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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-25
Erik
Lindahl
M
e
rge
b
ranch 'release-4-5-patch
e
s
'
o
f
git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Made sure all source files have some
copyri
g
h
t
header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
r
ik Lindahl
Re-added openmm paper
commit
|
commitdiff
|
tree
2010-08-24
Erik
L
indahl
M
e
rge branch 'release-4-5-pa
t
ches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Eri
k
Li
n
dahl
Up
d
ated
i
n
t
el synta
x
x86-6
4
asm files to also su
p
port
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
F
i
x
ed uniniti
a
l
i
z
ed
v
ariabl
e
e
rror in GB kernel w
i
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Fixed an u
n
signe
d
/signed int
e
g
e
r compa
r
ison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
ixed
t
wo m
o
re in
s
tances
of strcasec
m
p->g
m
x_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindahl
Co
p
ied SSE intri
n
s
ic
s
kernels
f
rom
x
8
6
-
64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Re
p
laced all occurences
o
f
str(n)ca
s
e
c
mp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lind
a
hl
Fix
e
d
s
tupid
mist
a
ke where
a
sta
t
ement wa
s
placed before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindah
l
Replaced t
e
sting of git version
w
ith testing for featu
r
es
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed namin
g
p
r
o
blems f
o
r d
o
ubl
e
pr
e
c
is
i
on
F
ort
r
an
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik
L
in
d
ahl
Fixed a t
y
p
o in fu
t
il
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Merge branch 'release
-
4-5-patches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
C
leaned up a
l
l install
e
d header
s
to remov
e
strict depend
e
n
ce
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Linda
h
l
Remove
d
som
e
u
nn
e
cessary #ifdefs from string2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lind
a
h
l
Amber for
c
e fields now
pass
v
a
l
idation
.
B
e
t
a status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k
Lindahl
Added F7
7
kernel setup headers
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indah
l
Fixed synchronization coun
t
er update for f77 kernels
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindah
l
Fixed a bug for G
B
OBC
b
orn radius calculati
o
n i
n
SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fixed an uninitialized variable bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
F
i
x
e
d a minor bug that caus
e
d For
t
ran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
Don
t
write nonpolar
surfac
e
energy to energy file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Linda
h
l
Fixed
s
o Fortran kerne
l
s work
a
gain
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
U
p
g
r
aded to latest autoconf pl
a
tform detecti
o
n scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
Fixed a chain rule
erro
r
in doub
l
e
p
rec
.
S
S
E2 GB
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
ri
k
Linda
h
l
Merge br
a
nch 'release-4-5-patches' o
f
git
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
i
k Lindahl
Do
u
b
le pr
e
cision SSE2 kern
e
ls f
o
r
G
e
n
erali
z
ed B
o
rn
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lin
d
ahl
Upd
a
t
e
d GB S
S
E2 kern
e
ls, t
e
sting
i
n p
r
ogress
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge
b
ranch
'r
e
lease-4-5-
p
atc
h
e
s
'
of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Mo
d
ifi
e
d atom order
in
A
m
ber
n
ucleo
t
ide
i
mproper to
r
sions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Modified improper torsion
atom
ord
e
r in Am
b
er TRP r
e
sidu
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lindah
l
Merge
b
ranch
'
r
e
lease-4-5-
p
atches' of gi
t
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Fix to write GB and surface energ
y
t
o separat
e
terms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge
b
r
anch 'release-4-
5
-patches' of
git
.
gro
m
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
hl
Ena
b
led dou
b
le prec
i
sion a
l
l
-vs-all kernels
.
Te
s
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
F
ixed simple typo i
n
last commit
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lin
d
ahl
Fixed pre
v
ious nasm
-
segv bug for
i
ntel-syntax
S
SE
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fix
e
d 64-bit b
u
g in SSE ass
e
mbly
(o
n
ly visible wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Worked around an internal compiler error fo
r
M
SVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lin
d
ah
l
Merge bran
c
h
'
releas
e
-4-5-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecated -ins opt
i
on to g_hbond since nobody s
e
ems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindah
l
Copie
d
all-vs-all chan
g
e
from x86-64
to
ia32 kernels too
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Merge branch 'release-4-
5
-p
a
tches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
i
n
dahl
Fixed potential error in cou
l
omb e
n
e
rgy
,
and maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Mer
g
e
b
r
anch 'r
e
leas
e
-4-
5
-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
A
dded doub
l
e preci
s
ion S
S
E2 g
e
neralized born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
d
a
hl
A
dded ia32 al
l
-vs
-
all kernels
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
Up
d
ated autoconf to work with
renam
e
d SSE2
x86-64
a
sm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lindahl
Renamed SSE2 x86-64 asm test
f
ile
t
o be co
n
sistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
i
xed typo to detect both
x86_64->i386 and
i
386->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
M
erge branch
'release
-
4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
F
i
xed
a
naming err
o
r introduc
e
d yesterday in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
Lindah
l
F
ixe
d
c
omp
i
ler err
o
rs for MSVC i
n
line intrinsics
a
nd
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Fixed che
c
kpo
i
nt
p
roblem in
3
2 bit
s
.
