree
2014-06-23
Ross
e
n Ap
o
st
o
lov
Added
tip5
p
to the list of
w
a
t
e
rmodels in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Enable
4-letter resnam
e
in
PDB
o
ut
p
ut, k
e
eps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik Lindahl
Detect non-
f
a
t
al warnin
g
s when tr
y
ing C
F
lags for
sour
c
e
commit
|
commitdiff
|
tree
2014-06-23
Erik Li
n
dahl
Enable xvgr out
p
ut an
d
labels f
o
r g_
p
rinci
p
al
commit
|
commitdiff
|
tree
2014-06-23
Erik Lin
d
ahl
Disallow
e
x
t
rac
t
i
ng V/F from XTC files i
n
g
_
t
r
aj
commit
|
commitdiff
|
tree
2014-06-23
Erik
Lindahl
Wa
r
n
i
f
u
sing nsteps
=
0 without continuation=
y
es
commit
|
commitdiff
|
tree
2014-06-21
Vedran Mi
l
etić
Use ${CMA
K
E_INSTALL_LIBDIR} as
lib di
r
e
c
tory for tn
g
_io
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk
H
ess
Fix
g
_mindis
t
w
i
th pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
R
o
s
s
en Apostolov
Fixed typo in opls
a
a ASPH charges
.
commit
|
commitdiff
|
tree
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