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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-25
Erik L
i
ndahl
Merge
b
r
an
c
h 'rele
a
se-4-5-patches' of git
.
gromac
s
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
ri
k
L
i
ndahl
Made sure all sour
c
e files
h
a
v
e
s
ome
c
opyright header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik
Linda
h
l
R
e-adde
d
o
penmm paper
commit
|
commitdiff
|
tree
2010-08-24
Er
i
k Lindah
l
Merge branch 'release-4-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Eri
k
Lindahl
Updated
intel
syntax
x
8
6-64 asm files to al
s
o
s
upport
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
nd
a
h
l
F
i
xed
uninitializ
e
d variable
e
rror in GB kernel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
ixed an unsigned/sig
n
ed integer co
m
p
a
ri
s
on
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
ixed two more inst
a
n
ces
of strcasecmp->gmx_strcase
c
mp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cop
i
ed SSE intrins
i
cs ke
r
ne
l
s f
r
o
m x86-64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindahl
Replaced all occuren
c
es
o
f
str
(
n)casecmp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik L
i
nda
h
l
F
i
xe
d
stupid mistake
w
h
ere a statemen
t
was plac
e
d before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindahl
Repla
c
ed t
e
s
ting of git version
wi
t
h testi
n
g for fea
t
ures
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindah
l
Fixed naming
p
roblems for double precision For
t
ran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed a typo
in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lind
a
hl
Merge branch 'r
e
leas
e
-4-5-patc
h
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cleaned up al
l
installed headers to r
e
move strict depende
n
ce
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindah
l
Remov
e
d
some
unnecessar
y
#ifdefs from str
i
ng2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Li
n
dahl
Amber force fi
e
lds n
o
w pass
v
a
lidation
.
B
eta statu
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Added
F77 kerne
l
se
t
up
h
e
a
d
e
rs
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed synchronization counter upd
a
te for f
7
7 kernels
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fi
x
ed a bug
for GB OBC
b
orn radius
calcul
a
tion in SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
L
i
ndahl
Fixed an uninitial
i
zed variable bu
g
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindah
l
Fixe
d
a minor bug that caused Fortran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik
Lindahl
Do
n
t writ
e
nonpolar s
u
rface
e
nergy to energy file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed so Fortran ke
r
nels wor
k
again
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Li
n
da
h
l
Upgraded to latest autoconf
p
l
a
tf
o
rm detection
scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
d
a
hl
Fixed a chain r
u
le error in double prec
.
SSE2 GB f
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k L
i
n
d
ahl
Merge branch
'release-4-5-patches'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
dahl
Double p
r
e
c
ision
S
S
E
2 kernels for Gene
r
alized Bo
r
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Upd
a
ted G
B
S
S
E2 kernels, te
s
t
i
n
g
i
n
progress
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lin
d
ahl
M
erge bra
n
ch 'rel
e
as
e
-4-5-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Modified a
t
om or
d
er in Amber nucleotide improp
e
r tors
i
ons
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modified
improper torsion ato
m
orde
r
i
n
Ambe
r
TRP residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik L
i
ndahl
M
e
rge bran
c
h 'release
-
4
-5-p
a
tches' o
f
git
.
g
romacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Lind
a
hl
F
i
x
to
w
rite G
B
an
d
surface energy to
s
eparate t
e
r
ms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Merge branch 'release-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Enabled
d
o
uble precis
i
on all-vs-
a
ll kernels
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Linda
h
l
Fi
x
ed si
m
ple typo in
l
ast
commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
hl
Fixed prev
i
ous nasm-seg
v
bug for intel
-
s
yntax SSE i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
i
k Linda
h
l
Fixed 64-bit bu
g
in
S
SE assembl
y
(only visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
indahl
Wor
k
e
d around an internal compiler error for
MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
L
i
ndah
l
Merge branch '
r
elease
-
4-5-patches' of gi
t
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecated -ins option t
o
g_hbond since
n
o
b
o
dy seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Copied all-vs-al
l
change fr
o
m
x86-6
4
to ia32 kernels too
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik Lindahl
Merge branch 'release-4-5
-
patches
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik Lindahl
F
ixed potential error
in coulom
b
en
e
r
gy, and ma
y
be
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Merge br
a
n
ch 'release-4-5-p
a
tches' of
git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Added double precisi
o
n
S
S
E
2
gener
a
lized born kernel
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Ad
d
ed ia32 all-vs
-
all
kernels
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Updated a
u
toconf
to wo
r
k with renamed
SSE2 x86-6
4
as
m
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
Lindahl
Ren
a
m
e
d SSE2 x86-6
4
asm
t
e
st file
to
b
e
consis
t
ent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Fix
e
d typ
o
to detect bo
t
h x86_64->i386
and i
3
86->x
8
6_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Merge b
r
anch 'release-4-
5
-
p
atches
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Fixed a n
a
ming
erro
r
intr
o
duced yesterday in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik L
i
ndah
l
Fixed comp
i
ler
errors for
M
S
VC inline intrinsic
s
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed chec
k
point problem in 32 bits
.
