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Detect AVX-512 FMA units to choose best SIMD
2012-12-27
Erik
L
i
n
dahl
F
i
xed error me
s
sag
e
f
or z
w
itteri
o
n
residues
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
Fixed
AVX256 doubl
e
-pr
e
cision kernel
s
for gcc
commit
|
commitdiff
|
tree
2012-11-22
Eri
k
Lindahl
Fix for icc 13 optimi
z
atio
n
-rel
a
ted issue and
TIP4P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
E
r
ik L
i
nda
h
l
Implemente
d
R
M
S-b
a
sed force tolera
n
c
e
i
n
gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindahl
Fixed LJ-14 error in free
energy
commit
|
commitdiff
|
tree
2012-11-09
Eri
k
L
indahl
Removed old (now unused) blueg
e
ne
ker
n
e
l
s
.
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindah
l
Removed
u
n
u
sed old kerne
l
ge
n
erator
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
R
e
mov
a
l
of st
a
le Fo
r
t
ran/Po
w
er6
kernels
commit
|
commitdiff
|
tree
2012-11-09
Eri
k
Linda
h
l
Removal o
f
stale Fortran
kerne
l
s
commit
|
commitdiff
|
tree
2012-11-08
Erik Lindahl
Fixed bug i
n
the new switch-m
o
dified interactions in
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Erik
L
indahl
Allow rc
o
ulomb=rl
i
stlong for PME wi
t
h nstcalclr=1
commit
|
commitdiff
|
tree
2012-06-21
Erik L
i
ndahl
Fixed gc
c
inline assembly is
s
ue with PIC and ol
d
er
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
Erik Lindahl
N
e
w CPU det
e
ctio
n
&
AVX/SSE code, re
m
ov
e
d raw as
s
emb
l
y
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Erik Lindahl
Introduced diffe
r
ent options for pd
b
2gmx termini introduc
t
io
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Erik Lindahl
Fix
e
d
incorrecti
o
n Am
b
erGS
force
f
iel
d
(redmi
n
e #728)
commit
|
commitdiff
|
tree
2011-05-05
Erik
L
ind
a
h
l
Merge
b
ranch
'rele
a
s
e
-
4-5-patch
e
s' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
E
r
ik
L
i
n
dahl
Update
d
o
c
to clarify tha
t
A
m
b
e
r nucleic params
a
re
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
Merg
e
branc
h
'
master' o
f
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2011-05-05
Er
i
k Linda
h
l
Update d
o
c to clarify that Amber n
u
cleic params are
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Er
i
k Lindahl
Impr
o
ved
P
BC handling for large m
o
l
e
cules duri
n
g cluster PBC
commit
|
commitdiff
|
tree
2011-01-30
Erik
L
indahl
F
i
xed the pbc clus
t
er option of
t
r
j
conv by switching
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
E
r
ik Lindahl
Merge branch 'release
-
4-5-
p
at
c
h
e
s' of git
.
gro
m
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lindahl
Fixed u
n
ini
t
ialized
v
a
r
i
a
ble warning in
gro
m
pp
.
c
commit
|
commitdiff
|
tree
2010-09-01
E
r
ik Lind
a
hl
Removed lots of unnece
s
sary
messages to
s
tdout from
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Erik
L
indahl
Adde
d
G
errit to
t
h
e
l
ist of auth
o
rs
.
Sorry for forg
e
tting
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Linda
h
l
M
ad
e
the options program
f
or the latex manual
com
p
ile
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Eri
k
Lindahl
Fixed typ
o
in src/contrib/M
a
kefile
.
am
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k
L
in
d
ahl
F
ixed incorrect call to gmx_finalize()
i
n
gmx_pme_error()
commit
|
commitdiff
|
tree
2010-08-31
Erik Lind
a
hl
Added final newline
t
o avoid comp
i
ler warni
n
g
i
n sfactor
.
h
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindah
l
Merg
e
branch
'
release-4-5-pat
c
hes' of git
.
gr
o
ma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Ad
d
ed Cpack su
p
po
r
t
commit
|
commitdiff
|
tree
2010-08-31
E
rik
L
i
n
dahl
Added label writing capabil
i
ty to editconf w
h
e
n
used
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
E
r
ik Lindahl
A
dd
e
d ch
e
ck for
<2
f
rames wh
e
n a
u
to
c
o
r
relatio
n
is
r
equeste
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
E
rik Lindahl
Moved buggy and
u
n
suppo
r
ted g
_
sdf to contrib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lindahl
I
m
proved handling
of include
paths in gmxcpp from
Te
e
mu
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Merge branch 'rele
a
se-4-5-patches'
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Added
l
onge
r
l
i
s
t of authors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
M
e
rge bran
c
h 'release-4-
5
-
patches
'
of git
.
gro
m
acs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added
c
h
eck
f
or S
S
E2 su
p
port to us
e
generalized bor
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindahl
R
esolved
m
erge
c
onflict in g
m
x_membed
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindahl
Merge branch 'r
e
lease-
4
-5-patches' o
f
git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k Lindah
l
F
ixed g
m
xcpp to always use unix path separators
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Me
r
g
e bran
c
h 'rele
a
se-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
indahl
F
i
xed
a
nother uni
n
itialized var
i
able warning
in gm
x
_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lind
a
hl
Add current p
a
t
h
(
.
