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Merge branch release-5-1
2015-05-09
M
a
rk Abraham
Merge branch re
l
e
ase
-
5-0
commit
|
commitdiff
|
tree
2015-05-06
Mar
k
Abraham
Fix
e
d recently-in
t
r
o
duced couple
-
lam
b
da warning message
commit
|
commitdiff
|
tree
2015-05-06
Mark Abraham
Fix
S
IMD unit tests on BG/Q
commit
|
commitdiff
|
tree
2015-05-05
Ma
r
k A
b
raham
Merge release
-
4
-
6
i
nto release-5-0
commit
|
commitdiff
|
tree
2015-04-30
M
ark Abraham
Mov
e
GPU imple
m
e
n
tation to new inte
r
face
commit
|
commitdiff
|
tree
2015-04-28
Mark
A
braham
Add application-c
l
ock NVML-b
a
s
e
d support for Quadro
.
.
.
commit
|
commitdiff
|
tree
2015-04-27
Mark
A
b
r
aham
Clean up
r
e
m
n
a
nts
i
n m
d
run
commit
|
commitdiff
|
tree
2015-04-24
Mark Abra
h
am
Add develo
p
er
d
o
cs for n
e
w documentation infrastruct
u
re
commit
|
commitdiff
|
tree
2015-04-23
M
ark Abraham
First beta
r
ele
a
s
e of 5
.
1
commit
|
commitdiff
|
tree
2015-04-21
Mark
A
braham
Merge "Me
r
ge branch release-5-0"
commit
|
commitdiff
|
tree
2015-04-17
Mar
k
Abraham
Ad
d
comment abou
t
Andersen
themostat a
n
d constraints
commit
|
commitdiff
|
tree
2015-04-09
M
ark Abr
a
ham
M
e
rg
e
branch r
e
lease
-
5-0
commit
|
commitdiff
|
tree
2015-04-08
Ma
r
k Abraham
Update mdrun Dox
y
gen
commit
|
commitdiff
|
tree
2015-04-08
Mark Ab
r
aham
Made
p
me_work_t op
a
que
commit
|
commitdiff
|
tree
2015-04-01
Mark Ab
r
aham
Initiali
z
e n_tr
i
cvec fiel
d
of t_pbc always
commit
|
commitdiff
|
tree
2015-03-30
M
a
rk Abraham
Imp
r
o
v
e
d man-p
a
g
e machinery
commit
|
commitdiff
|
tree
2015-03-19
M
ark
A
b
raham
Made err
o
r message more generic
commit
|
commitdiff
|
tree
2015-03-19
Ma
r
k Abraham
Exten
d
Forc
e
sub-
c
o
u
nte
r
s
commit
|
commitdiff
|
tree
2015-03-13
Mark Abraham
Made GPU warning
m
essages more
u
ser friendly
commit
|
commitdiff
|
tree
2015-03-06
Mark A
b
raham
Restore wal
l
cycle
subco
u
nter name to "Bonde
d
F"
commit
|
commitdiff
|
tree
2015-03-05
Mark
A
b
raham
Fix
A
ndersen
thermostats
commit
|
commitdiff
|
tree
2015-03-03
Mark
A
br
a
h
am
Re-implement gmx
tune_
p
m
e
-cpi
commit
|
commitdiff
|
tree
2015-03-03
Mark Abrah
a
m
M
ov
e
m
d
run
signalling c
o
d
e
commit
|
commitdiff
|
tree
2015-03-03
Mark Ab
r
aham
A
dd test that pla
i
n mult
i
-simulation works
commit
|
commitdiff
|
tree
2015-03-02
Mar
k
Abr
a
ham
Run replica-exchan
g
e tests with MPI enabled
commit
|
commitdiff
|
tree
2015-03-02
Mark Abraham
Add infrastructure for running MPI integrat
i
on tests
commit
|
commitdiff
|
tree
2015-02-25
Mark Abraham
New and r
e
organized documenta
t
i
on
commit
|
commitdiff
|
tree
2015-02-25
Mark Abraham
Add conten
t
to user gui
d
e
commit
|
commitdiff
|
tree
2015-02-25
Mark Ab
r
ah
a
m
S
plit pme
.
c i
n
t
o
multiple
f
iles
commit
|
commitdiff
|
tree
2015-02-25
Mark Abraham
Add mdp-
o
ptions to us
e
r guide
commit
|
commitdiff
|
tree
2015-02-18
Mark Abraham
Reenable SIMD for
R-B dihedrals
commit
|
commitdiff
|
tree
2015-02-13
Ma
r
k Abraham
F
i
x mdrun-only build
commit
|
commitdiff
|
tree
2015-02-13
M
ark Abraham
Implemented documentation
w
ith sphinx
commit
|
commitdiff
|
tree
2015-02-04
Mark Abraham
Implement user guid
e
commit
|
commitdiff
|
tree
2015-02-02
Mark Abraham
Merge
b
ranch release-5-0
commit
|
commitdiff
|
tree
2015-02-02
Mark A
b
raham
A
v
oid nea
r
-silent ge
n
eration of zer
o
ener
g
i
e
s
commit
|
commitdiff
|
tree
2015-02-02
Mark Ab
r
aham
Fix use of
s
imd
.
