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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-09-01
Mark
Abraham
M
erg
e
"Mer
g
e branch releas
e
-4-6 into re
l
ease-5-0"
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Fixes and updates to BlueGene/Q s
u
p
p
ort
commit
|
commitdiff
|
tree
2014-09-01
Mark Abraham
Merge br
a
n
c
h rele
a
se-4-6 into release-5-0
commit
|
commitdiff
|
tree
2014-09-01
Mark Ab
r
aham
Merge "Merge
branch re
l
ease-4-6 int
o
rele
a
se-
5
-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-08-29
Mark Ab
r
ah
a
m
V
e
rsi
o
n bum
p
after 4
.
6
.
7
commit
|
commitdiff
|
tree
2014-08-29
Mark Abraham
Merge branch r
e
lease-4
-
6 into releas
e
-
5-0
commit
|
commitdiff
|
tree
2014-08-23
Mark
Abraham
Gener
a
li
z
e markdown configuratio
n
m
a
chine
r
y
commit
|
commitdiff
|
tree
2014-08-23
Mark Abraham
Unif
y
do
c
u
me
n
tation
f
or webpage bui
l
d
commit
|
commitdiff
|
tree
2014-08-22
M
ark Ab
r
a
h
am
Fix
z
lib usa
g
e
with TNG
commit
|
commitdiff
|
tree
2014-08-16
Mark
Abraham
Fix gmx tune_pm
e
with LJ
-
PME
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraha
m
Fix wallcy
c
le counting
wi
t
h md-v
v
, sd and sd
2
commit
|
commitdiff
|
tree
2014-07-09
Mark Abraham
Name th
e
tarball
h
ow
we
like i
t
commit
|
commitdiff
|
tree
2014-07-09
Mark
Ab
r
aham
Quieten
r
epeated cmake run
s
commit
|
commitdiff
|
tree
2014-07-07
Mark Abraham
Fix tarball and
i
nstall, particularly f
o
r
I
NSTAL
L
commit
|
commitdiff
|
tree
2014-07-07
Mark Abra
h
a
m
V
e
rsi
o
n bump af
t
e
r
4
.
6
.
6 release
commit
|
commitdiff
|
tree
2014-07-01
Mark Abra
h
am
Fix
GMock to
wor
k
on MS
V
C
commit
|
commitdiff
|
tree
2014-06-29
M
a
rk Abraham
Ver
s
i
o
n bump for 5
.
0
commit
|
commitdiff
|
tree
2014-06-29
Mark Abrah
a
m
A
dd forgotten licen
s
es
t
o COPYING
commit
|
commitdiff
|
tree
2014-06-29
Mark A
b
rah
a
m
Refer to "mixed"
precision
i
n
u
ser-facing documentati
o
n
commit
|
commitdiff
|
tree
2014-06-29
Mark
A
bra
h
am
Convert inst
a
ll
g
u
ide to markdown
commit
|
commitdiff
|
tree
2014-06-29
M
a
rk Abraham
Merge "Merge rel
e
ase-4-6 into r
e
lease-5-
0
" into release-5-0
commit
|
commitdiff
|
tree
2014-06-28
Mark A
b
ra
h
am
Merge
b
r
anch 'release-
4
-6' into relea
s
e-5-0
commit
|
commitdiff
|
tree
2014-06-28
Mark Abrah
a
m
Use p
a
rall
e
l terminology
m
ore consis
t
ently
commit
|
commitdiff
|
tree
2014-06-26
M
a
rk
A
bra
h
a
m
M
erge "M
e
r
ge
r
elease-4-6 into release-5-0
"
into release-5-0
commit
|
commitdiff
|
tree
2014-06-24
Mark
A
bra
h
a
m
Manual fixes
commit
|
commitdiff
|
tree
2014-06-18
Mark Abraham
Made m
d
run w
a
r
n when
g
eneric kernels are used
commit
|
commitdiff
|
tree
2014-06-06
Mark Abraham
Merge
release-4-6 into relea
s
e-5-0
commit
|
commitdiff
|
tree
2014-06-05
Mark Abraham
New quotes
commit
|
commitdiff
|
tree
2014-06-03
Mark Abraham
Use RNG correc
t
ly for v-re
s
cale thermo
s
t
at
commit
|
commitdiff
|
tree
2014-05-30
Mark
Abraham
Finaliz
e
chan
g
e fr
o
m GMX_CPU_ACCELERATIO
N
to GMX_
S
IMD
commit
|
commitdiff
|
tree
2014-05-22
Mark
Abraham
Add
f
atal e
r
ro
r
s for VV and twin-ran
g
e
MTS
commit
|
commitdiff
|
tree
2014-05-22
M
ark Ab
r
a
h
am
Clarified docs for
u
se
o
f mdrun
-nstlist
commit
|
commitdiff
|
tree
2014-05-20
Mark Ab
r
aham
Fix copyright
y
ears f
o
r ne
w
code
commit
|
commitdiff
|
tree
2014-05-20
Mark Abraham
A
dd no
t
e
about c
o
rrect cal
l
ing
o
f wallcyc
l
e co
u
nter
commit
|
commitdiff
|
tree
2014-05-18
Mark Abraham
Fix in
d
enting of
.
tpr parameter
d
ump
in md
r
un log file
commit
|
commitdiff
|
tree
2014-05-13
Mark Abraham
Proh
i
bit AVX_256 with buggy
g
cc 4
.
