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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-09-01
M
a
rk Abraham
M
e
r
g
e
"Merge branch r
e
lease-
4
-
6
i
n
t
o
re
l
ease-5-0"
int
o
.
.
.
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Fixes and update
s
to BlueGene/Q support
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Merge "
M
erge br
a
n
ch release-4-6 in
t
o
r
e
l
ease-5-0
"
int
o
.
.
.
commit
|
commitdiff
|
tree
2014-08-31
E
r
i
k Lindahl
Added n
e
ga
t
ive
zero preprocesso
r
const
a
n
ts
commit
|
commitdiff
|
tree
2014-08-28
B
erk He
s
s
Fixed
two PME i
s
sues with
M
PI+OpenM
P
commit
|
commitdiff
|
tree
2014-08-24
B
e
rk Hess
Initialize
u
nus
e
d
v
elo
c
ity constraint comp
o
nents
commit
|
commitdiff
|
tree
2014-08-23
Ma
r
k
A
b
raham
Uni
f
y documenta
t
ion for web
p
age build
commit
|
commitdiff
|
tree
2014-08-22
Ma
r
k Abraham
Fix zlib usage
w
ith TNG
commit
|
commitdiff
|
tree
2014-08-21
Magn
u
s Lundbo
r
g
Fixed TNG
m
emory
alignment prob
l
em a
n
d reset pointers
.
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik Lin
d
ahl
Add
_
GNU_SOURCE
=
1 to fi
n
d c
l
one
(
)
w
ith PGI
commit
|
commitdiff
|
tree
2014-08-20
Roland Schulz
C
h
a
n
ge erro
r
to
war
n
ing
f
or missing OM
P
_NUM_THRE
A
DS
commit
|
commitdiff
|
tree
2014-08-20
Er
i
k Lindahl
F
i
x m
a
trix
pointer dereference b
u
g in up
d
ate
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Ena
b
le SIMD
r
egister calling
c
onvention
w
ith
g
m
x_
s
i
m
d
call
commit
|
commitdiff
|
tree
2014-08-20
E
rik Lin
d
a
h
l
Add cycle counters f
o
r
64-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik
L
indahl
S
horten plugin configur
a
tion
m
e
s
sage
commit
|
commitdiff
|
tree
2014-08-17
Erik Linda
h
l
Fix
P
o
rtla
n
d compiler
w
arnings
commit
|
commitdiff
|
tree
2014-08-17
B
erk He
s
s
Halved t
h
e cost of
t
he pull communication
commit
|
commitdiff
|
tree
2014-08-17
Rol
a
nd Sc
h
ulz
Don't build t
e
sts until they are r
u
n
commit
|
commitdiff
|
tree
2014-08-16
M
a
rk Abraham
Fi
x
gmx tune_pme
w
ith LJ-PM
E
commit
|
commitdiff
|
tree
2014-08-16
Mark Ab
r
ah
a
m
Fix wallcycle coun
t
in
g
with md-vv,
s
d and s
d
2
commit
|
commitdiff
|
tree
2014-08-16
Teem
u
Murtola
Disable analysisdata generic tests if not compilable
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Corrected SIMD math overflow documentatio
n
commit
|
commitdiff
|
tree
2014-08-11
Stef
a
n
F
leisc
h
ma
n
n
A
void stack overflow on Windows
w
it
h
CMake >
2
.
8
.
10
.
