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Moved buggy and unsupported g_sdf to contrib directory and removed its documentation...
2010-08-31
Eri
k
Lindahl
Moved bugg
y
a
n
d unsupported g_sdf to contrib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Li
n
d
ahl
Impro
v
ed handling of incl
u
de
pa
t
hs in
gmxcpp from Teemu
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lind
a
hl
Add
e
d l
o
n
g
er li
s
t of
a
u
t
hors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Mer
g
e branch 'releas
e
-4-5-p
a
tches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
A
dded c
h
ec
k
for
SSE2 support to us
e
genera
l
ized born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
Added trjconv che
c
k for topology prescence, see b
u
g
z
illa 52
6
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
Merge branch 'rel
e
as
e
-
4-5-patches' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
indahl
Fixed gmxcpp to alw
a
ys use unix pat
h
separa
t
ors in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lind
a
hl
Merg
e
branch 'release-4-5-patch
e
s
'
of
g
i
t
.
gro
m
acs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Linda
h
l
Fix
e
d ano
t
h
e
r uninitialized variable
w
arning in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
A
d
d
c
u
rre
n
t path (
.
/
) to topol
.
top
includ
e
when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Dont write EOF warnings
t
o
stdout every time w
e
checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Merge branch 're
l
ease-4-5-p
a
tche
s
' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindah
l
Fixed
f
i
r
st s
t
a
temement occuring
b
efore variabl
e
declaration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik
L
indahl
Merge bra
n
ch 'release-4-
5
-p
a
tch
e
s' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Modified pdb2gmx to
auto
m
atic
a
lly pick the force f
i
eld
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
hl
Fixed po
i
nter typo in patch from
A
lexey Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Added PBC checkin
g
patch to g_cluster from
A
lexe
y
Sh
v
etsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
nda
h
l
M
erge branch 'release-4-5-p
a
tche
s
' of gi
t
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Modified p
d
b
2
gmx to not acce
p
t ex
t
ra hydrogen a
t
o
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lin
d
ahl
F
ixed i
n
clude
path in vmd
i
o
.
h
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Forgot to act
u
ally do
t
h
e
char->i
n
t chang
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Ch
a
ng
e
d boo
l
t
o
signed
i
ntege
r
i
nstead
o
f unsigne
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik
L
indahl
Added m
i
ssing hea
d
e
r
include
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Me
r
ge bran
c
h 'rele
a
se-4
-
5-p
a
tche
s
' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lin
d
a
hl
Made
sure
a
l
l
source files
have
s
o
me copyright he
a
der
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Li
n
dahl
Re-added openm
m
paper
commit
|
commitdiff
|
tree
2010-08-24
E
r
i
k Lindahl
Merge
b
ranc
h
'release-4-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lin
d
ahl
Updated
intel sy
n
tax x86-64 asm
f
iles to a
l
so support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindah
l
Fixed uninitialized
variable er
r
or in GB kernel wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Li
n
d
ahl
Fixed an unsigned/signed integer compar
i
son
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Fixed two more instan
c
e
s of
strcase
c
mp->gmx_strcase
c
m
p
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Co
p
ied SSE intrinsics ke
r
n
els from x8
6
-
64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Replac
e
d all o
c
c
u
re
n
ces of str(n)cas
e
cmp with gmx_s
t
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindahl
Fixed
s
tupid mistake
w
her
e
a
st
a
tement w
a
s plac
e
d before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Replaced testing of git version with te
s
ting fo
r
f
eatures
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed naming pr
o
bl
e
m
s
f
o
r double precision Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lin
d
ahl
F
i
x
ed a typo in f
u
til
.
h
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lin
d
ahl
Merge b
r
anch 'rel
e
ase-4-5-patch
e
s'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lindahl
C
l
e
aned up all installed h
e
aders to remove stri
c
t dependence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lin
d
ahl
Removed some unn
e
cessary #i
f
defs
f
rom string2
.
h;
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
Am
b
er force fie
l
ds now pass v
a
l
idation
.
Beta s
t
atus
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Added F77
ke
r
nel setup headers
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
Fixe
d
synchronization counter up
d
ate for f
7
7 k
e
r
n
e
ls
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
inda
h
l
Fixed a bug f
o
r
GB OBC born
r
adius c
a
lculati
o
n in
SS
E
2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed an uninitial
i
zed var
i
ab
l
e bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
i
xed a minor bug that caused
F
ortran builds to fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Dont write nonp
o
lar surface energy to energy fi
l
e if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed so Fortran kerne
l
s wo
r
k again
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lindahl
U
p
grad
e
d to latest autoc
o
nf platform detection scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindah
l
Fi
x
ed a chain rule e
r
ror in
d
ouble prec
.