6
.
1
commit
|
commitdiff
|
tree
2014-04-29
Mar
k
A
b
raham
Mer
g
e
branch release-
4
-6
i
nto r
e
lease-5-0
commit
|
commitdiff
|
tree
2014-04-16
Mark Ab
r
aham
Fix and simplify version matchin
g
for running tests
commit
|
commitdiff
|
tree
2014-04-10
Mark Ab
r
aham
Merge branc
h
'release-4
-
6
'
i
nto release
-
5-0
commit
|
commitdiff
|
tree
2014-04-10
Mark Abraham
F
u
r
t
her fix to
gmx tune-pme
commit
|
commitdiff
|
tree
2014-04-07
Mark Abra
h
am
Fi
x
invalid
dereferen
c
e in g
_
t
u
ne_pme
commit
|
commitdiff
|
tree
2014-04-07
Mark Abraha
m
Version bump f
o
r
5
.
0
-
rc
1
commit
|
commitdiff
|
tree
2014-04-03
Mark Abrah
a
m
Move stri
n
g-parsing
co
d
e to
where
i
t ca
n
b
e
reuse
d
commit
|
commitdiff
|
tree
2014-04-02
Mark
Abrah
a
m
F
ixes for g_tune
_
pme f
o
r 5
.
0
commit
|
commitdiff
|
tree
2014-04-02
Mark Abraham
Fix bu
g
accumulating nra
n
k_pp_
i
n
tranode on PME ranks
commit
|
commitdiff
|
tree
2014-04-02
M
ark Abraham
Re-use gmx
_
greate
s
t_c
o
mmon_divisor()
commit
|
commitdiff
|
tree
2014-03-31
Mark Abraham
Remove quot
e
commit
|
commitdiff
|
tree
2014-03-26
Mark Abraham
F
ix use of i
n
li
n
e in
IM
D
commit
|
commitdiff
|
tree
2014-03-23
Mark Abraha
m
Ke
e
p CMake quiet ab
o
ut non-de
t
e
c
t
ion of optional
s
t
uf
f
commit
|
commitdiff
|
tree
2014-03-23
Mark Abraham
Merge branch
r
e
l
eas
e
-4-
6
commit
|
commitdiff
|
tree
2014-03-23
M
ark Abraham
Fix pr
i
nt_date_an
d
_time
commit
|
commitdiff
|
tree
2014-03-18
Mark
A
b
r
aham
Rev
e
rt
"Added new amber99
s
b-ild
n
-
b
sc0 force field
.
"
commit
|
commitdiff
|
tree
2014-03-18
M
a
r
k Ab
r
aham
R
e
m
o
ved more stuff rel
a
t
ed
t
o gmx
.
ff an
d
gmx2
.
ff
commit
|
commitdiff
|
tree
2014-03-17
M
a
rk Abraham
Ho
u
s
e-keeping for MTTK
commit
|
commitdiff
|
tree
2014-03-17
Mar
k
Abraham
Merge "Mer
g
e branch rel
e
ase-4-6"
commit
|
commitdiff
|
tree
2014-03-17
M
a
rk A
b
raham
Merge bran
c
h
rel
e
ase-4
-
6
commit
|
commitdiff
|
tree
2014-03-17
M
ar
k
Abraham
Fix
perturb
a
tion to Verlet scheme
when not perturbing
commit
|
commitdiff
|
tree
2014-03-11
M
ark Ab
r
ah
a
m
Fix MKL linking
commit
|
commitdiff
|
tree
2014-03-11
Mark A
b
rah
a
m
Avoid a
r
r
ay-bounds warni
n
gs with
gcc 4
.
8
.
2
commit
|
commitdiff
|
tree
2014-03-10
Mark Abra
h
am
Fix dependency on sw
a
pcoords enu
m
s
commit
|
commitdiff
|
tree
2014-03-06
Mark
A
braham
Fix format
t
ing in i
n
stall g
u
ide
commit
|
commitdiff
|
tree
2014-03-06
Mark Abraham
Fix CMake
s
yntax error
commit
|
commitdiff
|
tree
2014-03-05
M
ark Abra
h
a
m
M
e
r
g
e "
M
erge r
e
lease-4-6 into master"
commit
|
commitdiff
|
tree
2014-03-04
Mark Ab
r
aham
Add enum and do
c
s f
o
r
u
s
ing tpx_version
commit
|
commitdiff
|
tree
2014-03-03
Mark Ab
r
a
ham
Fix calling SIMD gr
o
up kern
e
ls
commit
|
commitdiff
|
tree
2014-03-01
Mark Abr
a
ham
Add fatal error
for Andersen
+
constrai
n
ts+DD
commit
|
commitdiff
|
tree
2014-02-26
Ma
r
k Abraham
Add T
h
r
eadSani
t
izer
buil
d
type
commit
|
commitdiff
|
tree
2014-02-25
Mark Abraham
Keep c
o
mp
i
lers happ
y
on BG/Q
commit
|
commitdiff
|
tree
2014-02-24
Mark Ab
r
aham
Cl
e
an up
options fo
r
domain de
c
ompositi
o
n
commit
|
commitdiff
|
tree
2014-02-24
Mark
A
braham
Permit warning
-
free use o
f
Andersen thermo
s
t
a
t
commit
|
commitdiff
|
tree
2014-02-24
Mark Abraham
S
u
ppress
icc warn
i
n
g
for Boost
1
.
