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grompp: fix the -ref <file> option
2019-11-04
Teemu Murtola
Updat
e
c
lang-format co
n
fig
commit
|
commitdiff
|
tree
2019-01-29
T
eemu M
u
rtola
A
v
o
id
w
arnings with Apple
C
l
ang
commit
|
commitdiff
|
tree
2019-01-13
Teem
u
Murtola
Use label to sel
e
ct
d
ox
y
gen versi
o
n
commit
|
commitdiff
|
tree
2018-12-24
Teem
u
M
urtola
Use
l
a
b
el to selec
t
d
oxygen version
commit
|
commitdiff
|
tree
2017-09-04
Teemu Mur
t
ola
In
t
roduce s
e
lf-p
a
irs search
i
n nbs
e
a
r
ch
commit
|
commitdiff
|
tree
2017-09-04
Teemu Murtola
Refac
t
or
a
nalysis nbsearch
t
ests
commit
|
commitdiff
|
tree
2017-08-21
T
e
emu Murt
o
la
Si
m
ple union-find structure
commit
|
commitdiff
|
tree
2017-07-19
Teemu Murt
o
l
a
P
r
une u
n
necessa
r
y
c
ells in ana
l
ysi
s
n
bsearch
commit
|
commitdiff
|
tree
2017-07-17
Teemu
M
urtola
Fix hwloc detection
commit
|
commitdiff
|
tree
2017-07-11
Teem
u
Murtola
Support scoped key-va
l
u
e tree transform rules
commit
|
commitdiff
|
tree
2017-07-06
T
e
emu Murtola
Detect unknown mdp options in gmx du
m
p/check
commit
|
commitdiff
|
tree
2017-06-30
Teemu Mur
t
ola
Fix boo
l
ean
serialization
commit
|
commitdiff
|
tree
2017-06-30
Teemu Murt
o
la
Extend
key-value tree comparison and tests
commit
|
commitdiff
|
tree
2017-06-29
T
ee
m
u
Mu
r
tola
Gener
a
lize IFor
c
eProvider
commit
|
commitdiff
|
tree
2017-06-28
Teemu Murtola
Extend key-value tree se
r
ialization a
n
d tests
commit
|
commitdiff
|
tree
2017-06-27
Te
e
mu Mur
t
o
la
Do not use conf-m
a
n
.
py for non
-
manpage doc build
s
commit
|
commitdiff
|
tree
2017-05-29
Teemu
Murtola
Avoid so
m
e incorrect be
h
avior
with gmx solvate
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murtola
Remove pbcutil
<
-> mdtypes cyclic
d
epe
n
dency
commit
|
commitdiff
|
tree
2017-05-11
Teemu Murt
o
la
Generaliz
e
com
m
and-line test output
f
ile checking
commit
|
commitdiff
|
tree
2017-04-17
Teemu Murto
l
a
Consi
s
tent
appro
a
ch for
whole-program tests
commit
|
commitdiff
|
tree
2017-04-11
Teemu Murtola
Improve key-value tree
g
m
x
dump support
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murtola
Fix
m
emor
y
access
i
s
s
ues in
g
m
x
s
o
lvate
commit
|
commitdiff
|
tree
2017-04-06
Teemu
M
urtol
a
Consistent naming f
o
r
g
mx
a
na
t
ests
commit
|
commitdiff
|
tree
2017-04-04
Tee
m
u
M
urtola
U
tility functions for formatting string val
u
e
s
commit
|
commitdiff
|
tree
2017-03-13
Te
e
mu
M
u
r
tola
Impro
v
e
o
p
t
i
on support
& t
e
sts for
key-value trees
commit
|
commitdiff
|
tree
2017-03-13
T
e
emu Mu
r
t
ola
Remove manual alignment
from InMem
o
ryS
e
r
ializer
commit
|
commitdiff
|
tree
2017-03-12
T
e
e
mu M
u
rtola
Consisten
t
Te
x
t
Wri
t
er tr
a
i
lin
g
whi
t
e
spa
c
e handli
n
g
commit
|
commitdiff
|
tree
2017-03-11
Teemu Murtola
Up
d
ate copy
r
ight
y
ear f
o
r gmx
-
v
ersion
commit
|
commitdiff
|
tree
2017-03-04
Te
e
mu Murtol
a
R
e
move MDModule
s
use f
r
om
m
d
l
ib
commit
|
commitdiff
|
tree
2017-03-04
Teemu Murtola
Sp
l
it
md m
o
du
l
e facets to different inter
f
aces
commit
|
commitdiff
|
tree
2017-02-28
Teemu Murto
l
a
More docu
m
entation for ke
y
-
value tr
e
es
commit
|
commitdiff
|
tree
2017-02-27
Teemu Murtola
Dec
o
u
p
le
t_
i
nputrec from MDModules
commit
|
commitdiff
|
tree
2017-02-27
Teem
u
M
ur
t
o
l
a
Remov
e
mo
d
ule re
f
erences from t_inputrec
commit
|
commitdiff
|
tree
2017-02-10
Teemu Murtola
Check lo
g
ou
t
