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Merge branch 'release-4-5-patches'
2010-08-27
Erik L
i
ndahl
Merge
b
ra
n
c
h
'release-4-5-patches'
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Add
e
d longer list
o
f authors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Li
n
d
a
h
l
M
e
r
g
e
bra
n
c
h 'rele
a
s
e-4-5-pat
c
hes'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added check for SSE2 support to us
e
generalized born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik L
i
ndah
l
Resol
v
ed
merge conflict in gmx
_
m
e
mbed
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Merge branch 'rel
e
ase-4-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed
gmxcpp to always
us
e
unix pa
t
h separators in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
Merge branch 'release-4-5-patches' of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
F
i
xed a
n
other uninit
i
ali
z
ed variable warn
i
ng in g
m
x
_
energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Add current path
(
.
/
)
to topol
.
top include when
force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
D
o
nt write
EOF warning
s
to stdo
u
t every time we checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
M
erge branch 'release-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindahl
Fixed firs
t
state
m
ement occuring before va
r
iab
l
e
dec
l
arati
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lind
a
hl
Added trjconv check for
topology pre
s
c
enc
e
, se
e
bugzilla 526
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik
L
indahl
Merge bran
c
h 'release-4
-
5-patc
h
e
s' of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
M
o
dified
p
d
b2gmx
to au
t
o
mat
i
c
a
l
l
y pick the forc
e
fiel
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Fixed poin
t
er ty
p
o in pat
c
h from Alex
e
y
S
h
v
etsov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Add
e
d PBC checking
p
atch to g_cluster f
r
om A
l
exey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge br
a
nch 'release-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Mod
i
fied pdb2gmx t
o
not accept e
x
t
r
a hyd
r
ogen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge br
a
n
ch 'release-4-5-patc
h
es'
of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Li
n
dahl
true/false input settings sh
o
u
l
d be cal
l
ed
bo
o
l i
n
stead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
M
e
rge b
r
anch
'release
-
4-
5
-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
L
indahl
Revert "Mad
e
pdb
2
gmx be slightly more helpfu
l
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
Up
d
a
t
ed compl
e
tions
f
or
4
.
5 release
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Ma
d
e
/
usr/loca
l
/gromacs d
e
f
a
ult
i
n
s
tal
l
ation path
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Updated html documentation
for rel
e
ase 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
U
pdated manual pa
g
e
s
, no
w
wi
t
h correct version (
4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
F
i
x
for
w
a
r
n
i
ng
i
n ngmx mak
e
file
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Changed version to
beta4
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indah
l
U
pdated
s
c
r
ipts t
o
p
r
o
duce 4
.
5 man pages
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Updated manpages for
4
.
5 release
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Remov
e
d use
l
ess g_logo and g_highw
a
y programs from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
g_kinet
i
cs removed from
automatica
l
ly bu
i
l
t programs
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Linda
h
l
Fixed include path in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
For
g
ot to actually do the char->int change
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Eri
k
Linda
h
l
Changed
bo
o
l
to
s
i
g
n
e
d
i
nte
g
er instead of uns
i
gned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik Lindahl
A
d
d
e
d
m
is
s
ing header include
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k Lindahl
Merge branch 'release-4-5-p
a
tch
e
s' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Li
n
dahl
Made sure all sou
r
ce
files have some copyrig
h
t
he
a
der
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Er
i
k Lind
a
hl
Re-a
d
ded openmm
p
aper
commit
|
commitdiff
|
tree
2010-08-24
Er
i
k Lindahl
Merge branch 'releas
e
-4-5-patc
h
es' of
g
it
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
r
ik L
i
ndahl
Up
d
ated intel
s
yntax
x
8
6-64 asm files to a
l
so su
p
port
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindah
l
Fixed uninitializ
e
d
v
ariable error in GB
k
ernel wit
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindahl
Fi
x
ed an unsig
n
ed/sig
n
ed
i
nteger c
o
mparison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed two more instanc
e
s of strcas
e
c
mp-
>
gmx_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
L
indahl
Copied S
S
E in
t
rin
s
i
cs kernels from x86-6
4
to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
h
l
Re
p
lac
e
d
a
ll occ
u
rences of s
t
r(n
)
casecmp with gm
x
_
s
tr
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
n
dahl
Fix
e
d
stupid mistake where a statement was p
l
aced before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
R
ep
l
a
c
ed testing of gi
t
version with
t
esting for featur
e
s
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Lindahl
Fixed naming prob
l
ems for doub
l
e
p
r
ecision
F
ortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Lind
a
hl
Fixed a typo
in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
M
e
r
g
e branch 're
l
e
ase-4
-
5-patch
e
s' o
f
g
i
t
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Cleaned
u
p all inst
a
lled
h
e
a
ders to remove stri
c
t
dep
e
ndence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Removed some unnecessary #ifdefs from stri
n
g
2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Amber
f
orce f
i
elds now pas
s
v
alid
a
t
ion
.
