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Updated intel syntax x86-64 asm files to also support MS win64 call convention (ifdef...
2010-08-24
Erik Lindahl
Updated i
n
tel syn
t
ax x86-64 asm files to also sup
p
ort
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed uninitializ
e
d
variable error in G
B
kernel wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik L
i
ndahl
Fixed
a
n u
n
signed/signed integer comparison
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lindahl
Fixe
d
t
w
o
more instances of str
c
asecmp->gmx_strcas
e
c
m
p
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
C
opied SS
E
i
n
trinsics kerne
l
s from x
8
6-64
t
o ia3
2
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Replaced
all
occurences of str(n)casecmp with
g
m
x_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lin
d
ah
l
Fixe
d
stupid mi
s
take where a sta
t
ement w
a
s placed
before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
i
ndahl
Rep
l
aced testing of
git
ver
s
io
n
with test
i
ng fo
r
fe
a
tures
commit
|
commitdiff
|
tree
2010-08-22
E
rik
Lindahl
Fi
x
ed naming problems fo
r
double pr
e
c
i
sion Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lindahl
Fixed a
t
ypo in f
u
til
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
M
e
rge bran
c
h
'rele
a
se-4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lind
a
hl
Cleaned up a
l
l insta
l
le
d
headers to remove strict
d
ependence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Removed some u
n
nece
s
sary #i
f
defs
f
rom string2
.
h;
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Amber f
o
rce f
i
elds now pass valida
t
ion
.
Beta status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ah
l
Added F77 kern
e
l setup headers
commit
|
commitdiff
|
tree
2010-08-21
E
rik Li
n
da
h
l
Fix
e
d synchronizat
i
o
n counter update for
f
77
k
ernels
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a
b
ug
for GB OBC born
r
adius
c
a
l
culati
o
n in
SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
n
dahl
F
i
xed an uninitialized variable bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
F
i
xed a minor bug
t
hat cau
s
ed
Fortran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
Do
n
t write no
n
polar surface en
e
rgy to energ
y
f
i
le
if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lindahl
F
i
xed so Fortran ke
r
nels work
again
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Li
n
da
h
l
Upg
r
aded to latest autoconf platform
d
etection scri
p
t
s
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
F
i
xed
a chain rule e
r
r
or in dou
b
le
p
rec
.
SSE2 GB for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Merge
b
r
anch '
r
e
lease-4-5-patches' o
f
gi
t
.
g
r
omacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Doubl
e
p
r
ecisi
o
n
SSE2 ker
n
els f
o
r
Generalized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Updated GB SSE2 kernels, te
s
t
i
ng i
n
progress now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindahl
Merg
e
branch 'release-
4
-5-patches' o
f
git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Modifi
e
d atom order in Amber nucleotide i
m
proper torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
h
l
M
o
dif
i
e
d
improper torsion atom o
r
de
r
in Amb
e
r TRP
residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
hl
Merge bran
c
h
'release-4-5-patches'
of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Fix to write GB a
n
d surface e
n
ergy to sepa
r
at
e
terms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
n
d
ahl
Merge branch
'release-4-5-patches
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Enabled double p
r
ec
i
sion all-vs-all kern
e
ls
.
Test
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik L
i
n
d
ahl
Fixed simple typo
in last
c
ommit
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lind
a
h
l
Fixed previous
n
as
m
-segv
b
u
g for inte
l
-synta
x
SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed 64-bit
bug
in
S
SE assembly (only
visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik Li
n
dahl
Wor
k
ed arou
n
d an
i
n
ternal
c
ompil
e
r error for MSVC
w
h
en
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lind
a
h
l
Merge branch 'release-4-5
-
patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
D
eprecated -ins option to g_h
b
ond sinc
e
n
o
body se
e
ms
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Copied all-vs-all change f
r
om x86-64 to
i
a32 kernels
t
o
o
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Lindahl
Merge branch 'release-4-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fi
x
ed
potential error in
c
o
ulo
m
b energ
y
, and maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Linda
h
l
Merge branch
'
release-4-5
-
pa
t
ches
'
of
g
it
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lin
d
a
hl
A
dded doubl
e
precision SSE2 g
e
neralized b
o
rn kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lin
d
ahl
Added ia32 all-vs-all kernels
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Updated
au
t
o
conf
t
o wor
k
with
renamed
S
SE2 x86-64 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lind
a
hl
Renamed SSE2 x86-64 asm te
s
t
f
ile to be cons
i
s
t
e
nt
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
indahl
Fix
e
d typ
o
to dete
c
t both x86
_
64->i38
6
and i386->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge branch 'release
-
4-5-
p
a
tches' of git
.
gro
m
ac
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindah
l
Fixed
a
n
a
ming error introdu
c
ed
y
esterda
y
i
n
32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
ix
e
d
c
ompiler errors for M
S
V
C
inli
n
e intrin
s
i
c
s
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Li
n
dahl
Fixed checkpoint
problem in
3
2
bits
.
