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Generalize IForceProvider
2017-06-29
Teemu Murtola
General
i
ze IForceProvi
d
er
commit
|
commitdiff
|
tree
2017-06-28
Teemu Murt
o
la
Extend key-value
tree serialization and t
e
sts
commit
|
commitdiff
|
tree
2017-06-27
Teemu
M
urt
o
la
Do not use conf-man
.
p
y
f
or non
-
m
a
n
p
age doc builds
commit
|
commitdiff
|
tree
2017-05-29
T
eemu M
u
rtola
A
void some incorr
e
c
t
b
ehavio
r
with gmx solvate
commit
|
commitdiff
|
tree
2017-05-29
Teemu
M
urtola
R
e
move
p
bcutil <-> mdtypes cyclic
depend
e
ncy
commit
|
commitdiff
|
tree
2017-05-11
Teemu Mur
t
ola
Gener
a
lize comman
d
-line test o
u
tput f
i
l
e
checking
commit
|
commitdiff
|
tree
2017-04-17
Teemu Mu
r
tola
Consisten
t
approach for whole-p
r
ogram tests
commit
|
commitdiff
|
tree
2017-04-11
Teemu Murt
o
la
I
mpro
v
e
key-value tree gm
x
d
ump support
commit
|
commitdiff
|
tree
2017-04-06
Teemu M
u
rtola
F
i
x
memory access issu
e
s
in gmx solvate
commit
|
commitdiff
|
tree
2017-04-06
T
e
em
u
Murtola
Consistent naming for
gmxana tests
commit
|
commitdiff
|
tree
2017-04-04
Teemu Murto
l
a
Utility
functio
n
s for formatt
i
ng
string values
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtola
Imp
r
ove op
t
i
o
n
s
upport & tests for key-value t
r
ee
s
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtola
R
e
move manua
l
al
i
gnment fr
o
m InMemorySerial
i
zer
commit
|
commitdiff
|
tree
2017-03-12
Teemu
M
urtola
Consistent
T
extWriter trai
l
in
g
whit
e
space handling
commit
|
commitdiff
|
tree
2017-03-11
Teemu Murtola
Update cop
y
r
i
ght year for gmx
-versi
o
n
commit
|
commitdiff
|
tree
2017-03-04
T
eemu Murtola
Remove MDModules u
s
e fro
m
mdlib
commit
|
commitdiff
|
tree
2017-03-04
Teemu Murt
o
la
Split
m
d modul
e
fac
e
t
s
to different interfaces
commit
|
commitdiff
|
tree
2017-02-28
Te
e
mu Murtola
More documentation for key-value
t
r
ees
commit
|
commitdiff
|
tree
2017-02-27
Tee
m
u Murtola
Decouple t
_
i
nputrec from MD
M
odules
commit
|
commitdiff
|
tree
2017-02-27
Teemu
Murtol
a
R
e
move
m
od
u
le
refe
r
e
n
ces
f
r
om t_i
n
p
u
trec
commit
|
commitdiff
|
tree
2017-02-10
Te
e
mu Mur
t
ola
Chec
k
log
o
utput i
n
t
hread affinity
t
ests
commit
|
commitdiff
|
tree
2017-02-09
Teem
u
Murtol
a
M
ulti-rank thread affinit
y
tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu Murtol
a
D
ocu
m
ent key-value
t
re
e
transfo
r
m
s
and improve checks
commit
|
commitdiff
|
tree
2017-02-09
Teemu
M
urtola
Overview documentation for new mdp inpu
t
scheme
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
G
e
neric KeyValue
T
re
e
broadcast
commit
|
commitdiff
|
tree
2017-02-08
T
e
emu Mu
r
tola
Generic g
m
x check impl
e
m
e
ntat
i
on wit
h
KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Gen
e
ri
c
gmx d
u
mp implementation for
K
eyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Te
e
mu Murt
o
la
G
ener
i
c tpr h
a
ndling for electric field
commit
|
commitdiff
|
tree
2016-12-12
T
eem
u
Murto
l
a
M
erge branch
r
e
l
e
as
e
-20
1
6
commit
|
commitdiff
|
tree
2016-12-10
T
e
emu Murtola
Minor CMake clean
u
p & modernization
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtola
Build scripts for impro
v
e
d relea
s
e
workflow
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtola
Fix and clean up hand
l
ing of som
e
li
n
k
i
ng
commit
|
commitdiff
|
tree
2016-12-08
T
e
em
u
Murtola