h
commit
|
commitdiff
|
tree
2015-01-23
M
ark Abraham
Change some listed-forces
h
eaders to be library-only
commit
|
commitdiff
|
tree
2015-01-23
Mark
A
braham
Update Fi
n
dCUDA work-around
commit
|
commitdiff
|
tree
2015-01-20
Mark Abr
a
ham
Removed
g
m
x
_he
a
der_co
n
f
ig
.
h
commit
|
commitdiff
|
tree
2015-01-16
M
a
r
k Abraha
m
F
i
x
BlueGe
n
e/Q bui
l
d with r
e
cent CMa
k
e
commit
|
commitdiff
|
tree
2015-01-15
Ma
r
k
A
b
raham
Merge branch
r
elease-
5
-
0
commit
|
commitdiff
|
tree
2015-01-14
Mar
k
Abraham
Fix
and suppre
s
s warning
s
on BlueGene/Q
commit
|
commitdiff
|
tree
2015-01-14
M
a
rk Abra
h
am
Refactor O
p
enMP initial
i
z
a
tion
commit
|
commitdiff
|
tree
2015-01-14
Mark Abraham
Remove temporary symlinks from pre-5
.
0 t
o
ol names
commit
|
commitdiff
|
tree
2015-01-09
M
a
r
k
Abra
h
am
Remove mdrun -testverlet
commit
|
commitdiff
|
tree
2015-01-08
Mark
A
br
a
h
am
Handle ivec*
c
orrectly in DD error messa
g
e
commit
|
commitdiff
|
tree
2015-01-08
Ma
r
k
A
brah
a
m
F
i
x fl
o
a
t
ing-point exception
commit
|
commitdiff
|
tree
2014-12-16
M
ar
k
Abrah
a
m
Move code to prepare for GPU int
e
rface rework
commit
|
commitdiff
|
tree
2014-12-15
Mark
A
b
raham
Merge branch
'release-5-0'
commit
|
commitdiff
|
tree
2014-12-15
Mark
Abraham
Removing i
t
eration + constraints fra
m
ework
commit
|
commitdiff
|
tree
2014-12-15
Mark A
b
r
aham
Versio
n
bumps
aft
e
r new releas
e
commit
|
commitdiff
|
tree
2014-12-15
Mark A
b
raham
Version 5
.
0
.
4
commit
|
commitdiff
|
tree
2014-12-15
Mark
A
braham
Fix
c
onstraints checks
i
n
gromp
p
commit
|
commitdiff
|
tree
2014-12-15
Mark Abraham
Merge "M
e
rge relea
s
e-4
-
6 into rele
a
se-5-0" int
o
release-5-0
commit
|
commitdiff
|
tree
2014-12-13
Mark A
b
raham
Remove heuristic group-sc
h
eme neighbour-list up
d
a
te
s
commit
|
commitdiff
|
tree
2014-12-13
Mark Abraham
F
ix laten
t
bu
g
in
O
penMP initializati
o
n
commit
|
commitdiff
|
tree
2014-12-12
Mark Abraham
Add Strin
g
Forma
t
ter and formatAndJoin to stri
n
gutil
commit
|
commitdiff
|
tree
2014-12-11
Mark Abraham
Merge release-4
-
6
into release-5-
0
commit
|
commitdiff
|
tree
2014-12-09
Mark
A
b
raha
m
Versi
o
n
b
u
m
p
s
after new r
e
lease
commit
|
commitdiff
|
tree
2014-12-09
Mark Abra
h
am
Ve
r
si
o
n
5
.
0
.
3
commit
|
commitdiff
|
tree
2014-12-08
Mark Ab
r
ah
a
m
M
e
rge "Merge
r
e
l
ease-5-0 into master"
commit
|
commitdiff
|
tree
2014-12-08
Mark Abraha
m
Fix group-sc
h
e
m
e
bug wit
h
ch
a
ng
i
ng
L
J p
a
rame
t
ers in FE
commit
|
commitdiff
|
tree
2014-12-08
Mark Abraham
Add basic GPU support for
g
mx tune
-
pme
commit
|
commitdiff
|
tree
2014-12-05
M
a
rk Abraham
C
l
e
a
n up no
n
-PME p
a
r
t
o
f
ewal
d
m
o
dule
commit
|
commitdiff
|
tree
2014-12-05
M
a
rk Ab
r
aham
M
ake
m
drun pr
i
nt the list of compa
t
i
b
l
e
G
PUs
commit
|
commitdiff
|
tree
2014-12-05
Mark Ab
r
aham
Move threading
s
uppo
r
t into lis
t
e
d
-
forces modu
l
e
commit
|
commitdiff
|
tree
2014-12-05
Mar
k
Abraham
C
r
eated do_for
c
e_listed an
d
m
o
ved
code to the modul
e
commit
|
commitdiff
|
tree
2014-11-27
M
ar
k
Abraham
Convert remaining callers
of do_force
t
o C++
commit
|
commitdiff
|
tree
2014-11-27
Mark Abraham
Remove us
e
of interaction_mask_indices on BG/Q
commit
|
commitdiff
|
tree
2014-11-27
Ma
r
k Abraham
M
erg
e
branch
re
l
e
ase-4-6 into rel
e
ase-
5
-0
commit
|
commitdiff
|
tree
2014-11-27
Ma
r
k
A
braham
M
e
r
g
e "Mer
g
e
r
elease-5-0 into master"
commit
|
commitdiff
|
tree
2014-11-26
Mark A
b
raham
Fix trjconv modi
f
yin
g
fr
.
