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Change use of t_inpfile to std::vector
2017-09-04
Te
e
mu Murtola
Intr
o
duce self
-
pairs search in n
b
search
commit
|
commitdiff
|
tree
2017-09-04
Te
e
mu M
u
rt
o
la
R
ef
a
ctor ana
l
ysis n
b
search test
s
commit
|
commitdiff
|
tree
2017-08-21
T
e
emu Murtola
Simple union-f
i
nd s
t
ruct
u
re
commit
|
commitdiff
|
tree
2017-07-19
T
eemu Murtola
Prune
unnece
s
sary cells in
anal
y
sis nbsearch
commit
|
commitdiff
|
tree
2017-07-17
Teemu
Murtola
Fix hwloc
d
ete
c
tion
commit
|
commitdiff
|
tree
2017-07-11
Teemu Murtola
Suppo
r
t sc
o
p
e
d key-value tree t
r
ansform ru
l
es
commit
|
commitdiff
|
tree
2017-07-06
Teemu Murtola
Detect un
k
nown mdp optio
n
s in g
m
x dum
p
/check
commit
|
commitdiff
|
tree
2017-06-30
T
eemu
M
urtol
a
Fix boolean
s
erialization
commit
|
commitdiff
|
tree
2017-06-30
Teemu Mur
t
ola
Extend key-value tree comp
a
rison
a
nd t
e
sts
commit
|
commitdiff
|
tree
2017-06-29
Teemu Mu
r
tol
a
G
e
neralize
I
Force
P
ro
v
ider
commit
|
commitdiff
|
tree
2017-06-28
T
eemu Murto
l
a
Ext
e
nd
k
e
y
-
value tree serializati
o
n
a
nd test
s
commit
|
commitdiff
|
tree
2017-06-27
Teemu Murtola
Do not use
c
onf-ma
n
.
py for non-manpage doc b
u
ilds
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murt
o
l
a
Av
o
id some
i
ncorrect be
h
avior with gm
x
solvate
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murtola
R
emov
e
pbcu
t
il <-> mdt
y
pes cyc
l
ic dependency
commit
|
commitdiff
|
tree
2017-05-11
Tee
m
u Murtola
Genera
l
ize comma
n
d
-lin
e
test out
p
ut
f
ile check
i
ng
commit
|
commitdiff
|
tree
2017-04-17
Teemu Murtola
Consistent approach
f
or
wh
o
le-program tests
commit
|
commitdiff
|
tree
2017-04-11
T
eem
u
Murtola
Im
p
ro
v
e key
-
value
t
ree gmx dump sup
p
ort
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murto
l
a
Fix memory access issues
i
n
gmx solvat
e
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murtola
Consistent naming
for gmxana tests
commit
|
commitdiff
|
tree
2017-04-04
Teemu Murt
o
la
U
t
ility fun
c
tions for formatting stri
n
g
values
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtola
Improve option support & tests for key-va
l
ue trees
commit
|
commitdiff
|
tree
2017-03-13
Teemu
M
urtola
Remov
e
man
u
al alignment from I
n
M
e
morySerializer
commit
|
commitdiff
|
tree
2017-03-12
Teemu Murtola
Cons
i
st
e
nt TextWriter trailing whit
e
space handling
commit
|
commitdiff
|
tree
2017-03-11
T
eemu
M
urtola
Update cop
y
rig
h
t
yea
r
for
g
mx -version
commit
|
commitdiff
|
tree
2017-03-04
Tee
m
u M
u
rt
o
la
Remove MDModules use
from mdlib
commit
|
commitdiff
|
tree
2017-03-04
T
eemu Mur
t
o
l
a
Spli
t
md
modu
l
e fac
e
ts t
o
different in
t
erfaces
commit
|
commitdiff
|
tree
2017-02-28
Teemu Murtola
More documentation for key-value trees
commit
|
commitdiff
|
tree
2017-02-27
Teemu Murtola
D
e
cou
p
l
e
t_inputrec
f
rom MDM
o
dules
commit
|
commitdiff
|
tree
2017-02-27
Teemu M
u
r
t
o
la
Remove
m
o
d
ule r
e
f
erence
s
fro
m
t_input
r
ec
commit
|
commitdiff
|
tree
2017-02-10
Teemu Murtola
Check
l
og
out
p
ut i
n
thread
af
f
inity tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu Murtola
Multi-rank t
h
read affinity tes
t
s
commit
|
commitdiff
|
tree
2017-02-09
Teemu Murto
l
a
D
