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When writing TNG include file closing in wallcycle.
2014-09-01
Magnus Lundborg
When writing TN
G
includ
e
file c
l
osing in wa
l
l
c
ycle
.
commit
|
commitdiff
|
tree
2014-09-01
Ma
r
k Ab
r
aham
Fix and
d
ocument
iss
u
es wit
h
te
m
plate
.
c
pp
commit
|
commitdiff
|
tree
2014-09-01
Mar
k
Abra
h
am
Me
r
ge "Merg
e
branch re
l
e
ase-4-6
i
nto rel
e
ase-5-
0
" into
.
.
.
commit
|
commitdiff
|
tree
2014-09-01
Mar
k
Abraham
Fixes and
updates to BlueGene/
Q
s
u
p
p
ort
commit
|
commitdiff
|
tree
2014-09-01
M
a
rk Abraham
M
erg
e
"Merge branch release
-
4-6
i
nto r
e
l
e
ase-5-
0
"
into
.
.
.
commit
|
commitdiff
|
tree
2014-08-31
Erik Lindahl
Added n
e
gative zero prep
r
oce
s
sor
cons
t
ants
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fixed two
PME iss
u
es w
i
th MPI+OpenM
P
commit
|
commitdiff
|
tree
2014-08-24
B
erk Hess
I
n
itia
l
ize unused velocity const
r
aint c
o
mponents
commit
|
commitdiff
|
tree
2014-08-23
Mark Ab
r
aham
Unify documentation for webpage bu
i
ld
commit
|
commitdiff
|
tree
2014-08-22
Mark Abraham
Fix z
l
ib usa
g
e with TNG
commit
|
commitdiff
|
tree
2014-08-21
Magnus Lundborg
Fixed TNG
m
e
m
ory alignment pr
o
blem and rese
t
pointer
s
.
commit
|
commitdiff
|
tree
2014-08-20
E
r
i
k Lindahl
Add _GNU
_
SOURCE=1
t
o
find
clone()
with
PGI
commit
|
commitdiff
|
tree
2014-08-20
R
oland Schulz
Change err
o
r to warning
f
o
r mi
s
sin
g
O
MP_NUM_T
H
READS
commit
|
commitdiff
|
tree
2014-08-20
Erik
Lindahl
Fix matrix pointer d
e
reference bug
in
u
pdat
e
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Enab
l
e
SIMD
register calling convention with gmx_s
i
mdcall
commit
|
commitdiff
|
tree
2014-08-20
Erik L
i
nd
a
hl
Ad
d
cycle counters for 6
4
-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Eri
k
Lindahl
Shorten plugin config
u
r
a
ti
o
n
message
commit
|
commitdiff
|
tree
2014-08-17
Erik Lin
d
a
hl
Fi
x
Portland
c
ompiler w
a
rnings
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
Ha
l
v
ed the cost
of the p
u
ll commu
n
icatio
n
commit
|
commitdiff
|
tree
2014-08-17
Rola
n
d Schulz
Don't build t
e
sts unt
i
l they
a
re run
commit
|
commitdiff
|
tree
2014-08-16
Mark
A
braham
Fix gmx tune_pme
w
ith LJ-PME
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraham
Fix wallcycle counting with
md-
v
v, sd and sd2
commit
|
commitdiff
|
tree
2014-08-16
Teemu
Murtola
Disa
b
l
e anal
y
si
s
data generic tes
t
s if not compilable
commit
|
commitdiff
|
tree
2014-08-14
B
e
rk Hes
s
Co
r
rected SIMD
m
ath
overflow documentation
commit
|
commitdiff
|
tree
2014-08-11
S
tefan Fl
e
is
c
h
mann
Avoid stack overflow on
Wind
o
ws with CMake > 2
.
8
.
10
.
