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Change use of t_inpfile to std::vector
2017-09-04
Teemu Murtola
Introduc
e
self-pairs se
a
rch in nbs
e
a
r
ch
commit
|
commitdiff
|
tree
2017-09-04
Teemu Mu
r
tola
Refactor
analy
s
is nbs
e
arch tests
commit
|
commitdiff
|
tree
2017-08-21
T
e
emu
Murtola
Simple union-find
struc
t
ure
commit
|
commitdiff
|
tree
2017-07-19
Te
e
m
u
M
ur
t
ola
Prune u
n
nece
s
sary
c
e
lls in analysis nbsearch
commit
|
commitdiff
|
tree
2017-07-17
T
e
e
m
u Mu
r
tola
Fi
x
hwloc detection
commit
|
commitdiff
|
tree
2017-07-11
Teemu Murtola
Suppo
r
t scoped k
e
y-value tre
e
transform rul
e
s
commit
|
commitdiff
|
tree
2017-07-06
Teemu M
u
rtola
Detect unknown m
d
p
o
ptions in gmx
d
ump
/
c
h
e
ck
commit
|
commitdiff
|
tree
2017-06-30
Teemu
M
ur
t
ol
a
Fix
b
o
o
lean s
e
r
ialization
commit
|
commitdiff
|
tree
2017-06-30
Te
e
mu Murtola
Ex
t
en
d
key-value
t
ree co
m
parison
a
nd tests
commit
|
commitdiff
|
tree
2017-06-29
Teemu Murtola
G
eneral
i
ze IF
o
r
c
eProvider
commit
|
commitdiff
|
tree
2017-06-28
T
eemu M
u
r
t
ola
Extend key-value tree serializat
i
on and tests
commit
|
commitdiff
|
tree
2017-06-27
Teem
u
Murtola
Do not use conf
-
man
.
p
y for non-manpage do
c
builds
commit
|
commitdiff
|
tree
2017-05-29
Tee
m
u Murtola
Avoid
s
om
e
in
c
orrect
b
ehavior with
g
mx sol
v
at
e
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murtola
Remo
v
e pbcutil <-> mdty
p
es cyclic dep
e
ndency
commit
|
commitdiff
|
tree
2017-05-11
Teemu
Murtola
Generalize command-line test outpu
t
file checki
n
g
commit
|
commitdiff
|
tree
2017-04-17
Teem
u
M
u
rtola
Consistent approach for
w
hole-program tests
commit
|
commitdiff
|
tree
2017-04-11
Te
e
mu Mur
t
ola
Imp
r
ove
key-value tree
g
mx dump support
commit
|
commitdiff
|
tree
2017-04-06
Teemu Mu
r
tola
Fix
m
e
mory a
c
ce
s
s issues
i
n gmx solva
t
e
commit
|
commitdiff
|
tree
2017-04-06
T
eemu Murtola
Consistent
naming for gmxa
n
a tes
t
s
commit
|
commitdiff
|
tree
2017-04-04
Teem
u
Mu
r
t
ola
Utility func
t
ions for formatting string v
a
lues
commit
|
commitdiff
|
tree
2017-03-13
Te
e
mu Murtola
Improve option
s
uppor
t
&
tests
f
or key
-
value trees
commit
|
commitdiff
|
tree
2017-03-13
Teem
u
Murtola
Remove manual a
l
ignmen
t
fr
o
m
InMemorySerializer
commit
|
commitdiff
|
tree
2017-03-12
T
e
emu Murtol
a
Consistent
TextWriter trai
l
i
n
g whitespace handling
commit
|
commitdiff
|
tree
2017-03-11
Teemu
M
urtola
Update copy
r
ight y
e
ar for gmx -version
commit
|
commitdiff
|
tree
2017-03-04
T
e
emu
M
u
rtola
Remove MDModule
s
use
f
r
om
mdlib
commit
|
commitdiff
|
tree
2017-03-04
T
e
emu
M
urtola
Split
md
m
o
dule
f
acets to different i
n
terfaces
commit
|
commitdiff
|
tree
2017-02-28
Teemu Murt
o
la
More documentation for key-va
l
u
e tr
e
es
commit
|
commitdiff
|
tree
2017-02-27
Teem
u
Murto
l
a
Decouple t_inputrec from MD
M
odules
commit
|
commitdiff
|
tree
2017-02-27
Teemu
M
ur
t
ola
Remove module references from t_inputr
e
c
commit
|
commitdiff
|
tree
2017-02-10
Teemu Murtola
Check log outpu
t
in
t
hread
affinity tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu
M
urtol
a
Multi-rank
thread
affi
n
ity
t
ests
commit
|
commitdiff
|
tree
2017-02-09
Tee
m
u Mur
t
ola
Do
c
ument key-value tre
e
