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Refactor SD update
2018-04-25
M
a
rk Abraham
Ref
a
c
t
o
r
SD update
commit
|
commitdiff
|
tree
2018-04-18
M
a
r
k A
b
raham
I
n
troduce gmx
_
used_i
n
_
debu
g
commit
|
commitdiff
|
tree
2018-04-17
Mark
A
braham
Shift per-step
c
ontr
o
l
lo
g
ic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark
Abra
h
am
B
r
eak
a
part update_const
r
aints
commit
|
commitdiff
|
tree
2018-04-16
Mar
k
Abraham
Updated
mdrun co
m
parison
i
nfrastructure
commit
|
commitdiff
|
tree
2018-04-13
Mark
Ab
r
aham
Merge bra
n
c
h
r
e
l
ease-
2
018
commit
|
commitdiff
|
tree
2018-04-13
Mark A
b
raham
Clean
up
c
o
nstraints code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remove
use of w
h
ere
(
), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reorganize energy evaluation
f
o
r EM
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Simp
l
ified handling of si
m
u
l
ation r
u
nner
s
commit
|
commitdiff
|
tree
2018-04-05
M
ark Abraham
Create grom
a
c
s/mdrun module and m
o
ve
co
d
e th
e
re
commit
|
commitdiff
|
tree
2018-04-04
Mark Abrah
a
m
Quiet chec
k
poi
n
t
reading
commit
|
commitdiff
|
tree
2018-04-03
Mar
k
Abr
a
ham
Remo
v
e
leftover mention of
tw
i
n-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
M
erge "Me
r
ge
br
a
nc
h
r
e
le
a
s
e
-
2018"
commit
|
commitdiff
|
tree
2018-03-28
Mark Abra
h
am
F
ree more memory
i
n grompp an
d
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Mar
k
Abraham
Merge branch
release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Clarified md
p
options relating to bonds
commit
|
commitdiff
|
tree
2018-03-27
M
a
r
k A
b
raham
More gcc-8 fixes for POWER
commit
|
commitdiff
|
tree
2018-03-22
Mark Abrah
a
m
Updat
e
d to
prepare for 2018
.
2 rel
e
ase
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abr
a
h
a
m
Version 2
0
1
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark
Abraham
M
e
rg
e
"Merge branch release-20
1
6
int
o
r
e
lease-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Ab
r
aham
Update release n
o
tes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Merge branch
release-2
0
1
6
into release-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update
use
o
f gpu_
i
d
in J
e
n
kins
commit
|
commitdiff
|
tree
2018-03-20
M
ark Ab
r
aham
U
pdate u
s
e of gpu
_
id
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update us
e
o
f
g
pu_id in Jen
k
i
ns
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
Add hel
p
er
f
unction t
o
make a vector
f
rom an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark A
b
raham
Fix VSX SIMD with
gcc
8
commit
|
commitdiff
|
tree
2018-03-14
Mar
k
Abraham
Make a persistent physica
l
node
communicator
commit
|
commitdiff
|
tree
2018-03-13
Mark
Abraham
Add more
const t
o
u
ses
o
f t_commrec an
d
t_inpu
t
rec
commit
|
commitdiff
|
tree
2018-03-13
M
a
rk Ab
r
aham
In
t
roduce con
s
train_shake
commit
|
commitdiff
|
tree
2018-03-13
Mar
k
Abra
h
a
m
Merge "Merge bran
c
h
r
e
l
ease-2018"
commit
|
commitdiff
|
tree
2018-03-12
Mark Abra
h
am
Test gcc-6 and cuda-9
.
