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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-27
Erik Lind
a
hl
M
e
rge branch 'relea
s
e-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindahl
Added
c
heck f
o
r SSE2 support
to use gen
e
r
a
lized born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ah
l
Ad
d
ed trjconv check for topology p
r
e
s
cence,
s
ee bugzilla
5
2
6
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
d
ah
l
Merge
b
r
anch 'r
e
l
e
ase-
4
-5-patch
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k
Lindahl
Fixed gmxc
p
p
to always use unix path se
p
arators i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindahl
Merge
branch 'release-4-5-patche
s
' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
ind
a
hl
F
i
xed
another
u
ninitia
l
ized vari
a
ble warning i
n
gmx_en
e
r
g
y
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Linda
h
l
Add current path (
.
/) to topol
.
top include when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Dont wri
t
e EOF
w
a
rnings to stdout
every
t
ime we
checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Merg
e
branch 'release-4-5-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik
Lindah
l
Fix
e
d first statem
e
ment
occur
i
ng
b
e
fore
v
ariable declaration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik
Lind
a
hl
Merge branch 'release-4-
5
-p
a
t
c
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lin
d
ahl
M
o
difi
e
d pdb2gmx to automaticall
y
p
i
ck the force f
i
eld
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik
L
indahl
F
ixed
pointer typo in
p
atch from Alexey Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
i
ndahl
A
d
d
ed PBC
c
h
e
c
king patc
h
to g_clus
t
er from Alexey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
erge branch '
r
ele
a
se-4-5-patches' o
f
git
.
gro
m
ac
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Modified
p
db2gmx t
o
not accept e
x
t
ra h
y
dro
g
e
n
at
o
ms
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Fixed include path in
v
mdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
Eri
k
Lindahl
Fo
r
go
t
to a
c
tual
l
y
do t
h
e char
-
>i
n
t change
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
inda
h
l
Chan
g
e
d
boo
l
to signed integer
instead of
unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Li
n
d
a
hl
Added missing heade
r
i
n
clude
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Merg
e
bran
c
h 'release-4-5-patches' of gi
t
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik Lindahl
Mad
e
sure
a
ll source fil
e
s hav
e
some copyri
g
ht hea
d
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindah
l
R
e
-ad
d
ed op
e
nmm pa
p
er
commit
|
commitdiff
|
tree
2010-08-24
Erik
L
inda
h
l
Mer
g
e b
r
anch
'release-
4
-5-patches' of git
.
groma
c
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Eri
k
Lindahl
Updated i
n
tel syntax x86-6
4
asm
files to
als
o
support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
indahl
Fixed
u
n
initiali
z
ed variable er
r
or
in
G
B kernel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lin
d
ahl
Fixed an
unsigned/si
g
ned
integer
comparison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fix
e
d
t
w
o
more
i
nstan
c
es of strca
s
ecmp->gm
x
_strcase
c
mp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cop
i
e
d
SSE
i
n
t
r
insics kernels from x8
6
-6
4
to ia3
2
commit
|
commitdiff
|
tree
2010-08-22
E
r
i
k
Li
n
d
ah
l
Replaced all
occurences of str(n)casecmp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lind
a
hl
Fixed stupid mistake where a statement was
p
laced before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Rep
l
aced t
e
sting
o
f git vers
i
on with te
s
t
i
n
g for feat
u
res
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
Fixed naming problems for double precision Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik
Li
n
d
a
hl
Fixed a t
y
po in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Merge branch 'r
e
le
a
s
e-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lindahl
C
l
e
aned
u
p
all install
e
d head
e
rs t
o
r
e
move
s
trict depen
d
ence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
L
i
ndahl
Removed some unnecessary
#
i
fdefs f
r
om string2
.
h;
all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
nda
h
l
Amber
force fields
n
ow pass validation
.
Beta status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik L
i
ndahl
Added F77
kernel setup he
a
der
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fi
x
ed synchronization cou
n
t
e
r up
d
ate for f77 kern
e
ls
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lind
a
hl
Fixed
a bug for GB
O
BC born r
a
dius calculatio
n
in
S
S
E2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
Fixed an un
i
nitialized variab
l
e
bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Linda
h
l
Fixed a minor bug that caused Fortr
a
n builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik
L
indahl
D
o
nt write nonpol
a
r sur
f
ace energy to energy
file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Linda
h
l
Fixed so Fortran kernel
s
work
a
gain
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lindahl
Upgraded to latest autoco
n
f
platform dete
c
ti
o
n scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik
Linda
h
l
Fixed a chain rule error in
d
ouble prec
.
