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Fix data block length when uncompressing TNG data.
2014-09-02
Magnus Lundborg
F
i
x
data block
length when uncompressing TNG
d
ata
.
commit
|
commitdiff
|
tree
2014-09-01
M
a
gn
u
s Lundborg
T
NG: Handle
large files
on 32
b
it systems
.
commit
|
commitdiff
|
tree
2014-09-01
J
usti
n
Lemkul
Updated
x-ax
i
s
l
a
bel
f
or g_w
h
am
.
commit
|
commitdiff
|
tree
2014-09-01
Magnus Lundb
o
rg
When writing TNG include file cl
o
sing
i
n
wallcy
c
le
.
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Fix and
d
o
cument issues w
i
t
h temp
l
a
t
e
.
cpp
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Merge "Merge bra
n
c
h re
l
ease-
4
-6 into release-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-09-01
Mar
k
Ab
r
aham
Fixes and updates to BlueGene
/
Q
s
upport
commit
|
commitdiff
|
tree
2014-09-01
Mark
A
b
raham
Merge
"Merge branch re
l
ease-4
-
6 into release-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-08-31
Erik Lindahl
Added
n
egative z
e
ro preprocessor constants
commit
|
commitdiff
|
tree
2014-08-28
Berk H
e
ss
Fixed two PME issue
s
with MPI+O
p
enMP
commit
|
commitdiff
|
tree
2014-08-24
Berk
Hess
I
n
i
t
ia
l
ize unu
s
ed velo
c
ity con
s
train
t
c
omponents
commit
|
commitdiff
|
tree
2014-08-23
Mark
A
braham
U
nify documenta
t
ion for webpage b
u
ild
commit
|
commitdiff
|
tree
2014-08-22
Mark Abr
a
ha
m
Fi
x
z
lib usage with TNG
commit
|
commitdiff
|
tree
2014-08-21
Magnus Lundborg
Fixed TNG memory alignment problem and r
e
set
pointers
.
commit
|
commitdiff
|
tree
2014-08-20
Erik
L
indahl
Add _GNU_SOURC
E
=1
t
o find clone() with
P
G
I
commit
|
commitdiff
|
tree
2014-08-20
Roland Schulz
Change err
o
r to
warning for missing O
M
P
_
NUM_THREAD
S
commit
|
commitdiff
|
tree
2014-08-20
Er
i
k Lindahl
Fix m
a
tri
x
pointer
d
erefe
r
ence
bug in update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Eri
k
L
ind
a
hl
Enable SIMD
r
egister calling conve
n
ti
o
n
w
ith gmx_simdcall
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik L
i
n
d
a
hl
Add c
y
cle c
o
unters for 64-bit
ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Shor
t
e
n
p
lugi
n
c
o
nfiguration
m
e
ssage
commit
|
commitdiff
|
tree
2014-08-17
E
r
ik Linda
h
l
Fi
x
Portland compiler warnings
commit
|
commitdiff
|
tree
2014-08-17
Ber
k
Hess
H
a
l
ved
the cost of t
h
e pull
communica
t
ion
commit
|
commitdiff
|
tree
2014-08-17
R
oland
S
chulz
Do
n
't
buil
d
t
e
s
t
s u
n
t
i
l
they ar
e
run
commit
|
commitdiff
|
tree
2014-08-16
Mark Abra
h
am
Fix gmx tune_pme with LJ-PME
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraham
Fix wallcy
c
l
e
cou
n
t
i
n
g
with md-vv, s
d
and sd2
commit
|
commitdiff
|
tree
2014-08-16
T
eemu Murt
o
la
D
isab
l
e analysisdata generic tests if not c
o
m
p
ilable
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Corrected SIMD math o
v
er
f
low
docum
e
ntation
commit
|
commitdiff
|
tree
2014-08-11
Stefan
Fl
e
isch
m
ann
Avoid stack
overfl
o
w on Windo
w
s
w
ith CMake > 2
.
8
.
10
.
