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Merge release-4-6 into release-5-0
2014-06-26
Roland Sch
u
l
z
Merge relea
s
e-4-6
i
nto
r
elease-5-0
commit
|
commitdiff
|
tree
2014-06-05
Berk
H
ess
Fi
x
ed shift and switch modifiers, particularly for
.
.
.
commit
|
commitdiff
|
tree
2014-06-02
Eri
k
Lindahl
Ad
d
e
d grompp checks for zero atom mass
e
s in state B
commit
|
commitdiff
|
tree
2014-06-01
Erik Lindah
l
Tw
o
quote
s
contributed by Vedr
a
n Mileti
c
commit
|
commitdiff
|
tree
2014-05-27
Ro
l
a
n
d Schulz
Merge relea
s
e-4
-
6 into rel
e
ase-5-0
commit
|
commitdiff
|
tree
2014-05-20
Mark Abraham
Fix copyright
years for new code
commit
|
commitdiff
|
tree
2014-05-13
Mark Ab
r
aham
Prohibit AVX_256 with bu
g
gy
gcc 4
.
6
.
1
commit
|
commitdiff
|
tree
2014-04-29
M
a
rk
A
braham
Merge br
a
nch
r
elease-4-6 in
t
o
r
elease-5
-
0
commit
|
commitdiff
|
tree
2014-04-10
Mark A
b
raham
Mer
g
e bra
n
c
h
're
l
ease-4-6' in
t
o rel
e
ase-5-0
commit
|
commitdiff
|
tree
2014-04-07
Mar
k
Abraham
Version bump for 5
.
0
-rc1
commit
|
commitdiff
|
tree
2014-03-31
Te
e
mu Mur
t
ol
a
Rem
o
ve #
i
nclude <
.
.
.
>
f
o
r
local
f
i
l
es
i
n gmx-v
i
ew
commit
|
commitdiff
|
tree
2014-03-26
Mark Abraham
Fix
u
se of
i
nlin
e
in IMD
commit
|
commitdiff
|
tree
2014-03-23
Mark Abraham
Merge branch release-4-6
commit
|
commitdiff
|
tree
2014-03-18
Mark
Ab
r
aham
Revert "Added new ambe
r
99sb-ildn-bsc0
force field
.
"
commit
|
commitdiff
|
tree
2014-03-17
M
ark
A
b
raham
House
-
keeping for MTTK
commit
|
commitdiff
|
tree
2014-03-17
Mark
A
braham
Merge
b
ranch release-4-6
commit
|
commitdiff
|
tree
2014-03-11
R
o
s
s
en Apo
s
t
o
l
o
v
Remove
d
.
itp
f
iles from t
o
p
l
e
vel
d
i
rectory
.
commit
|
commitdiff
|
tree
2014-03-06
Mark Abraham
Fix formatt
i
ng
i
n
i
nstall guide
commit
|
commitdiff
|
tree
2014-03-06
Mark Abr
a
ham
Fix C
M
ake syntax
e
r
r
or
commit
|
commitdiff
|
tree
2014-03-03
Mark A
b
raham
Fix calling SIMD group kernel
s
commit
|
commitdiff
|
tree
2014-02-26
R
o
la
n
d
S
chul
z
Use r
e
duce in
p
me
commit
|
commitdiff
|
tree
2014-02-26
Erik Lin
d
ahl
R
edesi
g
n
e
d SIMD module and unit tests
.
commit
|
commitdiff
|
tree
2014-02-24
Berk Hess
Implemented LJ-PME nbn
x
n k
e
rnel
s
commit
|
commitdiff
|
tree
2014-02-21
Szilard Pall
porta
b
i
l
ity
a
sp
e
c
ts in ins
t
all guid
e
+ mino
r
t
w
eaks
commit
|
commitdiff
|
tree
2014-02-19
Berk Hess
Imp
l
emented nbnxn LJ switch functions
commit
|
commitdiff
|
tree
2014-02-18
Ma
r
k
Abraham
Fix out
s
tanding
r
eferences to "CP
U
accel
e
ration"
commit
|
commitdiff
|
tree
2014-02-18
Ma
r
k Abra
h
am
Extend TestFileMana
g
e
r
commit
|
commitdiff
|
tree
2014-02-16
Mark Abr
a
ham
Fix
t
est reference data accidentally broken
commit
|
commitdiff
|
tree
2014-02-11
Mar
k
Abraham
U
p
date stuff f
o
r old Blue
G
en
e
commit
|
commitdiff
|
tree
2014-02-09
T
e
emu Mur
t
ola
M
a
ke 'gm
x
-h
'
invaria
n
t wrt
.
p
r
ovided options
commit
|
commitdiff
|
tree
2014-02-09
Te
e
mu Murtola
Remove old help forma
t
ting code
commit
|
commitdiff
|
tree
2014-02-09
Teemu
Murtola
Make FileNameOption behave more lik
e
o
ld filenm
p
arser
commit
|
commitdiff
|
tree
2014-02-09
Teemu Murt
o
la
Implem
e
n
t s
y
nopsis f
o
r
h
elp output
commit
|
commitdiff
|
tree
2014-02-04
Mark
A
br
a
ham
Use feature to explain th
a
t tpbconv h
a
s moved
commit
|
commitdiff
|
tree
2014-02-01
Eri
k
Lindahl
Add
e
d A
V
X2 d
e
t
e
c
tion
t
o
cmake
and crea
t
ed
CP
U
acceleration
.
