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Resolved merge conflict in gmx_membed.c
2010-08-27
E
rik
Lindahl
Resolv
e
d me
r
g
e
conflict in
gmx_memb
e
d
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
nd
a
h
l
Merge
branch 'rel
e
a
s
e-4-5-pat
c
hes' of git
.
gro
m
ac
s
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Fi
x
ed gm
x
c
p
p to
a
l
ways use
u
nix path separators in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
ndahl
Merge branch
'
release-4-5-patches
'
of
g
it
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
ind
a
hl
Fix
e
d another uni
n
itialized variable w
a
rni
n
g in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Add
c
urrent
p
ath (
.
/)
t
o topol
.
top in
c
lude when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik L
i
nda
h
l
D
ont write EOF w
a
rnings to stdout every time we
checkpo
i
nt
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
ind
a
hl
Merge
b
ranch
'
release-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
F
ixed
first sta
t
em
e
men
t
occur
i
ng before
v
ariable decl
a
rati
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge branc
h
'relea
s
e-4-
5
-patche
s
'
of git
.
g
romacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Mod
i
fied
pd
b
2
g
mx
to automatically pick th
e
force f
i
eld
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
Fixed pointer
t
ypo
i
n patch from Alexey Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Added
PBC checking
p
a
t
ch t
o
g_cluster from
A
lexey
S
hvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lin
d
ahl
Merge bra
n
ch
'
releas
e
-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
n
dahl
Mo
d
ified pdb2gmx to not accept extra hydr
o
gen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
F
i
xed i
n
clu
d
e pat
h
i
n
vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k Lindahl
F
o
rgot to a
c
tual
l
y do the
c
h
ar->in
t
c
h
ange
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k
L
indahl
Changed b
o
ol to sign
e
d inte
g
er instea
d
of unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lindahl
Added m
i
ssing header inc
l
ude
commit
|
commitdiff
|
tree
2010-08-25
Erik Li
n
dahl
Merge
b
r
a
nch 'release-4-5-
p
atches' of git
.
g
r
o
m
ac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
indahl
Made sure all source
files
h
a
ve some copyright header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Er
i
k L
i
n
d
ahl
Re-added
op
e
nmm paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Li
n
dahl
Merge br
a
nch 're
l
ea
s
e
-4-5-patche
s
' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Updated in
t
el sy
n
tax x86-64 asm fil
e
s t
o
a
l
s
o
suppo
r
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
Fixed u
n
initializ
e
d var
i
able e
r
ror in
GB kernel wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Lindahl
Fixed an unsigne
d
/signed
integer compar
i
s
o
n
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed two more inst
a
nces of
st
r
casecmp->
g
mx_str
c
asecmp
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
L
i
n
d
a
hl
Copied SSE intrinsics
k
ernels from
x
86
-
64
t
o ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Replaced all occu
r
ences of
s
tr(n)casecmp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
s
t
upid mistake wh
e
re a st
a
t
ement was placed
b
efore
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Replaced testing of
g
it ver
s
ion w
i
th test
i
ng for features
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed naming problems for double
p
recision Fortra
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
ri
k
Lindahl
F
i
xed a ty
p
o in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
Merge
branch '
r
el
e
ase-4-5-patches' of
git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Cleaned up
a
l
l
ins
t
a
l
led headers to remove strict d
e
pendence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Re
m
oved s
o
me u
n
nece
s
s
ary #ifdefs
f
rom string2
.
h
; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
A
mber force fields now pa
s
s
validat
i
on
.
Beta status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
a
hl
Added F77
k
ernel se
t
up headers
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lind
a
hl
Fi
x
ed synchroniz
a
tion counter u
p
da
t
e for f77
kernels
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Li
n
dahl
Fi
x
ed a bug f
o
r GB OBC b
o
rn
radius ca
l
culation in SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Lindahl
Fixed an uni
n
it
i
alized va
r
ia
b
le bug
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik
L
indahl
Fixed
a
m
i
n
o
r bug that caused Fortran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lind
a
hl
Dont write n
o
npolar surface energy to e
n
erg
y
file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
i
xed so
Fortran ke
r
nels w
o
rk again
commit
|
commitdiff
|
tree
2010-08-21
Erik Linda
h
l
U
p
graded
t
o late
s
t
a
utoc
o
n
f
p
latform de
t
e
ction
s
c
ripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed
a
chain rule error in double prec
.
SSE2 GB
for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Linda
h
l
Merge br
a
nch 'release
-
4-5-patches' of
g
it
.
g
r
oma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lin
d
a
h
l
Dou
b
l
e precis
i
o
n SSE2
ker
n
els
fo
r
Generalized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
i
ndah
l
Upda
t
ed GB SSE2
kernels, te
s
t
ing in p
r
o
gress now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
inda
h
l
Mer
g
e bra
n
ch 'release-4-5-patches'
of git
.
g
r
o
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindahl
Modified at
o
m order in Amber
n
ucleotide i
m
p
rop
e
r torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Li
n
dahl
Mod
i
fied
i
m
proper torsion ato
m
or
d
er in
A
mber TRP residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
M
e
rge branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Li
n
dahl
F
i
x to
writ
e
GB and surface e
n
ergy to se
p
arate
t
erms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
M
e
r
ge b
r
anch 'release-4-5-patches'
o
f
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Enabled d
o
uble precision al
l
-vs-all ke
r
nels
.
