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Merge "fixed bug in nbnxn OpenMP non-bonded force reduction" into release-4-6
2012-11-27
E
rik Lindahl
Merge "fixed bug in n
b
nx
n
Open
M
P n
o
n-bonded force r
e
d
uction
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
E
rik
Linda
h
l
Mer
g
e
"Use stat fo
r
gmx_is
_
fi
l
e
.
Fix g
e
t_libdir with
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
Erik Lindahl
Merge "E
x
tended build
i
nformation output and reference
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
E
ri
k
Lindahl
Fix
f
or icc
13
o
p
timization-rela
t
ed issue and
T
IP
4
P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindah
l
Implem
e
nted RMS-based force tolerance in gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
Erik
Lindahl
F
i
xed LJ-14 error i
n
fr
e
e energy
commit
|
commitdiff
|
tree
2012-11-19
Erik Lindahl
SSE4
.
1
si
n
g
le-precision kernels
commit
|
commitdiff
|
tree
2012-11-16
E
rik L
i
ndahl
S
S
E2 single-pre
c
is
i
on kernels
commit
|
commitdiff
|
tree
2012-11-13
Erik
Lindahl
Remove
d
some unnecessary instructio
n
s, and fixed a
.
.
.
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
Rem
o
ved old (now unused) bluegene kernels
.
commit
|
commitdiff
|
tree
2012-11-09
Erik Lin
d
ahl
Removed unuse
d
old kernel generator
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
Removal of stale Fort
r
an/Power6 k
e
r
ne
l
s
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
R
e
mova
l
of st
a
le Fortran ker
n
els
commit
|
commitdiff
|
tree
2012-11-08
Erik Lindahl
Fixed
bug i
n
t
he new switch-m
o
d
ified interact
i
o
ns in
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Erik Linda
h
l
A
llow rcoulomb=rlistlong
for
PME
with nstca
l
clr=1
commit
|
commitdiff
|
tree
2012-11-08
Erik Lindahl
In
f
rastructure for new
g
roup kernels
,
an
d
new C kernels
commit
|
commitdiff
|
tree
2012-06-21
Erik
L
ind
a
hl
Fixed gcc in
l
ine
assembly
i
ssue with P
I
C and
older
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
Erik Lindahl
N
ew CPU detecti
o
n &
A
VX/SSE code, remo
v
ed raw assemb
l
y
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Erik Lindahl
M
e
rge "made
alloc
a
tion for LINCS with
p
article decomposi
t
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
E
r
ik
L
i
n
dahl
Introduced di
f
feren
t
op
t
io
n
s
f
o
r pdb2gmx termini
introductio
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Er
i
k
L
inda
h
l
Fixe
d
i
n
correction AmberGS fo
r
ce field (re
d
mine #728)
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
M
erge b
r
anc
h
'
r
e
lease-4
-
5
-p
a
tches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik Li
n
dahl
Update
d
o
c to clarify that A
m
ber nuc
l
e
ic params are
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Eri
k
Lindahl
I
mproved PB
C
handling for large molecules during
cluste
r
PBC
commit
|
commitdiff
|
tree
2011-01-30
Eri
k
Lindahl
Fixed the pbc cluster option of
t
rjconv by switc
h
ing
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Li
n
d
a
h
l
Merge branch 'release-4-5-patches
'
of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Eri
k
Li
n
d
a
hl
F
i
xed uninit
i
alized va
r
i
a
ble warning
i
n grompp
.
c
commit
|
commitdiff
|
tree
2010-09-01
Erik L
i
ndah
l
Removed lots o
f
unnece
s
s
ar
y
messag
e
s to stdout f
r
om
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Erik
L
indahl
Added Gerri
t
to
the li
s
t of authors
.
Sorry f
o
r
f
orgetting
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
Lin
d
a
h
l
Made t
h
e
options program f
o
r th
e
latex manual c
o
mpile
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
E
rik
Lindahl
F
ixed t
y
po
i
n src/c
o
nt
r
ib
/
Makefil
e
.
am
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k Lindahl
Fixed incorrect call to gmx
_
fina
l
ize() i
n
g
m
x_pme_error
(
)
commit
|
commitdiff
|
tree
2010-08-31
Erik Linda
h
l
Added final newline to avoid compiler
warning
in sfactor
.
h
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k L
i
ndah
l
Merge branch 'release-4-5-patches
'
of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k Lindahl
A
dded Cpack sup
p
ort
commit
|
commitdiff
|
tree
2010-08-31
Erik
Linda
h
l
Added
l
abel
w
r
i
ti
n
g capability to editconf when
used
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Added check for <2
f
rame
s
when autocorrelation is requested
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
L
indahl
Moved
b
uggy
a
nd unsu
p
po
r
ted g_
s
df
t
o contrib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lindahl
Improved handling of
i
n
clude paths
i
n
gmxcpp fr
o
m Teemu
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
Added longe
r
lis
t
of authors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindahl
Merge branch 'relea
s
e
-
4-5-patches'
o
f
gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
nd
a
hl
Adde
d
ch
e
ck for SSE2 su
p
por
t
to use general
i
zed b
o
rn
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
ri
k
Lindah
l
Added trjc
o
nv check
f
or topology prescence, see bu
g
z
i
lla 526
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
Li
n
dahl
M
e
rge b
r
anch
'
r
e
lease-4
-
5-patche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Linda
h
l
Fixed gmxcpp to always
us
e
unix path se
p
arator
s
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
M
erg
e
b
r
anch 'rele
a
se-4-5-patches
'
of git
.
g
romacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
da
h
l
Fi
x
ed ano
t
her uniniti
a
lized vari
a
b
l
e warning in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
Add cu
r
rent path (
.
