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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-27
Eri
k
Lind
a
hl
Me
r
ge
branch 'release-4-5-patche
s
' of git
.
grom
a
c
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
A
d
d
e
d
ch
e
c
k for SSE2 support to u
s
e generalized born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
Added trjcon
v
check for topolo
g
y
prescence, see bug
z
illa 526
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k Lindahl
M
e
rge bra
n
ch 'release-4-5-patches' of git
.
gro
m
ac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
da
h
l
Fixed gm
x
cpp to always use
unix path separators
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindahl
Merg
e
branch
'
release-4-5-patches' of gi
t
.
gr
o
macs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Li
n
dahl
Fixed another uniniti
a
lized variable wa
r
ning in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lin
d
ahl
Add cur
r
e
nt path (
.
/) to topol
.
top include when forc
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Dont
write
EOF warnings to std
o
u
t
e
very time we checkpoin
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Merge branch 'release-4-5-patches
'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k Lindahl
Fixed first st
a
temem
e
nt
o
c
curing before variable d
e
cla
r
a
tion
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Merge branc
h
'r
e
lease-4
-
5-patches'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik L
i
ndahl
Modifi
e
d pdb2gmx to automa
t
ic
a
l
ly
p
ick the force fie
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k L
i
n
d
ahl
Fixed poin
t
er typo in patch from Alexey Shvets
o
v
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Added PBC
check
i
n
g
patch to g_cluste
r
from Alexey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Li
n
dahl
Merge branch 'release-4-5-patches' of g
i
t
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Mo
d
ified pdb2gmx to not accept ex
t
ra
h
ydrogen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
i
k Lindahl
Mer
g
e
b
ranc
h
're
l
ease-4-5-patches
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
i
n
d
ahl
true
/
false
i
nput setti
n
gs sh
o
uld be c
a
ll
e
d bool inst
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge
br
a
nch '
r
el
e
ase-4-5-patches' of
git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
Rev
e
r
t "Made pdb2gmx
b
e
s
lightly more helpful when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Update
d
comp
l
etion
s
for 4
.
5
r
e
l
ease
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Made /usr/local/g
r
omacs defaul
t
i
nstallation path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
U
p
dated htm
l
d
o
cumentation for
r
e
le
a
se 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
in
d
ahl
Up
d
ate
d
manual pages, no
w
with corre
c
t v
e
rsion (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
Fi
x
f
or
w
arning in
ngmx
mak
e
f
il
e
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
C
ha
n
g
e
d ve
r
sion to beta4
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
Updated scri
p
ts
t
o p
r
oduce
4
.
5
m
a
n pages
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lindahl
Upd
a
ted
m
anpages
for
4
.
5
r
elea
s
e
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Remove
d
u
s
eless g_
l
ogo and
g
_highway p
r
o
gr
a
ms from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
g_kinetics
rem
o
v
ed from au
t
omatically
b
u
ilt programs
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Fixed include path in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lind
a
hl
Forgot to actuall
y
do the char->int c
h
ange
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
in
d
ahl
C
hange
d
bool to si
g
ned integer ins
t
ead of
unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Added missing
header
i
nclu
d
e
commit
|
commitdiff
|
tree
2010-08-25
Erik Linda
h
l
M
erge branc
h
're
l
eas
e
-4-5-patches' of git
.
grom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Eri
k
Lind
a
hl
Made sure all
sour
c
e fil
e
s
have
so
m
e copyright header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
r
ik Lin
d
ahl
Re
-
a
dde
d
openmm paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Merg
e
branch 'release
-
4-5-patc
h
es' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Eri
k
Lindahl
U
p
da
t
ed
i
ntel syntax x86-64
a
sm files to also support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Lind
a
hl
Fixed
uniniti
a
lized variable
error in GB kern
e
l wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
F
ixed an u
n
signed/signed integer
c
omparison
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
F
i
xed two m
o
re insta
n
ces of strc
a
secmp->gmx_s
t
rcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Li
n
dahl
C
opied
SSE int
r
insics kernels from x86-64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndah
l
R
e
p
laced
a
l
l
occurences of st
r
(n)casecmp wi
t
h gm
x
_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
i
xed st
u
pid mistake where a statement was place
d
be
f
o
re
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Replaced t
e
s
ting of git versio
n
w
i
th
t
esting for f
e
atures
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
n
aming pr
o
blems
for double precis
i
on F
o
rt
r
an
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik
L
i
n
dahl
Fixed a typo in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
n
da
h
l
Merge
b
r
a
nch 'release-4-5-
p
atches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
C
l
e
a
ned
up
all ins
t
a
l
led
h
e
a
ders
to remove
s
trict depen
d
ence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Rem
o
ved some
un
n
ecessar
y
#ifdefs from string2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Li
n
d
ahl
Amber force fie
l
ds now pass validation
.