2
commit
|
commitdiff
|
tree
2014-08-10
Erik
L
indahl
Improv
e
Gromacs portability
commit
|
commitdiff
|
tree
2014-08-10
E
r
ik Lindahl
R
e
pla
c
e __LP64__ with
c
h
ec
k
f
or po
i
nter s
i
ze
commit
|
commitdiff
|
tree
2014-08-10
Berk Hess
Added checks for TPI + Verlet scheme
commit
|
commitdiff
|
tree
2014-08-10
Roland Schulz
Check MD5sum for r
e
gressiontest
commit
|
commitdiff
|
tree
2014-08-07
Erik Linda
h
l
Fix portability issue with ArrayRef initial
i
zer overloading
commit
|
commitdiff
|
tree
2014-08-07
Er
i
k Lindahl
C
hanged names
o
f
test files to
avoid Fujitsu compiler bug
commit
|
commitdiff
|
tree
2014-08-05
B
erk
H
e
ss
Fix ha
n
g wi
t
h LJ-PME a
n
d emp
t
y domains
commit
|
commitdiff
|
tree
2014-08-05
Roland
S
chulz
Workaround for ICC 14
commit
|
commitdiff
|
tree
2014-08-01
E
r
ik Lindahl
Added tests for
denorm
a
l an
d
un
d
er
f
low
f
o
r s
i
md exp
(
)
commit
|
commitdiff
|
tree
2014-07-28
Roland Sch
u
lz
Fix build of bi
n
ar
y
pa
c
k
age
commit
|
commitdiff
|
tree
2014-07-28
Rol
a
nd Schulz
Remove Random123/features
commit
|
commitdiff
|
tree
2014-07-25
Roland Schulz
Workarou
n
d
f
o
r ICC 14 bug
commit
|
commitdiff
|
tree
2014-07-24
R
oland Schulz
Fix
Cygw
i
n+Shar
e
d-
L
ibs
+
FFTW
commit
|
commitdiff
|
tree
2014-07-21
Roland Schulz
Fix GMX_NO
N
BO
N
DED
_
NUM
_
THREADS!=GMX_PAIRSEARCH_NUM_THREADS
commit
|
commitdiff
|
tree
2014-07-16
Teemu Murto
l
a
Fix HTML help a
n
d man pages
for commands
w
ith dashes
commit
|
commitdiff
|
tree
2014-07-13
Erik
Lindahl
Avoid clan
g
/32
o
p
timization
a
f
fect
i
ng IEEE endian det
e
ction
commit
|
commitdiff
|
tree
2014-07-11
T
e
emu
M
u
r
tola
Fix HTML
lin
k
s that conta
i
n file extensions
commit
|
commitdiff
|
tree
2014-07-09
M
a
rk
A
braham
Quieten repeated cmake runs
commit
|
commitdiff
|
tree
2014-07-09
Roland Schulz
Fix Cygwin build
commit
|
commitdiff
|
tree
2014-07-08
Erik Lindahl
Ma
k
e IEEE7
5
4 check more ro
b
ust
commit
|
commitdiff
|
tree
2014-07-08
Te
e
m
u
Murtola
Make s
e
lecti
o
ns
i
gnore \r in in
p
ut
commit
|
commitdiff
|
tree
2014-07-07
Mark Abra
h
am
Fix tarball and in
s
t
all,
p
a
rticula
r
ly for INS
T
ALL
commit
|
commitdiff
|
tree
2014-07-05
Mag
n
us
L
undborg
Fi
x
bug
c
ausing reading next
frame not to stop
.
commit
|
commitdiff
|
tree
2014-07-05
M
a
gnus
Lundborg
Fix
t
n
g
_nu
m
_frame_sets_
g
et()
w
ith no frame set
s
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu
M
ur
t
ola
Reinsta
n
tiate un
s
o
rt
e
d index group check
commit
|
commitdiff
|
tree
2014-07-05
Rol
a
nd Schu
l
z
Add runni
n
g t
e
sts
t
o install-guide
commit
|
commitdiff
|
tree
2014-07-05
Te
e
mu Murt
o
la
Update so
m
e
installatio
n
-related do
c
s
commit
|
commitdiff
|
tree
2014-07-01
M
a
rk
A
b
rah
a
m
Fix GMock
t
o wor
k
on M
S
VC
commit
|
commitdiff
|
tree
2014-06-29
Ma
r
k
Abraham
R
e
f
e
r
to
"
mixed"
precision i
n
us
e
r-fac
i
n
g
docu
m
entat
i
on
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
ess
T
ake
LJ
-
PME
i
nto a
c
count for table spaci
n
g
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindahl
Fixed free
energ
y
with LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
C
o
nvert install guide to markdown
commit
|
commitdiff
|
tree
2014-06-29
M
a
rk Abra
h
a
m
Merge "Merge release-
4
-
6 i
n
t
o
release-5-0"
into release-5-0
commit
|
commitdiff
|
tree
2014-06-29
Berk H
e
ss
Up
d
ated LJ-PME do
c
umentation
commit
|
commitdiff
|
tree
2014-06-29
R
o
ssen Apostolo
v
Us
e
c
o
si
s
t
e
nt
s
ty
l
e when ref
e
rring to f
o
rce fields
.
commit
|
commitdiff
|
tree
2014-06-29
Teemu Murtola
Re
m
ove
s
o
me hardc
o
ded
s
el
e
ction strin
g
b
u
ffers
commit
|
commitdiff
|
tree
2014-06-29
R
o
l
a
nd
S
chu
l
z
Fix detection of i38
6
i
n
tmpi
commit
|
commitdiff
|
tree
2014-06-29
Er
i
k
Li
n
dahl
Enable rtp angle/di
h
edr
a
l entrie
s
not connected by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Michael Shir
t
s
Allow p
r
intin
g
potenti
a
l e
n
ergies to dhd
l
.