ocument k
e
y-value
t
ree tra
n
sforms and im
p
rove
checks
commit
|
commitdiff
|
tree
2017-02-09
T
e
emu
Murtola
Overv
i
ew doc
u
men
t
ation for ne
w
mdp inpu
t
scheme
commit
|
commitdiff
|
tree
2017-02-08
Teemu M
u
rtola
G
e
ne
r
ic KeyValueTre
e
broad
c
ast
commit
|
commitdiff
|
tree
2017-02-08
Tee
m
u
M
urtola
G
en
e
ric gmx check implementation
w
i
th KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teem
u
Murtola
Generic gmx dump impl
e
me
n
tation for K
e
yValueTree
commit
|
commitdiff
|
tree
2017-02-08
T
ee
m
u Murtol
a
Generic tpr
handling for
electric field
commit
|
commitdiff
|
tree
2016-12-12
Teem
u
Murtola
Merge b
r
anch release-2
0
16
commit
|
commitdiff
|
tree
2016-12-10
Teemu
M
urtol
a
Minor CMake c
l
eanup &
modern
i
zation
commit
|
commitdiff
|
tree
2016-12-10
Te
e
mu Murtola
B
uild s
c
ripts for
improved
relea
s
e w
o
r
k
flow
commit
|
commitdiff
|
tree
2016-12-08
T
eem
u
Mu
r
tola
F
ix and clean up
h
a
ndling of so
m
e link
i
ng
commit
|
commitdiff
|
tree
2016-12-08
T
eemu Murtola
Fix
p
os
s
ib
l
e memory error with long sele
c
ti
o
ns
commit
|
commitdiff
|
tree
2016-12-07
T
eem
u
Murt
o
la
Fix use of
position varia
b
l
e
s with plus/merge
commit
|
commitdiff
|
tree
2016-11-29
Teemu Murtola
A
dd
i
tional s
e
lection help
commit
|
commitdiff
|
tree
2016-11-06
Teemu Murtola
Add
s
election-enabled gmx tra
j
commit
|
commitdiff
|
tree
2016-10-30
Teemu Murto
l
a
S
upport
normalizi
n
g values i
n
Key
V
alueTr
e
e
commit
|
commitdiff
|
tree
2016-10-24
Teemu
M
urtol
a
El
e
ctric field mdp parsing usi
n
g options
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murto
l
a
S
u
p
po
r
t for de
f
ault values from Optio
n
s to
K
eyV
a
lueTree
commit
|
commitdiff
|
tree
2016-10-21
Teemu Murtola
Clean up option (default) v
a
lue access
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murt
o
la
Serialization suppor
t
for KeyValueTre
e
commit
|
commitdiff
|
tree
2016-10-17
Teemu
Murt
o
l
a
Supp
o
rt op
t
io
n
ass
i
gnme
n
t f
r
om diff
e
r
e
n
t precision
commit
|
commitdiff
|
tree
2016-10-17
Teemu Mu
r
tola
Ad
d
support
f
or reading values from
r
efdata
commit
|
commitdiff
|
tree
2016-10-16
T
ee
m
u
Murtola
Impr
o
ved error hand
l
ing fo
r
KeyV
a
lueTree operation
s
commit
|
commitdiff
|
tree
2016-10-15
Tee
m
u Murto
l
a
I
m
p
roved address sanitiz
e
r
s
u
pport
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Work around memory le
a
k
i
n t_stat
e
commit
|
commitdiff
|
tree
2016-10-15
Teemu
Murtola
Fix most memory leak
s
re
c
ently i
n
troduced
commit
|
commitdiff
|
tree
2016-10-14
Teem
u
Murtola
Use gmx_mtop_t
in
s
el
e
c
t
ions, part 3
commit
|
commitdiff
|
tree
2016-10-14
Tee
m
u Murtola
Use gmx_mtop_
t
in selections, pa
r
t 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu M
u
rtola
Us
e
gmx_mtop_t in selections, part
2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
A
d
d bac
k
-
m
a
p
ping to K
e
yValueTr
e
eTransf
o
r
m
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murto
l
a
Update bundled TNG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
G
e
tt
e
r fo
r
ma
p
ped paths from
K
eyValu
e
Tr
e
eTransfor
m
commit
|
commitdiff
|
tree
2016-10-12
Te
e
mu Murtol
a
Us
e
gmx_mtop_t in
selections, par
t
1
commit
|
commitdiff
|
tree
2016-10-12
Teemu Mur
t
ola
Wrap
s
e
l
.
