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Changed bool to signed integer instead of unsigned char.
2010-08-25
Erik Lindahl
Ch
a
nged b
o
ol to s
i
gned integ
e
r instead of unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik Lindahl
Added missing h
e
ader include
commit
|
commitdiff
|
tree
2010-08-25
Erik Li
n
d
a
hl
Merge branc
h
'release-
4
-
5
-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Made
sure all source files have some copyright he
a
der
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lind
a
hl
Re-added
openm
m
paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lin
d
ahl
Merge bran
c
h
'releas
e
-4-5-patches
'
of
git
.
groma
c
s
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
r
i
k Lindah
l
Updated inte
l
syn
t
a
x x86-6
4
a
s
m
fi
l
es
t
o also support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lindahl
Fixed
u
ni
n
itial
i
z
e
d var
i
able error in GB
kernel wit
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindahl
Fixed
a
n uns
i
gned
/
sig
n
e
d
int
e
ger comp
a
rison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed tw
o
more
i
n
stances
of st
r
casecmp->gmx_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Copied
S
S
E intrinsic
s
k
e
rn
e
ls fro
m
x86-64 t
o
ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Rep
l
aced all occurences of st
r
(n)ca
s
e
c
mp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik
Lin
d
ahl
Fixed stupid mistake where a statement was plac
e
d before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Repl
a
ced
t
est
i
ng of
git v
e
rsion
w
ith testing
f
or feat
u
res
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
i
n
dahl
Fixed naming pr
o
blems for double precis
i
on Fortr
a
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindahl
Fixed
a typo in
futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Linda
h
l
Merge branch 'release-4-5-
p
atc
h
es' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cleaned u
p
a
ll inst
a
l
l
ed hea
d
ers t
o
remove strict dependence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Remo
v
ed s
o
me
u
nn
e
ce
s
sary #ifdefs f
r
om string2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
ri
k
L
i
ndahl
Am
b
er force fiel
d
s
now pass valid
a
tion
.
B
e
ta st
a
tus
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lindahl
Ad
d
e
d
F77 kernel setup head
e
rs
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lin
d
ahl
Fixed sync
h
ro
n
ization counter update for f
7
7
k
ern
e
l
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a bug for GB
OBC born radius c
a
lculation in
S
SE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
i
k Lindahl
Fixed
a
n
uninitiali
z
ed
v
ar
i
ab
l
e bug
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
Fixe
d
a mi
n
o
r bug that caused F
o
rtran
b
uil
d
s to f
a
il
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Dont w
r
ite nonpo
l
ar surface e
n
ergy to energy fi
l
e i
f
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed s
o
For
t
ran
k
ernels work again
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lind
a
hl
Upgrad
e
d to latest autoconf platf
o
rm de
t
ection scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
Fixed a chain ru
l
e error
i
n
d
ouble prec
.
SSE2 GB for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
Merge branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
D
o
uble precision
S
SE
2
k
e
rnels for General
i
z
ed Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Upda
t
ed GB SSE2
kernels
,
te
s
ting in pr
o
gr
e
ss
n
ow
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
i
k
Lindahl
M
erge branch 'r
e
lease
-
4-5-pa
t
ches' o
f
git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
M
odified atom
order in Amb
e
r nucleotid
e
improper tor
s
ions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
ndahl
Modified improper torsion atom order in Amber TRP resid
u
es
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge
b
ranch 'release-
4
-5-pat
c
hes' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
F
i
x
to write GB and surface energy to separa
t
e ter
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Li
n
dahl
Merge branch '
r
elease-4-
5
-
patch
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Enabled
d
ouble precision all-vs-all kernels
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik
Lindahl
Fixe
d
simple typo in
last commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
hl
F
ixed pre
v
i
o
us n
a
sm-segv
b
ug for
i
ntel-synta
x
S
SE
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lindahl
Fixed 64
-
bit bug
i
n SSE
a
sse
m
bly
(
only visible
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Linda
h
l
Worked around an internal
c
o
mpiler error for MSVC
w
hen
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
L
i
ndahl
Merge branch
'
release-4-5
-
pat
c
h
es
'
of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k Lindahl
Dep
r
e
c
ated
-
i
ns optio
n
to g_h
b
ond
since n
o
body seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k
L
indahl
Copied all-vs-all change from x86-64 to ia32 ke
r
nels too
commit
|
commitdiff
|
tree
2010-08-17
Erik L
i
ndahl
Merge branc
h
'relea
s
e-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
i
k L
i
n
d
ahl
Fix
e
d
potential error i
n
coulomb energy, a
n
d
maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Merge
b
ranch 'relea
s
e
-4-5-patches'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Added d
o
ub
l
e pr
e
c
ision SSE2 gen
e
ralized born ker
n
els
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
A
dded ia
3
2 all-v
s
-all
ke
r
nels
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
U
p
dated
autoconf to work w
i
th rename
d
S
S
E2 x86
-
64 as
m
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
R
e
n
amed S
S
E2
x
86-64 asm test file to be consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik
Lindahl
Fixed typo to detect
both x
8
6
_64->i386 and i386->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
L
i
n
d
a
hl
Merge branch
'relea
s
e-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Fixed a naming e
r
ror introduced yest
e
r
d
ay in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed compi
l
er err
o
rs fo
r
MSVC inline intrinsics a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Li
n
dahl
Fixed checkpoint
p
roblem
in 3
2
bits
.