transforms
a
nd
i
mprove che
c
ks
commit
|
commitdiff
|
tree
2017-02-09
Teemu
Mur
t
ola
Over
v
iew
docum
e
n
tation f
o
r new mdp
input scheme
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murt
o
la
Generic KeyValueT
r
e
e
b
r
oa
d
cast
commit
|
commitdiff
|
tree
2017-02-08
T
eemu
M
urtola
Generi
c
gmx
c
heck im
p
le
m
e
ntation wi
t
h
K
e
yValueTree
commit
|
commitdiff
|
tree
2017-02-08
T
e
e
mu
M
u
rtola
Gen
e
ric gmx
dump imple
m
entati
o
n
f
or KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Generic tpr hand
l
ing f
o
r
el
e
ctric field
commit
|
commitdiff
|
tree
2016-12-12
Te
e
mu Murtola
Merge br
a
nch rele
a
se-
2
01
6
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtol
a
Minor CMa
k
e
c
leanu
p
&
mod
e
rnization
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtola
B
uild scripts for imp
r
oved relea
s
e
workflow
commit
|
commitdiff
|
tree
2016-12-08
Teemu M
u
r
t
ola
Fix
a
nd clean up handl
i
n
g
of some
l
i
nking
commit
|
commitdiff
|
tree
2016-12-08
T
e
e
m
u
Murtola
Fix possible m
e
mory error
with lo
n
g
s
elec
t
i
on
s
commit
|
commitdiff
|
tree
2016-12-07
Teemu Murtola
Fi
x
use of position varia
b
les with
p
lus/merge
commit
|
commitdiff
|
tree
2016-11-29
Tee
m
u Murtola
Additiona
l
selection help
commit
|
commitdiff
|
tree
2016-11-06
Teemu Mur
t
ola
Add selec
t
ion-
e
nabled
g
mx tr
a
j
commit
|
commitdiff
|
tree
2016-10-30
Te
e
mu Murto
l
a
Support normaliz
i
ng values in KeyValueTree
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Ele
c
tric field
mdp pa
r
sing
using opti
o
ns
commit
|
commitdiff
|
tree
2016-10-24
T
e
emu
M
u
rtola
Support for d
e
f
aul
t
values from
O
pti
o
ns to
KeyValueT
r
ee
commit
|
commitdiff
|
tree
2016-10-21
Teemu Murt
o
l
a
C
l
ean up option (defa
u
lt)
v
alue access
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murtol
a
S
e
r
i
alization support
for
KeyValue
T
ree
commit
|
commitdiff
|
tree
2016-10-17
Teemu Murto
l
a
Support option ass
i
g
n
ment
f
rom different
p
r
eci
s
i
o
n
commit
|
commitdiff
|
tree
2016-10-17
Teemu Murtola
Add s
u
pport for reading values from refdata
commit
|
commitdiff
|
tree
2016-10-16
T
e
emu
Murtola
Impro
v
ed error handlin
g
f
or
K
ey
V
alueTree operations
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murto
l
a
Improved
address sanitizer support
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Work around memory leak in t_state
commit
|
commitdiff
|
tree
2016-10-15
T
e
e
mu Murto
l
a
Fix most
memory l
e
aks recently introdu
c
ed
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Us
e
gmx_mtop_t in se
l
ections,
pa
r
t 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu
Murto
l
a
Use
g
m
x
_
m
t
o
p_t in selections,
p
a
r
t 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mur
t
ola
Use
g
mx_mtop_t in selections, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mu
r
tola
Add ba
c
k-mapp
i
ng to KeyVal
u
eTre
e
Trans
f
orm
commit
|
commitdiff
|
tree
2016-10-13
T
e
e
mu
Murt
o
la
Update
b
u
n
dled T
N
G
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Getter for
mapped
pat
h
s from KeyValueTreeTransform
commit
|
commitdiff
|
tree
2016-10-12
Tee
m
u Murt
o
la
Use gmx_mtop_t in selections, pa
r
t 1
commit
|
commitdiff
|
tree
2016-10-12
Teem
u
Murtola
Wrap
s
el
.