.
.
commit
|
commitdiff
|
tree
2014-01-29
M
a
rk A
b
raham
Keep cla
n
g Address Sanitize
r
ha
p
py
commit
|
commitdiff
|
tree
2014-01-28
Mark
A
braham
Merge
b
ranch 're
l
e
ase-4-6'
commit
|
commitdiff
|
tree
2014-01-28
M
ark Abraha
m
Remove unused fplog
commit
|
commitdiff
|
tree
2014-01-27
Ma
r
k Abraham
Don't
n
umb
e
r a list manual
l
y
commit
|
commitdiff
|
tree
2014-01-21
Mark Abrah
a
m
Remove hidden option t
o
gmx dum
p
commit
|
commitdiff
|
tree
2014-01-20
Mark Abr
a
ham
R
e
mov
e
var
i
ous outd
a
ted thing
s
from
th
e
repo
commit
|
commitdiff
|
tree
2014-01-20
Mark Abraham
Rename 'gmx tpbconv'
to 'gmx convert-tpr'
commit
|
commitdiff
|
tree
2014-01-20
Magnus Lundborg
A
d
d TNG writing
a
n
d reading sup
p
o
rt
commit
|
commitdiff
|
tree
2014-01-09
R
oland Schu
l
z
Remove
r
emai
n
i
ng usage of SIZEOF*
commit
|
commitdiff
|
tree
2014-01-08
M
ark Abraham
C
r
eate ma
t
h module
commit
|
commitdiff
|
tree
2013-12-05
Mark Abraham
Ve
r
s
i
on bump after 5
.
0
-beta1 releas
e
commit
|
commitdiff
|
tree
2013-12-05
Mark Abraham
Fix administ
r
ivia
commit
|
commitdiff
|
tree
2013-12-02
Mark
A
braham
Version b
u
mp a
f
ter 4
.
6
.
5
release
commit
|
commitdiff
|
tree
2013-12-02
Ber
k
Hess
Made
c
u
t
o
ff-scheme=Verlet the default
commit
|
commitdiff
|
tree
2013-12-02
B
erk
H
e
ss
Rename
d
verlet-buffer-dr
i
ft
t
o
verlet-
b
uffer-tolera
n
c
e
commit
|
commitdiff
|
tree
2013-12-02
Mark Abra
h
a
m
Versio
n
bumps
b
e
f
ore release
commit
|
commitdiff
|
tree
2013-12-02
Mark Abraham
Merge br
a
nch 'release
-
4-6'
commit
|
commitdiff
|
tree
2013-11-28
Teemu Murtola
Fix some #inc
l
ude
problems
.
commit
|
commitdiff
|
tree
2013-11-27
Mark Abr
a
ham
Fix stra
n
ge character in
m
anual
commit
|
commitdiff
|
tree
2013-11-26
Be
r
k
H
ess
Fixed return value of gmx_mtop_bo
n
deds_free_ene
r
g
y
commit
|
commitdiff
|
tree
2013-11-19
Ma
r
k Abr
a
ham
Fix inc
o
rrect var
i
able name in documentation
commit
|
commitdiff
|
tree
2013-11-15
Mark Abraham
Merge b
r
a
n
ch r
e
l
e
a
se-4-6
commit
|
commitdiff
|
tree
2013-11-13
Mark Abraham
Bump version after 4
.
6
.
4 release
commit
|
commitdiff
|
tree
2013-11-08
Ma
r
k A
b
raham
Fi
x
m
a
lformed CMake
commit
|
commitdiff
|
tree
2013-10-26
Rola
n
d
Schulz
Fix NBNxN SIMD reference kernels
commit
|
commitdiff
|
tree
2013-10-26
Mar
k
A
b
raham
Enca
p
su
l
ate gmx_wall
c
lock_accounting
_
t in
t
o
new
t
iming
.
.
.
commit
|
commitdiff
|
tree
2013-10-23
Mar
k
A
b
rah
a
m
Mer
g
e branch release-4-6 in
t
o master
commit
|
commitdiff
|
tree
2013-10-20
Ma
r
k
Ab
r
aham
Remove
html
t
a
rg
e
t from and exce
s
sive PDFs for manual
commit
|
commitdiff
|
tree
2013-10-14
Szilard P
a
ll
u
s
e CUDA textu
r
e obj
e
c
ts whe
n
supported
commit
|
commitdiff
|
tree
2013-10-08
Mark Abraham
Remove so
m
e unus
e
d variables from MD l
o
op
commit
|
commitdiff
|
tree
2013-10-06
Ma
r
k Abraham
Fixed t
r
igger
i
ng of CPU ac
c
el
e
ration-s
c
heme de
t
ection
commit
|
commitdiff
|
tree
2013-10-04
Teemu Murtola
Clean up CTest usage
.
commit
|
commitdiff
|
tree
2013-10-03
Chr
i
sto
p
h Junghans
Fix parallel
b
ui
l
d for GMX
_
BUI
L
D
_
O
W
N_
F
FTW
commit
|
commitdiff
|
tree
2013-09-26
Mark Abraham
Merge branch
release
-
4-6
commit
|
commitdiff
|
tree
2013-09-26
Mark
A
b
r
aham
Remove Gen
e
ral Coupling Theory s
t
uff
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraha
m
Merge branch '
r
elea
s
e-
4
-6'
commit
|
commitdiff
|
tree
2013-08-15
Mar
k
A
b
raham
Prod
u
ctive afternoon of meetings
.