Beta status
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lindahl
Added F
7
7 k
e
rnel setup headers
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k L
i
n
dahl
Fixed syn
c
hronization counter update for f77 k
e
rnels
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
F
i
xed
a bug for
G
B OBC
born radius
calculat
i
on in
SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
ixed
a
n
u
ninitialized var
i
abl
e
bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a mino
r
bug that caused Fortran
build
s
t
o
fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
dahl
Don
t
wr
i
te
nonp
o
la
r
surface energy to energy file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fi
x
ed so Fortra
n
k
e
rnels w
o
r
k
a
gain
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lindahl
Upgr
a
d
ed to lates
t
autoconf platfor
m
detection s
c
ripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
Fixed a chain rule error in doubl
e
prec
.
SSE2
G
B for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Li
n
dahl
Merge branch 'release-
4
-5-patche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
n
dahl
Double precision SSE2 k
e
rne
l
s
for Gener
a
lized
B
orn
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
i
k Lindahl
U
pdated GB S
S
E2 kernels, testing in p
r
ogress now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge
b
ranch 'r
e
l
e
a
se-4-5-patch
e
s' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Modified ato
m
order in Amber nucleotide i
m
pr
o
per tor
s
io
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik
L
indah
l
Mo
d
ified impro
p
er
torsi
o
n atom order in Amber TRP res
i
dues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge bra
n
ch 'release
-
4-
5
-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
L
i
n
d
ahl
F
i
x to writ
e
GB and s
u
rface
en
e
rgy to
s
e
p
a
r
ate terms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Mer
g
e
br
a
n
c
h 'release-4-5-p
a
tches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
E
na
b
led doubl
e
precision all-v
s
-a
l
l
kernels
.
Test
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik L
i
ndahl
F
ix
e
d simpl
e
typo in last
co
m
mit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fixed previous nasm-se
g
v bug for intel-syntax SSE
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fi
x
ed 64-bit bug in SSE assembly (only visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Lin
d
ahl
W
orke
d
around an internal compiler error for MSVC w
h
en
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
rik
Lindahl
M
e
rge b
r
anch 'rele
a
se-4-
5
-patches' of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecated
-ins option to g_hbond s
i
nce no
b
ody se
e
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lind
a
hl
Copied all-vs-all chan
g
e from
x
86
-
64 to
ia
3
2 kernels
to
o
commit
|
commitdiff
|
tree
2010-08-17
Erik Li
n
da
h
l
Merge
b
ranch 're
l
ease-4-5-patc
h
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
F
ixed potential error in coulomb energy,
a
n
d maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Merge br
a
nch
'relea
s
e
-4-
5
-
p
atches'
o
f git
.
gromac
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Added
d
ouble
p
recision
SSE2 generalized b
o
rn kerne
l
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Added ia32 all-vs-all kerne
l
s
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Updated autoconf to w
o
rk with renamed SSE2 x86-64 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Renamed
S
SE2 x86-64 asm test
f
il
e
t
o
b
e consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
inda
h
l
Fixed typo
t
o
d
e
t
ect both x86_64->i386 and i386->x86_
6
4
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Merge branch 'relea
s
e-
4
-
5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
i
n
dahl
Fixed a naming error int
r
oduced yester
d
ay
i
n 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
F
i
xed compiler e
r
rors fo
r
MSVC
inline intrinsics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lin
d
ahl
Fixed checkpoint proble
m
in
3
2 bits
.
W
e
should always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
ind
a
hl
Removed extra TER r
e
cords
aft
e
r chains
we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Me
r
ge branch 'release-4-5-pa
t
ches' o
f
gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
h
l
Fixed SSE k
e
r
n
els in doub
l
e precision for Cmake, work
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Merge branch 'releas
e
-4-5-
p
atche
s
' of
g
it
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Linda
h
l
Cmake and Nas
m
sup
p
or
t
for windo
w
s
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Li
n
dahl
Moved four mor
e
SSE assembly files to avoi
d
d
oub
l
e
.
.
.
commit
|
commitdiff
|
tree
next