2
commit
|
commitdiff
|
tree
2014-08-10
E
rik Lindahl
Improve Gromacs po
r
tab
i
lity
commit
|
commitdiff
|
tree
2014-08-10
E
r
ik Lindahl
Replace __LP64__
w
i
th check for pointer siz
e
commit
|
commitdiff
|
tree
2014-08-10
B
e
rk Hess
Added
checks for TPI
+ Verlet s
c
he
m
e
commit
|
commitdiff
|
tree
2014-08-10
Roland Sch
u
lz
Chec
k
MD5sum for re
g
ressiontest
commit
|
commitdiff
|
tree
2014-08-07
Erik
L
indahl
F
ix po
r
t
a
bility issue wi
t
h ArrayRef initiali
z
e
r overloading
commit
|
commitdiff
|
tree
2014-08-07
E
r
ik
Lindahl
Changed
n
a
m
es of
test
f
iles to avoi
d
Fu
j
itsu compiler bug
commit
|
commitdiff
|
tree
2014-08-05
Berk Hess
Fix
hang
with
L
J-PME and empty domai
n
s
commit
|
commitdiff
|
tree
2014-08-05
R
o
land Schu
l
z
W
o
r
k
arou
n
d for ICC 14
commit
|
commitdiff
|
tree
2014-08-01
Erik Lindahl
Added tests
for denor
m
al and under
f
low for simd exp()
commit
|
commitdiff
|
tree
2014-07-28
Roland Schulz
Fix build of bi
n
ary
p
ackage
commit
|
commitdiff
|
tree
2014-07-28
Roland Schulz
Remove
R
a
ndom123/features
commit
|
commitdiff
|
tree
2014-07-25
Roland Schulz
Workaround for
ICC
1
4
b
u
g
commit
|
commitdiff
|
tree
2014-07-24
Ro
l
an
d
Schul
z
Fix
C
y
gw
i
n+Shared-L
i
bs+FF
T
W
commit
|
commitdiff
|
tree
2014-07-21
Roland
Schu
l
z
Fix GMX_NONBOND
E
D_NUM_THREADS!=GMX_PAIRSE
A
R
CH_N
U
M
_TH
R
EA
D
S
commit
|
commitdiff
|
tree
2014-07-16
Teem
u
Murto
l
a
Fix HTML hel
p
and ma
n
pages for
c
ommands with das
h
es
commit
|
commitdiff
|
tree
2014-07-13
Erik
Lindahl
Av
o
i
d clang/32 optimizatio
n
a
ffecting
I
EEE endia
n
dete
c
tion
commit
|
commitdiff
|
tree
2014-07-11
Te
e
mu Murtola
Fi
x
H
TML links that
c
ontain file extension
s
commit
|
commitdiff
|
tree
2014-07-09
Mark Abraham
Quieten r
e
pe
a
te
d
cmake runs
commit
|
commitdiff
|
tree
2014-07-09
R
o
la
n
d Sc
h
ulz
Fix Cygwin build
commit
|
commitdiff
|
tree
2014-07-08
E
rik Lindahl
Make IEEE754 check mor
e
robust
commit
|
commitdiff
|
tree
2014-07-08
Te
e
mu
M
urtola
Make se
l
ections ignore \r
in
i
nput
commit
|
commitdiff
|
tree
2014-07-07
Mark Abraham
Fix tarb
a
ll and
ins
t
a
ll, particul
a
rly for
I
NSTALL
commit
|
commitdiff
|
tree
2014-07-05
Magn
u
s Lundborg
Fix bug cau
s
in
g
reading next frame
n
o
t to s
t
op
.
commit
|
commitdiff
|
tree
2014-07-05
Ma
g
nus Lundborg
Fix
tng_n
u
m_frame
_
sets_g
e
t() with no
f
r
ame sets
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu Murtola
Rein
s
tantiate
u
n
sor
t
ed index group
c
he
c
k
commit
|
commitdiff
|
tree
2014-07-05
Roland
S
chul
z
A
d
d running tes
t
s
to install
-
guide
commit
|
commitdiff
|
tree
2014-07-05
T
e
emu Murtola
Updat
e
some
i
ns
t
allatio
n
-
r
e
l
a
ted
d
ocs
commit
|
commitdiff
|
tree
2014-07-01
Mark
A
brah
a
m
Fix GMock
t
o
work
o
n MSVC
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Refer to "mixed" precision in use
r
-
facing docu
m
enta
t
io
n
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
ess
Tak
e
L
J
-PME into account for table sp
a
cing
commit
|
commitdiff
|
tree
2014-06-29
Er
i
k Lin
d
ahl
Fi
x
ed
free
e
nergy with LJ
-
PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
C
onvert in
s
tall guide to ma
r
kdown
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Merge "Merge releas
e
-4-6
i
n
t
o release-5-0
"
into release-5-0
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
Updated
LJ-PME docume
n
tat
i
o
n
commit
|
commitdiff
|
tree
2014-06-29
Rossen Apostolov
Use cosi
s
tent s
t
y
l
e wh
e
n refe
r
ring to
f
orce fields
.
commit
|
commitdiff
|
tree
2014-06-29
Teemu M
u
r
t
o
la
Re
m
o
v
e
some
h
ardcoded s
e
lection s
t
ring bu
f
fers
commit
|
commitdiff
|
tree
2014-06-29
R
oland Schulz
Fix det
e
ction of i386 i
n
tmpi
commit
|
commitdiff
|
tree
2014-06-29
E
r
i
k
Lin
d
ahl
Enable r
t
p
angl
e
/d
i
hedral entries not connected b
y
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Mich
a
el Shirts
Allow pr
i
nting pot
e
n
t
ial energies to
d
hdl
.
xvg file
commit
|
commitdiff
|
tree
2014-06-29
David van
d
er Spoel
Fixes
#1532, S
E
GV i
n
g_c
u
rrent
.