Bet
a
status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
d
ahl
Adde
d
F
77 kernel set
u
p head
e
rs
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Fixed sy
n
chroniz
a
tion
c
o
unter
u
pdate for f77 kernels
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Li
n
dahl
Fixed
a bug for GB OBC born radius calculation in SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fixed an un
i
nit
i
alized variable bug
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
ndahl
Fi
x
ed a minor bug t
h
a
t caused Fortran builds
to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
Do
n
t write
nonpola
r
surface e
n
ergy
to ener
g
y file i
f
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
a
h
l
Fixed so For
t
ran kernels work again
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
ndahl
U
pgraded to latest autocon
f
platform
d
et
e
ction script
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindah
l
Fixed a
chain rule error i
n
dou
b
le p
r
ec
.
SSE2 GB f
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Merge branch 'r
e
lease-4-5-patches'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Lin
d
a
h
l
D
o
uble precision SSE2 kernels for Ge
n
er
a
lized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
i
ndahl
U
pdat
e
d GB SSE2 kern
e
ls, testing in
progress no
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Me
r
ge
branc
h
'release-4-5-
p
atches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modified ato
m
order in Amber
n
ucleotide imprope
r
t
o
r
sions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Li
n
dahl
M
odified imprope
r
t
o
rsi
o
n a
t
om
o
r
d
er
i
n Amber
T
RP
r
esi
d
ues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
ind
a
hl
Merge branch
'releas
e
-4-5-pat
c
hes' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fix to write GB and surfa
c
e energy to
separat
e
t
e
rms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Merge
b
ranch
'relea
s
e-4-5-patches' of gi
t
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Enable
d
doubl
e
precision al
l
-vs-all
k
e
r
n
e
ls
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lindahl
Fixed simple
typo i
n
l
a
st c
o
mmit
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
L
indah
l
Fi
x
e
d
p
r
evious nasm-segv bug for
i
nt
e
l
-
s
y
ntax S
S
E in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Li
n
dahl
Fixed 64-bi
t
b
ug in
S
S
E assemb
l
y
(only visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lind
a
hl
Worked around an
i
nternal
c
ompile
r
error
f
or
M
SVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Merge
b
ranch 'release-4-5-pat
c
hes' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecate
d
-ins option to g_h
b
ond since no
b
ody seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
C
o
p
ied all-vs-all
c
h
ange fro
m
x
8
6
-64 to
i
a
3
2
k
erne
l
s too
commit
|
commitdiff
|
tree
2010-08-17
Erik L
i
ndahl
Me
r
ge branch 'relea
s
e-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
F
ixed p
o
tentia
l
e
r
ror in coulom
b
energy, and
m
aybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik L
i
ndahl
Merge bra
n
ch
'r
e
l
ease-4-5-p
a
tches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lindahl
Added
doub
l
e precisio
n
SSE2 generalized born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Added ia32 all-
v
s-a
l
l
k
er
n
els
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Updated autoco
n
f to wor
k
with re
n
amed SSE
2
x86-
6
4 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
R
e
nam
e
d
SSE2 x
8
6
-64 asm test file to b
e
consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
Fixed typ
o
to detect bo
t
h x
8
6_64->i386 and
i
3
8
6->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge
b
r
a
nch
'
rel
e
ase-4-5-p
a
tches'
of git
.
gro
m
ac
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Fixed a naming
error introduced yest
e
rday in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fix
e
d
compiler errors for MS
V
C
inline int
r
ins
i
cs
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
a
h
l
F
ixed checkpoint problem
i
n 3
2
b
i
ts
.
W
e should always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Re
m
oved
extra T
E
R records after
ch
a
ins we think a
r
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Mer
g
e bran
c
h 'release
-
4
-
5-pa
t
ches' of git
.
grom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindah
l
F
ix
e
d SS
E
kernels in double precision
f
or Cmak
e
, worki
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
E
rik L
i
ndahl
Merge branch 'release
-
4-
5
-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lind
a
hl
Cmake an
d
Nasm support for w
i
n
d
o
ws
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
ndahl
M
o
v
ed f
o
ur
more
S
SE as
s
em
b
ly files to avoid doubl
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lin
d
ahl
M
erge bra
n
ch 'releas
e
-4-5-patches' of git
.
g
ro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Li
n
da
h
l
Chan
g
es to mak
e
Cmake work u
n
der win
d
ows
a
gain
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2010-08-10
E
rik Lindahl
R
ename
d
intel s
y
nta
x
assembly files to avoid do
u
ble
.
.
.
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