method eva
l
uation para
m
eters to
stru
c
t
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murt
o
la
Support
c
o
n
curre
n
t
t
_t
o
pology and g
m
x_mtop_t use
commit
|
commitdiff
|
tree
2016-10-11
Tee
m
u Murtola
Check at
o
m ma
s
s availability
in se
l
ect
i
o
n
s
commit
|
commitdiff
|
tree
2016-10-05
Teemu Murtola
S
u
pport different key matc
h
ing in Key
V
alu
e
TreeTransfo
r
m
commit
|
commitdiff
|
tree
2016-10-05
Teemu M
u
rtola
Me
r
ge "
M
erge br
a
nch release-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Te
e
mu
M
u
rto
l
a
Fix
d
efault ni
c
e level in
m
dru
n
-
only bui
l
d
commit
|
commitdiff
|
tree
2016-09-12
T
e
emu Murto
l
a
Fix
variou
s
me
m
o
r
y
leaks
commit
|
commitdiff
|
tree
2016-09-07
Teemu Murt
o
la
Clean
up CTest te
s
t management
commit
|
commitdiff
|
tree
2016-08-30
Teemu Mu
r
t
ola
Basic supp
o
rt for transforming Ke
y
ValueTre
e
s
commit
|
commitdiff
|
tree
2016-08-27
Teem
u
Murtola
Sup
p
o
r
t
K
ey
V
alueTr
e
e
objects in refda
t
a
commit
|
commitdiff
|
tree
2016-08-18
Te
e
mu
M
urtol
a
Check for unused refdata values
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Generic structu
r
ed key-
v
alue tree
f
or options
commit
|
commitdiff
|
tree
2016-08-18
Tee
m
u Murto
l
a
S
u
pport for non-string option
value assignment
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murt
o
la
Basi
c
s
u
p
p
ort for
a
r
r
ay-of-st
r
u
c
ts i
n
o
p
tions
commit
|
commitdiff
|
tree
2016-08-17
Teemu
M
urtola
Generalize and simplify option value storage
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Generalize option section internals
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
R
e
implement subsections in Options
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murtola
Fi
x
/improv
e
d
o
c li
n
ks in templat
e
/README
commit
|
commitdiff
|
tree
2016-08-01
Teemu M
u
rto
l
a
Function t
o
split de
l
imited strings
commit
|
commitdiff
|
tree
2016-07-14
Teemu Murtola
U
s
e n
e
wer gcc
f
o
r coverage
commit
|
commitdiff
|
tree
2016-07-07
T
eemu Murt
o
la
Change handling for missing releng do
c
s
commit
|
commitdiff
|
tree
2016-06-30
Teemu Mu
r
t
o
la
Extract stri
n
g parsing ro
u
ti
n
es to utility
commit
|
commitdiff
|
tree
2016-06-28
Teemu
Murtola
S
p
lit up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Mu
r
tola
Factory for c
r
eating
t_inputre
c
commit
|
commitdiff
|
tree
2016-06-01
T
eemu Murtola
Use C++ re
p
l
a
cem
e
n
t for md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Mu
r
tola
Ba
s
i
c
C+
+
loggin
g
interface
commit
|
commitdiff
|
tree
2016-05-31
Teemu Mu
r
tola
Improve make_ndx help text
commit
|
commitdiff
|
tree
2016-05-25
Te
e
mu Murtol
a
Support
f
or real MPI
u
nit tests
commit
|
commitdiff
|
tree
2016-05-24
Teem
u
Murtola
Tests for single-rank thread
a
ffinity settin
g
commit
|
commitdiff
|
tree
2016-05-21
T
eemu
M
u
r
t
ola
Pass nu
m
ber of local threa
d
s to thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
A
llow creat
i
ng mock
H
ardwareTopology objects
commit
|
commitdiff
|
tree
2016-05-21
Tee
m
u Murtol
a
Use on
l
y H
a
rdwareTopology for t
h
read affi
n
ity
commit
|
commitdiff
|
tree
2016-05-21
T
eemu Murto
l
a
Merge
b
ranch re
l
ease-2016
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu M
u
rtol
a
Bump version number
s
fo
r
2017
d
eve
l
op
m
ent
commit
|
commitdiff
|
tree
2016-05-17
T
eemu
M
ur
t
o
la
F
ix
some th
r
ead af
f
ini
t
y cas
e
s
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murto
l
a
Ad
d
itional Jenkins docume
n
t
a
t
ion
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
urtola
Inc
l
ude releng documentation to develop
e
r
guide
commit
|
commitdiff
|
tree
next