2
commit
|
commitdiff
|
tree
2014-08-10
E
rik
Lind
a
hl
Improve Gromacs
p
o
rtability
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Replace __LP64__ wit
h
check
f
o
r
p
oi
n
ter size
commit
|
commitdiff
|
tree
2014-08-10
Ber
k
H
e
ss
Add
e
d c
h
e
c
ks for TPI + Verlet
scheme
commit
|
commitdiff
|
tree
2014-08-10
Roland
Sc
h
ulz
Chec
k
MD5sum for
reg
r
es
s
ion
t
est
commit
|
commitdiff
|
tree
2014-08-07
Eri
k
Lindahl
Fi
x
portability issue with ArrayRef initia
l
i
z
er o
v
erl
o
adi
n
g
commit
|
commitdiff
|
tree
2014-08-07
Erik
Li
n
dahl
Changed names of test f
i
le
s
to
avoid Fujits
u
com
p
iler
b
u
g
commit
|
commitdiff
|
tree
2014-08-05
B
e
r
k
H
e
ss
Fix hang with LJ
-
PME and empty domains
commit
|
commitdiff
|
tree
2014-08-05
Roland Schulz
Worka
r
o
u
n
d for I
C
C 14
commit
|
commitdiff
|
tree
2014-08-01
Erik Lindahl
Added
t
e
s
ts
for
d
enor
m
a
l and underflow
f
or simd exp()
commit
|
commitdiff
|
tree
2014-07-28
Rol
a
nd Schulz
Fi
x
build
o
f binary package
commit
|
commitdiff
|
tree
2014-07-28
Ro
l
and Schulz
Remove Rand
o
m
123/featu
r
es
commit
|
commitdiff
|
tree
2014-07-25
Rol
a
nd Sch
u
l
z
Workaround
f
o
r
ICC 1
4
bug
commit
|
commitdiff
|
tree
2014-07-24
R
oland Sch
u
l
z
Fix
C
y
gwin+Sh
a
red-Libs+FFTW
commit
|
commitdiff
|
tree
2014-07-21
Ro
l
an
d
Schulz
Fix GMX_N
O
NBONDE
D
_NUM_THREADS!=GMX_PAIRSEARCH_NU
M
_
T
HREA
D
S
commit
|
commitdiff
|
tree
2014-07-16
Tee
m
u Murto
l
a
Fix
HTML help and man pages f
o
r
c
o
mmands wi
t
h d
a
shes
commit
|
commitdiff
|
tree
2014-07-13
Erik Lindahl
A
void clang/32 optimiza
t
i
on affecting IEEE endian det
e
ction
commit
|
commitdiff
|
tree
2014-07-11
Teemu
Mu
r
t
ola
Fix H
T
ML
l
i
n
k
s
t
hat
c
ontain
f
i
le e
x
ten
s
i
o
ns
commit
|
commitdiff
|
tree
2014-07-09
Mark Abraham
Quiete
n
re
p
eated c
m
ake runs
commit
|
commitdiff
|
tree
2014-07-09
Roland Schulz
Fix Cygwin bu
i
ld
commit
|
commitdiff
|
tree
2014-07-08
Erik Lindahl
Make IEEE75
4
c
heck m
o
re
r
o
b
ust
commit
|
commitdiff
|
tree
2014-07-08
Teemu M
u
r
tola
Make sele
c
tions ignore \
r
i
n
input
commit
|
commitdiff
|
tree
2014-07-07
Mark Abraham
Fi
x
t
a
rball and install
,
particularly fo
r
INSTA
L
L
commit
|
commitdiff
|
tree
2014-07-05
Mag
n
us Lundborg
Fix bug causing readin
g
next frame n
o
t to stop
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus L
u
nd
b
org
Fix
tng_num_
f
r
ame_sets_get(
)
with no f
r
ame
s
ets
.
commit
|
commitdiff
|
tree
2014-07-05
T
eemu
Murtola
Reins
t
antiate unsorted index group check
commit
|
commitdiff
|
tree
2014-07-05
Roland Schulz
Add
r
u
nning tests to i
n
stall-gui
d
e
commit
|
commitdiff
|
tree
2014-07-05
Teemu
Murtola
Update so
m
e instal
l
a
t
ion-related docs
commit
|
commitdiff
|
tree
2014-07-01
Mark Abraham
F
ix GMock to work on MS
V
C
commit
|
commitdiff
|
tree
2014-06-29
M
ark
A
braham
Refer to "mixed
"
precision in
use
r
-facing documentati
o
n
commit
|
commitdiff
|
tree
2014-06-29
Berk
Hess
Take LJ-PM
E
i
nto a
c
count for table
s
p
a
cing
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindahl
Fixed free
e
n
e
rgy with LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Conve
r
t insta
l
l guide t
o
m
a
rkdo
w
n
commit
|
commitdiff
|
tree
2014-06-29
Mar
k
Abr
a
ha
m
M
erge "Merge release-4-6 into release-5-0" i
n
to
release-5-0
commit
|
commitdiff
|
tree
2014-06-29
Berk H
e
ss
Updated
LJ-PM
E
documentation
commit
|
commitdiff
|
tree
2014-06-29
Rossen Apostolov
Use cosistent style whe
n
re
f
erring to forc
e
fields
.
commit
|
commitdiff
|
tree
2014-06-29
Te
e
m
u M
u
rtol
a
Remo
v
e s
o
me hardcoded select
i
on s
t
ring buffers
commit
|
commitdiff
|
tree
2014-06-29
Roland
Schulz
F
ix detect
i
on of i386 i
n
tmpi
commit
|
commitdiff
|
tree
2014-06-29
Erik L
i
ndahl
Enable rtp angle/dihe
d
ral entries not connected
by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Michael
S
h
irts
A
l
l
o
w pri
n
ting potential e
n
erg
i
e
s
to dhdl
.
xvg file
commit
|
commitdiff
|
tree
2014-06-29
D
avid van der
Spo
e
l
Fixes #1532, SEGV in
g
_current
.
