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Support normalizing values in KeyValueTree
2016-10-30
Teemu Murt
o
la
Sup
p
o
rt
normalizing values
in K
e
yValueTr
e
e
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Electric f
i
eld mdp parsing using o
p
ti
o
ns
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Suppo
r
t fo
r
d
efault valu
e
s f
r
om Options to KeyVal
u
eT
r
ee
commit
|
commitdiff
|
tree
2016-10-21
Teemu M
u
rt
o
l
a
Clean up option (d
e
faul
t
)
value
a
cce
s
s
commit
|
commitdiff
|
tree
2016-10-19
Tee
m
u
Murtola
Seria
l
i
za
t
i
on supp
o
r
t for KeyV
a
lueTree
commit
|
commitdiff
|
tree
2016-10-17
Teemu
Mur
t
ola
Su
p
port
optio
n
ass
i
gnme
n
t from differe
n
t precision
commit
|
commitdiff
|
tree
2016-10-17
Teemu Murtola
Add support
for reading
v
alues from refdata
commit
|
commitdiff
|
tree
2016-10-16
Teemu Mu
r
tola
Impr
o
v
e
d error
h
andling for KeyV
a
lueTree operations
commit
|
commitdiff
|
tree
2016-10-15
T
e
emu Mur
t
ola
Impr
o
ved address sa
n
itizer support
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murt
o
l
a
W
ork ar
o
und me
m
or
y
leak in t_s
t
ate
commit
|
commitdiff
|
tree
2016-10-15
Te
e
mu Murtola
Fix most m
e
mory leaks re
c
ently introduced
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use gmx_mtop_t in selecti
o
ns, part 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu M
u
rtola
Use gmx_mtop_t in selections,
p
art
2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mur
t
ola
Use gmx_mt
o
p_t
in selections, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mur
t
ola
Add back-m
a
pping
to
K
eyValueTr
e
eTransform
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mur
t
ola
Update bu
n
dled TNG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Getter for
mapped paths from Ke
y
V
alueTreeTran
s
form
commit
|
commitdiff
|
tree
2016-10-12
Teemu
M
urto
l
a
U
se gmx_mtop_t in sele
c
tions, par
t
1
commit
|
commitdiff
|
tree
2016-10-12
T
e
emu Murtola
Wrap sel
.
meth
o
d
evalu
a
tion parameters to struct
commit
|
commitdiff
|
tree
2016-10-11
Teemu
Murtola
Suppor
t
concurrent
t
_topology and gmx
_
mtop_t use
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murtola
C
hec
k
at
o
m mass availabilit
y
in s
e
lections
commit
|
commitdiff
|
tree
2016-10-05
Teemu Mur
t
ola
Support different key
m
atching in
KeyValu
e
TreeTransform
commit
|
commitdiff
|
tree
2016-10-05
Te
e
mu Murtola
Merge "Merge branch
release-5-1 in
t
o release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Murtola
F
i
x
d
efault nice level
in mdrun-only bui
l
d
commit
|
commitdiff
|
tree
2016-09-12
Teem
u
Mu
r
to
l
a
Fix various memory leaks
commit
|
commitdiff
|
tree
2016-09-07
Teemu Murt
o
l
a
Clean
up C
T
est test
ma
n
agement
commit
|
commitdiff
|
tree
2016-08-30
Teemu
Murto
l
a
Basic support for tran
s
forming KeyValueT
r
e
es
commit
|
commitdiff
|
tree
2016-08-27
Teemu Mu
r
tola
S
upport KeyVal
u
e
T
ree
objec
t
s in r
e
fdat
a
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Check f
o
r unused refdata
v
alues
commit
|
commitdiff
|
tree
2016-08-18
T
eemu Murtola
Generic str
u
ct
u
red
ke
y
-v
a
lue tre
e
for o
p
t
i
ons
commit
|
commitdiff
|
tree
2016-08-18
Te
e
mu Mur
t
ola
S
u
pport for
non-
s
tring option value assignment
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
B
a
sic suppo
r
t
f
o
r
arra
y
-of-stru
c
t
s
in options
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murtola