W
e
should
always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Re
m
oved
e
x
tra TE
R
re
c
ords after chains
we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Merge branch
'release-4-5-pat
c
hes' of
git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Fix
e
d SSE k
e
rne
l
s in double precisi
o
n for
Cmake, wor
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
E
ri
k
Li
n
d
a
hl
Me
r
ge branch 'release-4-5-patches' o
f
git
.
g
r
omacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
E
rik Lind
a
hl
C
m
ake and Nasm suppo
r
t for wi
n
dows
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Moved
four more SSE assembly files to a
v
oid
d
ouble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Lin
d
ahl
Merge branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik
L
indahl
Changes to make Cmake work under windo
w
s again
commit
|
commitdiff
|
tree
2010-08-10
Erik
Li
n
dahl
R
enamed in
t
el syntax as
s
embly fil
e
s to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik
Lindahl
Added NASM Cmake
sup
p
ort
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Lindahl
Merge
b
ranch 'rele
a
se-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Er
i
k Linda
h
l
MAYBE a fix
f
or Berk
'
s Heme
p
roblem
.
Needs test
i
ng
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
M
erge branch 'release
-
4-5-pa
t
c
h
e
s'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik
Lindahl
Added NHE as an A
m
ber aminoacid
r
esidue type
commit
|
commitdiff
|
tree
2010-08-08
Er
i
k Lindahl
C
o
pied CK-CB-N*-CT Am
b
er improper to also list CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Er
i
k
Lind
a
hl
Merge branc
h
'release
-
4-5-
p
atches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Fix
e
d incorre
c
t #endif -> #els
e
t
hat caused the C
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Eri
k
Li
n
d
ahl
Mer
g
e b
r
a
nch 'release-4-5-patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixed a b
u
g in
i
ndex generation for non-adjacent protein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
rik L
i
n
dahl
Fix
e
d n
o
n
e
xistent return type on
gmx_mm_sincos_pd
commit
|
commitdiff
|
tree
2010-08-04
E
rik Lindahl
Added out int-extraction macro to
d
o
u
ble precision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lin
d
ah
l
Added doubl
e
precision SS
E
2 transc
e
n
d
ental
f
u
n
ctions
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lind
a
hl
Fi
x
ed accuracy issues in gm
x
_
mm_log_ps(), an
d
added
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Eri
k
Lindahl
Merge bra
n
ch 're
l
ease-4
-
5-pat
c
h
e
s' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lin
d
ahl
Modifie
d
TER r
e
c
o
rd writing behaviour (only add
a
fter
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Eri
k
L
indah
l
Merge branch '
r
elease-4-5
-
patches'
of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
E
rik
Li
n
dahl
F
i
xed buil
d
i
s
sue for templa
t
e pr
o
gram in do
u
ble precision
commit
|
commitdiff
|
tree
2010-08-02
Erik
L
indahl
Removed un
u
sed variab
l
e
that cause
d
a warning
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k Linda
h
l
Tempora
r
i
l
y di
s
abled double precision SSE2 generali
z
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindahl
F
ixed error in (unused) SS
E
2
d
oubl
e
p
r
ecision
i
nline
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lindahl
Mod
i
fied index proces
s
ing to rei
n
stat
e
r
es
i
due-
s
plitting
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lindahl
A
d
ded ion
c
lasses to residue
t
ype
s
.
d
at
commit
|
commitdiff
|
tree
2010-07-30
E
r
ik
L
i
ndahl
Merge branch 'master' of g
i
t
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-30
E
r
ik Lindahl
Replaced non-t
h
read-safe
calls to c
t
ime(
)
with our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
E
rik Lindahl
A
d
d
e
d por
t
able gmx_ct
i
m
e
_
r() to
e
n
a
b
le replac
e
ment
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge branch
'master
'
o
f
gi
t
.
gromacs
.
org:gr
o
mac
s
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Replaced
l
ocaltime w
i
t
h l
o
calt
i
me_r()
o
n
uni
x
and
l
ocalt
i
me_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge
b
r
anch
'
m
a
s
ter' of
gi
t
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k L
i
nda
h
l
R
e
placed readdir(
)
with readdir_r() to
a
voi
d
futur
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik
Li
n
dah
l
Merge b
r
anch '
m
ast
e
r' of gi
t
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
ndahl
Port
e
d x86-64 single
p
r
e
c
i
s
ion
S
SE2 all-vs-all patch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Commented o
u
t
calls to double
p
r
ec
.
SSE2 all
-
vs-al
l
.
.
.
commit
|
commitdiff
|
tree
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