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Convert gmx_mtop_t to C++
2018-04-03
B
e
rk Hess
Convert gmx_
m
t
op
_
t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Ab
r
a
h
a
m
Merge "Merge bra
n
ch r
e
l
ea
s
e-2
0
1
8"
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hess
M
ove
f
ile opening
o
ut
o
f
init_pul
l
(
)
commit
|
commitdiff
|
tree
2018-03-29
Sz
i
lárd Pál
l
Tweak/enable icc 18
p
ost-submit
te
s
ts
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus Lundbor
g
Imp
r
oved
c
heck of if only f
o
rces are comput
e
d in do_
p
airs()
commit
|
commitdiff
|
tree
2018-03-29
Paul
B
auer
Fix c
m
ake
S
phinx
det
e
ctio
n
for
v
ersions
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
S
w
itc
h
CUD
A
9
.
0/gcc 5 test
t
o
CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modulari
z
e pull_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Free more
memory in g
r
o
mp
p
a
n
d
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Ber
k
He
s
s
R
emove mols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Ab
r
aham
Merge b
r
anch release-
2
018
commit
|
commitdiff
|
tree
2018-03-27
Mar
k
Abraham
More
g
cc-8 f
i
xes for
PO
W
E
R
commit
|
commitdiff
|
tree
2018-03-21
D
avid
v
an der Spoel
R
e
named
e
ntropy
.
*
to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Ab
r
aham
V
e
rsion 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk Abraham
Merge "Merge b
r
anc
h
release-2016 into relea
s
e-
2
018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraha
m
Up
d
ate release notes
for
2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Merge branch
release-2016 into release-2
0
1
8
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraha
m
Updat
e
use of gpu_id
i
n
Je
n
kin
s
commit
|
commitdiff
|
tree
2018-03-20
B
e
r
k
Hess
Disallow single sim
u
lation
with mult
i
sim
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braha
m
U
p
date use
of gpu_
i
d in Jenkin
s
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
Update use of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
A
d
d
h
elper functi
o
n
t
o
m
ake a vector fr
o
m an
A
rr
a
yRef
commit
|
commitdiff
|
tree
2018-03-19
M
ark
A
braham
Fix VSX SIMD
w
ith gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free
t
opology when a
l
located
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF sign error
in AWH bias sh
a
ring
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk H
e
ss
Improve inter-si
m
ulation
si
g
naling
commit
|
commitdiff
|
tree
2018-03-14
M
a
r
k
Abr
a
ham
Ma
k
e a p
e
rsistent physical node communicator
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
Fix mdrun signalli
n
g with AWH bias
sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH
f
ixes
t
o release
n
otes
commit
|
commitdiff
|
tree
2018-03-13
S
z
il
á
r
d Páll
Require Open
C
L 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
i
x AWH
e
nsemble
c
heckpointi
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix A
W
H deco
n
v
olut
i
on w
h
e
n
sharing a bias
commit
|
commitdiff
|
tree
2018-03-13
M
a
rk Abraham
I
ntroduce c
o
nstrain
_
sh
a
ke
commit
|
commitdiff
|
tree
2018-03-13
S
zilá
r
d Páll
F
i
x
clang
6
.
0
w
i
th C
U
DA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Ma
r
k Abraham
Merge "Mer
g
e branc
h
r
e
l
ease-20
1
8"
commit
|
commitdiff
|
tree
2018-03-09
Berk
H
e
ss
Correct pd
b
2gmx -
m
issi
n
g
op
t
io
n
commit
|
commitdiff
|
tree
2018-03-06
Ber
k
H
ess
Conv
e
rt
t_filenm to
C
++
commit
|
commitdiff
|
tree
2018-03-06
M
ark A
b
raham
M
erge branch
release
-
2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abrah
a
m
Fixed dvdlambda for
SHAKE
+ FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Páll
A
d
d to t
h
e contributor secti
o
n
commit
|
commitdiff
|
tree
2018-03-01
Berk
H
e
ss
Detect
A
M
D
SMT top
o
log
y
commit
|
commitdiff
|
tree
2018-02-28
M
a
rk Abraham
Moved and removed constraint
code
commit
|
commitdiff
|
tree
2018-02-28
Mark Abrah
a
m
R
eorganiz
e
d c
o
nstr
a
in
t
c
o
de
commit
|
commitdiff
|
tree
2018-02-27
Ma
r
k Abraha
m
Fix GPU
u
t
ils
t
est
commit
|
commitdiff
|
tree
2018-02-26
Paul Bauer
C
h
ange TNG
f
ile
o
pening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Perm
i
t
d
e
fine
.