0
commit
|
commitdiff
|
tree
2018-03-06
Mar
k
Abraham
M
erge branch releas
e
-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark
A
b
r
aham
Fixed
d
v
dlambda for SHAKE
+
FE
commit
|
commitdiff
|
tree
2018-02-28
Mark
A
braham
Moved and r
e
moved constraint code
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
Reorganized c
o
n
s
tr
a
int cod
e
commit
|
commitdiff
|
tree
2018-02-27
Mark Abraham
F
i
x GPU ut
i
ls test
commit
|
commitdiff
|
tree
2018-02-26
Mark
Abraham
Permit def
i
ne
.
mdp field
t
o ass
i
gn
values
commit
|
commitdiff
|
tree
2018-02-26
Mar
k
Abraha
m
O
rgani
z
e
for recording 2016-era release notes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-21
Mar
k
Abraham
En
h
anced
d
ocs of pim
p
l
po
i
nter help
e
r
commit
|
commitdiff
|
tree
2018-02-19
M
a
rk Abrah
a
m
R
emove cy
c
l
e s
u
ppr
e
ssion
commit
|
commitdiff
|
tree
2018-02-19
Mark Abraham
Disal
l
owed change of ensemble for checkpoint restart
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Merg
e
branch release-
2
0
1
6 into
r
elease
-
201
8
commit
|
commitdiff
|
tree
2018-02-16
Mark
Abrah
a
m
Bump
e
d patc
h
version for next release
commit
|
commitdiff
|
tree
2018-02-16
M
ark A
b
raham
Merge branch release-2
0
18 into
m
aster
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraha
m
V
ersion 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
M
ark Abraham
Use str
u
ct
for che
c
kpoi
n
t header contents
commit
|
commitdiff
|
tree
2018-02-14
Mark Abra
h
am
Remove read_checkpoi
n
t_state
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
U
s
e std::vector for chec
k
poi
n
t
o
utpu
t
f
ile
s
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Merge branch release-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-14
Mark Abrah
a
m
Fi
x
b
u
g i
n
check
p
o
int error checking
commit
|
commitdiff
|
tree
2018-02-14
Mark Ab
r
a
h
a
m
Pr
e
pare release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mar
k
Abraham
Use d
e
ath t
e
st only whe
n
supported
commit
|
commitdiff
|
tree
2018-02-13
Mark Abrah
a
m
Separat
e
m
ultisim from
comm
r
ec
commit
|
commitdiff
|
tree
2018-02-12
M
a
rk Abraham
R
emove commre
c
from hard
w
are d
e
tection
commit
|
commitdiff
|
tree
2018-02-12
M
ar
k
Abraham
Ana
l
yse
threa
d
s on
no
d
e befo
r
e setting affin
i
ties
commit
|
commitdiff
|
tree
2018-02-12
Mark Ab
r
aham
Fix r
e
ading old
force field files
commit
|
commitdiff
|
tree
2018-02-09
M
a
r
k
Abra
h
am
Merge
br
a
nc
h
release-20
1
8
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Us
e
more
po
r
t
a
ble python shebangs
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraha
m
Merge
"Merge branc
h
release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge branch releas
e
-201
6
i
nto release-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark Ab
r
a
h
am
Me
r
ge "M
e
rge branch 're
l
e
a
s
e
-2018
'
into mas
t
er"
commit
|
commitdiff
|
tree
2018-02-06
Ma
r
k Abraha
m
Prevent log fi
l
e
energy average printing dividin
g
by
.
.
.
commit
|
commitdiff
|
tree
2018-02-06
Mark Abra
h
am
Use isfin
i
te
una
m
big
u
ously
commit
|
commitdiff
|
tree
2018-01-30
Mark Abraha
m
R
eplace macros for multi-sim
commit
|
commitdiff
|
tree
2018-01-30
Mark
A
braham
Update GoogleTest to 1
.
8
.
