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Break apart update_constraints
2018-04-17
M
ark Abraha
m
B
reak ap
a
rt update_constra
i
n
t
s
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
A
dd post-
s
u
b
m
i
t
test with hwloc o
f
f
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Mo
v
e
natoms_mol out of gm
x
_molbloc
k
_t
commit
|
commitdiff
|
tree
2018-04-16
Mark A
b
raha
m
Up
d
a
ted m
d
run
c
o
m
parison infr
a
structure
commit
|
commitdiff
|
tree
2018-04-13
Mark Ab
r
aham
Cle
a
n up
constraints code
commit
|
commitdiff
|
tree
2018-04-12
Mark
A
braham
R
e
m
ove
u
se of where
(
), if DEBUG
etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark
A
b
raham
Reorganize energy e
v
a
l
uation for EM
commit
|
commitdiff
|
tree
2018-04-10
Alek
s
ei
I
u
p
inov
Prevent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-04-09
Be
r
k
Hess
Convert
gmx_molblock
_
t to C++
commit
|
commitdiff
|
tree
2018-04-05
M
ark Abra
h
a
m
Simpl
i
fied handling of simulation runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abrah
a
m
Cr
e
ate gr
o
macs/mdrun
module and m
o
ve code there
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
R
e
fa
c
tor
c
j
p
r
eload in the nonbonded O
p
enCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Mark Abra
h
am
Quiet ch
e
c
k
poin
t
r
e
a
di
n
g
commit
|
commitdiff
|
tree
2018-04-04
P
a
s
c
a
l
Merz
Move checkNumberOfBondedInt
e
raction
s
commit
|
commitdiff
|
tree
2018-04-03
Berk He
s
s
Con
v
ert gmx_mtop_t to
C
+
+
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remove l
e
ftove
r
mention of twin
-
range
s
c
h
eme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abrah
a
m
M
e
rge "Merge bran
c
h release-2018"
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hess
Move
f
ile ope
n
ing
out of ini
t
_pu
l
l()
commit
|
commitdiff
|
tree
2018-03-29
Sz
i
l
á
rd Páll
Twe
a
k/enable i
c
c 18 post-su
b
mi
t
test
s
commit
|
commitdiff
|
tree
2018-03-29
Mag
n
us Lundborg
Improved check of if o
n
ly
f
orces are compu
t
ed in
do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
P
aul Ba
u
er
F
ix cmake Sphinx detectio
n
f
o
r ve
r
sions
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd P
á
ll
S
w
itch CU
D
A 9
.
0
/
gcc 5
t
e
s
t
t
o
CUDA 9
.
1/
g
cc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk He
s
s
Modularize pull_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Free more memory in
grompp and mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk He
s
s
R
e
move mols
f
r
o
m gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
bra
h
am
Merge
b
r
anc
h
release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark
A
braham
Clarified mdp opt
i
ons
r
e
lating
t
o bo
n
d
s
commit
|
commitdiff
|
tree
2018-03-27
Mark A
b
r
a
h
am
More g
c
c-8
f
ixes for POW
E
R
commit
|
commitdiff
|
tree
2018-03-21
Dav
i
d
v
an der Spoel
Renamed e
n
tropy
.
* to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraha
m
Versi
o
n 201
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Merge
"Merg
e
br
a
n
ch r
e
lease-2016 into relea
s
e-20
1
8
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraha
m
Update release n
o
t
es for 201
8
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abrah
a
m
Merge branch
r
e
lease-
2
01
6
i
n
to release
-
20
1
8
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abraham
Update
use of gpu
_
i
d
i
n
Jenkin
s
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k
He
s
s
Disallo
w
single
s
i
m
ulati
o
n with multisim
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Updat
e
use of gpu
_
id in J
e
nki
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
r
aha
m
Update use of
gpu_id
in Jenki
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Add hel
p
er functio
n
to
m
a
k
e a
v
ector
f
r
o
m an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
F
ix VSX S
I
MD with gcc
8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only f
r
e
e
topology when allocated
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Cor
r
ect
P
MF sign error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hes
s
I
mprove i
n
ter-sim
u
lat
i
on signaling
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a persistent phy
s
ica
l
n
o
de communicator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix
m
drun signal
l
ing
w
ith AWH bias sha
r
ing
commit
|
commitdiff
|
tree
2018-03-13
B
erk
H
ess
Add AWH fixes to relea
s
e notes
commit
|
commitdiff
|
tree
2018-03-13
Sz
i
lárd Páll
Require OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Fix AW
H
e
n
semble chec
k
poin
t
ing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvol
u
ti
o
n when sharing a bi
a
s
commit
|
commitdiff
|
tree
2018-03-13
Mark A
b
raham
Introduce constrain_s
h
ake
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Fi
x
clang 6
.