/) to topol
.
t
op includ
e
when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Linda
h
l
Dont write EOF warn
i
ngs to st
d
out every time we checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Linda
h
l
M
e
r
ge bran
c
h 'r
e
lease-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
F
ixed first statemement occur
i
ng befo
r
e
variable decl
a
rati
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Added
t
r
j
conv c
h
eck for
t
opology prescen
c
e, s
e
e
b
u
g
zi
l
la 526
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lin
d
ahl
Merge
branch
'release
-
4-5-patche
s
' of git
.
g
ro
m
a
c
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dah
l
Modified p
d
b
2gmx to
a
utomatically pick th
e
force
f
ield
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik L
i
ndah
l
Fixed
pointer typ
o
in patch from Alexey Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
E
r
i
k Lindahl
Ad
d
ed PBC c
h
ecking pa
t
ch to g_cluster
from Alexey Shv
e
tsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
i
ndah
l
M
erge
b
ranch
'
release-
4
-5
-
patches
'
of gi
t
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
M
o
difi
e
d
p
d
b
2g
m
x to not accep
t
extra hydrogen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Me
r
ge branch 'release-4-5-patches'
of git
.
g
r
oma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
tru
e
/fa
l
s
e
i
n
p
u
t settings s
h
ould be c
a
lled boo
l
instead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
M
er
g
e branch 'rele
a
se-4-5-
p
atches' of g
i
t
.
grom
a
cs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
h
l
R
evert "Made pdb2g
m
x be slightly more helpful when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated completions
for 4
.
5
r
e
lease
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
inda
h
l
Made /usr/local/g
r
o
macs
d
ef
a
ult installat
i
on path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Updated ht
m
l documentation for release 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updat
e
d ma
n
ual
p
ages,
n
ow w
i
th corre
c
t version (
4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Fix f
o
r
w
arning in ngmx m
a
kefile
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Changed version t
o
beta4
commit
|
commitdiff
|
tree
2010-08-26
E
r
i
k
Lindahl
Upd
a
ted scripts
to produce 4
.
5 man pages
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Updated ma
n
p
ages for
4
.
5 rele
a
se
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Removed us
e
le
s
s g_log
o
and
g
_highway
programs
from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ah
l
g_kinetics removed f
r
om automati
c
a
l
ly built
pro
g
ra
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lindahl
Fixe
d
includ
e
path in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Forgot to act
u
ally do
t
he char
-
>int
c
hang
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindah
l
Chan
g
ed bool to signed integer
i
nstead of
unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lin
d
a
hl
Added m
i
ssing hea
d
er i
n
c
l
ude
commit
|
commitdiff
|
tree
2010-08-25
Erik Li
n
dahl
M
erge branch
'
releas
e
-4-5-patches
'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k
L
indahl
Made sur
e
all source files have
s
ome
copyright header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
rik
L
indahl
R
e
-a
d
ded openmm
paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Me
r
ge bra
n
c
h 'release-4-5-p
a
tc
h
e
s
' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
E
rik Lindahl
Upda
t
ed intel synta
x
x86-64 asm files to also
support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
F
ixed
u
nin
i
tialized variable
error in GB kernel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed an uns
i
gned/si
g
ned integer comparison
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Fixed two more instances
of strcasecmp
-
>
g
mx_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
E
r
i
k
L
indahl
Cop
i
ed SS
E
intrins
i
cs kernels from x86
-
6
4 to i
a
32
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lindahl
R
e
p
l
a
ced
a
ll occurences of str(n)cas
e
c
m
p with
gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
s
t
up
i
d m
i
stake
w
here a s
t
atement wa
s
placed before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Replaced test
i
ng of git ver
s
ion
with
t
est
i
ng for features
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixe
d
naming proble
m
s for do
u
ble precision F
o
rtra
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Li
n
dahl
Fi
x
ed a typo in
futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
M
e
rge b
r
anch 'release-4-
5
-p
a
tch
e
s' of git
.
gr
o
macs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k
Lindahl
Cl
e
aned up all installed headers to
remove strict depende
n
ce
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Removed
s
o
me unnece
s
sary
#if
d
efs from string
2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
A
mber force fields now
pass validat
i
on
.
Bet
a
st
a
tus
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
A
dded F77 kernel setup headers
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
F
i
x
ed synchronization counter update for f77 kernels
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Fixed a bug for GB OBC bor
n
ra
d
ius calculat
i
on
in SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fixed an uniniti
a
lized var
i
able bug
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fi
x
ed a minor bug that caused For
t
ran builds t
o
fai
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k
Linda
h
l
Dont write nonpol
a
r surface e
n
e
r
gy to energy file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
Fi
x
ed so Fort
r
an kernels wo
r
k aga
i
n
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Upgraded to lat
e
st auto
c
onf p
l
at
f
orm dete
c
tion sc
r
ipt
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a c
h
a
i
n r
u
le error
i
n double prec
.
SSE2 GB f
o
r
.
.
.
commit
|
commitdiff
|
tree
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