.
.
more quot
e
s
!
commit
|
commitdiff
|
tree
2013-08-09
Mark Abra
h
am
Reordered
FFTW fatal erro
r
; avoid
s
using unset variables
commit
|
commitdiff
|
tree
2013-07-26
Mark Abraha
m
Merge branch release-
4
-6 into m
a
s
t
er
commit
|
commitdiff
|
tree
2013-07-24
Mark Abraham
Merg
e
bra
n
ch release-4-6 into ma
s
ter
commit
|
commitdiff
|
tree
2013-06-27
Roland Schulz
Merge
branch
'
release-4-6'
int
o
maste
r
commit
|
commitdiff
|
tree
2013-06-16
Jeff
H
ammond
Define
both C and
C
++
c
om
p
il
e
rs in BGQ toolchains;
.
.
.
commit
|
commitdiff
|
tree
2013-06-16
Jeff
Ham
m
ond
Use
m
ore
o
bvi
o
us na
m
e o
f
BGQ compiler
MPI
wrappers
commit
|
commitdiff
|
tree
2013-06-16
J
e
ff
Hammond
fix
CMake bug rel
a
ted to TestQPX
.
c location
commit
|
commitdiff
|
tree
2013-06-16
Jeff Hammond
f
i
xed
a
t
y
po (un
c
losed brac
k
et)
that cau
s
e CMake to
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
Ma
r
k Abraha
m
Ne
w
patc
h
release
4
.
6
.
2
commit
|
commitdiff
|
tree
2013-05-26
Micha
e
l Sh
i
rt
s
Fix of mem
o
ry leak
commit
|
commitdiff
|
tree
2013-05-07
Mark Ab
r
aham
F
i
x e
x
tan
t
refe
r
e
nce
s
to
f
o
r
m
e
r GPL
l
icensing
commit
|
commitdiff
|
tree
2013-04-26
Michae
l
Shirts
Fixing a p
r
oblem
w
i
t
h dh/dl 1-4 intera
c
t
i
o
ns
commit
|
commitdiff
|
tree
2013-04-26
Mark Abraham
Update linking to
M
KL and
d
ocume
n
t sam
e
commit
|
commitdiff
|
tree
2013-04-19
Mark
Abraham
v-r
e
scale works
with tau
-
t >= 0
commit
|
commitdiff
|
tree
2013-03-11
Mar
k
Abraham
Adde
d
in
s
t
a
ll guide section for BLAS/LAPACK
commit
|
commitdiff
|
tree
2013-03-05
Ma
r
k Abraham
War
n
i
f X11 was not fo
u
nd and the u
s
er
w
a
n
ted it
commit
|
commitdiff
|
tree
2013-03-05
M
ark Abraham
f
i
x
broken things i
n
mkh
t
ml
commit
|
commitdiff
|
tree
2013-02-26
Mark A
b
raham
Unc
r
ustified cod
e
changes since 4
.
6
commit
|
commitdiff
|
tree
2013-02-20
Mark
Abraham
Mer
g
e
r
elease
-
4
-
5-pa
t
ches into release-4-6
commit
|
commitdiff
|
tree
2013-02-18
R
oland Schulz
Issue errors/
w
arnings for
I
CC before 12
.
0
.
0
commit
|
commitdiff
|
tree
2013-02-15
Michae
l
Shirts
bugfix for
m
d-vv +
n
o
s
e-hoover +
(
nstcalcenergy > nsttcouple)
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Us
e
explicit kernel
p
oint
e
r typecas
t
s
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraha
m
Bump shared obje
c
t version to 7
commit
|
commitdiff
|
tree
2013-02-15
Peter Kasson
Unwi
n
ds flag
d
ep
e
ndencies in g_o
r
d
e
r
.
commit
|
commitdiff
|
tree
2013-02-13
Mark Abrah
a
m
Fi
x
cod
e
bug w
i
th
t
hread-MPI
o
n Powe
r
P
C with xlc
commit
|
commitdiff
|
tree
2013-02-13
Mar
k
Abra
h
am
Mor
e
d
escriptive V
e
rl
e
t k
e
rnel macro para
m
e
t
er names
commit
|
commitdiff
|
tree
2013-02-13
M
ark Abrah
a
m
Fix and add Verlet kernel error
messages
commit
|
commitdiff
|
tree
2013-02-13
Mark Abraham
Re-ge
n
erated
group ke
r
nels
commit
|
commitdiff
|
tree
next