We should a
l
w
ay
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Removed
e
x
tra TER re
c
o
rds after chains
w
e thi
n
k a
r
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Mer
g
e b
r
anch 'release-4-5-patc
h
es' of
g
i
t
.
gro
m
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
ixed SSE
k
ern
e
ls in double pr
e
c
i
sion for Cmake, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Er
i
k Lindahl
Mer
g
e bra
n
ch 'relea
s
e-4-5-patches' o
f
git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Cmake and Nasm support fo
r
wind
o
ws
commit
|
commitdiff
|
tree
2010-08-10
Erik
Linda
h
l
Mov
e
d four m
o
re
S
S
E a
s
sembl
y
files t
o
avoid do
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
M
e
rge
br
a
n
c
h 'release-4-5-patches' of gi
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Change
s
to
m
ake Cmake work
under w
i
n
d
ows aga
i
n
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik
Lindahl
R
ename
d
intel syntax assem
b
ly f
i
l
e
s
to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
E
rik Lindahl
A
dde
d
NASM
C
m
ake support
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge b
r
anc
h
'release-4-5
-
pat
c
hes' of git
.
gromac
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
L
i
ndahl
MAYBE a fi
x
for
B
erk's
Heme p
r
oble
m
.
N
e
eds testing
commit
|
commitdiff
|
tree
2010-08-08
E
rik
L
indahl
M
erg
e
branch '
r
elease-4
-
5-pa
t
ch
e
s
'
of gi
t
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
E
r
ik
L
in
d
ahl
A
d
ded NHE as a
n
A
m
ber
am
i
noacid residue type
commit
|
commitdiff
|
tree
2010-08-08
E
r
ik Lindahl
Co
p
ied CK-CB-N*-C
T
Ambe
r
improper
t
o also l
i
st CK-
C
B
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindah
l
Merge b
r
a
nch 'r
e
lea
s
e-4-5-patc
h
es'
o
f git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik L
i
ndahl
Fixed inc
o
rrect #endif ->
#
else
that caused the C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Merge branch 'release-
4
-5-patches' o
f
git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Er
i
k L
i
ndahl
Fixe
d
a bug in ind
e
x
generati
o
n for non-adjacent
protein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lin
d
ahl
Fixed
n
onexistent return type on gm
x
_m
m
_sincos_pd
commit
|
commitdiff
|
tree
2010-08-04
E
r
i
k
L
i
ndahl
Added out i
n
t-ex
t
raction macro to
d
ouble precision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lindahl
Adde
d
double precisi
o
n SSE2 tr
a
nscendental f
u
nctions
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Linda
h
l
Fixed
accuracy issue
s
in gmx_mm_
l
og_ps(),
a
nd added
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindahl
Merge branch 'r
e
lease-4
-
5-patches' of
g
i
t
.
g
roma
c
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindahl
Modified TE
R
record writing be
h
aviour (only add after
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
E
r
ik Linda
h
l
Merge bran
c
h 'relea
s
e-4
-
5
-
p
atches
'
of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k Li
n
dahl
Fi
x
e
d
build
i
ssue
f
o
r
t
e
mplat
e
program in double precision
commit
|
commitdiff
|
tree
2010-08-02
Erik
Lindahl
Rem
o
v
e
d unused variable t
h
a
t cau
s
ed a warning
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindahl
Temporarily
disabled double pr
e
ci
s
i
o
n SSE
2
gen
e
ralized
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Linda
h
l
Fi
x
ed error in (unused) SSE2 doub
l
e
p
rec
i
sion inline
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lindahl
Modif
i
e
d index proce
s
sin
g
to
r
einstate residue-split
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik L
i
n
dahl
Added ion
c
lasses to residu
e
types
.
dat
commit
|
commitdiff
|
tree
2010-07-30
E
r
ik Lindahl
M
erge
b
ranch 'maste
r
' of
g
it
.
g
romacs
.
or
g
:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindah
l
Rep
l
aced non-thread-safe cal
l
s
t
o ctime(
)
wit
h
our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k Lindahl
Added po
r
ta
b
le gmx_
c
time_r() to enable
r
epla
c
ement
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
ndahl
M
erge branc
h
'master' of
g
it
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Replaced localt
i
me with loca
l
time_r() on
unix
an
d
localti
m
e_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
ndahl
Merge branch 'master' o
f
g
i
t
.
groma
c
s
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik
Lind
a
hl
Replaced readdir(
)
w
i
t
h readdir
_
r
() t
o
avoid future
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge branch
'ma
s
t
er' of g
i
t
.
gromacs
.
or
g
:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lin
d
ahl
Ported x86-64 si
n
gle precision SSE2 al
l
-vs-all p
a
t
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
E
r
ik
Lindahl
Com
m
ente
d
out calls to double p
r
ec
.
SSE2 all-vs-
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k Lindahl
Worked
a
ro
u
nd cross-i
n
clusion problem between g
r
o
mpp
.
.
.
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2010-07-29
Erik Lindahl
Rem
o
ved deprecated nsb
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h header
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