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Fix duplicate warning
2017-09-04
Teemu Murtola
I
nt
r
oduce self-pairs search
i
n
nbsearch
commit
|
commitdiff
|
tree
2017-09-04
Teem
u
Murt
o
la
Refactor analysis nbsear
c
h
t
ests
commit
|
commitdiff
|
tree
2017-08-21
Teem
u
Murtola
Simple union-
f
i
n
d
structure
commit
|
commitdiff
|
tree
2017-07-19
Teemu Murtola
Prune un
n
ecessar
y
cel
l
s
in
analysis nbsearch
commit
|
commitdiff
|
tree
2017-07-17
Teemu M
u
rtola
Fix hwl
o
c
d
etect
i
on
commit
|
commitdiff
|
tree
2017-07-11
Tee
m
u Murtola
Sup
p
ort
scoped key
-
value tre
e
transform rules
commit
|
commitdiff
|
tree
2017-07-06
T
eemu Murtola
Detect unknown mdp optio
n
s in gmx
d
ump/check
commit
|
commitdiff
|
tree
2017-06-30
Teemu M
u
rtola
Fix boolean seria
l
ization
commit
|
commitdiff
|
tree
2017-06-30
Teemu Murtola
Extend key-va
l
ue tree
c
omparison an
d
tests
commit
|
commitdiff
|
tree
2017-06-29
Teemu Murtola
Ge
n
e
ralize IForceP
r
ovid
e
r
commit
|
commitdiff
|
tree
2017-06-28
Teemu Murtola
E
x
tend key-value tree serializa
t
ion and tests
commit
|
commitdiff
|
tree
2017-06-27
Tee
m
u
M
urtola
Do n
o
t use
c
onf-man
.
p
y
for non-manpage doc
build
s
commit
|
commitdiff
|
tree
2017-05-29
Tee
m
u Murtola
Avoid so
m
e inco
r
rect b
e
h
a
vior
w
ith gmx solvate
commit
|
commitdiff
|
tree
2017-05-29
Te
e
mu Murtola
Rem
o
ve
p
bcu
t
il <-> mdtype
s
c
y
cli
c
depe
n
den
c
y
commit
|
commitdiff
|
tree
2017-05-11
Teemu Murtola
Gene
r
aliz
e
c
o
mman
d
-
l
ine test
output file check
i
ng
commit
|
commitdiff
|
tree
2017-04-17
Teemu
M
u
r
t
o
l
a
C
o
nsistent approach fo
r
whole-p
r
ogram tests
commit
|
commitdiff
|
tree
2017-04-11
Teemu Murtola
Improve key-value tre
e
gmx dump supp
o
rt
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murtola
Fix me
m
ory access
i
ssues in gmx solvate
commit
|
commitdiff
|
tree
2017-04-06
Teemu Murt
o
l
a
Co
n
sis
t
en
t
na
m
i
n
g
for gmxana tests
commit
|
commitdiff
|
tree
2017-04-04
Teem
u
Murtola
Utility functions fo
r
formattin
g
string valu
e
s
commit
|
commitdiff
|
tree
2017-03-13
Teem
u
Murt
o
la
Improve
o
ption su
p
por
t
& test
s
for key-value
t
rees
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtol
a
Remove
manual alignment from
InMe
m
ory
S
erializer
commit
|
commitdiff
|
tree
2017-03-12
Teemu Murtola
Consistent Text
W
r
i
t
e
r trai
l
ing
whi
t
espace handling
commit
|
commitdiff
|
tree
2017-03-11
Teemu Murtola
Upd
a
te copyri
g
ht year fo
r
gmx -ver
s
ion
commit
|
commitdiff
|
tree
2017-03-04
Teem
u
Mu
r
tola
Remov
e
M
DMod
u
les
use
f
rom mdlib
commit
|
commitdiff
|
tree
2017-03-04
Teemu Mu
r
tol
a
Split md
m
odu
l
e facets
t
o different interfaces
commit
|
commitdiff
|
tree
2017-02-28
Teemu Mu
r
to
l
a
Mor
e
document
a
tion
f
o
r key-
v
alu
e
tr
e
es
commit
|
commitdiff
|
tree
2017-02-27
Teemu Mu
r
tola
Dec
o
u
ple t_inp
u
tre
c
f
rom MDModules
commit
|
commitdiff
|
tree
2017-02-27
Teemu
M
urtola
Remo
v
e modu
l
e r
e
feren
c
es from t_inputrec
commit
|
commitdiff
|
tree
2017-02-10
Teemu Mu
r
tola
Check
l
o
g
o
u
tput in th
r
ead
a
ffinity tes
t
s
commit
|
commitdiff
|
tree
2017-02-09
Teemu
Murtola
Multi-rank th
r
ead affinity tests
commit
|
commitdiff
|
tree
2017-02-09
T
e
emu Murtola
Document key
-