G
eneralize and simplif
y
o
p
tion value
storage
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murtola
G
eneralize option section intern
a
ls
commit
|
commitdiff
|
tree
2016-08-17
Teemu Mu
r
tola
Reimplement subsections in Opti
o
n
s
commit
|
commitdiff
|
tree
2016-08-04
T
eemu Murtola
Fix/i
m
p
r
o
v
e
doc
li
n
ks in tem
p
late/
R
EADME
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtola
Functio
n
to split del
i
m
ited strings
commit
|
commitdiff
|
tree
2016-07-14
T
eemu Murt
o
la
Use newer gcc
f
or coverage
commit
|
commitdiff
|
tree
2016-07-07
Te
e
mu
Murtola
Chan
g
e
h
andling for
m
issing rele
n
g docs
commit
|
commitdiff
|
tree
2016-06-30
Te
e
mu Mu
r
tola
Extr
a
ct string parsing rout
i
nes to util
i
ty
commit
|
commitdiff
|
tree
2016-06-28
Teem
u
Murtola
Split up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Tee
m
u Mu
r
tola
Factory for creating
t_inp
u
tr
e
c
commit
|
commitdiff
|
tree
2016-06-01
Te
e
mu Murto
l
a
Use C+
+
replacement
f
o
r md_log
g
ing
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murtola
B
asi
c
C++ loggi
n
g interface
commit
|
commitdiff
|
tree
2016-05-31
Teem
u
M
urto
l
a
Improve make_ndx hel
p
te
x
t
commit
|
commitdiff
|
tree
2016-05-25
Teemu Murto
l
a
Support for
real M
P
I
un
i
t test
s
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
Te
s
ts for sin
g
le-ran
k
t
hread affinity setting
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
urtola
P
ass
n
u
m
ber o
f
local threads to t
h
rea
d
affini
t
y
commit
|
commitdiff
|
tree
2016-05-21
T
e
emu Murtola
Allow cre
a
ting mock H
a
r
dwareT
o
pology
objects
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu M
u
rtola
U
se
only Hardware
T
opolo
g
y fo
r
t
hread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teem
u
Murto
l
a
Merg
e
bra
n
ch release
-
2016
commit
|
commitdiff
|
tree
2016-05-21
T
e
e
mu M
u
rtol
a
Bum
p
version
n
umbers
f
or 2017 development
commit
|
commitdiff
|
tree
2016-05-17
T
ee
m
u Murtola
Fix some t
h
read af
f
i
n
ity cas
e
s
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtol
a
Additional Jenkins documentatio
n
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
urtola
Include releng documentat
i
on to de
v
elo
p
e
r guide
commit
|
commitdiff
|
tree
2016-05-08
Teemu Murtola
S
upport for OpenCL CI
b
u
ilds
commit
|
commitdiff
|
tree
2016-05-05
Tee
m
u
M
u
r
tola
Merge bra
n
c
h release-5
-
1
commit
|
commitdiff
|
tree
2016-05-05
Teemu
M
u
r
tol
a
Make Sphinx b
u
i
l
d
s
ilent fo
r
ve
r
sion 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Te
e
mu Murtola
M
ark o
p
t
i
o
nal
in
p
u
t
/
o
utput
f
iles in gm
x
order
commit
|
commitdiff
|
tree
2016-04-28
Te
e
m
u
M
u
rtola
Use Hard
w
are
T
opology to se
t
nthrea
d
s_hw_a
v
a
i
l
commit
|
commitdiff
|
tree
2016-04-28
Teemu
Murtol
a
Remove gmx_hw_info_t::nco
r
e
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murt
o
l
a
Impr
o
ve relea
s
e
w
orkflow testing
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Disab
l
e
m
ult
i
pl
e
ranks fo
r
non-
M
PI unit tests
commit
|
commitdiff
|
tree
2016-04-27
Tee
m
u Murtola
Fix issues with faili
n
g th
r
ead
affin
i
ty se
t
tin
g
commit
|
commitdiff
|
tree
2016-04-27
Tee
m
u
M
urtola
Mer
g
e "Merge b
r
anch
r
ele
a
se-5-1"
commit
|
commitdiff
|
tree
2016-04-18
Teem
u
Murtola
M
a
k
e
threa
d
affinity fa
i
lures
a
lways end up in log
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Make includeso
r
ter
.
