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Merge branch 'release-4-5-patches'
2010-08-27
Erik Lindah
l
Merge
b
ranch 'releas
e
-4-5-patche
s
'
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added longer
l
ist of authors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
Lindahl
Mer
g
e
branc
h
're
l
ease-
4
-5
-
p
a
tches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
Added check for SSE2 suppor
t
t
o
use g
e
neralize
d
born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
i
n
dahl
Resolved merge conflict in gmx_mem
b
ed
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik L
i
ndahl
Merge br
a
nch 'release-4
-
5-p
a
t
ches' of git
.
g
r
omac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Fixe
d
gmxcpp
t
o
always use unix path
sep
a
rators
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
nd
a
hl
M
erge br
a
nch 're
l
e
a
se-4-5-patc
h
e
s'
o
f git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
Fixed another un
i
n
i
t
i
alized
variabl
e
wa
r
n
i
ng
i
n gmx_e
n
ergy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
L
i
ndahl
Add c
u
rrent pa
t
h (
.
/)
t
o to
p
o
l
.
top inclu
d
e when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Li
n
dahl
Do
n
t write EO
F
warnings to stdout every time
we chec
k
point
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
Li
n
d
a
hl
Merge branc
h
'relea
s
e-4
-
5-patches' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed
f
i
rst statemement occ
u
ring before variable declaration
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Added trjc
o
nv check
for
t
o
pology prescence, see
b
u
gzilla 526
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
Linda
h
l
Merge br
a
nch 're
l
eas
e
-
4-5-
p
atches'
o
f
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
Modified p
d
b2g
m
x to
a
utoma
t
ically
pick
the force
field
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lindahl
Fixed po
i
nt
e
r
typo
in patch from Alexey Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Ad
d
e
d PBC
c
heck
i
ng patch to g_
c
luster
from Ale
x
ey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
Merge
b
r
anch
'
rel
e
ase-4-5
-
patches
'
o
f git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
o
dified p
d
b2gmx to no
t
accept extra hydrogen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
Lind
a
hl
F
i
xed
i
ncl
u
de p
a
th
i
n vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik L
i
nd
a
hl
For
g
ot t
o
actu
a
ll
y
do the char
-
>int ch
a
n
ge
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lindahl
Changed bool t
o
signed i
n
teger
i
n
s
tead of u
n
signed
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lind
a
hl
A
d
d
e
d missi
n
g heade
r
in
c
lude
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Me
r
ge branch 'release-4-
5
-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Made s
u
re
a
ll source
files have
so
m
e copyright
h
eader
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
r
ik Li
n
da
h
l
Re-added op
e
n
m
m paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Merge branch 'release-4-5-patches' of gi
t
.
g
romac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Upda
t
ed intel synt
a
x
x86-64 asm
f
iles to also su
p
p
o
r
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindahl
Fixed
uni
n
itialize
d
variable error
i
n GB ke
r
nel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
i
n
dahl
Fixed an unsigned/signed integer compa
r
i
s
on
commit
|
commitdiff
|
tree
2010-08-22
E
rik
L
ind
a
hl
Fixed two
m
ore instances of strcasecmp
-
>gmx_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
C
o
pied
SSE intr
i
nsic
s
kernels f
r
om x86-64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
i
ndahl
Replaced
all
o
ccurences o
f
str(n)casecmp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed stu
p
id mistake where
a
statement was placed before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Replaced testing of
g
it version with testing f
o
r features
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Fixed naming problems for double pr
e
cision Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
ixed a t
y
po
in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Merge
b
ranch 'rele
a
se-4-5-pat
c
hes' of git
.
g
romac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik L
i
ndahl
C
l
ea
n
ed up
a
ll installed headers to remove strict de
p
endence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Removed some
u
nnecess
a
ry
#
ifdef
s
from string2
.
h; a
l
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
A
mber force fields
n
o
w pas
s
validati
o
n
.
Beta status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lindahl
A
d
de
d
F77
kernel set
u
p heade
r
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
dahl
Fixed sy
n
chron
i
zat
i
on counter
u
pdate for f77 ke
r
n
e
ls
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lin
d
ahl
Fixed
a bug
f
o
r GB OBC
born radius calc
u
lation i
n
SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fi
x
ed an uninitialized varia
b
le bug
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lindahl
Fix
e
d a m
i
nor bug
that c
a
use
d
Fortran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Linda
h
l
Dont write no
n
polar surface
e
ne
r
g
y
to energy file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
ndahl
Fixed s
o
For
t
ran kerne
l
s wor
k
ag
a
i
n
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
inda
h
l
Upgraded to latest autoconf
p
lat
f
orm
d
etection scrip
t
s
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik
Lindah
l
Fixed a cha
i
n ru
l
e er
r
or
in double prec
.