We
s
ho
u
l
d always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lindahl
Rem
o
ve
d
extra TER
records after c
h
ains we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindah
l
Me
r
ge branch
'release-4-5-patche
s
' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
F
i
xed SSE kernels in double pre
c
ision for
C
make, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik
Lindahl
M
er
g
e branch '
r
elease-4-5-patches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
E
r
ik
L
indahl
Cmake and Nasm support
for wi
n
do
w
s
commit
|
commitdiff
|
tree
2010-08-10
Erik Li
n
dahl
Move
d
f
o
ur more
S
SE
assembly fil
e
s to a
v
oid doub
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
M
erge bran
c
h 'r
e
l
e
a
s
e
-4-5-pa
t
ches'
of gi
t
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
nd
a
hl
Chang
e
s
t
o mak
e
Cmake w
o
r
k
u
n
der windows again
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindah
l
R
e
named
intel syntax
a
ssembl
y
files to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Added NASM
C
make support
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
ndahl
Merge branch 'r
e
le
a
se-4
-
5-patches' of g
i
t
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
MAYBE a f
i
x
f
or B
e
rk's Heme p
r
o
blem
.
Needs testing
commit
|
commitdiff
|
tree
2010-08-08
Erik Lin
d
ahl
Merge branc
h
'release-4-
5
-patches'
o
f
git
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik L
i
nda
h
l
Added
NHE as an A
m
b
e
r aminoacid residue type
commit
|
commitdiff
|
tree
2010-08-08
Erik L
i
ndahl
Copied CK-CB-
N
*-CT Amber improp
e
r
to
a
lso l
i
st CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Merg
e
branc
h
'r
e
l
ea
s
e-4-5-patches' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Li
n
dahl
Fixe
d
i
ncorrect #endif -> #else that ca
u
sed
t
he C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Merge br
a
nch 'rel
e
a
se-4-5-p
a
tches
'
of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik L
i
n
d
ahl
Fixed a
b
ug in
i
nde
x
g
e
neration f
o
r non-adjacent prot
e
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lindahl
Fixed nonexistent return type on gmx_mm_sincos_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Added out
int-extraction macro to double p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik
L
indahl
Added d
o
uble prec
i
sion SSE2 transcendental functio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
F
ixed accuracy issues in gm
x
_
m
m_log_ps(), and
a
dd
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik
L
indah
l
M
e
r
g
e branch 'release-4-5-patches' of git
.
gr
o
ma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k
L
i
ndahl
Modified T
E
R record w
r
iting be
h
aviour (only add af
t
er
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Li
n
dahl
M
erg
e
branch 'rel
e
ase-4-5-patches' of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
E
r
ik Lindahl
Fixed bu
i
l
d
issue for
template p
r
ogram
in double pr
e
cisi
o
n
commit
|
commitdiff
|
tree
2010-08-02
Erik
Lindahl
R
emoved unused va
r
ia
b
le that caused
a warnin
g
commit
|
commitdiff
|
tree
2010-08-02
Erik Linda
h
l
T
emporarily
d
isabled double precision SSE2 generalized
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Eri
k
L
indahl
Fixed er
r
or
in
(
unuse
d
) S
S
E2 dou
b
le precisi
o
n inline
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
E
r
i
k Li
n
da
h
l
Modifi
e
d inde
x
pr
o
cessing to r
e
instate residue-splitti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lin
d
ahl
Add
e
d
i
on
c
lasses to res
i
duetypes
.
dat
commit
|
commitdiff
|
tree
2010-07-30
Erik
Lindah
l
Merge branch 'master' of git
.
gromacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lin
d
ahl
Replac
e
d non-thread-safe
c
alls
to cti
m
e
(
) with our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Added p
o
rtable gmx_ctime_r() to enable replacement
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindah
l
Merge
b
r
a
n
ch 'master' of git
.
g
romacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-30
Erik Li
n
dahl
Replaced localtime with localtime_r() on unix and loca
l
ti
m
e_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
E
rik
Lindahl
Merge branch
'master' of git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Repla
c
ed r
e
a
ddir
(
)
w
i
t
h readdir_r(
)
to av
o
id
future
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
M
e
rge branch
'
m
aster' of g
i
t
.
gromacs
.
org:
g
r
o
mac
s
commit
|
commitdiff
|
tree
2010-07-30
Erik
Lind
a
hl
Porte
d
x
8
6-64 single
prec
i
s
ion SSE2 all-v
s
-
al
l
patch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
E
rik Lin
d
ahl
Commen
t
ed out
ca
l
ls to
d
ouble
p
rec
.
SSE2 all-vs-all
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik
L
inda
h
l
Wor
k
e
d
arou
n
d cross-inclus
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2010-07-29
E
rik Lindahl
Rem
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