commit
|
commitdiff
|
tree
2014-06-29
Roland Schulz
Me
r
ge "Merge branch 'releas
e
-
4
-6' into rele
a
se-5-0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Ro
l
and Sc
h
u
l
z
F
i
x er
r
or for no 64bit
file suppor
t
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindahl
F
ixed CMA
P
g
eneration for alanine dipeptide
s
pecial
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
M
a
g
n
us Lund
b
org
Update TNG build
s
ystem
commit
|
commitdiff
|
tree
2014-06-28
Mark Abraham
Use parallel terminology
m
ore consist
e
n
t
ly
commit
|
commitdiff
|
tree
2014-06-28
ngoga
Default SD
i
n
tegrator is now sd1 by N
i
cu
Goga
commit
|
commitdiff
|
tree
2014-06-27
E
r
ik Linda
h
l
Always set b-state posres, ev
e
n
if iden
t
ical to a-state
commit
|
commitdiff
|
tree
2014-06-27
E
rik Lindahl
Up
d
ate g_density to
handle bilayers
b
etter
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
indahl
F
i
x LJPM
E
L
orentz
-
Berthelot combination rules
commit
|
commitdiff
|
tree
2014-06-27
Ro
s
s
e
n Apostolov
Changed link
i
ng o
r
de
r
to
make
Extrae wo
r
k
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Linda
h
l
I
m
p
r
ove P
D
B
I/O (kee
p
occ
u
p
a
n
c
y, b-f
a
ctor, eleme
n
t
)
commit
|
commitdiff
|
tree
2014-06-27
Car
s
ten
K
utzner
Remov
e
obso
l
e
t
e
p
ull-
g
eometry opt
i
on 'positi
o
n'
from
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland S
c
hulz
F
i
x Phi Platform file
f
o
r
MPI
commit
|
commitdiff
|
tree
2014-06-27
E
r
ik
Lindahl
Avoid
w
a
r
ning
s
a
bout coupl
i
ng when
f
ree
_
ene
r
g
y
=
n
o
commit
|
commitdiff
|
tree
2014-06-27
Rossen Aposto
l
ov
Added i
n
formation about dihedral rest
r
ai
n
ts
.
commit
|
commitdiff
|
tree
2014-06-27
R
ossen Apostolov
Remo
v
e install_manifest
.
txt during make
c
le
a
n
.
commit
|
commitdiff
|
tree
2014-06-26
Mark Abraham
Merge "Merge r
e
lease-4-6 into r
e
le
a
se-5-0" into r
e
lea
s
e
-
5-0
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k Li
n
dahl
Upda
t
ed Amber GBSA par
a
m
e
te
r
s
commit
|
commitdiff
|
tree
2014-06-25
Erik Li
n
dahl
Mak
e
source c
o
m
p
i
l
e under Linux X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Erik Linda
h
l
Ma
k
e it harde
r
for
compi
l
er to opti
m
ize away SIMD
C
M
a
ke
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Abraham
Manual fix
e
s
commit
|
commitdiff
|
tree
2014-06-24
Magnus Lundbor
g
Improved check
to decide
if
t
o add chain/residue
.
commit
|
commitdiff
|
tree
2014-06-24
Dav
i
d van der Spoel
Added check
i
n
g
romp
p
fo
r
s
h
ell
s
a
nd inp
u
tre
c
issues
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fixed GROMOS
ass
i
gnment of
P
R
O
-NH ter
m
inus torsion
s
commit
|
commitdiff
|
tree
2014-06-24
Erik Lin
d
ahl
Mak
e
su
r
e dup
l
icate
s
bond
e
ds are set
from
hackb
l
ocks
commit
|
commitdiff
|
tree
2014-06-24
Erik
L
indahl
Clean
u
p CMAP pla
c
ement in p
a
rameter list
commit
|
commitdiff
|
tree
2014-06-24
E
r
i
k
Lind
a
hl
Added mul
t
isimu
l
at
i
on
inf
o
to log/output
commit
|
commitdiff
|
tree
2014-06-24
R
o
s
sen Apo
s
tolov
Extend ve
r
sion che
c
king/wa
r
nings
f
o
r checkpoint continuation
commit
|
commitdiff
|
tree
2014-06-23
Ro
s
sen
Apostolo
v
Ad
d
ed tip
5
p to the lis
t
o
f watermode
l
s
in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Ena
b
l
e
4-letter resna
m
e in PDB ou
t
put, ke
e
ps
m
ore pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Erik
Lin
d
a
hl
Det
e
ct no
n
-fatal wa
r
nings
w
hen trying CF
l
ags
f
or sourc
e
commit
|
commitdiff
|
tree
2014-06-23
Erik L
i
ndahl
Enabl
e
xvg
r
output a
n
d
labels fo
r
g_pr
i
ncipal
commit
|
commitdiff
|
tree
2014-06-23
Erik L
i
ndahl
Di
s
a
llow extractin
g
V/F from
X
TC fil
e
s in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
W
arn if usin
g
nstep
s
=
0
without
c
ontinuatio
n
=ye
s
commit
|
commitdiff
|
tree
2014-06-21
Vedran
Miletić
Use ${CMA
K
E_INSTALL_LIBD
I
R} as l
i
b directory for tng
_
io
.
.
.
commit
|
commitdiff
|
tree
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