x
v
g f
i
le
commit
|
commitdiff
|
tree
2014-06-29
D
avid van der Spoel
Fixes
#153
2
, SEGV
in g_current
.
commit
|
commitdiff
|
tree
2014-06-29
R
o
land Schulz
Merge "Merg
e
branch
'
releas
e
-
4-6' into r
e
le
a
se
-
5-0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Ro
l
and
S
chulz
Fix error f
o
r no 6
4
bit file support
commit
|
commitdiff
|
tree
2014-06-28
Erik Li
n
da
h
l
F
ix
e
d CMAP genera
t
i
o
n for
alani
n
e
d
ipepti
d
e special
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Ma
g
nus Lundborg
Upda
t
e TNG build system
commit
|
commitdiff
|
tree
2014-06-28
Mar
k
A
braha
m
Use parallel ter
m
inol
o
gy more consistently
commit
|
commitdiff
|
tree
2014-06-28
ngoga
Def
a
ult SD integrator i
s
no
w
sd1 by Nicu
G
o
ga
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Al
w
ays set
b-state posres,
even i
f
identical to a-s
t
a
te
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
in
d
ahl
Update g_
d
ensity
t
o
h
andle
b
i
l
ay
e
rs bette
r
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindah
l
Fix LJP
M
E L
o
rentz-Berthelot
c
ombinatio
n
rule
s
commit
|
commitdiff
|
tree
2014-06-27
Ro
s
sen Apostolov
Changed
l
inking
order to make
E
xtrae
work
.
commit
|
commitdiff
|
tree
2014-06-27
Eri
k
Lind
a
hl
Imp
r
o
v
e PD
B
I/O (keep occupancy,
b-factor,
e
lement)
commit
|
commitdiff
|
tree
2014-06-27
Carsten
K
utzner
Re
m
ove
o
bs
o
l
ete pull-ge
o
metry option 'posi
t
i
o
n' fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Rola
n
d Schulz
Fix Phi Platform fil
e
for
M
PI
commit
|
commitdiff
|
tree
2014-06-27
Erik Lin
d
ahl
Avoid war
n
in
g
s about
c
oupling w
h
e
n
free_e
n
ergy=no
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apost
o
lov
Adde
d
information about dihedral r
e
s
tr
a
ints
.
commit
|
commitdiff
|
tree
2014-06-27
Ros
s
en Apostolov
Remove install
_
m
a
nifest
.
t
x
t
during make
c
l
ean
.
commit
|
commitdiff
|
tree
2014-06-26
Ma
r
k Abraham
Merge
"
Me
r
ge rel
e
ase-4-6 into release-5-0" into release-5-0
commit
|
commitdiff
|
tree
2014-06-25
Erik
Lindahl
Updated Amber G
B
SA
p
arameter
s
commit
|
commitdiff
|
tree
2014-06-25
Erik Linda
h
l
Make sourc
e
com
p
ile under Linux
X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Erik Li
n
dah
l
Make it
harder for
c
o
mpiler to optimize awa
y
S
IMD CM
a
ke
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mar
k
Abraham
Manual fix
e
s
commit
|
commitdiff
|
tree
2014-06-24
Magn
u
s Lundborg
I
m
proved c
h
eck to decide
if to add ch
a
in/res
i
due
.
commit
|
commitdiff
|
tree
2014-06-24
Dav
i
d van der Spoe
l
A
dded check in grompp for shells
and i
n
putrec issues
.
commit
|
commitdiff
|
tree
2014-06-24
E
r
ik Lin
d
a
hl
Fi
x
ed GROMOS assignment o
f
PRO-NH terminu
s
torsions
commit
|
commitdiff
|
tree
2014-06-24
Erik
Lind
a
hl
Make sure
du
p
licates bondeds are
set
from hackblocks
commit
|
commitdiff
|
tree
2014-06-24
Eri
k
Linda
h
l
C
lean up C
M
AP placement in paramete
r
li
s
t
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Ad
d
ed m
u
ltisi
m
ulati
o
n
info to lo
g
/output
commit
|
commitdiff
|
tree
2014-06-24
Rossen
Apostolov
Extend ver
s
i
on checking/warnings
f
or checkpoint conti
n
uation
commit
|
commitdiff
|
tree
2014-06-23
Rosse
n
A
p
ost
o
lov
Ad
d
ed
t
ip5p to
the
l
ist
o
f watermode
l
s in som
e
FF
.
commit
|
commitdiff
|
tree
2014-06-23
E
rik Linda
h
l
Enable 4-letter res
n
am
e
i
n
PDB output, ke
e
ps more
p
dbinf
o
.
commit
|
commitdiff
|
tree
2014-06-23
Erik
Lindah
l
Detect non
-
fat
a
l
warnings whe
n
trying C
F
lags for
s
ource
commit
|
commitdiff
|
tree
2014-06-23
Eri
k
Linda
h
l
Enab
l
e xvgr outpu
t
and lab
e
ls for g_principal
commit
|
commitdiff
|
tree
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