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Change naming convention for C++ interfaces
2015-07-18
Teemu Mu
r
tola
Chan
g
e naming conventio
n
for C++ interfac
e
s
commit
|
commitdiff
|
tree
2015-07-10
Teemu Murtola
M
ore gmxf
i
o
simplification
commit
|
commitdiff
|
tree
2015-07-07
Teemu Mur
t
ola
Wra
p
u
ses of thr
e
ad_mpi/mutex
.
h
commit
|
commitdiff
|
tree
2015-07-05
Te
e
mu Mur
t
o
la
Improve gmx he
l
p
-
export Sphi
n
x
r
ebuild
b
ehav
i
or
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
F
i
x e
r
ro
r
wrappin
g
in interact
i
ve
selection input
commit
|
commitdiff
|
tree
2015-07-04
T
e
emu Murt
o
la
T
e
sts for
i
n
t
eractiv
e
s
e
l
ection input
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
Fix copy
-
p
a
ste bu
g
in gmx
dis
t
ance
commit
|
commitdiff
|
tree
2015-07-04
T
e
emu Mur
t
ola
Refacto
r
fo
r
testing interac
t
iv
e
sel
e
ct
i
o
n
inp
u
t
commit
|
commitdiff
|
tree
2015-07-04
Teemu M
u
rtol
a
Remove gmx::File
(except
f
o
r File::exist
s
()
)
commit
|
commitdiff
|
tree
2015-07-04
T
e
e
m
u M
u
rt
o
la
Replace direc
t
uses of gmx::File w
i
th streams
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
Bump various version numb
e
rs
commit
|
commitdiff
|
tree
2015-07-04
T
ee
m
u Murtola
Make so
m
e u
n
it te
s
t
s
u
se moc
k
f
ile output
commit
|
commitdiff
|
tree
2015-07-02
Teem
u
Murto
l
a
C
onvert gmxfio to
C
++
commit
|
commitdiff
|
tree
2015-07-02
Teemu M
u
rtola
R
e
move sta
t
u
s messag
e
s
a
bo
u
t
Sphinx
d
etecti
o
n
commit
|
commitdiff
|
tree
2015-07-02
Teemu
M
u
r
to
l
a
Cl
e
an up gmxfio
i
ncludes
commit
|
commitdiff
|
tree
2015-07-02
Tee
m
u Murtola
R
eo
r
der code within gmxfio
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Furt
h
e
r
gmxfio cleanup re
l
ated
to xdr handli
n
g
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtol
a
Mino
r
include sorting changes
commit
|
commitdiff
|
tree
2015-07-01
Teemu
Murtola
Cl
e
an up unused code
f
rom gmx
f
io
commit
|
commitdiff
|
tree
2015-06-29
Teemu Murtola
O
n
l
y accept e
x
ac
t
matches for
s
election
keywor
d
s
commit
|
commitdiff
|
tree
2015-06-29
T
eemu Murtola
Make
s
ome unit tests skip fil
e
s
ystem access
commit
|
commitdiff
|
tree
2015-06-27
Teemu Murto
l
a
Document
t
o
o
l
c
h
anges
i
n 5
.
1
commit
|
commitdiff
|
tree
2015-06-25
Tee
m
u M
u
r
tola
Move docu
m
e
n
tation on
t
o
ol changes
from wiki
commit
|
commitdiff
|
tree
2015-06-17
T
eemu Murtola
Minor clean
u
p
for refd
a
ta
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teem
u
Murtola
Improve logi
c
for
automatic selection names
commit
|
commitdiff
|
tree
2015-06-16
Teemu Murtol
a
Fi
x
brok
e
n li
n
ks
from t
h
e
old
f
low chart
commit
|
commitdiff
|
tree
2015-06-12
Tee
m
u Murtola
U
p
date
h
e
lp ou
t
p
ut
commit
|
commitdiff
|
tree
2015-06-12
Te
e
mu Murtola
I
m
prove uncrustify Jen
k
ins buil
d
s
commit
|
commitdiff
|
tree
2015-06-12
T
eemu Murtola
Initia
l
d
ocs for Jenk
i
ns integr
a
tion
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Ini
t
ial
bui
l
d sy
s
tem docu
m
entation
in
dev gu
i
de
commit
|
commitdiff
|
tree
2015-06-12
Teemu
M
urtola
Impro
v
e Je
n
k
i
ns docs build
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Exten
d
s
o
urce layout description in dev guide
commit
|
commitdiff
|
tree
2015-06-11
T
e
emu Murtola
Script f
o
r Jenkins doc
u
mentation build
commit
|
commitdiff
|
tree
2015-06-09
Teemu Murtola
M
i
s
c
.
i
m
provement
s
to docs
b
u
il
d
system
commit
|
commitdiff
|
tree
2015-06-09
Teemu Murtola
Add desc
r
iption of relocatable binar
i
es
commit
|
commitdiff
|
tree
2015-06-09
Te
e
mu
M
u
r
tola
Resolve one TODO for comma
n
d line
h
elp
t
ests
commit
|
commitdiff
|
tree
2015-06-09
Teemu Mur
t
ola
Improv
e
user
g
ui
d
e text for command lin
e
in
t
erfac
e
commit
|
commitdiff
|
tree
2015-06-04
Teem
u
Mur
t
ola
Fix
p
ote
n
tial
FP
E
in selection te
s
ts
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
R
e
factor rst parsi
n
g for console output
commit
|
commitdiff
|
tree
2015-06-04
T
eemu
M
urto
l
a
Replace gromacs
.
