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Fix portability issue with ArrayRef initializer overloading
2014-08-07
E
rik Lindahl
Fix
portabili
t
y iss
u
e with Array
R
ef initializer overl
o
a
d
ing
commit
|
commitdiff
|
tree
2014-08-07
Erik
Lindah
l
Changed names of test fil
e
s to a
v
oid F
u
j
i
tsu com
p
iler bug
commit
|
commitdiff
|
tree
2014-08-01
E
r
i
k Lindahl
Added tests for
d
e
n
ormal and u
n
derflow for sim
d
e
xp()
commit
|
commitdiff
|
tree
2014-07-27
Erik Lindah
l
Fix
s
electi
o
n of xtc groups not starti
n
g at inde
x
0
commit
|
commitdiff
|
tree
2014-07-13
Erik
L
i
ndah
l
Avoid clang/
3
2
o
ptimiza
t
ion affecting
IEEE en
d
ian de
t
e
c
tion
commit
|
commitdiff
|
tree
2014-07-11
Er
i
k Lindah
l
Make
AVX2 check more
r
obust
commit
|
commitdiff
|
tree
2014-07-08
Eri
k
Lindahl
Make IEEE
7
5
4
check m
o
re ro
b
ust
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindahl
Fixe
d
free ene
r
gy with
L
J-PME
commit
|
commitdiff
|
tree
2014-06-29
Erik L
i
ndahl
E
n
abl
e
rtp
a
ngle/dihedral entri
e
s not
c
onnected by
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindahl
Fixed
CMAP
ge
n
eration for alanine dipeptide special
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Er
i
k
L
i
ndah
l
Always
set b-s
t
ate posre
s
,
even if identical to a-state
commit
|
commitdiff
|
tree
2014-06-27
E
rik Lindahl
Update g_
d
ensity to handle bilayers better
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Fix LJPME
Lo
r
ent
z
-Bert
h
elot
co
m
bination rules
commit
|
commitdiff
|
tree
2014-06-27
Erik Lind
a
hl
Improve
P
DB I/O (keep
o
ccupancy, b-f
a
c
t
o
r
,
e
lement)
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Avoid warnings about coupling when f
r
ee_energy=n
o
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Upd
a
ted Amber GB
S
A paramete
r
s
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Make source compile under Linux X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k Lindahl
M
ake
i
t hard
e
r f
o
r compiler to optimiz
e
away SIM
D
CMake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Li
n
dahl
F
ixed GROMOS assi
g
nment
o
f P
R
O
-NH terminus torsions
commit
|
commitdiff
|
tree
2014-06-24
E
r
i
k
Lindahl
Make sure duplicates bo
n
deds are set
f
r
o
m
hackblo
c
ks
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Clean
u
p
CMAP
p
lacement in paramete
r
list
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Added multisimula
t
ion info to log
/
output
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindah
l
F
i
xed recent
bug with disp
.
corr
.
and vdwtype=shift
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
E
nable terminu
s
-sp
e
cific ato
m
tran
s
lation
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
En
a
bl
e
4-letter resname in
P
DB output, keeps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Er
i
k Lindahl
Detect n
o
n-fatal warni
n
gs when
trying CFla
g
s
f
o
r
source
commit
|
commitdiff
|
tree
2014-06-23
Er
i
k Lindahl
Enable xvgr ou
t
put and la
b
els f
o
r
g_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Di
s
a
l
low
extracting V
/
F from XTC files in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Warn if usi
n
g ns
t
e
p
s
=0
w
itho
u
t con
t
inuation=y
e
s
commit
|
commitdiff
|
tree
2014-06-22
Eri
k
Lindah
l
Make log file option listi
n
g
s
i
milar t
o
m
dp
names
commit
|
commitdiff
|
tree
2014-06-21
Erik Lindahl
Make sure m
a
sse
s
a
r
e
copied from termini databases
commit
|
commitdiff
|
tree
2014-06-18
Erik Lindahl
Fixed CMake 2
.
8
.
12+
CUDA
d
ylib bugs a
n
d warnings on
.
.
.
commit
|
commitdiff
|
tree
2014-06-17
Erik Lindahl
Di
s
abled
replic
a
exc
h
ange when T
n
ot in order
commit
|
commitdiff
|
tree
2014-06-14
Erik Lindahl
Make
s
u
re figu
r
e
l
egends ar
e
adapted
t
o x
m
gr/xmgrace
commit
|
commitdiff
|
tree
2014-06-13
Erik
L
indahl
Forc
e
g_bon
d
to use structur
e
fil
e
commit
|
commitdiff
|
tree
2014-06-12
Erik
L
ind
a
hl
Added dummy
mass f
o
r charmm TYR
aromat
i
c vs
i
te
s
commit
|
commitdiff
|
tree
2014-06-12
E
rik Lindahl
Make s
u
re
g
enres
t
r uses the disre_up2 parameter
commit
|
commitdiff
|
tree
2014-06-12
Erik
Lin
d
ahl
Remo
v
ed
u
n
d
ocumen
t
ed -map and -mda
t
a options fr
o
m
g_sh
a
m
.