t
i
m
e
u
n
n
ecess
a
rily
commit
|
commitdiff
|
tree
2014-11-26
Mark Abra
h
a
m
Mo
v
e code
t
o domdec
m
o
d
u
l
e
folder
commit
|
commitdiff
|
tree
2014-10-17
Mark
Abraham
E
xten
d
gmock to turn off s
o
cket
l
ist
e
ner
commit
|
commitdiff
|
tree
2014-10-17
M
a
rk A
b
raham
M
ov
e
code
t
o what wil
l
b
e
come the ewald
m
od
u
le
commit
|
commitdiff
|
tree
2014-10-15
Mark Abraham
Converted many integrator-loop
files
to C++
commit
|
commitdiff
|
tree
2014-10-13
Mar
k
Ab
r
a
ham
Merge release-4-
6
into re
l
ease-5-0
commit
|
commitdiff
|
tree
2014-10-09
Mark
A
braham
Fixed minor iss
u
e with NPT conserv
e
d energy
commit
|
commitdiff
|
tree
2014-10-09
Mar
k
Abraham
Clean up cshake() and resolve o
l
d issu
e
s
commit
|
commitdiff
|
tree
2014-10-06
Ma
r
k Abraham
Fix trjconv -spli
t
not clos
i
ng files
commit
|
commitdiff
|
tree
2014-10-03
Ma
r
k Abr
a
ham
M
ove pair-i
n
terac
t
ion co
d
e
into listed-forces module
commit
|
commitdiff
|
tree
2014-10-03
Mark Abrah
a
m
U
n
ite code
f
or h
a
nd
l
ing listed pair
s
commit
|
commitdiff
|
tree
2014-10-01
Mark Abraham
Merge
re
l
ease-5-0 into master
commit
|
commitdiff
|
tree
2014-10-01
Mark Abrah
a
m
Version bumps afte
r
n
ew rel
e
ase
commit
|
commitdiff
|
tree
2014-10-01
M
a
rk
A
braha
m
V
ersion 5
.
0
.
2
commit
|
commitdiff
|
tree
2014-09-29
Mark Abraham
Merg
e
"Merge
r
ele
a
se-4-6 into
r
elease-5-0" into
r
elease-
5
-0
commit
|
commitdiff
|
tree
2014-09-23
Ma
r
k Ab
r
aham
Renamed bonded module as 'listed-
f
orce
s
'
commit
|
commitdiff
|
tree
2014-09-23
Mark Abr
a
ham
Refactor mdrun integrati
o
n
t
e
s
ts
commit
|
commitdiff
|
tree
2014-09-22
Mark Abr
a
h
am
More quote
s
commit
|
commitdiff
|
tree
2014-09-18
Mark Abraham
Mer
g
e branch release-4-6 into
r
elease-5-
0
commit
|
commitdiff
|
tree
2014-09-13
M
a
rk Abraha
m
Teach git that some f
i
l
es are bina
r
y
commit
|
commitdiff
|
tree
2014-09-12
Mark Abraham
M
i
nor chan
g
e
s to mdru
n
-h descri
p
tions
commit
|
commitdiff
|
tree
2014-09-11
Mark Abraham
Remo
v
e docume
n
tatio
n
references t
o
op
t
imize-fft
commit
|
commitdiff
|
tree
2014-09-11
Ma
r
k
Abr
a
ham
Conver
t
d
omdec code to C++
commit
|
commitdiff
|
tree
2014-09-05
Mark A
b
raham
Version bumps after new
r
el
e
ase
commit
|
commitdiff
|
tree
2014-09-05
Mark Abra
h
a
m
Version 5
.
0
.
1
commit
|
commitdiff
|
tree
2014-09-04
Mark Abraham
C
r
e
a
t
ed bonded module
commit
|
commitdiff
|
tree
2014-09-03
Ma
r
k Ab
r
a
h
am
F
i
x
mis
-
use of fabs in
L
APAC
K
commit
|
commitdiff
|
tree
2014-09-03
Mar
k
Abraham
More hacki
n
g
t
o get the te
m
plate to d
e
tect
a
nd build
commit
|
commitdiff
|
tree
next