7 ma
n
page wi
t
h gmx
.
1
commit
|
commitdiff
|
tree
2015-06-04
Te
e
mu Murtola
Document curre
n
t help forma
t
ting
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtol
a
B
a
sic suppor
t
fo
r
titles wit
h
in tool help
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Sup
p
o
r
t r
s
t tables in tool he
l
p texts
commit
|
commitdiff
|
tree
2015-05-28
Teemu Murto
l
a
Improve lists in
u
ser guide for selections
commit
|
commitdiff
|
tree
2015-05-28
Teem
u
Murto
l
a
Additional selec
t
ion examples
commit
|
commitdiff
|
tree
2015-05-25
Tee
m
u Murto
l
a
O
ve
r
view docs fo
r
anal
y
sis nbsea
r
c
h
commit
|
commitdiff
|
tree
2015-05-24
T
e
e
m
u
Murtola
Include selection key
w
or
d
det
a
il
s
in user gui
d
e
commit
|
commitdiff
|
tree
2015-05-22
T
e
emu M
u
rtola
Allow an
y
or
d
er for
s
ections in 'gmx he
l
p -export
'
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murt
o
la
Base to
g
et all 'gmx h
e
lp' contents
t
o u
s
er
g
uide
commit
|
commitdiff
|
tree
2015-05-22
Te
e
mu
M
urtol
a
Merge releas
e
-5-0 into master
commit
|
commitdiff
|
tree
2015-05-22
Teemu M
u
rtola
Avoid c
r
ash with empty refere
n
ce for 's
a
me as' selecti
o
n
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Add subsect
i
on depth to HelpWriterCont
e
xt
commit
|
commitdiff
|
tree
2015-05-22
Te
e
mu Murtola
Add
no
t
e about atom
order
in selecti
o
ns
commit
|
commitdiff
|
tree
2015-05-21
Teemu Murtola
Restruc
t
ure C
o
mma
n
dLineM
o
d
uleManager
t
e
s
ts
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtola
Fix
handli
n
g of real-valued 'to
'
selectio
n
ran
g
es
commit
|
commitdiff
|
tree
2015-05-20
Te
e
mu Murtola
Fix dep
e
ndencies
for regression test
cust
o
m
t
a
rget
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtol
a
Some tests for 'gmx help -
e
xport
r
st
'
commit
|
commitdiff
|
tree
2015-05-18
Tee
m
u Murto
l
a
Merge "Merge branc
h
origin/release-5-0"
commit
|
commitdiff
|
tree
2015-05-17
Teem
u
Murtola
Move
a few defines to buildin
f
o
.
h
commit
|
commitdiff
|
tree
2015-05-13
Teemu Murtola
Remove rem
a
ining
o
ld-html conten
t
commit
|
commitdiff
|
tree
2015-05-11
T
e
e
mu Mur
t
ola
Use single
v
a
r
iable
for e
x
p
ected Dox
y
gen
v
ersion
commit
|
commitdiff
|
tree
2015-05-10
T
e
emu Murtola
M
ove som
e
testut
i
ls
and
o
vervie
w
docs to dev guide
commit
|
commitdiff
|
tree
2015-05-10
T
eemu M
u
rt
o
la
Print
c
or
r
e
ct
o
rder for include
o
rder/style issues
commit
|
commitdiff
|
tree
2015-05-10
T
e
e
mu Mu
r
tola
I
mprove
build sy
s
tem
f
or Sphinx
commit
|
commitdiff
|
tree
2015-05-10
Teemu Mu
r
tola
Convert developer
manual to rst
commit
|
commitdiff
|
tree
2015-05-05
Teemu Murtola
A
v
oid rounding
errors affect
i
n
g r
e
sult
s
in on
e
test
commit
|
commitdiff
|
tree
2015-04-24
Teemu Mu
r
t
o
la
A
d
d
s
ection on n
a
ming conventions t
o
de
v
manual
commit
|
commitdiff
|
tree
2015-02-13
T
eemu
M
urtola
Repla
c
e
more [
B
R
]
with
rst bu
l
l
et lists
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Replace some
[BR] in h
e
lp
t
e
xt
s
with rst literals
commit
|
commitdiff
|
tree
2015-02-13
Tee
m
u Murtola
Move flow ch
a
rt from old-html t
o
Sphinx
commit
|
commitdiff