py
w
ork
w
i
t
h Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
T
eemu Murtola
Fix
e
rror
r
eporting for documenta
t
ion build
commit
|
commitdiff
|
tree
2016-03-28
Teemu Murtola
M
ore suppor
t
fo
r
r
e
l
e
ase workflow
commit
|
commitdiff
|
tree
2016-03-26
Te
e
mu Murt
o
la
Ig
n
ore empty
GMXLIB
commit
|
commitdiff
|
tree
2016-03-14
Teemu M
u
rtola
Add tests fo
r
e
m
p
ty st
r
ings in ref
d
a
t
a
commit
|
commitdiff
|
tree
2016-03-13
Tee
m
u
M
urtola
Su
p
port repla
c
ing
s
olvent in in
s
e
r
t-mole
c
ules
commit
|
commitdiff
|
tree
2016-02-01
Teemu Murt
o
la
H
andle pdbinfo
i
n Atoms
B
uilde
r
commit
|
commitdiff
|
tree
2016-01-28
Teemu Murtola
Upd
a
te build scrip
t
s to releng chang
e
s
commit
|
commitdiff
|
tree
2016-01-24
T
eemu Murtola
Document l
i
mitations on
32-bit Linux
commit
|
commitdiff
|
tree
2016-01-12
Teem
u
Murtola
Ma
k
e G
M
X_MPI
a
l
w
ays defi
n
e
d
to 0/1
commit
|
commitdiff
|
tree
2016-01-12
T
ee
m
u
M
u
r
tola
Mo
v
e flag
s
out of t_trxframe
commit
|
commitdiff
|
tree
2016-01-12
Teemu
Mur
t
ola
Remove histori
c
al times from t_trxframe
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Support pa
s
sin
g
t
arball MD5 for
web
p
age bui
l
d
commit
|
commitdiff
|
tree
2016-01-12
Teemu
M
u
rtola
Remove vmdplugin
from
t_tr
x
fr
a
me
commit
|
commitdiff
|
tree
2016-01-11
Teemu Murt
o
la
Convert
mo
r
e config
.
h defin
e
s to 0
/
1
commit
|
commitdiff
|
tree
2016-01-10
Teemu M
u
rtola
Suppor
t
tra
j
ectory analysis with any
atom s
u
bset
commit
|
commitdiff
|
tree
2016-01-10
Teemu
M
urt
o
la
S
upport frames with atom
subs
e
ts in sele
c
tions
commit
|
commitdiff
|
tree
2016-01-10
T
eemu Murtola
Support
ar
b
itr
a
r
y subset traj
e
ctories in
p
oscal
c
.
*
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Make
f
ile names in fa
t
al error me
s
sages mor
e
robust
commit
|
commitdiff
|
tree
2016-01-10
T
e
emu Murtola
Do not warn ab
o
ut missing OpenMP wi
t
h GMX_GPU=OFF
commit
|
commitdiff
|
tree
2016-01-10
Teemu
M
u
r
tola
More
config
.
h macr
o
s
to
0/1
commit
|
commitdiff
|
tree
2016-01-10
T
e
e
mu M
u
rtola
C
o
nv
e
rt some config
.
h
macros to use 0/1
commit
|
commitdiff
|
tree
2016-01-05
T
e
emu
M
u
r
tola
Update pack
a
g
ing build
commit
|
commitdiff
|
tree
2015-12-31
T
e
e
m
u
Murtol
a
Report used defines in
check-sou
r
ce
commit
|
commitdiff
|
tree
2015-12-29
Teemu Murt
o
la
Packaging
b
uild script for web site
commit
|
commitdiff
|
tree
2015-12-29
Teemu Murtola
Re
d
uc
e
inputre
c
.
h dependencies
commit
|
commitdiff
|
tree
2015-12-27
Teemu Murtola
Im
p
rove tex
t
writin
g
in he
l
p ou
t
put
commit
|
commitdiff
|
tree
2015-12-27
Teemu Murtol
a
Sour
c
e packagi
n
g with new rele
n
g
commit
|
commitdiff
|
tree
2015-12-27
Teemu Murt
o
la
Further
v
ec
.
h clean
u
p
commit
|
commitdiff
|
tree
2015-12-26
T
eemu Murtola
Clean
up vec
.
h
commit
|
commitdiff
|
tree
2015-12-24
Tee
m
u Murtola
Add functionality t
o
TextWriter
commit
|
commitdiff
|
tree
2015-12-20
Teemu
M
u
rto
l
a
Fix most war
n
in
g
s
with Do
x
ygen 1
.
8
.
1
0
commit
|
commitdiff
|
tree
2015-12-19
Teemu
M
urtola
Update
version
i
ng for new sch
e
m
e
commit
|
commitdiff
|
tree
2015-12-16
T
e
emu Murtola
M
o
ve calcgrid
.
* to fft/
commit
|
commitdiff
|
tree
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