5
5
use of #pragma
.
.
.
commit
|
commitdiff
|
tree
2014-02-21
M
a
rk
Abraham
Rei
n
state shell code with DD
commit
|
commitdiff
|
tree
2014-02-20
Mark Abraham
Remove particle decomposition
commit
|
commitdiff
|
tree
2014-02-20
Mark Abraham
avoid mdrun crash w
h
en rdtsc
p
is not supporte
d
commit
|
commitdiff
|
tree
2014-02-20
Mark Abraham
Add integration tests for
r
eplica e
x
change
commit
|
commitdiff
|
tree
2014-02-19
Mark Abraham
M
ake s
o
m
e
variable names less
cryptic
commit
|
commitdiff
|
tree
2014-02-18
Mark
A
b
r
a
ham
F
i
x outst
a
nding
r
efe
r
ences to "CPU acceleration"
commit
|
commitdiff
|
tree
2014-02-18
M
ark Abraham
Fix harmless bug w
i
th co
m
b
i
natio
n
of gro
u
p
a
nd twin
.
.
.
commit
|
commitdiff
|
tree
2014-02-18
Mark Abra
h
am
Extend TestFileManager
commit
|
commitdiff
|
tree
2014-02-16
Mark Ab
r
aham
Fix test refer
e
nce data accide
n
t
a
lly
b
roken
commit
|
commitdiff
|
tree
2014-02-16
Ma
r
k Abraham
Remove suppor
t
f
o
r
.
g87
an
d
.
xyz I/
O
formats
commit
|
commitdiff
|
tree
2014-02-12
M
ark Abraham
Refactored 'solvate
'
and '
i
nsert-
m
o
l
ecules'
commit
|
commitdiff
|
tree
2014-02-12
Mark Abraham
R
e-fix compiler
warn
i
ngs with sc
a
nner
.
cpp
commit
|
commitdiff
|
tree
2014-02-11
M
ark Abraham
S
p
lit gen
b
ox into 'solvate' and 'in
s
ert-m
o
l
e
cules'
commit
|
commitdiff
|
tree
2014-02-11
Mark Abraham
Update
stuff
f
or old BlueGen
e
commit
|
commitdiff
|
tree
2014-02-09
Mark Abraham
M
o
ve orientation r
e
straints
c
heck
s
inside init function
commit
|
commitdiff
|
tree
2014-02-08
Mark Abraham
Cl
e
an
up
.
log file
d
ump of inputrec
commit
|
commitdiff
|
tree
2014-02-08
M
a
rk Abraham
Issue fatal error
s
rather tha
n
use broken s
h
ell code
commit
|
commitdiff
|
tree
2014-02-07
M
a
rk Abraham
Initial
i
ze i
n
putrec bet
t
er in genbox
commit
|
commitdiff
|
tree
2014-02-06
Mark
A
braham
Remove antiquated an
d
unused gmxpa
r
.
tex documentation
commit
|
commitdiff
|
tree
2014-02-05
Mark A
b
raha
m
Update
d
escription of genrestr
commit
|
commitdiff
|
tree
2014-02-04
Mark Abr
a
ham
Use
feature
to
e
xplain
that t
p
b
c
onv h
a
s
moved
commit
|
commitdiff
|
tree
2014-02-03
M
ark Abraham
A
dd hack to
fix ge
n
box
commit
|
commitdiff
|
tree
2014-02-03
Ma
r
k Abraha
m
C
l
e
an
u
p g
e
n
box
and asso
c
iated code
commit
|
commitdiff
|
tree
2014-02-03
Mark A
b
ra
h
a
m
I
mpr
o
ved wallcycle reporting
commit
|
commitdiff
|
tree
2014-01-30
Mark Ab
r
aham
Mi
n
or impr
o
vements to ewald_LR
c
orrection
commit
|
commitdiff
|
tree
2014-01-29
Mark Abraha
m
Imp
r
oved dependencies on maths inc
l
ud
e
s
commit
|
commitdiff
|
tree
2014-01-29
Mark Abraham
Ke
e
p
clang Address Sanitizer
h
ap
p
y
commit
|
commitdiff
|
tree
2014-01-28
Mark Abraham
Merge b
r
anch 're
l
ease
-
4-6'
commit
|
commitdiff
|
tree
2014-01-28
Mar
k
Abraham
Remov
e
"gmx trjconv -app"
commit
|
commitdiff
|
tree
next