SSE2 GB
f
or
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
h
l
M
erg
e
bran
c
h '
r
ele
a
se
-
4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
D
o
uble precision SSE2 kernels for Gene
r
alized
B
orn
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Lindah
l
Up
d
ated
G
B SSE2 kernels, testing in progr
e
ss
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
M
e
r
ge
b
ranch 're
l
ease-4-5-patches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
Modified atom o
r
der in
A
mber nucle
o
tide im
p
r
o
per torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
n
d
ahl
M
odifi
e
d improper to
r
sio
n
a
tom order in Ambe
r
TRP r
e
sidues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lind
a
hl
M
e
rge branch 'r
e
lease-
4
-5-patches' of git
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fix
t
o wri
t
e G
B
a
nd surface ener
g
y to separate
t
erms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik
Li
n
d
a
h
l
Merge branc
h
'
r
elease-4-5-patches'
of
g
it
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik L
i
ndahl
Enabled do
u
ble
p
r
ecisio
n
all-vs-all
ke
r
nel
s
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
F
ixed simple typo in
last com
m
i
t
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Fixed p
r
e
viou
s
nasm-segv bug for intel-syn
t
a
x SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed 64-bit bug in SSE assem
b
ly (o
n
ly
v
isi
b
le with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
indahl
W
orked around an internal compiler err
o
r for
MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Li
n
dahl
Merge br
a
nch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik L
i
ndahl
D
ep
r
e
c
a
ted -i
n
s
opti
o
n
to g_hbond
since nobod
y
see
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Eri
k
Lind
a
hl
Copie
d
all-vs-al
l
change
fr
o
m x86-64 to ia32
k
erne
l
s too
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
Merge branch
'
rele
a
se-4-5-
p
atches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed
p
otential error in coulo
m
b e
n
e
rgy, and maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge bra
n
ch 'release-4-5-patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
L
i
nd
a
hl
Added do
u
ble precision SSE
2
generalized born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Ad
d
ed ia32
a
ll-vs-al
l
ke
r
nels
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Upd
a
ted
a
utoconf
to work with renamed SSE2 x86-64
a
sm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
ri
k
Lindahl
Renamed SSE2 x
8
6-64 asm t
e
s
t
file
t
o be
consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
i
n
dahl
Fixed typ
o
to detect
b
oth x
8
6_
6
4->i3
8
6 an
d
i386->x8
6
_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Li
n
dahl
Merge branch 'release-4-5-pat
c
h
e
s
'
of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixe
d
a naming error introduce
d
yest
e
rday
i
n 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed compiler errors for MS
V
C
inline in
t
rinsics
an
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed checkpoint problem
i
n
32 bits
.
W
e
should always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Linda
h
l
Removed extra TER records after chain
s
we thi
n
k are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
i
k
Lindahl
Me
r
g
e bran
c
h 'release-4-
5
-p
a
tches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Li
n
d
a
hl
Fixed SSE
k
e
r
nels
in double precis
i
on
for Cmake, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik
Lindah
l
Merge br
a
n
ch
'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lin
d
ahl
Cmake
a
nd Nasm support
f
o
r
windows
commit
|
commitdiff
|
tree
2010-08-10
Erik
L
indahl
Moved four more SSE assembly files to avoid doub
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Linda
h
l
Merge branch 'release-4-5-patches' of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
C
han
g
e
s
t
o
mak
e
Cmake work un
d
er
w
indows again
commit
|
commitdiff
|
tree
2010-08-10
Erik Linda
h
l
Renamed intel
syntax assembly files to a
v
oid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik L
i
ndahl
Added NASM Cm
a
ke support
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch 'release-4-5-patches'
o
f git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
Lindahl
MAYBE a fix for Berk
'
s Heme p
r
oblem
.
Nee
d
s testin
g
commit
|
commitdiff
|
tree
2010-08-08
Erik Lin
d
ahl
Me
r
g
e branch
'
re
l
e
a
se-4-5-patch
e
s' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Er
i
k
Lindahl
Added
N
HE as an Amber am
i
noa
c
i
d
r
esi
d
ue t
y
p
e
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Copied CK-C
B
-N*-CT Am
b
er
imprope
r
to also list CK-C
B
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik
L
indahl
M
erge
branch 'release-4-
5
-patc
h
e
s
' of git
.
grom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik L
i
n
d
ah
l
F
i
xed
i
ncorrect #endif -> #else that caused the
C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik
Lindahl
Merge branch '
r
el
e
as
e
-
4
-5-patches' of g
i
t
.
gromac
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lin
d
ahl
Fixe
d
a
bug in index generation f
o
r
n
on-adjacent
p
rote
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik L
i
ndahl
Fixed no
n
existent return type on gmx_
m
m_sincos_pd
commit
|
commitdiff
|
tree
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