S
SE2 GB fo
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
M
erge
br
a
nch 'release-4-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
i
ndahl
Doub
l
e precision
S
SE2 kernels for Generalized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Updated GB SSE2 kern
e
ls, te
s
t
i
n
g in progress
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge branch 'release-4
-
5-patch
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lindahl
Modi
f
i
ed at
o
m order in Amber nucl
e
otide imp
r
oper torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lind
a
hl
Modified improper
t
orsion at
o
m ord
e
r in Amber TR
P
re
s
idues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k
Lindahl
M
e
rge branch 'release-4-5-patches
'
of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
Fix to w
r
ite GB and surface energy to se
p
arat
e
terms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
M
erge branch 're
l
ease-4-5-
p
atches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Lindahl
E
n
able
d
double
precisio
n
all-
v
s-all kern
e
ls
.
Te
s
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fixed s
i
m
ple typo
in
last commit
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
nda
h
l
Fixed previous nasm-s
e
g
v bu
g
for i
n
tel-syntax SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik Lindahl
Fix
e
d 64-
b
it bug
i
n SSE
a
ssembly (onl
y
visibl
e
with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
Worked ar
o
und an inter
n
a
l c
o
mpiler error for
MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Lindahl
Me
r
ge
b
ranch 'release-4-5-pat
c
hes' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Depreca
t
ed -ins opti
o
n to g_hbond s
i
nce nobody seem
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Li
n
da
h
l
C
o
pied a
l
l-vs-all cha
n
ge from x86-64 to ia32
kernels too
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lind
a
hl
Merge branch 'r
e
lease-4-5-patches
'
o
f
g
i
t
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lindahl
Fixed
potential error in coulomb energy, an
d
maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
M
e
r
ge branch 'release-4-5-patches' of git
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
d
a
h
l
Added double pr
e
ci
s
ion
SSE2 generalized bo
r
n ke
r
nels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Linda
h
l
Added ia32 all-vs-
a
l
l
kernels
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindah
l
Updated autoconf to
w
ork w
i
th renam
e
d
S
S
E
2 x8
6
-64 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Renamed
SSE2 x86-64 asm t
e
st fil
e
to be con
s
ist
e
nt
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Fixed
t
y
po to detec
t
both x86_64->i386 and i386-
>
x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ah
l
Me
r
ge branch 'rel
e
ase-
4
-5-pat
c
hes' of
g
it
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Li
n
d
ahl
Fixed a naming error introduced yesterday
i
n 32
b
it
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Linda
h
l
Fixed compiler errors
f
or MS
V
C
inline intrinsics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik
Li
n
dahl
Fixed checkpoint prob
l
em i
n
32
bits
.
We should a
l
w
a
ys
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
Lindahl
Removed extra TER recor
d
s af
t
er chains
w
e think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge bran
c
h 'release-4-5-patches' of git
.
gro
m
acs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Fixed SSE
kernels
in double precision for C
m
ake, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Er
i
k
L
indahl
Merg
e
branch 're
l
ease-4-5-patches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik L
i
nda
h
l
Cmake an
d
Nasm
s
u
pp
o
rt for
w
indows
commit
|
commitdiff
|
tree
2010-08-10
E
r
i
k Lindahl
Mov
e
d f
o
ur
more S
S
E assembly
f
iles to av
o
i
d do
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch
'release-4-5-
p
atches'
of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik
L
inda
h
l
Chan
g
es to make
Cma
k
e work und
e
r
windows again
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Linda
h
l
Ren
a
m
e
d in
t
el
syntax assembly
f
iles t
o
a
void
d
o
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Linda
h
l
Add
e
d NAS
M
Cmake suppo
r
t
commit
|
commitdiff
|
tree
2010-08-10
E
rik
L
in
d
ahl
M
e
r
g
e
branch 're
l
ease-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik
Lind
a
hl
MAYBE a fix for
B
e
r
k's Heme problem
.
Nee
d
s testing
commit
|
commitdiff
|
tree
2010-08-08
Erik L
i
nd
a
hl
Merge
branch
'release-4-5-patc
h
es' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Er
i
k
L
indahl
Added NHE
a
s an
Amber aminoacid residue type
commit
|
commitdiff
|
tree
2010-08-08
Erik
L
indahl
Copi
e
d CK
-
CB-N*-
C
T
A
mber
i
m
proper to
also
list C
K
-
C
B
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Merge
bran
c
h 'release-4-5-pa
t
ches'
o
f
git
.
g
r
omacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
E
r
ik L
i
ndahl
Fixed incorr
e
ct #e
n
dif -> #else that caused t
h
e C
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lindah
l
Merge branch
'
r
elease-4-5-patc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fi
x
ed a bug in index generation for non-a
d
jacent pro
t
ein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
rik Lindahl
Fixed nonex
i
stent return type on gmx_
m
m_sinc
o
s_pd
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