W
e
s
h
o
u
ld al
w
ays
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Remov
e
d extra TER record
s
a
f
ter chains w
e
thin
k
ar
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Me
r
ge branch 'release-4-5-patch
e
s' of git
.
grom
a
cs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fix
e
d S
S
E
k
ernels in double precision for C
m
a
k
e, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindah
l
M
e
rge branch 'rel
e
ase-4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Cmake
and
N
asm support for windows
commit
|
commitdiff
|
tree
2010-08-10
E
rik Lindahl
Moved fou
r
more S
S
E assembly
files
to
a
v
oid d
o
uble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Er
i
k Lin
d
ahl
M
erge branch 'release-4-
5
-patche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Li
n
dahl
Cha
n
ges
t
o
make Cmake
w
ork
under window
s
aga
i
n
commit
|
commitdiff
|
tree
2010-08-10
Erik Linda
h
l
Rename
d
i
n
tel synt
a
x
assembl
y
files to
avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Added NASM Cmake sup
p
ort
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch 'release-4-5-p
a
tches' of g
i
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik L
i
ndah
l
MAYBE a fix f
o
r Berk'
s
Heme problem
.
Needs testing
commit
|
commitdiff
|
tree
2010-08-08
Er
i
k Lindahl
Merge branch 'release-4-5-patc
h
es
'
of gi
t
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Added NHE
as an Amber aminoac
i
d
r
esi
d
u
e
t
y
pe
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Copied CK-CB-N*-CT Amb
e
r
improper to also l
i
st CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lin
d
ahl
Me
r
ge bran
c
h
'
release-4
-
5
-
patches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Fixed incor
r
ect #endif -> #else that
c
au
s
ed the C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Me
r
ge branch 'release-4-5-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lin
d
ahl
Fixed a bug in index
gen
e
rati
o
n
f
or non-adjacent pro
t
ein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik L
i
nd
a
hl
Fixed nonexi
s
tent ret
u
rn t
y
pe on gm
x
_mm_sin
c
os_
p
d
commit
|
commitdiff
|
tree
2010-08-04
E
r
i
k
L
inda
h
l
A
d
ded out in
t
-ex
t
raction
macro t
o
double prec
i
s
i
on
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Added double
precision SSE2 trans
c
endental funct
i
ons
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik
Lindahl
F
i
xe
d
a
cc
u
ra
c
y issues in gmx_mm_log_
p
s(), and added
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik L
i
n
d
a
h
l
Modified in
d
ex
p
rocessing to
r
e
ins
t
ate residu
e
-spl
i
tti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
E
r
i
k
L
indahl
A
d
ded i
o
n classes to residue
t
ypes
.
dat
commit
|
commitdiff
|
tree
2010-07-30
Erik Li
n
dahl
M
e
rge
b
ra
n
ch '
m
aste
r
'
o
f
git
.
gromac
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Repla
c
ed n
o
n-thread
-
safe calls to cti
m
e() with our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik
L
indahl
A
d
d
e
d po
r
t
able gmx_ctime_r() to
e
n
abl
e
replacement
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge branch
'
master' o
f
git
.
gro
m
acs
.
o
r
g
:
gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik
Lindahl
R
eplaced lo
c
altime with lo
c
a
ltime_r() on unix and localtime_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge br
a
nch
'
master' of git
.
gr
o
m
a
cs
.
org
:
g
ro
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-30
E
rik Lindahl
Replac
e
d
readdir()
w
i
th readdir_
r
() to
a
voi
d
future
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k
L
indahl
Merge
b
ra
n
c
h 'ma
s
ter' of git
.
gromac
s
.
or
g
:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-30
E
rik
Lindahl
Po
r
ted x86-64 sin
g
le precisi
o
n
SS
E
2
a
ll-vs
-
all patch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik
L
indahl
Commented ou
t
calls to double prec
.
SSE2 all-vs-a
l
l
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lin
d
ahl
Worke
d
aro
u
nd cross-inclusion
p
robl
e
m
b
etw
e
en grompp
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Remo
v
ed
d
eprec
a
ted nsb
.
h
h
eader
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k
Lindahl
Merge branch '
m
as
t
er' of git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-07-29
Erik Linda
h
l
Changed inde
x
group
analy
s
is t
o
only create water_and_ions
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
E
rik Lind
a
hl
Merge branch
'
maste
r
' of git
.
g
r
omacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-29
Erik Lind
a
hl
A
d
ded residuedef
i
nitions for water, and intr
o
duced
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
R
e
ve
r
t
e
d in
c
orrect Makefile edit earlier
t
oday
commit
|
commitdiff
|
tree
2010-07-29
Eri
k
Li
n
dahl
Merge branch 'master'
o
f git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-07-29
Erik Linda
h
l
Imp
r
oved
c
hain s
e
para
t
ion detecti
o
n
for
p
db2gmx, and
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Erik
L
i
ndahl
Merge branch 'master'
of git
.
gromacs
.
or
g
:
g
romacs
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
Added
missing double p
r
ec
.
SSE2 header file
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
T
e
mpo
r
a
r
ily disabled a new pdb2gmx opti
o
n
commit
|
commitdiff
|
tree
2010-07-27
E
r
ik L
i
nd
a
hl
Mo
d
ified PDB io code to merely store the chain _identifier_
.
.
.
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