SS
E
2 G
B
for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
Merge branch 'releas
e
-
4
-
5
-patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Lindahl
Double pre
c
i
sion SSE2 kernels for Generalized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
Updated
G
B
SSE2 k
e
rnels,
testing in progress
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Merge br
a
n
ch
'release-4-5-patches' of
gi
t
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modifi
e
d
atom order in
A
mber nucleotide im
p
rope
r
torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modified imp
r
o
per t
o
rsion atom or
d
er
i
n Amber TRP
r
esidues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
M
erge
branch '
r
elease-4-5
-
patche
s
' o
f
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fix to write GB and surfa
c
e energy to
sepa
r
ate t
e
rms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge br
a
nch 'releas
e
-4-5-
p
atc
h
es'
of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
L
in
d
ahl
Enabled double
prec
i
sion all-vs-all
kernels
.
Te
s
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Lindahl
Fix
e
d
si
m
ple
t
ypo
in last commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
F
i
xed previous nasm
-
s
e
gv bug
f
or intel-sy
n
ta
x
SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik Lind
a
h
l
F
i
x
ed 64
-
bit bug in SSE
a
ssembly
(only visibl
e
with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Worke
d
around an int
e
r
n
al compiler
erro
r
for MSVC
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lind
a
h
l
Merge bra
n
c
h 'relea
s
e-4
-
5-p
a
t
ches'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
De
p
recated -ins option to g_hbond si
n
ce nobody seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Copi
e
d al
l
-
vs-all
chan
g
e from
x
86
-
6
4
to ia32 kern
e
ls too
commit
|
commitdiff
|
tree
2010-08-17
Erik Lin
d
ahl
Merge bra
n
ch 're
l
e
as
e
-4-5-p
a
tches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k Lindahl
Fixed potential
error in coulomb ener
g
y
, and
m
aybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindah
l
Merge
branch 'rel
e
a
s
e-4-5-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
A
dded dou
b
le precisio
n
SSE2 gen
e
ralized born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Ad
d
ed ia32 all-vs
-
all kernels
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Updated autoconf to work wi
t
h r
e
named SSE2 x86-
6
4
asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Linda
h
l
Rena
m
e
d
SSE2 x86-64 asm test
file
to be consist
e
nt
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik L
i
n
d
a
h
l
Fixed t
y
po to detect bot
h
x86_64->i386 and i386->x86
_
64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge branch 'release-4
-
5-p
a
tches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed a naming error introduced yeste
r
day i
n
32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Linda
h
l
Fixed compile
r
errors for MSVC inline intrinsic
s
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
inda
h
l
F
i
x
ed checkpoint proble
m
i
n
32
b
its
.
W
e should
a
l
w
ays
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
L
i
nd
a
hl
Removed ex
t
ra TER record
s
af
t
er chains w
e
think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
i
k L
i
ndahl
Merge branch 're
l
ease-4-5-patc
h
es' of git
.
g
roma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
i
x
ed SSE kernels
i
n
double
p
r
ecision
f
or
Cmake, w
o
r
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Merge bran
c
h 'release-
4
-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Eri
k
Lin
d
ahl
Cmak
e
and Nasm suppor
t
f
or
windo
w
s
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Moved four
m
ore SSE a
s
sembly files to avoid do
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
n
dahl
Merge branch
'
rel
e
a
se-4-5-patches' of
git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
ndahl
Changes to make
C
ma
k
e
work under
windows again
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
nd
a
h
l
Rena
m
ed int
e
l
syntax assembly
files to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
L
i
ndahl
Added NASM
Cmake supp
o
rt
commit
|
commitdiff
|
tree
2010-08-10
Erik
Linda
h
l
Me
r
ge branch 'release-4-5-pat
c
hes' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
MAYBE a fix for
Berk's
Heme p
r
oblem
.
N
e
eds testing
commit
|
commitdiff
|
tree
2010-08-08
Erik Lind
a
hl
Merge b
r
a
n
ch 'release-4-5-p
a
t
c
hes' of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik Li
n
dahl
Added
NHE as an Amber aminoaci
d
r
e
sid
u
e
type
commit
|
commitdiff
|
tree
2010-08-08
E
rik Li
n
dahl
Copied
C
K-CB-N*-C
T
Amber
i
mproper to al
s
o list CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
M
erge
branch
'rele
a
se-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Fixed incorr
e
ct #
e
ndif -
>
#els
e
t
hat caused the C
all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Merge br
a
nch 'release-
4
-5-pat
c
h
e
s
'
o
f
git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik L
i
ndahl
Fixed a bu
g
in i
n
d
ex generation
f
o
r non-adjacent protein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixed nonex
i
stent
r
e
turn
t
ype
on gmx_mm_s
i
ncos_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik Lind
a
hl
Added
o
ut int-extraction macro to double precision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Add
e
d double p
r
e
cision SSE2 tr
a
n
sc
e
ndental fu
n
c
t
ions
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
rik Lindahl
Fixed acc
u
racy issues in gmx_
m
m_lo
g
_
p
s(
)
, and a
d
ded
.
.
.
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