Fix possible memory error with long
s
e
lection
s
commit
|
commitdiff
|
tree
2016-12-07
Tee
m
u Murtola
F
ix
u
se of positio
n
v
ariables
w
i
t
h plus/merge
commit
|
commitdiff
|
tree
2016-11-29
Te
e
m
u
Murtol
a
Ad
d
itional selec
t
io
n
help
commit
|
commitdiff
|
tree
2016-11-06
Teemu Murto
l
a
A
dd selection-enabled gmx tra
j
commit
|
commitdiff
|
tree
2016-10-30
Teemu Murtola
Support normalizing v
a
lues
in Ke
y
V
a
lueTree
commit
|
commitdiff
|
tree
2016-10-24
Teemu M
u
rt
o
la
E
l
e
ctric field md
p
parsing
u
sing options
commit
|
commitdiff
|
tree
2016-10-24
Teemu Mu
r
t
ola
Supp
o
r
t
for d
e
fault
v
a
l
u
es from Options
to KeyValueTree
commit
|
commitdiff
|
tree
2016-10-21
Teemu M
u
rto
l
a
Clean up option (defa
u
lt)
v
a
lue access
commit
|
commitdiff
|
tree
2016-10-19
T
e
emu Murtola
S
e
rializati
o
n supp
o
rt for KeyValueT
r
ee
commit
|
commitdiff
|
tree
2016-10-17
Teemu
M
urto
l
a
Support option
a
s
s
ign
m
ent
f
rom different preci
s
ion
commit
|
commitdiff
|
tree
2016-10-17
T
eem
u
M
urtola
A
d
d supp
o
r
t
for re
a
din
g
v
a
lues
f
rom refdata
commit
|
commitdiff
|
tree
2016-10-16
T
e
emu
M
urtola
Imp
r
oved error handling for KeyValueTre
e
ope
r
atio
n
s
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtol
a
Imp
r
oved address saniti
z
er support
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
W
o
r
k
around memory leak
in t_state
commit
|
commitdiff
|
tree
2016-10-15
Teemu Mur
t
ola
Fix most memory leaks recently
i
n
troduced
commit
|
commitdiff
|
tree
2016-10-14
Teem
u
Mur
t
ola
Us
e
gm
x
_m
t
op_t
i
n selections, part 3
commit
|
commitdiff
|
tree
2016-10-14
T
e
emu Murtola
Use gmx_mtop_t
in selection
s
, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu
M
urtola
Use gmx_mto
p
_t in selectio
n
s,
p
a
rt 2
commit
|
commitdiff
|
tree
2016-10-13
Te
e
mu Murtola
Add back-mapp
i
ng to
KeyValueTreeTran
s
f
orm
commit
|
commitdiff
|
tree
2016-10-13
T
e
e
mu Murtola
Update bundle
d
TNG
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
Gett
e
r
for mapped paths from K
e
yVal
u
eT
r
ee
T
ransform
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murtola
Use gm
x
_m
t
op_t in
selections, par
t
1
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murt
o
la
Wrap sel
.
m
e
thod evaluation parameters to struct
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murtola
Suppo
r
t co
n
cur
r
ent t_topolog
y
an
d
gmx
_
mtop_t use
commit
|
commitdiff
|
tree
2016-10-11
Te
e
mu M
u
rtola
Check ato
m
m
a
ss a
v
ail
a
b
i
l
ity in selec
t
ion
s
commit
|
commitdiff
|
tree
2016-10-05
Tee
m
u Murt
o
la
Support
d
ifferen
t
key mat
c
hing in
K
eyValueTreeTransform
commit
|
commitdiff
|
tree
2016-10-05
Teemu Murtola
Merge "Merge branch release-5-1
into release-2016
"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Murtola
F
i
x
d
ef
a
ult nice level in
mdrun-only buil
d
commit
|
commitdiff
|
tree
2016-09-12
Teem
u
Murtola
Fix various memory le
a
k
s
commit
|
commitdiff
|
tree
2016-09-07
Teem
u
M
urto
l
a
Clean up
CTest
t
e
st management
commit
|
commitdiff
|
tree
2016-08-30
Teem
u
M
urtola
Basic
su
p
port
f
or transf
o
rming
K
e
yValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murt
o
la
S
u
pport KeyValueTree
o
b
jects
in
refda
t
a
commit
|
commitdiff
|
tree
2016-08-18
Te
e
m
u
Murtola
Check for u
n
us
e
d re
f
data v
a
lues
commit
|
commitdiff
|
tree
2016-08-18
Teemu
M
urtola
Gen
e
ric stru
c
ture