v
a
lue tree tran
s
forms
a
n
d
improve checks
commit
|
commitdiff
|
tree
2017-02-09
Te
e
mu Murtola
O
v
erview docume
n
tation for
new m
d
p input sch
e
me
commit
|
commitdiff
|
tree
2017-02-08
Teem
u
Mur
t
ola
G
eneric KeyValueT
r
ee bro
a
dcast
commit
|
commitdiff
|
tree
2017-02-08
T
e
emu M
u
rtola
Generic gmx ch
e
ck
implementation with KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu
M
u
r
tol
a
Generic gmx d
u
mp implementati
o
n
fo
r
KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
T
e
em
u
Murtola
Gene
r
ic tpr handli
n
g for electric field
commit
|
commitdiff
|
tree
2016-12-12
Teemu
M
urto
l
a
M
e
r
g
e branch rele
a
s
e-2
0
16
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtola
Minor CMa
k
e
clean
u
p & modernization
commit
|
commitdiff
|
tree
2016-12-10
T
eemu Murtola
Build scripts for improv
e
d release wo
r
kflow
commit
|
commitdiff
|
tree
2016-12-08
Te
e
mu
Murtola
F
i
x
a
n
d clean up handling of some
l
inki
n
g
commit
|
commitdiff
|
tree
2016-12-08
Tee
m
u Murtola
Fix
possible
m
em
o
r
y e
r
ror with long selections
commit
|
commitdiff
|
tree
2016-12-07
Tee
m
u
M
u
r
tola
Fix use of position variables with plus/me
r
ge
commit
|
commitdiff
|
tree
2016-11-29
Teemu Murtola
Addit
i
onal selection h
e
lp
commit
|
commitdiff
|
tree
2016-11-06
Teemu Murto
l
a
Add
s
e
l
e
ction-enabled gmx traj
commit
|
commitdiff
|
tree
2016-10-30
Teemu Mu
r
tola
Support norma
l
izing values in KeyVa
l
ueTree
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Electric fi
e
ld mdp pa
r
sing
usi
n
g
options
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Support f
o
r default va
l
ues from Options to
K
eyValueTree
commit
|
commitdiff
|
tree
2016-10-21
Teemu
Mu
r
t
ola
Clean
up
o
p
t
ion (de
f
ault) v
a
lue acce
s
s
commit
|
commitdiff
|
tree
2016-10-19
Teemu
M
urto
l
a
Se
r
ializa
t
ion su
p
p
o
rt for
K
eyValueTree
commit
|
commitdiff
|
tree
2016-10-17
Teemu Mur
t
ol
a
Support option assignment from
diff
e
re
n
t pre
c
ision
commit
|
commitdiff
|
tree
2016-10-17
Te
e
mu
M
urtola
Add
s
upport
for r
e
ading
val
u
es from ref
d
ata
commit
|
commitdiff
|
tree
2016-10-16
Teemu Murt
o
l
a
Improve
d
error hand
l
ing for
KeyVa
l
ueTre
e
operations
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Improved address saniti
z
er sup
p
ort
commit
|
commitdiff
|
tree
2016-10-15
Teemu M
u
rtola
Work around
m
emory leak in t_state
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murto
l
a
Fix
m
ost memory leak
s
recently introduced
commit
|
commitdiff
|
tree
2016-10-14
T
e
emu Murto
l
a
Use g
m
x_
m
top_t in
selections,
p
a
r
t 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use
gmx_mtop_t in
selecti
o
ns, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Use gm
x
_m
t
op_
t
in se
l
ecti
o
ns,
p
art 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtol
a
Add back-mapping to KeyVal
u
e
T
reeT
r
ansf
o
r
m
commit
|
commitdiff
|
tree
2016-10-13
Tee
m
u M
u
rtola
Update bundl
e
d TNG
commit
|
commitdiff
|
tree
2016-10-13
T
eemu M
u
r
t
ola
G
e
tter
for mapped paths from KeyValueTre
e
Tr
a
nsform
commit
|
commitdiff
|
tree
2016-10-12
T
eem
u
Murtol
a
U
se gmx_mtop_t in sele
c
tions, part 1
commit
|
commitdiff
|
tree
2016-10-12
Teemu Mu
r
tola
Wrap sel
.