/) to t
o
p
o
l
.
top incl
u
de when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Li
n
dahl
Dont write EOF warning
s
to stdout
ev
e
r
y t
i
me we chec
k
point
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Merge branch 'r
e
l
e
ase-4-5-patc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
Lindahl
Fixed fi
r
st st
a
teme
m
ent occur
i
ng befo
r
e
variable decl
a
ration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
Mer
g
e
branch
'rel
e
ase-4
-
5-patches' of gi
t
.
gr
o
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Mo
d
ified pdb2gmx to automatical
l
y p
i
ck the
f
orce field
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
ind
a
hl
Fixe
d
po
i
nter typo in
p
at
c
h fr
o
m
Alexey Shv
e
ts
o
v
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Added
P
BC check
i
ng patch to g_cluster fro
m
A
l
exe
y
Shvets
o
v
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Merg
e
br
a
nch 'relea
s
e-4-5-pa
t
ches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lin
d
ahl
Modif
i
ed pd
b
2
g
mx to not a
c
cept extra hydroge
n
at
o
ms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
M
erg
e
b
ranc
h
'release-4
-
5-patches'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
true/false in
p
u
t settings s
h
o
u
ld
b
e called bool inste
a
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
i
n
da
h
l
Merge bra
n
ch '
r
eleas
e
-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Revert
"
M
a
de pdb
2
gmx be
s
lig
h
tly
m
or
e
helpf
u
l whe
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
Updated comp
l
e
t
i
o
n
s
for 4
.
5 r
e
leas
e
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Made /usr/lo
c
al/g
r
om
a
cs default ins
t
a
l
lati
o
n path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindah
l
Updat
e
d html documenta
t
i
on for re
l
e
a
se 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Up
d
ated manual pages, now
w
ith cor
r
ect version (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik
L
indahl
Fix
f
o
r warning in ngmx makefile
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Changed
version to beta4
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Updated scripts to pro
d
uc
e
4
.
5 m
a
n
p
ages
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated manpa
g
es for 4
.
5 release
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
i
ndahl
Removed useless g_logo
and g_highway programs
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
g_kin
e
t
ics rem
o
v
ed f
r
om aut
o
matically
b
u
ilt p
r
ogram
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik L
i
ndahl
F
i
xed includ
e
path in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
E
ri
k
Lindahl
Forgot to actu
a
lly do the char->
i
nt
c
hange
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Changed boo
l
to si
g
ned integer in
s
tead of
u
n
s
igned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
rik
Lindahl
Added mis
s
i
n
g he
a
de
r
include
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
i
ndahl
Merge branch
'
r
e
l
eas
e
-4
-
5
-patches'
o
f git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Made sure all source files have some copyright header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik
L
indahl
Re-ad
d
ed
o
penm
m
paper
commit
|
commitdiff
|
tree
2010-08-24
E
r
ik Lindahl
Me
r
ge branch 'release-4-
5
-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lin
d
a
h
l
Update
d
intel syntax x86-64 as
m
files
to also support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Fixed uni
n
itialized variab
l
e erro
r
i
n GB kernel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
i
x
e
d an
un
s
i
gned/signed int
e
g
e
r compa
r
ison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed t
w
o more i
n
stances of strcasecmp->gmx_strcas
e
cmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cop
i
ed SSE int
r
insics kernels from x86-64
to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
R
e
place
d
all occure
n
ces of
s
t
r(n)case
c
mp with
g
mx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
Fixed stupi
d
mistake w
h
ere a statement
w
as placed be
f
or
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lindahl
Replaced testing
o
f
git version w
i
t
h
testing for featu
r
es
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
na
m
ing
p
roblems fo
r
do
u
ble
p
r
e
cis
i
on Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Fi
x
ed
a typo in
f
util
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lin
d
ahl
Merge bra
n
ch '
r
elease-4-5-patches
'
of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
Cle
a
ned up all i
n
sta
l
led h
e
aders to remo
v
e strict depend
e
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Li
n
dahl
R
e
moved som
e
un
n
ec
e
s
s
ary
#
ifdefs from stri
n
g2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Amber force fields
no
w
pass
validation
.
Bet
a
stat
u
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Linda
h
l
Add
e
d F77
kernel setup
head
e
rs
commit
|
commitdiff
|
tree
2010-08-21
E
r
i
k Lind
a
hl
Fi
x
ed sy
n
chronization co
u
nter update for f77 kernels
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
i
xed a bug f
o
r GB O
B
C born
r
adius calculation
i
n SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lindahl
Fixed
an
uninitialized var
i
ab
l
e bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixe
d
a
minor bug tha
t
caused F
o
rt
r
a
n bu
i
lds t
o
fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Dont wri
t
e nonpolar surface
e
nergy to en
e
r
g
y fil
e
if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lind
a
hl
Fixed so
F
ort
r
an ke
r
nels work again
commit
|
commitdiff
|
tree
next