commit
|
commitdiff
|
tree
2014-06-12
Er
i
k Li
n
dahl
Always write output from genio
n
commit
|
commitdiff
|
tree
2014-06-11
Eri
k
Lind
a
hl
Avoid writing
x
vgr f
o
rmatting with
-
xvg n
o
ne
commit
|
commitdiff
|
tree
2014-06-10
E
r
ik Lindahl
Process n
e
gat
i
ve sigma correctly wit
h
c
ombrule
2
or 3
commit
|
commitdiff
|
tree
2014-06-09
E
rik Lin
d
a
h
l
Fix
e
d th
e
output f
o
rmat of g_p
r
incipal
commit
|
commitdiff
|
tree
2014-06-09
Erik Lindahl
Modif
y
singl
e
/double EPS
t
o agree
with ISO C
commit
|
commitdiff
|
tree
2014-06-07
Erik Lindahl
Added p
a
ckage versio
n
to tng_io
CMa
k
eli
s
ts
.
tx
t
commit
|
commitdiff
|
tree
2014-06-02
Erik Lind
a
hl
Added grompp ch
e
cks for zero atom
masses in state B
commit
|
commitdiff
|
tree
2014-06-01
Erik Lind
a
hl
Fixed typ
o
i
n
m
anual
commit
|
commitdiff
|
tree
2014-06-01
Erik
L
i
ndahl
Two quot
e
s c
o
n
tribut
e
d by Vedra
n
Mil
e
ti
c
commit
|
commitdiff
|
tree
2014-04-07
Eri
k
Lind
a
hl
M
a
ke sure wa
t
er o
p
tim
i
za
t
ion is disabled for eso
t
eric
.
.
.
commit
|
commitdiff
|
tree
2014-03-16
Erik
L
in
d
a
hl
U
se a const
a
nt inste
a
d of sizeof
(
in
t
) for SSE
2
immediate
.
.
.
commit
|
commitdiff
|
tree
2014-02-26
E
rik
L
indahl
Adde
d
message to
w
a
rn that gro
u
p kernel
s
are depre
c
a
t
ed
.
commit
|
commitdiff
|
tree
2014-02-26
Erik Lind
a
hl
R
e
desi
g
n
e
d
S
IMD m
o
dule
and unit tests
.
commit
|
commitdiff
|
tree
2014-02-11
Erik Lin
d
ahl
First pa
r
t of commit
for redesigned SIM
D
mod
u
le - na
m
echanges
.
commit
|
commitdiff
|
tree
2014-02-01
E
r
ik
L
indah
l
Add
e
d
AVX2 detect
i
on to
c
make and
creat
e
d
C
PU a
c
c
elerat
i
on
.
.
.
commit
|
commitdiff
|
tree
2014-02-01
Erik Lindahl
U
se ps
e
udo-random instead
o
f
r
a
n
dom streams to in
t
i
a
lize
.
.
.
commit
|
commitdiff
|
tree
2013-12-17
Erik Lind
a
hl
Added a bunch
o
f quotes from
t
he 2013 No
b
el lectures
commit
|
commitdiff
|
tree
2013-12-16
E
r
i
k Lindahl
Moved
s
hared/s
t
atic libra
r
y det
e
ction to separ
a
te module
commit
|
commitdiff
|
tree
2013-12-16
Erik
L
indahl
Moved FF
T
library pro
c
e
ssing to separate module
commit
|
commitdiff
|
tree
2013-12-16
Erik Lindahl
Moved compiler pro
b
l
em detectio
n
into separa
t
e
module
commit
|
commitdiff
|
tree
2013-12-16
Erik Lindahl
Moved OpenMP detection to separa
t
e
f
i
le
.
commit
|
commitdiff
|
tree
2013-11-15
Erik
Lindahl
Merge
"
Merge
b
r
anch release-4-6"
commit
|
commitdiff
|
tree
2013-09-25
Eri
k
Lindahl
Fix bug in (
l
ong
)
neig
h
borlist SIMD paddin
g
when addin
g
.
.
