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Fix duplicate warning
2017-09-04
Teemu
M
urtola
Introduce self-pairs search in nbs
e
a
r
c
h
commit
|
commitdiff
|
tree
2017-09-04
T
e
emu Mur
t
o
la
R
e
fa
c
tor analysis
nbsearch
tests
commit
|
commitdiff
|
tree
2017-08-21
Teemu Murtola
Simple union-find
str
u
c
ture
commit
|
commitdiff
|
tree
2017-07-19
Teemu Murtol
a
Pr
u
ne un
n
ecess
a
ry cells in analysis nbs
e
a
r
c
h
commit
|
commitdiff
|
tree
2017-07-17
Teemu Murtol
a
Fix hwloc
d
etec
t
i
o
n
commit
|
commitdiff
|
tree
2017-07-11
Te
e
m
u
Murtola
Support sco
p
e
d
key-v
a
lue tree transf
o
rm rules
commit
|
commitdiff
|
tree
2017-07-06
Te
e
m
u
Murtola
Det
e
ct unknown mdp options in gmx d
u
mp/che
c
k
commit
|
commitdiff
|
tree
2017-06-30
T
ee
m
u Mu
r
tola
Fix boolean serializa
t
i
o
n
commit
|
commitdiff
|
tree
2017-06-30
T
e
emu
M
ur
t
o
la
Extend k
e
y-
v
a
lue tree comparis
o
n
and tests
commit
|
commitdiff
|
tree
2017-06-29
Teem
u
M
urt
o
la
Genera
l
ize IForcePr
o
vider
commit
|
commitdiff
|
tree
2017-06-28
Teemu
M
u
r
t
o
la
Extend key
-
value tree serialization and tests
commit
|
commitdiff
|
tree
2017-06-27
Teemu Mur
t
ola
Do not use conf-man
.
py for non-manpage doc builds
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murtola
Avoid s
o
me incorrect
b
ehavior
w
ith
gmx sol
v
ate
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murt
o
la
Remove
p
bcutil <-> mdtypes c
y
clic de
p
ende
n
c
y
commit
|
commitdiff
|
tree
2017-05-11
Teemu M
u
rtola
Genera
l
ize
c
ommand-line test out
p
u
t
file
checki
n
g
commit
|
commitdiff
|
tree
2017-04-17
Teemu
M
u
r
tola
Consisten
t
a
ppro
a
ch for whole-p
r
ogr
a
m tests
commit
|
commitdiff
|
tree
2017-04-11
Te
e
mu Mu
r
t
o
la
Improve key
-
val
u
e
tree gm
x
dump suppor
t
commit
|
commitdiff
|
tree
2017-04-06
T
e
emu Mu
r
tola
Fix
m
emory acc
e
ss
issu
e
s in gmx s
o
lvate
commit
|
commitdiff
|
tree
2017-04-06
T
e
emu Murtola
C
o
nsiste
n
t namin
g
for gmxana te
s
ts
commit
|
commitdiff
|
tree
2017-04-04
Teemu
Murtola
Utility functions for form
a
t
tin
g
string values
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murt
o
la
Improve
option
suppo
r
t
& t
e
sts
f
or key-value trees
commit
|
commitdiff
|
tree
2017-03-13
Teemu M
u
rtola
Re
m
ove manua
l
a
l
ignme
n
t fr
o
m In
M
emo
r
y
S
e
rializer
commit
|
commitdiff
|
tree
2017-03-12
Teemu Murtola
C
o
nsiste
n
t TextWrite
r
trailing whitespac
e
ha
n
dling
commit
|
commitdiff
|
tree
2017-03-11
Teemu M
u
rtola
Upda
t
e copyr
i
ght year for gmx -version
commit
|
commitdiff
|
tree
2017-03-04
Teemu Mu
r
tola
Re
m
o
v
e MDModule
s
use from
m
dlib
commit
|
commitdiff
|
tree
2017-03-04
Tee
m
u Murtola
Sp
l
it m
d
m
odule facets to differe
n
t interfaces
commit
|
commitdiff
|
tree
2017-02-28
Teemu Mur
t
ola
M
ore d
o
c
umentation for key-value trees
commit
|
commitdiff
|
tree
2017-02-27
Teemu
M
urtola
Decouple t_inputrec from M
D
Modules
commit
|
commitdiff
|
tree
2017-02-27
T
e
emu M
u
rtola
Remove
m
o
dule
references fro
m
t_inputrec
commit
|
commitdiff
|
tree
2017-02-10
Teemu
M
ur
t
ola
Ch
e
ck
lo
g
ou
t
put in thre
a
d
affini
t
y tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu Mu
r
tola
Mult
i
-rank th
r
ead affini
t
y tests
commit
|
commitdiff
|
tree
2017-02-09
T
eemu Mu
r
tola
Docume
n
t key-value t