put in thread a
f
finit
y
t
e
s
ts
commit
|
commitdiff
|
tree
2017-02-09
T
ee
m
u M
u
r
t
o
la
Mu
l
t
i-ran
k
thr
e
ad affinity tests
commit
|
commitdiff
|
tree
2017-02-09
Te
e
mu Murtola
D
o
cument key-value tree tra
n
s
f
orm
s
and improve checks
commit
|
commitdiff
|
tree
2017-02-09
Teemu Murtola
Ov
e
r
view
documentation fo
r
new md
p
input sc
h
e
me
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murt
o
la
Generic K
e
yValueTree broadcast
commit
|
commitdiff
|
tree
2017-02-08
Teem
u
Murt
o
la
G
e
neric gmx check
i
mp
l
ementation with K
e
yVal
u
eT
r
ee
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Gen
e
ric gmx
d
u
m
p im
p
lementation for
K
eyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Gener
i
c tpr handling for
e
lectric f
i
e
ld
commit
|
commitdiff
|
tree
2016-12-12
Teemu Murtola
Merge branch release-2016
commit
|
commitdiff
|
tree
2016-12-10
Teem
u
Murtola
M
i
nor CMake cleanup & modernization
commit
|
commitdiff
|
tree
2016-12-10
Te
e
mu Mu
r
t
o
l
a
Buil
d
scri
p
ts
for imp
r
oved r
e
lease workflow
commit
|
commitdiff
|
tree
2016-12-08
Teem
u
M
urtol
a
Fix a
n
d clean up handling of some linking
commit
|
commitdiff
|
tree
2016-12-08
Teem
u
Murt
o
la
Fix possible memory er
r
o
r with long selections
commit
|
commitdiff
|
tree
2016-12-07
Tee
m
u Murtola
Fi
x
u
s
e of p
o
sit
i
o
n
var
i
ables wi
t
h
plus
/
merge
commit
|
commitdiff
|
tree
2016-11-29
Teemu Murtola
Additional
s
e
le
c
tion help
commit
|
commitdiff
|
tree
2016-11-06
Teemu Murtola
Add s
e
lection-enab
l
ed gmx t
r
aj
commit
|
commitdiff
|
tree
2016-10-30
T
e
emu Murtola
Support n
o
rmalizing va
l
u
e
s in Key
V
alueT
r
ee
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murt
o
la
Electric field mdp pa
r
s
i
ng using options
commit
|
commitdiff
|
tree
2016-10-24
T
e
emu Murtola
S
upport for defaul
t
va
l
u
e
s
from
O
ptions to KeyValueTree
commit
|
commitdiff
|
tree
2016-10-21
Tee
m
u M
u
rtola
Clean up option (default) value access
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murt
o
la
Se
r
ialization suppor
t
for KeyValueTree
commit
|
commitdiff
|
tree
2016-10-17
Teemu Murtola
Su
p
port
o
ption ass
i
gnme
n
t f
r
o
m
d
ifferent prec
i
sion
commit
|
commitdiff
|
tree
2016-10-17
Teemu Mur
t
ola
Add support f
o
r re
a
d
i
ng values from
r
ef
d
ata
commit
|
commitdiff
|
tree
2016-10-16
Teemu Murtola
Improv
e
d error h
a
ndling for
K
eyValueTree operations
commit
|
commitdiff
|
tree
2016-10-15
Teemu Mu
r
tola
Im
p
r
oved address
sanitize
r
support
commit
|
commitdiff
|
tree
2016-10-15
Teem
u
Murtola
Work
around memory leak in
t_sta
t
e
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
F
ix most memory leaks recently in
t
roduced
commit
|
commitdiff
|
tree
2016-10-14
T
eemu Murt
o
la
Us
e
gmx_mtop_t
i
n
sele
c
tions, p
a
r
t 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use
g
mx_mtop
_
t in
selecti
o
ns
,
p
a
rt 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Use gmx_
m
top
_
t in
sele
c
tions, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu
M
urtola
Add back-mapping to
K
eyV
a
l
ueTreeTransform
commit
|
commitdiff
|
tree
2016-10-13
T
eemu Mur
t
ola
Update bu
n
d
l
ed TNG
commit
|
commitdiff
|
tree
2016-10-13
T
eemu Mur
t
ola
Getter for m
a
p
p
ed
p
a
ths f
r
om KeyValu
e
T
r
ee
T
ran
s
form
commit
|
commitdiff
|
tree
2016-10-12
T
e
emu
Murtola
Use gmx_mtop_t in selections, part 1
commit
|
commitdiff
|
tree
2016-10-12
Teemu M
u
rtola
W
r
ap sel
.