.
commit
|
commitdiff
|
tree
2013-05-21
Erik L
i
ndahl
Fuj
i
tsu Sparc64
a
cceleration and ge
n
eral fixes for
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Erik Linda
h
l
Merge "re
m
ove unn
e
cessar
y
c
m
ake
mess
a
ge
s
"
into
rel
e
as
e
-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik
L
i
n
d
a
hl
Merge
"
fix
O
penMP detection on Mac OS
b
roken
by a
6
f
ee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Erik Lindahl
Fi
x
ed GB in
t
eractions for releas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik
Lindahl
Merge "ma
d
e SHAKE wor
k
again with partic
l
e decompostion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
A
d
ded ba
s
i
c
C
PU topo
l
o
gy in
f
ormation to
c
puid
c
ode
commit
|
commitdiff
|
tree
2013-01-11
E
r
ik Lindahl
M
er
g
e "fixed nbnxn no
LJ c
o
mb
.
rule AVX256 PME kerne
l
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Erik L
i
ndahl
Fix
e
d flop-
a
c
c
ounting
for peri
o
d
i
c i
m
p
r
oper dihedrals
commit
|
commitdiff
|
tree
2013-01-10
Erik Li
n
dahl
Dis
a
llow the use of
C
lang to
c
ompile AVX_128_FMA
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Re
m
o
v
e broke
n
g_dih tool
commit
|
commitdiff
|
tree
2013-01-10
E
rik Lindahl
Revert default rlist/rv
d
w
/
rcoulomb t
o
valid valu
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Eri
k
L
indahl
Fixes SSE/AVX compilation under
W
indows
commit
|
commitdiff
|
tree
2013-01-09
Erik Linda
h
l
Merge
"Cor
r
ecte
d
g
m
x
c
heck outp
u
t for
Gromos96 b
o
nds
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Er
i
k Lindahl
Added work-around for gc
c
bug in
A
VX
intr
i
nsin
c
s formal
.
.
.
commit
|
commitdiff
|
tree
2013-01-08
Erik Lindahl
Add ch
e
ck to remo
v
e zero Charm
m
dihedrals
commit
|
commitdiff
|
tree
2013-01-08
Erik Lind
a
hl
Do not always
a
dd -msse2 to releas
e
flags f
o
r icc
commit
|
commitdiff
|
tree
2012-12-30
Erik Linda
h
l
Fixed GMXRC so we are not polluting
s
tandard shell
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Erik Lindahl
Merg
e
"
T
h
r
ead-MPI f
i
xes fo
r
i
3
86 llvm & simp
l
ification
.
.
.
commit
|
commitdiff
|
tree
2012-12-27
Erik Li
n
dahl
Fixed error mess
a
g
e
for
zwitte
r
i
o
n
residues
commit
|
commitdiff
|
tree
2012-12-21
Erik L
i
ndahl
Fi
x
ed gmx_cpuid not working on non-x86
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
Merge
"
cmake: added op
t
ion to disabl
e
quote
s
"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Erik Lind
a
hl
Merge "Sm
a
ll fix for g_tune_pme" in
t
o rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-12-20
Erik
L
indahl
Mer
g
e "Fixes for
a
n
derse
n
tempe
r
a
t
u
re cont
r
ol" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Erik Li
n
dahl
Merge "F
i
xe
s
for expande
d
ens
e
mble a
n
d
HREPEX"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Erik Lind
a
hl
Fixed AVX256 doub
l
e-precision kernels for g
c
c
commit
|
commitdiff
|
tree
2012-11-29
Er
i
k Lindahl
Double precisi
o
n AVX
-
2
5
6
k
e
rnels
commit
|
commitdiff
|
tree
2012-11-29
Eri
k
Lin
d
a
h
l
Double p
r
ecisi
o
n
A
VX_128_FMA ker
n
els
commit
|
commitdiff
|
tree
2012-11-28
Erik
Lindahl
SSE
4
.
1 do
u
b
l
e
precision kernels
commit
|
commitdiff
|
tree
2012-11-28
Erik Lindahl
Dou
b
le precision SSE2 kernels
commit
|
commitdiff
|
tree
2012-11-28
Eri
k
Lindah
l
Por
t
ed
b
ack
some AVX25
6
optimiz
a
tion
s
to SSE2/SSE4
.
.
.
commit
|
commitdiff
|
tree
2012-11-28
Erik Li
n
dahl
128-bi
t
A
VX ker
n
els
,
w
i
th FMA instr
u
c
t
ions for Opteron
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
Erik
Lindahl
Nonbo
n
d
e
d gr
o
up
kernels for 256-bit AVX (In
t
el
C
PUs)
commit
|
commitdiff
|
tree
2012-11-27
E
r
i
k L
i
ndahl
Merge "Added a
f
f
inity s
u
ppor
t
check,
v
i
sibility macros
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
Erik Li
n
dahl
Merge "fixed b
u
g
in
nbnxn OpenMP n
o
n-bonde
d
forc
e
redu
c
ti
o
n
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
Erik
L
ind
a
h
l
Merge "Use stat for gm
x
_is_fil
e
.
Fix get_libd
i
r
with
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
Erik Lindahl
Merg
e
"Extende
d
build information output
and refere
n
ce
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindahl
F
ix for icc 13 optim
i
zation-r
e
lated issue
a
n
d TIP4P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Erik Linda
h
l
Im
p
le
m
ented
RMS-based f
o
rce to
l
erance in
gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindahl
Fi
x
e
d
L
J
-14 e
r
ror
in free energy
commit
|
commitdiff
|
tree
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