|
tree
2015-02-13
Teemu Mu
r
t
ola
Make (m
o
st) HTML links to file formats work ag
a
in
commit
|
commitdiff
|
tree
2015-02-13
T
e
emu Murtola
C
o
nvert file format
d
es
c
riptions to
rst
commit
|
commitdiff
|
tree
2015-02-13
Tee
m
u Murtola
Generate man pages through
Sphin
x
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Replace
tool HTML
h
elp with Sph
i
nx-generated do
c
s
commit
|
commitdiff
|
tree
2015-02-07
Teemu Murtol
a
Supp
o
rt more c
o
mpl
e
x fix
e
d
position sel
e
c
t
ions
commit
|
commitdiff
|
tree
2015-01-29
Teemu Mu
r
tol
a
Ad
d
inp
u
t file o
p
tions that acce
p
t
missing
f
il
e
s
commit
|
commitdiff
|
tree
2015-01-24
Teemu Murtola
R
e
move old
s
e
l
e
ctio
n
p
a
rser
er
r
or
h
andling c
o
de
commit
|
commitdiff
|
tree
2015-01-24
T
eemu Mu
r
tola
I
m
pro
v
e selection error messages (use exce
p
t
i
ons)
commit
|
commitdiff
|
tree
2015-01-23
Te
e
m
u
Murt
o
l
a
Ignor
e
te
s
t-only de
p
end
e
nc
y
cycles
commit
|
commitdiff
|
tree
2015-01-20
Teemu Murtola
Make data file path search more reusable
commit
|
commitdiff
|
tree
2015-01-20
Teemu
M
urtola
Convert force
f
i
e
ld search to C+
+
commit
|
commitdiff
|
tree
2015-01-19
Teemu Murtola
Rem
o
ve Anal
y
s
i
sNeighborhood::setU
s
eBou
n
dingBox
(
)
commit
|
commitdiff
|
tree
2015-01-17
Teemu M
u
r
tola
Merge "Merge b
r
anch release-5-0
"
commit
|
commitdiff
|
tree
2015-01-08
T
e
e
m
u Murtola
Refactor lo
g
i
c for fin
d
i
n
g
s
hare/top/ fi
l
es
commit
|
commitdiff
|
tree
2015-01-08
Teemu Murtola
Closed some
.
x
vg files that
were
b
eing left open
commit
|
commitdiff
|
tree
2015-01-07
T
e
emu Murto
l
a
Custom p
r
og
r
am co
n
text for
u
n
it
t
ests
commit
|
commitdiff
|
tree
2015-01-07
T
e
emu Mur
t
ola
Split unit test in
i
t
f
rom
te
s
topti
o
ns
.
cpp
commit
|
commitdiff
|
tree
2015-01-06
Teem
u
Murtola
Use analysis
nbsearch for surface area calculation
commit
|
commitdiff
|
tree
2015-01-06
Teemu
Murtola
Use xv
g
rclos
e
()
for
f
ile
s
opened with xvgropen()
commit
|
commitdiff
|
tree
2015-01-05
Te
e
mu Mu
r
tola
Support su
b
se
t
of rvec
a
rray as input for analysi
s
.
.
.
commit
|
commitdiff
|
tree
2015-01-05
Teemu M
u
rtola
Minimal C++ replacem
e
nt for
rvec
commit
|
commitdiff
|
tree
2015-01-05
Tee
m
u Murtola
Clarify GMX_MPI
m
ana
g
ement
commit
|
commitdiff
|
tree
2015-01-03
Teemu
M
ur
t
o
l
a
Minor selection c
l
arificati
o
ns
commit
|
commitdiff
|
tree
2015-01-03
Teemu Murtola
Fix c
r
as
h
with '
z
of
.
.
.
' w
i
thin an e
x
pres
s
ion
commit
|
commitdiff
|
tree
2015-01-02
Teemu Murtola
U
pdate copyr
i
ght year in
c
opyrite
.
cpp
commit
|
commitdiff
|
tree
2014-12-28
Te
e
mu Murtola
Conv
e
r
t
gmx-
i
nsert-molecules into proper C++
module
commit
|
commitdiff
|
tree
2014-12-28
Teemu Mu
r
to
l
a
A
dd helpe
r
for generic C++ co
m
ma
n
d
-line modu
l
es
commit
|
commitdiff
|
tree
2014-12-18
Te
e
mu
M
urtola
Re
w
or
k
gmx-solvate
to use analysis n
b
sea
r
ch
commit
|
commitdiff
|
tree
2014-12-17
T
e
e
mu M
u
r
t
ola
Make 'gmx
sasa' cal
c
ula
t
ion
thread-saf
e
commit
|
commitdiff
|
tree
2014-12-17
Teemu
Murtola
R
e
move
s
om
e
backwards-co
m
patibility glue for Jenk
i
ns
commit
|
commitdiff
|
tree
next