T
ested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
F
i
xed
s
im
p
le typo
in l
a
st commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
F
ixed previo
u
s nasm-segv bug for intel
-
s
yntax SSE
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Li
n
dahl
F
i
xed 64-bit bug in SSE as
s
emb
l
y (
o
nly v
i
sible
with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Lindahl
Work
e
d
around an internal compiler error for M
S
VC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Li
n
dahl
M
e
rge branch 'release-
4
-5-patch
e
s'
o
f
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
Deprecated -ins opti
o
n to g_hb
o
nd sin
c
e nobody seem
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
indahl
Copied
all-
v
s-all change from x86-64 to ia32 kerne
l
s too
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
inda
h
l
Merge
b
ranch
'r
e
lease-4-5
-
patch
e
s' of
git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed pot
e
ntial error in cou
l
omb ener
g
y
, and maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
h
l
M
e
rge branch '
r
elease-4
-
5-patc
h
es' of g
i
t
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindah
l
Added
double
p
recision SSE2 generalize
d
born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Linda
h
l
Added ia32 all-vs-all kerne
l
s
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
indahl
Upda
t
ed autoconf to w
o
rk
with re
n
amed SS
E
2
x
86-64 as
m
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Re
n
amed SSE2
x
86-64 asm test file t
o
be
c
onsistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixe
d
typo to
detect bot
h
x
8
6_64-
>
i
3
86 and
i
386->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Mer
g
e br
a
nc
h
'r
e
lease-
4
-5-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
i
xed a namin
g
error introduc
e
d ye
s
t
erday in 32b
i
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Fixe
d
c
o
mpile
r
errors for MSVC
inline int
r
insics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik L
i
ndahl
Fixed ch
e
c
kp
o
i
nt problem in 32 b
i
t
s
.
We shou
l
d al
w
ays
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Removed extra TER records after c
h
ains we th
i
nk are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge bran
c
h 'release-4-5-patches' of
g
it
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixe
d
S
SE
k
ernels in
d
oub
l
e pr
e
cision f
o
r Cmake, wor
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik L
i
ndahl
Merge branch '
r
elease
-
4-5
-
pa
t
ches' o
f
gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
C
make an
d
Nasm support for windows
commit
|
commitdiff
|
tree
2010-08-10
Er
i
k
Li
n
dahl
Moved four more SSE a
s
sembly f
i
les
to
av
o
id do
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
ndahl
Merge bra
n
ch 'release
-
4-5-pat
c
hes
'
o
f
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
C
hanges to make Cmake work under windows
again
commit
|
commitdiff
|
tree
2010-08-10
E
r
i
k
L
indahl
Renamed intel synt
a
x assembly
f
iles
t
o
a
v
o
i
d d
o
uble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik
L
indahl
A
dded
NASM Cmake support
commit
|
commitdiff
|
tree
2010-08-10
E
rik
L
i
n
dahl
Merge br
a
nch 'release-4-5
-
patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
MAYBE a fix for Berk
'
s
H
eme prob
l
em
.
Needs test
i
ng
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Merge branch 'release-4-5-p
a
tc
h
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik
Lindahl
Added
NHE
as an Amber am
i
n
o
a
cid residue type
commit
|
commitdiff
|
tree
2010-08-08
Eri
k
Lin
d
ahl
Co
p
ied CK
-
CB-N*
-
CT Amber improp
e
r to als
o
list CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Merge branch 'release-4-5-p
a
tch
e
s' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik
Li
n
d
a
hl
Fixed incorrec
t
#endif -> #else
that ca
u
sed the C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik
L
i
n
d
ahl
Merge
branch
'
rele
a
se-4-5-pat
c
hes' of
g
it
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Eri
k
Lindahl
Fix
e
d
a bug
i
n index ge
n
er
a
t
i
on for non-adjacent protei
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixe
d
n
on
e
xist
e
nt return typ
e
on gmx_m
m
_si
n
cos_pd
commit
|
commitdiff
|
tree
2010-08-04
Eri
k
Lindahl
A
dded out i
n
t-
e
xtraction macro to double precision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Adde
d
dou
b
le precision SSE2 transcendental func
t
ions
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik L
i
n
d
ahl
Fi
x
e
d accu
r
ac
y
i
ss
u
es in gmx_mm_log_ps
(
), and
a
dd
e
d
.
.
.
commit
|
commitdiff
|
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2010-08-04
Erik
Lindahl
Adde
d
double
prec
i
sion SSE2 trans
c
endenta
l
fun
c
tions
.
.
.
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2010-08-04
Erik L
i
nd
a
hl
Fixed accur
a
cy issues in gmx_mm_log_
p
s(), a
n
d added
.
.
.
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