commit
|
commitdiff
|
tree
2014-06-29
Roland Schu
l
z
Me
r
ge "Merg
e
branch 'release-4-6' int
o
release-
5
-0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Roland Sc
h
ulz
Fix error for no 64bit
file support
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindahl
Fixed CMA
P
g
e
nerati
o
n for alanine dip
e
ptide
special
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Ma
g
nus L
u
nd
b
org
Updat
e
TN
G
build syst
e
m
commit
|
commitdiff
|
tree
2014-06-28
Mark
A
b
ra
h
am
Use parallel te
r
m
i
n
olo
g
y more consi
s
t
e
ntly
commit
|
commitdiff
|
tree
2014-06-28
ngoga
D
e
f
ault SD integra
t
or is now sd
1
by Nicu Goga
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Always set b-stat
e
posres, even if id
e
ntical
to a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
U
pdate g_densit
y
to
han
d
le bilayers b
e
tter
commit
|
commitdiff
|
tree
2014-06-27
Erik
Lindahl
Fix
LJPME L
o
rentz-Be
r
thelo
t
combination rules
commit
|
commitdiff
|
tree
2014-06-27
R
ossen Apostolov
Chang
e
d link
i
ng order
to make Extrae
w
ork
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Linda
h
l
I
mprove PDB I/O
(
keep occupancy,
b
-fac
t
or, ele
m
e
nt)
commit
|
commitdiff
|
tree
2014-06-27
Carsten Kutzner
Remove obsole
t
e pu
l
l-geometry
option 'position' from
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland Schulz
F
i
x Phi Platform file for MPI
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
inda
h
l
Av
o
id warn
i
ng
s
about coupling when fr
e
e_energy
=
no
commit
|
commitdiff
|
tree
2014-06-27
R
o
ss
e
n Apostolov
A
d
ded informatio
n
ab
o
ut
dihedral res
t
raints
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apo
s
tolov
Remove
install_m
a
ni
f
est
.
txt
durin
g
make clean
.
commit
|
commitdiff
|
tree
2014-06-26
Mar
k
A
braham
Merge "Merge relea
s
e-4-6
i
nto
r
e
lea
s
e
-5-0"
i
n
to release
-
5
-0
commit
|
commitdiff
|
tree
2014-06-25
Eri
k
Linda
h
l
Upda
t
ed Amber GBSA pa
r
ameters
commit
|
commitdiff
|
tree
2014-06-25
Erik
L
i
n
d
ahl
Make source comp
i
le
u
n
der Lin
u
x X32
A
B
I
commit
|
commitdiff
|
tree
2014-06-25
Erik Lin
d
ahl
Make it har
d
er for
c
ompiler
t
o optimiz
e
away SIMD C
M
ake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Ab
r
aha
m
M
anual fixes
commit
|
commitdiff
|
tree
2014-06-24
Mag
n
us Lund
b
org
I
m
proved
c
heck to
decide if to add chain
/
r
e
sid
u
e
.
commit
|
commitdiff
|
tree
2014-06-24
David v
a
n der Spoe
l
Added check
in g
r
ompp for shells and inputre
c
is
s
ues
.
commit
|
commitdiff
|
tree
2014-06-24
Erik
Linda
h
l
Fixed GROMOS ass
i
gnment
o
f PRO-NH ter
m
i
nu
s
torsions
commit
|
commitdiff
|
tree
2014-06-24
Eri
k
Lin
d
ahl
M
a
ke sure duplicates bondeds are set fr
o
m
h
a
c
kblocks
commit
|
commitdiff
|
tree
2014-06-24
Erik Linda
h
l
Clean up CMAP placement in parameter
list
commit
|
commitdiff
|
tree
2014-06-24
Erik Linda
h
l
Adde
d
mu
l
tisimulation i
n
fo
t
o log/ou
t
put
commit
|
commitdiff
|
tree
2014-06-24
Rossen A
p
ostolov
Extend version
checking/warnings fo
r
checkpoint continuat
i
on
commit
|
commitdiff
|
tree
2014-06-23
Rossen Apostolov
Adde
d
tip5p to the list of watermodels
in some
F
F
.
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik Lindahl
Enabl
e
4-letter
r
esname in PD
B
outpu
t
, keeps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Linda
h
l
Detect non-fatal warnings when trying CFl
a
gs for source
commit
|
commitdiff
|
tree
2014-06-23
Eri
k
Lindahl
E
nab
l
e xvgr output
a
nd labels for
g
_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
D
isallow extracting V/F from
XTC files in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Warn
i
f using
n
steps=0 without
c
onti
n
uation=yes
commit
|
commitdiff
|
tree
2014-06-21
Vedran Miletić
Us
e
${CMAKE_INSTAL
L
_
LIB
D
IR} as l
i
b
directory fo
r
tng_
i
o
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk He
s
s
Fix g_mindist
w
ith pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Ro
s
sen Apostolov
Fixed ty
p
o in oplsaa ASP
H
charges
.
commit
|
commitdiff
|
tree
next