d
key-value
tree for op
t
ions
commit
|
commitdiff
|
tree
2016-08-18
Teemu
M
urtola
Su
p
port for
non-
s
tring
o
pt
i
on value
assignm
e
nt
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtol
a
B
asic suppo
r
t
for array-of-structs in options
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murt
o
l
a
Generalize and simplif
y
o
p
tion
v
alue
s
t
ora
g
e
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
G
eneralize
optio
n
s
e
ction inte
r
na
l
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Re
i
mplement subsections
i
n Option
s
commit
|
commitdiff
|
tree
2016-08-04
Te
e
mu Murtola
Fix/i
m
prove d
o
c links in template/REA
D
ME
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtol
a
Function to split d
e
limited stri
n
g
s
commit
|
commitdiff
|
tree
2016-07-14
Teem
u
M
u
rto
l
a
Use n
e
w
er gcc fo
r
cov
e
rag
e
commit
|
commitdiff
|
tree
2016-07-07
Teemu Mur
t
o
l
a
Chan
g
e handling for
m
issing releng docs
commit
|
commitdiff
|
tree
2016-06-30
Tee
m
u
Murtola
Ex
t
rac
t
string pars
i
ng routi
n
e
s
to
ut
i
lity
commit
|
commitdiff
|
tree
2016-06-28
Teemu M
u
rtola
Sp
l
it up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Murtola
Factor
y
for crea
t
ing
t_inputrec
commit
|
commitdiff
|
tree
2016-06-01
Teemu Mu
r
tola
Use C++ replacement for
m
d
_logg
i
ng
.
*
commit
|
commitdiff
|
tree
2016-06-01
T
eemu
M
urtola
Basic C++ logging interface
commit
|
commitdiff
|
tree
2016-05-31
Tee
m
u Murto
l
a
I
m
prove make_ndx help tex
t
commit
|
commitdiff
|
tree
2016-05-25
Te
e
m
u
M
urtola
Sup
p
ort for
real MPI unit
tests
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
Tests for sin
g
l
e-
r
an
k
thread af
f
in
i
ty se
t
ting
commit
|
commitdiff
|
tree
2016-05-21
T
e
emu M
u
rtola
Pass number of local thr
e
ads to thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Tee
m
u
M
urtola
All
o
w creating mock HardwareTopology
object
s
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Use onl
y
Har
d
wareTopology fo
r
t
h
r
ead affi
n
ity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
M
e
rg
e
branch release-2
0
1
6
commit
|
commitdiff
|
tree
2016-05-21
Teem
u
Murtol
a
Bump version n
u
mbers for 2
0
17 development
commit
|
commitdiff
|
tree
2016-05-17
Teemu
M
urtola
Fix some thread affini
t
y cases
commit
|
commitdiff
|
tree
2016-05-10
Teem
u
Murto
l
a
Addit
i
onal Jenkins documen
t
ation
commit
|
commitdiff
|
tree
2016-05-10
Teemu
Murtola
Includ
e
r
eleng documentatio
n
t
o developer g
u
ide
commit
|
commitdiff
|
tree
2016-05-08
T
e
emu Murtola
S
upport for
O
penCL C
I
b
uil
d
s
commit
|
commitdiff
|
tree
2016-05-05
Teemu Mu
r
tola
Mer
g
e br
a
nch rele
a
se-
5
-1
commit
|
commitdiff
|
tree
2016-05-05
Teemu Murto
l
a
Ma
k
e Sphinx build silent for vers
i
on 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Teemu Murtola
Mark
o
ptional input/output fi
l
es in gmx order
commit
|
commitdiff
|
tree
2016-04-28
T
e
em
u
M
urt
o
la
U
s
e Ha
r
dwareTopo
l
ogy to set nthreads_hw_av
a
il
commit
|
commitdiff
|
tree
2016-04-28
Teemu
Murto
l
a
Remove
g
mx_hw_info
_
t::ncore
commit
|
commitdiff
|
tree
2016-04-27
Teemu
M
urtola
Improve release wo
r
kf
l
ow tes
t
ing
commit
|
commitdiff
|
tree
2016-04-27
T
eemu Murt
o
la
Disable multiple
ranks for non-MPI
u
nit test
s
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix issues with failing t
h
read aff
i
nity s
e
tting
commit
|
commitdiff
|
tree
next