m
d
p field to
assign
value
s
commit
|
commitdiff
|
tree
2018-02-26
Al
e
k
s
ei
I
upin
o
v
Advice users
o
n
i
nfi
n
ite output of TP
I
commit
|
commitdiff
|
tree
2018-02-26
Mark
A
brah
a
m
Organize fo
r
recording 201
6
-
e
ra release no
t
es a
n
d ad
d
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
F
ix
m
d
i
n
tegrator with N
o
se-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-21
Mark Abraham
E
n
h
a
n
c
ed docs of pimpl pointer hel
p
er
commit
|
commitdiff
|
tree
2018-02-16
Mark Abra
h
am
Merge
branch release-2016 int
o
release-201
8
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
B
umped patc
h
v
e
r
sion for next r
e
lease
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
C
o
rrect
multisim M
P
I barrier
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abr
a
ham
Merge bra
n
ch r
e
le
a
se-
2
018 int
o
master
commit
|
commitdiff
|
tree
2018-02-16
Mark Abr
a
h
a
m
Version 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark Abraham
Use struct for che
c
kpoint header con
t
ents
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
Iupinov
Update FFTW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mark A
b
r
a
ham
Remove re
a
d_ch
e
ckpoint_stat
e
commit
|
commitdiff
|
tree
2018-02-14
B
e
r
k
Hess
Remove su
p
port for tpx version before 58
/
gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Use std::vector for c
h
eckpo
i
nt
outputfiles
commit
|
commitdiff
|
tree
2018-02-14
Mark
A
braham
Merge branch releas
e
-
2
0
1
6 into rel
e
a
se-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range bug in add_sel
e
ction_groups
i
n
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei
Iup
i
nov
Replac
e
t
he rem
a
ining
EXPECT_DEATH
with EXPECT_DEATH_IF
_
SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Ale
k
sei Iupinov
Add DeviceBuffer as a typ
e
def for cl_mem/device ponter
commit
|
commitdiff
|
tree
2018-02-14
Szilárd
Páll
R
e
move bar
r
ie
r
s preventin
g
t
e
xture re
f
e
rence
races
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
i
x gro
m
pp net ch
a
rge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
i
x grompp net cha
r
ge check
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Prepare rele
a
se n
o
t
es for 201
8
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mark Ab
r
aha
m
Use death test only when
supporte
d
commit
|
commitdiff
|
tree
2018-02-13
Ma
r
k Abraham
Se
p
ara
t
e multisi
m
from comm
r
e
c
commit
|
commitdiff
|
tree
2018-02-12
M
ark A
b
raham
Analyse threads on node bef
o
re setting a
f
finities
commit
|
commitdiff
|
tree
2018-02-12
Mark
Abrah
a
m
F
i
x reading old
f
orce field
files
commit
|
commitdiff
|
tree
2018-02-09
Mark
A
b
raham
M
e
rge bran
c
h release-2018
commit
|
commitdiff
|
tree
2018-02-08
M
ark Abraha
m
Me
r
g
e
"Me
r
g
e
branch release-2016 into rele
a
se-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge branch release-2016 in
t
o
releas
e
-2018
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupi
n
ov
E
nab
l
e deb
u
g FP exception
s
wit
h
out TPI, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Mer
g
e
"Me
r
ge branch 'releas
e
-2018' into
master"
commit
|
commitdiff
|
tree
2018-02-06
Mark Abr
a
ham
Pr
e
vent
log file
e
nergy average printi
n
g dividing by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei I
u
pinov
Don't
print impossibl
e
C
UDA version numbers
i
n
absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bauer
Add information fo
r
n2t file format
commit
|
commitdiff
|
tree
2018-01-27
Mark Abraham
Re
m
ove unused
de
c
la
r
ation
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
Remove unus
e
d fields of t_comm
r
ec
commit
|
commitdiff
|
tree
2018-01-25
Mark Abr
a
ham
Reduced
inc
l
u
des o
f
co
m
mon
h
eaders in
h
eaders
commit
|
commitdiff
|
tree
2018-01-25
Mark
A
b
raham
Removed
mdrun -multi
commit
|
commitdiff
|
tree
2018-01-24
Mar
k
Abr
a
ham
C
h
ange multi-sim t
e
st
s
to
u
s
e
-mult
i
dir
commit
|
commitdiff
|
tree
2018-01-24
Ma
r
k
A
b
r
aham
Re
m
ove gmx_inlin
e
commit
|
commitdiff
|
tree
2018-01-24
Mark Abrah
a
m
Teach include sorter to ignor
e
cmake-tes
t
files
commit
|
commitdiff
|
tree
2018-01-24
M
ark A
b
ra
h
am
Mo
v
e Wi
n
dows icc c
o
nfig to p
o
st-submit t
e
sting
commit
|
commitdiff
|
tree
2018-01-24
Mark
Abr
a
h
a
m
Rep
l
ace gmx_bool with bo
o
l
in bitmas
k
fun
c
tions
commit
|
commitdiff
|
tree
2018-01-23
Mark
Abraham
Re
m
ove
s
uppo
r
t
f
or impl
i
cit solvatio
n
commit
|
commitdiff
|
tree
2018-01-23
Mar
k
Abraham
Re
m
ove top
o
logy s
u
pport for implicit
s
olvation
commit
|
commitdiff
|
tree
2018-01-23
A
leks
e
i Iupinov
Test PME CPU/GPU with w
a
lls and box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Wra
p
the PME
testing loop in a method for extensibi
l
i
t
y
commit
|
commitdiff
|
tree
2018-01-23
Mark A
b
raham
P
r
eliminary clea
n
up
be
f
ore removing ifdef cplusplus
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Add a de
a
th test
f
or the du
p
li
c
ate inputrec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Merge "M
e
rge branc
h
'
release-2018' into master"
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Ren
a
me cla
s
s BiasReader t
o
struct Bias
O
utputS
e
tup
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
A
dd
d
ev-
g
uide docs for
au
t
omati
c
upda
t
e of regressiontests
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei
Iupinov
Mak
e
t
h
e referenc
e
d
a
ta
variable
s
loc
a
l in G
e
tIrTest
commit
|
commitdiff
|
tree
2018-01-19
Mark
A
braha
m
Fixes f
o
r
iss
u
es found by clang 6
commit
|
commitdiff
|
tree
next