0
commit
|
commitdiff
|
tree
2018-01-27
Mark Abraham
Remove
u
n
u
sed decl
a
rat
i
on
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
Remove unused fie
l
ds of t_commrec
commit
|
commitdiff
|
tree
2018-01-25
Mark Ab
r
aham
Reduced inclu
d
e
s of common headers in heade
r
s
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
R
e
move
d
mdrun -mu
l
t
i
commit
|
commitdiff
|
tree
2018-01-24
M
a
rk A
b
raham
Change mul
t
i-sim
t
e
s
ts
to
use -multidir
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Re
m
ove gmx_inlin
e
commit
|
commitdiff
|
tree
2018-01-24
Mark Abra
h
am
Teach include sorter to
i
gnore c
m
ake-test files
commit
|
commitdiff
|
tree
2018-01-24
M
ark Abraham
Move Windows
icc config to
post-su
b
mit testin
g
commit
|
commitdiff
|
tree
2018-01-24
M
ark Abraham
Replace
g
mx_bo
o
l with bool
in b
i
tmask f
u
nctions
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraham
Remove support for im
p
lici
t
solvat
i
on
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraham
R
e
m
o
ve topology support for
i
m
plicit solva
t
ion
commit
|
commitdiff
|
tree
2018-01-23
Mark Ab
r
aham
Preliminary cleanup befor
e
removin
g
if
d
ef cplu
s
pl
u
s
commit
|
commitdiff
|
tree
2018-01-19
M
a
rk
A
braham
Merge "M
e
rge br
a
n
ch 'rele
a
se-2018' into maste
r
"
commit
|
commitdiff
|
tree
2018-01-19
M
ark Abraham
Add dev-gu
i
de
d
ocs for
auto
m
atic update of regressiontests
commit
|
commitdiff
|
tree
2018-01-19
Mark Abra
h
a
m
Fixes for iss
u
es
f
o
und b
y
c
l
a
n
g
6
commit
|
commitdiff
|
tree
2018-01-18
Mar
k
Abra
h
am
Bump version nu
m
ber
s
for 2019 deve
l
o
pment
commit
|
commitdiff
|
tree
2018-01-18
Mark
A
braham
Remove sup
p
ort for Bl
u
eGene
commit
|
commitdiff
|
tree
2018-01-18
Mark Abr
a
ham
Port
t
hread-MPI to compile as C
+
+
commit
|
commitdiff
|
tree
2018-01-16
Mark Abraha
m
Merge "Merge
release-201
8
into master"
commit
|
commitdiff
|
tree
2018-01-11
Mark Abra
h
am
Re
m
ove contrib directory
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Bumped version for next
p
atch
relea
s
e
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraha
m
Ver
s
io
n
2018
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Annou
n
ce in user
lo
g
files t
h
a
t feature
s
are deprecate
d
.
commit
|
commitdiff
|
tree
2018-01-10
Mark Abr
a
ham
Fix automated GPU ID a
s
signment
commit
|
commitdiff
|
tree
2018-01-10
Mark Abr
a
h
a
m
Add releas
e
n
o
tes t
o
source repo
commit
|
commitdiff
|
tree
2018-01-10
Mark Abraham
H
andle errone
o
us command line
a
r
gs
b
ette
r
commit
|
commitdiff
|
tree
2018-01-09
Mark Abraham
Deac
t
ivate
a
utoselect o
f
PME on GPU on
s
e
par
a
t
e
ran
k
commit
|
commitdiff
|
tree
2018-01-09
Ma
r
k
Abrah
a
m
Clea
n
u
p us
e
r g
u
ide for release
commit
|
commitdiff
|
tree
2018-01-09
Ma
r
k A
b
rah
a
m
M
e
rg
e
b
ran
c
h releas
e
-2016 into releas
e
-
2
018
commit
|
commitdiff
|
tree
2018-01-05
Mark Abraham
R
e
move FindCUDA fro
m
source tarbal
l
commit
|
commitdiff
|
tree
2018-01-04
Mark A
b
raham
M
erge b
r
an
c
h
releas
e
-2
0
18
commit
|
commitdiff
|
tree
2018-01-04
Mark Abr
a
h
am
A
dd t
e
st config of GP
U
build on slave
without GPU
commit
|
commitdiff
|
tree
2018-01-03
Mark Abraham
Add cool quote
commit
|
commitdiff
|
tree
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