method evalu
a
tion parameters to
s
truct
commit
|
commitdiff
|
tree
2016-10-11
Teem
u
Murtol
a
Support
c
oncurrent t_t
o
pology and g
m
x_
m
top_t use
commit
|
commitdiff
|
tree
2016-10-11
T
e
emu Mu
r
tola
Chec
k
atom mass avail
a
b
i
lity
in
s
elections
commit
|
commitdiff
|
tree
2016-10-05
Teemu Murtola
Supp
o
rt diff
e
ren
t
key mat
c
hing in
K
e
y
V
al
u
eTree
T
ransform
commit
|
commitdiff
|
tree
2016-10-05
Teemu Mu
r
tola
Merge
"Merge branc
h
re
l
ea
s
e-5
-
1
into releas
e
-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Mu
r
tola
Fix default
ni
c
e level
in mdrun-only build
commit
|
commitdiff
|
tree
2016-09-12
Teemu Murtola
Fix var
i
o
u
s
m
emory leaks
commit
|
commitdiff
|
tree
2016-09-07
Teemu Murto
l
a
Clean up C
T
e
s
t tes
t
management
commit
|
commitdiff
|
tree
2016-08-30
T
e
emu Murtol
a
Basi
c
support for
t
r
a
nsforming KeyVa
l
ueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
Support KeyValu
e
Tree obj
e
c
ts in r
e
fdata
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murt
o
la
Check for unused ref
d
a
ta values
commit
|
commitdiff
|
tree
2016-08-18
T
e
emu Murtola
Gene
r
ic struc
t
ured key-value tree for op
t
ions
commit
|
commitdiff
|
tree
2016-08-18
Te
e
mu
Mur
t
ola
Suppor
t
for non-string option
val
u
e assign
m
ent
commit
|
commitdiff
|
tree
2016-08-17
T
e
e
mu M
u
rtola
Basic support for a
r
ray
-
of-struct
s
in op
t
io
n
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
General
i
ze
and s
i
mpl
i
fy option value
storage
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Genera
l
ize
o
ption
s
ect
i
on int
e
r
n
a
l
s
commit
|
commitdiff
|
tree
2016-08-17
T
eemu Murtola
Reimplement subsection
s
in Op
t
ions
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murtola
F
i
x/improve
d
oc li
n
ks in template/README
commit
|
commitdiff
|
tree
2016-08-01
Te
e
mu
Murtola
F
u
n
c
tion to spli
t
delimit
e
d strings
commit
|
commitdiff
|
tree
2016-07-14
Teemu
M
urtol
a
Use newer gcc fo
r
co
v
e
rage
commit
|
commitdiff
|
tree
2016-07-07
Teemu Murtola
Change
h
a
ndlin
g
for missing re
l
e
n
g
d
ocs
commit
|
commitdiff
|
tree
2016-06-30
Teemu Murto
l
a
Extrac
t
string parsing routines to
u
tili
t
y
commit
|
commitdiff
|
tree
2016-06-28
Te
e
mu Murtola
S
p
lit up
co
m
pare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Te
e
mu Murtola
Factory f
o
r creati
n
g
t_inputrec
commit
|
commitdiff
|
tree
2016-06-01
T
eemu Murtola
Use
C++ repl
a
cement for md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murt
o
la
Basic
C
+
+
lo
g
ging
i
nterface
commit
|
commitdiff
|
tree
2016-05-31
Te
e
mu Murtola
Im
p
rove make_ndx help text
commit
|
commitdiff
|
tree
2016-05-25
Teemu
M
urto
l
a
Support for real MPI unit tests
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
Tests fo
r
singl
e
-rank th
r
e
a
d aff
i
ni
t
y setting
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Murtola
Pass number of local threads to thread a
f
fin
i
ty
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtol
a
Allow creating mock Hardware
T
opology objects
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Murto
l
a
Use only Har
d
ware
T
opology fo
r
thread affi
n
i
ty
commit
|
commitdiff
|
tree
2016-05-21
Teem
u
Murtola
Merge
b
ranc
h
release-2016
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
urt
o
la
Bump version num
b
ers for 2017 dev
e
lo
p
ment
commit
|
commitdiff
|
tree
2016-05-17
Teemu Murtola
Fix som
e
thr
e
ad
a
ffinity cases
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
A
d
d
it
i
o
nal Jenkins docum
e
nta
t
i
on
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
In
c
lude r
e
leng docume
n
tation
to developer guide
commit
|
commitdiff
|
tree
next