r
ee transf
o
rms and im
p
rove c
h
ecks
commit
|
commitdiff
|
tree
2017-02-09
T
e
e
mu Murtola
Overview
documenta
t
ion
f
o
r
new md
p
input scheme
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Gener
i
c
KeyValu
e
T
re
e
broadcast
commit
|
commitdiff
|
tree
2017-02-08
Teemu Mur
t
ol
a
Gener
i
c gmx
c
heck im
p
l
e
mentation with KeyV
a
lueTree
commit
|
commitdiff
|
tree
2017-02-08
Tee
m
u Mur
t
o
l
a
Ge
n
eric g
m
x
dump implementa
t
i
o
n fo
r
KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Tee
m
u
Murtola
G
e
neri
c
tpr handling for ele
c
tric fie
l
d
commit
|
commitdiff
|
tree
2016-12-12
Teemu Murt
o
la
Mer
g
e
b
ra
n
ch
release-2
0
16
commit
|
commitdiff
|
tree
2016-12-10
T
eemu
M
urto
l
a
Minor CMak
e
cleanup & modern
i
zation
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtola
Bu
i
ld scripts for improved release workflow
commit
|
commitdiff
|
tree
2016-12-08
T
eemu Murtola
Fi
x
and cle
a
n
u
p
handling of some
l
inking
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtol
a
Fix possible memory error with lon
g
selecti
o
ns
commit
|
commitdiff
|
tree
2016-12-07
Teemu Mur
t
ola
Fix use of positio
n
vari
a
bles wi
t
h plus/me
r
ge
commit
|
commitdiff
|
tree
2016-11-29
Te
e
m
u
Murtola
Add
i
tional selection help
commit
|
commitdiff
|
tree
2016-11-06
T
e
emu
Murtola
A
d
d selection-e
n
abled gmx traj
commit
|
commitdiff
|
tree
2016-10-30
Teemu Murtola
Sup
p
ort normalizing values in KeyV
a
lueTree
commit
|
commitdiff
|
tree
2016-10-24
T
eemu
M
urtola
Electric fiel
d
mdp pa
r
sing using op
t
ions
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtol
a
Sup
p
or
t
for
d
ef
a
ult value
s
f
rom Options to KeyV
a
l
u
e
T
ree
commit
|
commitdiff
|
tree
2016-10-21
Teemu Murtola
Clean
u
p option (def
a
ult) v
a
lue
a
c
cess
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murtola
S
e
rializati
o
n support for KeyVa
l
ueTree
commit
|
commitdiff
|
tree
2016-10-17
T
e
emu Murtola
Support
o
ption as
s
ignment from d
i
fferen
t
precision
commit
|
commitdiff
|
tree
2016-10-17
T
e
e
m
u M
u
rtola
Add
support
f
or readi
n
g valu
e
s from
r
e
fdata
commit
|
commitdiff
|
tree
2016-10-16
Teem
u
Murtola
Impr
o
ve
d
e
r
ror handl
i
ng for KeyValue
T
ree operati
o
ns
commit
|
commitdiff
|
tree
2016-10-15
T
eemu Murtola
Improv
e
d address sanit
i
z
e
r su
p
p
ort
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
W
o
rk around me
m
ory leak
i
n t_st
a
te
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Fix most
memory l
e
a
k
s re
c
ently i
n
troduced
commit
|
commitdiff
|
tree
2016-10-14
Teemu
M
urtol
a
U
s
e gmx
_
m
top_t in selections, part 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu
M
urto
l
a
U
s
e gmx_
m
top_t
i
n
sel
e
c
t
ions,
part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murto
l
a
U
s
e gm
x
_mtop_t in
sele
c
tions, pa
r
t 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Add b
a
ck-mapping to KeyValueTre
e
Transform
commit
|
commitdiff
|
tree
2016-10-13
Teemu M
u
rtola
Update bundl
e
d TNG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
G
ett
e
r f
o
r mapp
e
d
p
aths from KeyVa
l
ueTreeTr
a
n
sform
commit
|
commitdiff
|
tree
2016-10-12
Teem
u
Mu
r
tola
U
se gmx_mtop_t
i
n selections, pa
r
t 1
commit
|
commitdiff
|
tree
2016-10-12
T
ee
m
u M
u
rto
l
a
Wrap
sel
.