metho
d
evaluation
parame
t
ers to struc
t
commit
|
commitdiff
|
tree
2016-10-11
Tee
m
u Mur
t
ola
Sup
p
ort concurr
e
nt
t_topology and g
m
x_mto
p
_t use
commit
|
commitdiff
|
tree
2016-10-11
Teem
u
M
urtola
C
h
eck
a
tom mass
a
v
ailability in s
e
le
c
tio
n
s
commit
|
commitdiff
|
tree
2016-10-05
Teemu Mu
r
tola
Support di
f
ferent key matching
i
n KeyValueTreeTransform
commit
|
commitdiff
|
tree
2016-10-05
T
e
e
m
u Mu
r
tola
M
erge "Merge branch release-5-1 into relea
s
e
-
2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Mur
t
ola
Fix default n
i
ce l
e
ve
l
in mdrun-on
l
y buil
d
commit
|
commitdiff
|
tree
2016-09-12
T
e
e
m
u Murt
o
la
F
ix various
m
emory
l
eaks
commit
|
commitdiff
|
tree
2016-09-07
Teemu M
u
rtola
C
l
ean u
p
CTest test management
commit
|
commitdiff
|
tree
2016-08-30
Teemu Murtola
Basic s
u
pport for transfo
r
m
i
ng
K
eyValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
Supp
o
rt
Key
V
al
u
eTree objects in refda
t
a
commit
|
commitdiff
|
tree
2016-08-18
Teemu
M
urto
l
a
Check for unu
s
ed
r
efdata va
l
ues
commit
|
commitdiff
|
tree
2016-08-18
Teem
u
M
u
rtol
a
G
e
neric structu
r
ed ke
y
-value tree f
o
r option
s
commit
|
commitdiff
|
tree
2016-08-18
Teemu
Murt
o
la
S
upport
f
or
non-string option value a
s
signment
commit
|
commitdiff
|
tree
2016-08-17
Teemu Mur
t
ola
Basic support
f
or a
r
ra
y
-of-
s
tructs in o
p
tions
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Generalize a
n
d simplify option val
u
e storage
commit
|
commitdiff
|
tree
2016-08-17
T
e
emu Murto
l
a
Ge
n
e
r
aliz
e
op
t
ion section internals
commit
|
commitdiff
|
tree
2016-08-17
Teemu
M
urto
l
a
Reimplement sub
s
ectio
n
s in
O
ptio
n
s
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murt
o
la
Fix/improve d
o
c lin
k
s in tem
p
late/READM
E
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtol
a
Function to
s
plit
deli
m
it
e
d str
i
ngs
commit
|
commitdiff
|
tree
2016-07-14
T
e
emu Murtola
Us
e
newe
r
gcc for
cover
a
ge
commit
|
commitdiff
|
tree
2016-07-07
Te
e
mu Murt
o
la
Chan
g
e handlin
g
for miss
i
n
g releng doc
s
commit
|
commitdiff
|
tree
2016-06-30
Teemu
M
urto
l
a
Extract str
i
ng par
s
ing routine
s
to u
t
ility
commit
|
commitdiff
|
tree
2016-06-28
Teemu Murtola
Split up compa
r
e
.
*
commit
|
commitdiff
|
tree
2016-06-27
Te
e
mu Murtola
Factory for creating t_inputrec
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murtola
Use C++
r
e
pl
a
cement
for md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu
M
urtola
Basic
C
++
loggin
g
inte
r
face
commit
|
commitdiff
|
tree
2016-05-31
Teemu Murtola
Improve ma
k
e_ndx help text
commit
|
commitdiff
|
tree
2016-05-25
T
e
emu
Mu
r
t
o
la
S
u
pport for
r
ea
l
M
P
I unit tes
t
s
commit
|
commitdiff
|
tree
2016-05-24
T
e
em
u
M
u
rtola
Tests for single-
r
ank thread a
f
f
i
nity setting
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Pass number o
f
loc
a
l threads t
o
thread affin
i
ty
commit
|
commitdiff
|
tree
2016-05-21
Teemu M
u
r
t
ola
A
llow creati
n
g mock HardwareTopology objec
t
s
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
u
r
t
ola
Use only
Har
d
w
a
reTopology
for thread
af
f
inity
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Murtola
Merg
e
b
ra
n
ch
r
el
e
a
s
e
-
20
1
6
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Bump ver
s
ion numbers for
2017 dev
e
lop
m
ent
commit
|
commitdiff
|
tree
2016-05-17
T
eemu Murto
l
a
Fix some t
h
rea
d
affinity cases
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Murtola
Ad
d
itional Jen
k
ins documentati
o
n
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Include releng
d
o
cument
a
ti
o
n to d
e
velop
e
r
g
uid
e
commit
|
commitdiff
|
tree
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