0 with CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Merge
"Merge b
r
anch release-2018"
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correct pdb2gmx
-
missing option
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
C
o
nv
e
rt t_fil
e
nm to C++
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Me
r
g
e
b
ranch release-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Fixed d
v
dlambda
for SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
S
zilárd Páll
Add to the
contributor se
c
tion
commit
|
commitdiff
|
tree
2018-03-01
Berk
H
ess
Detect AMD SMT topol
o
gy
commit
|
commitdiff
|
tree
2018-02-28
M
ark Abraham
Mo
v
e
d
and remo
v
ed constraint
c
ode
commit
|
commitdiff
|
tree
2018-02-28
M
a
rk Abr
a
ham
R
eorganized
c
onstraint code
commit
|
commitdiff
|
tree
2018-02-27
M
a
rk Abrah
a
m
Fix GPU utils
t
est
commit
|
commitdiff
|
tree
2018-02-26
Pa
u
l Bau
e
r
Change TNG file opening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit define
.
mdp fie
l
d
to
a
ssign values
commit
|
commitdiff
|
tree
2018-02-26
Alek
s
e
i
Iupi
n
o
v
Advice users on infinite
output of TPI
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abraham
Organize for reco
r
ding 2016-e
r
a release notes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix m
d
integrator w
i
t
h Nose
-
Hoover coupling
commit
|
commitdiff
|
tree
2018-02-21
Ma
r
k A
b
raha
m
Enhance
d
doc
s
of
pi
m
pl pointer h
e
lp
e
r
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraha
m
M
e
rg
e
bran
c
h r
e
lease
-
2016 in
t
o release-2018
commit
|
commitdiff
|
tree
2018-02-16
Mark Ab
r
aham
Bumped
p
a
t
ch ve
r
sion fo
r
next release
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct
multisim MP
I
bar
r
ier
commit
|
commitdiff
|
tree
2018-02-16
M
a
r
k Abraham
M
er
g
e branch release-2018 into master
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraham
Version 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
M
a
rk Ab
r
aham
Use struct for checkpoint he
a
d
e
r con
t
ents
commit
|
commitdiff
|
tree
2018-02-15
A
l
eksei Iu
p
inov
U
pdate FFTW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mar
k
Abraham
Remove read_checkpoint_state
commit
|
commitdiff
|
tree
2018-02-14
Berk
He
s
s
Remove sup
p
ort for t
p
x vers
i
on b
e
fo
r
e 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark Abr
a
ham
Use std::vector for checkpoint out
p
utfi
l
e
s
commit
|
commitdiff
|
tree
2018-02-14
Mark Abra
h
am
Merg
e
branch relea
s
e-2016 into r
e
lease-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk He
s
s
Fi
x
ra
n
ge bug
in a
d
d
_
se
l
ecti
o
n_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Alek
s
ei I
u
pinov
R
e
place the rem
a
ining EXPE
C
T_D
E
ATH wit
h
EXPECT_DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei
Iu
p
in
o
v
A
d
d
DeviceBuffer as a typedef for cl_mem/d
e
vice
ponter
commit
|
commitdiff
|
tree
2018-02-14
Szilárd Pál
l
Re
m
ove barriers preven
t
i
n
g text
u
r
e
ref
e
re
n
c
e ra
c
es
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk Hess
Fix grompp ne
t
char
g
e check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fix g
r
ompp net cha
r
ge
ch
e
c
k
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Prepare release
not
e
s
for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
M
ark Abraha
m
U
se death test only
w
hen supp
o
r
t
ed
commit
|
commitdiff
|
tree
2018-02-13
Ma
r
k A
b
r
a
h
am
S
epar
a
te multisim from commrec
commit
|
commitdiff
|
tree
2018-02-12
M
ark A
b
raham
A
n
aly
s
e
thre
a
ds on node
b
e
fo
r
e setting af
f
i
n
ities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Fix reading old force
field
files
commit
|
commitdiff
|
tree
2018-02-09
Ma
r
k Abraham
Merge branch releas
e
-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark Ab
r
aham
Merge "Merge branch release-
2
0
1
6 into r
e
l
ease-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark
A
braham
Merge
b
r
a
nch release-
2
016 in
t
o
rel
e
a
s
e
-2018
commit
|
commitdiff
|
tree
2018-02-08
A
l
eksei Iupin
o
v
Enable de
b
ug FP exceptions without TPI, not wi
t
h
T
P
I
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Mer
g
e "
M
erge bra
n
ch 'rel
e
ase-2
0
18' into master"
commit
|
commitdiff
|
tree
2018-02-06
Mark
Abraha
m
Prevent
l
og file energy ave
r
age printing divi
d
ing by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don't print impo
s
sible CU
D
A v
e
rsion numbers in
absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bauer
Add information for n
2
t
file fo
r
mat
commit
|
commitdiff
|
tree
2018-01-27
Mark Abrah
a
m
Remove unuse
d
de
c
lar
a
tion
commit
|
commitdiff
|
tree
2018-01-25
M
a
r
k
A
br
a
ham
Remo
v
e unused fiel
d
s of t_commrec
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
R
e
duced includes o
f
common header
s
in
h
e
aders
commit
|
commitdiff
|
tree
2018-01-25
M
ark
A
braham
R
e
moved mdrun -m
u
lti
commit
|
commitdiff
|
tree
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