method ev
a
luation parameters to struct
commit
|
commitdiff
|
tree
2016-10-11
T
e
emu Murtol
a
Support concurr
e
nt t_
t
o
p
ology and
gmx_mtop_t use
commit
|
commitdiff
|
tree
2016-10-11
Teemu M
u
rtola
Check atom mass av
a
il
a
bili
t
y
i
n selections
commit
|
commitdiff
|
tree
2016-10-05
Teemu Mu
r
tola
Suppor
t
diffe
r
ent key ma
t
chi
n
g
in KeyValueTreeTra
n
sfo
r
m
commit
|
commitdiff
|
tree
2016-10-05
Teemu
Murto
l
a
M
erg
e
"Merge
br
a
nch release
-
5
-
1 into rel
e
ase-2016
"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Tee
m
u Murtola
Fix
d
efaul
t
n
ice
l
evel
in mdrun-
o
n
ly
b
uild
commit
|
commitdiff
|
tree
2016-09-12
Tee
m
u Murtola
Fix var
i
ous
memory leaks
commit
|
commitdiff
|
tree
2016-09-07
T
eemu
M
urtola
Clean up
C
Test
t
est
management
commit
|
commitdiff
|
tree
2016-08-30
Teemu
Murtola
B
a
si
c
s
u
pp
o
rt for transfo
r
m
in
g
KeyValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu
Murtola
Support Key
V
alueTree
o
bject
s
in refdata
commit
|
commitdiff
|
tree
2016-08-18
T
e
e
m
u M
u
r
tola
Check for unuse
d
r
e
f
data values
commit
|
commitdiff
|
tree
2016-08-18
Teem
u
Murtola
Gen
e
ric
s
tructured key-value t
r
ee for
o
ptions
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Support for non-st
r
ing op
t
io
n
value as
s
ign
m
ent
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murtola
Basic support fo
r
array-of-
s
truc
t
s
in option
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtol
a
General
i
ze and simplify
o
p
t
ion val
u
e st
o
ra
g
e
commit
|
commitdiff
|
tree
2016-08-17
Teemu Mur
t
ola
Gener
a
l
ize option secti
o
n
i
nternals
commit
|
commitdiff
|
tree
2016-08-17
T
eemu M
u
rtola
Reimple
m
e
n
t
subsections in Optio
n
s
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murtola
F
i
x/impro
v
e
doc lin
k
s
i
n
t
empla
t
e/README
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtola
Function
to sp
l
it
d
elimited st
r
i
n
gs
commit
|
commitdiff
|
tree
2016-07-14
T
e
emu
M
urtola
U
se newer gcc f
o
r coverage
commit
|
commitdiff
|
tree
2016-07-07
T
eemu Mur
t
ola
Change handling for missin
g
r
ele
n
g docs
commit
|
commitdiff
|
tree
2016-06-30
Teem
u
Murtola
E
x
tr
a
ct string parsi
n
g ro
u
tine
s
to utility
commit
|
commitdiff
|
tree
2016-06-28
Tee
m
u
Murtol
a
S
plit up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu
M
u
rt
o
l
a
Fac
t
or
y
f
or creatin
g
t
_
inputrec
commit
|
commitdiff
|
tree
2016-06-01
T
eemu Murtola
Use C++ re
p
lacem
e
nt fo
r
md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
T
eemu Murtola
Ba
s
ic C+
+
loggi
n
g interface
commit
|
commitdiff
|
tree
2016-05-31
Teemu Murtola
Improve m
a
ke_ndx
help text
commit
|
commitdiff
|
tree
2016-05-25
Teemu Murt
o
la
Support f
o
r
real MPI
u
n
i
t
t
es
t
s
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
Te
s
ts f
o
r sing
l
e-rank t
h
rea
d
affinity setting
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murto
l
a
Pass num
b
er of loca
l
threads
to
thread affinit
y
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
A
l
low creating mock
H
ardwareTopology objects
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Us
e
only Hardw
a
r
eT
o
po
l
ogy
for t
h
re
a
d af
f
in
i
ty
commit
|
commitdiff
|
tree
2016-05-21
T
eemu
Murt
o
la
Merge
b
ranc
h
release
-
2
016
commit
|
commitdiff
|
tree
2016-05-21
Teemu
Mu
r
tola
Bump
v
ersion numb
e
rs
f
or 2017
d
e
velopment
commit
|
commitdiff
|
tree
2016-05-17
Teemu Murtola
Fix some threa
d
a
ffinity cases
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu
Murtola
Additional Jenkins doc
u
menta
t
ion
commit
|
commitdiff
|
tree
2016-05-10
T
e
em
u
Murt
o
la
In
c
lud
e
releng documentation to developer guide
commit
|
commitdiff
|
tree
next