method evaluation p
a
rame
t
ers to struc
t
commit
|
commitdiff
|
tree
2016-10-11
Teem
u
M
urtola
Support
concurrent t_topology and
gmx_mtop
_
t use
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murtola
Check ato
m
mass availab
i
lity
i
n
s
elections
commit
|
commitdiff
|
tree
2016-10-05
T
eem
u
Murtola
Su
p
p
o
rt di
f
f
e
rent key matching
i
n KeyValueTree
T
ran
s
f
or
m
commit
|
commitdiff
|
tree
2016-10-05
T
eemu Mu
r
tol
a
Merge "Merge bran
c
h
r
e
l
ease-5
-
1 into release-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Mu
r
tol
a
Fix defau
l
t nice l
e
v
e
l
i
n mdrun-
o
nly build
commit
|
commitdiff
|
tree
2016-09-12
Teemu Murtola
Fix various memory lea
k
s
commit
|
commitdiff
|
tree
2016-09-07
T
e
e
mu Murtola
C
l
e
an
up CTest test man
a
gemen
t
commit
|
commitdiff
|
tree
2016-08-30
Teemu Murtola
Basic support for tra
n
sforming KeyVal
u
e
T
rees
commit
|
commitdiff
|
tree
2016-08-27
Teemu M
u
rto
l
a
Support KeyValueTree
objects in re
f
data
commit
|
commitdiff
|
tree
2016-08-18
T
eemu
M
urtol
a
Check for
un
u
sed ref
d
a
t
a values
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murt
o
la
Generic structure
d
key-value tree f
o
r options
commit
|
commitdiff
|
tree
2016-08-18
Teemu
M
urtola
Support f
o
r
n
on-string opt
i
on
v
a
lue
a
s
s
ig
n
ment
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murtola
Basic
su
p
port
f
or ar
r
ay
-
of-st
r
ucts in
o
ptions
commit
|
commitdiff
|
tree
2016-08-17
Tee
m
u Murtol
a
Generalize and
simplify optio
n
v
alue
st
o
rage
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murto
l
a
Gen
e
ralize
o
pti
o
n
s
e
ction intern
a
ls
commit
|
commitdiff
|
tree
2016-08-17
Teemu
M
u
rtola
Reimple
m
ent subsectio
n
s in Options
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murtola
Fix/impr
o
v
e
d
o
c
l
inks
i
n template/READ
M
E
commit
|
commitdiff
|
tree
2016-08-01
T
eemu
M
urt
o
l
a
Func
t
ion to split
d
e
lim
i
t
ed str
i
ngs
commit
|
commitdiff
|
tree
2016-07-14
T
e
emu M
u
r
tola
Use newer
g
cc fo
r
coverage
commit
|
commitdiff
|
tree
2016-07-07
T
e
emu Murtola
C
h
a
n
g
e
h
andling for missing r
e
leng
docs
commit
|
commitdiff
|
tree
2016-06-30
Teemu Mur
t
ola
E
xtract string p
a
rsing routines t
o
ut
i
l
i
ty
commit
|
commitdiff
|
tree
2016-06-28
Teemu Mu
r
tol
a
Split up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Te
e
mu Murtola
Factory for c
r
eat
i
n
g t_inputrec
commit
|
commitdiff
|
tree
2016-06-01
T
e
emu Mur
t
ola
Use C++
r
ep
l
acement for md_l
o
gging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murtola
Bas
i
c
C
++ logging
i
n
t
e
rface
commit
|
commitdiff
|
tree
2016-05-31
Tee
m
u Mur
t
ola
I
mprove ma
k
e_ndx he
l
p
t
ext
commit
|
commitdiff
|
tree
2016-05-25
Teemu Murtola
Support fo
r
real
MPI unit tests
commit
|
commitdiff
|
tree
2016-05-24
T
e
e
m
u
Murto
l
a
Tests fo
r
s
ingle-rank thread affinity
s
etting
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
urtol
a
Pass
num
b
er of
l
ocal threads to thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
A
llow
creating moc
k
HardwareTopol
o
gy
o
bjects
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
urto
l
a
Use on
l
y
HardwareTopology f
o
r thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu M
u
rtola
M
erge b
r
anch relea
s
e-2016
commit
|
commitdiff
|
tree
next