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Split g96 I/O routines from confio.cpp
2015-07-22
Teemu M
u
rt
o
la
Split
g96 I/O rout
i
nes from
con
f
io
.
cpp
commit
|
commitdiff
|
tree
2015-07-22
T
eemu Murtola
Move read_tps_conf(
)
to c
o
n
f
i
o
.
h
commit
|
commitdiff
|
tree
2015-07-22
Teemu
M
ur
t
ola
Add basic
tests f
o
r reading/writing structure files
commit
|
commitdiff
|
tree
2015-07-18
Teemu Mu
r
t
o
la
Mov
e
Options::setD
e
scription() elsewhe
r
e
commit
|
commitdiff
|
tree
2015-07-18
T
eemu M
u
rt
o
la
C
hange namin
g
convent
i
on for C++
interfaces
commit
|
commitdiff
|
tree
2015-07-10
Teemu Murtola
More gmxfi
o
simpli
f
icatio
n
commit
|
commitdiff
|
tree
2015-07-07
T
eemu Murtola
W
rap
u
s
es of th
r
ead_mpi/
m
ut
e
x
.
h
commit
|
commitdiff
|
tree
2015-07-05
Teemu Murto
l
a
Improve gmx he
l
p -ex
p
or
t
S
ph
i
nx rebu
i
ld b
e
havior
commit
|
commitdiff
|
tree
2015-07-04
Teem
u
M
u
rt
o
la
Fix error wrap
p
ing
in interac
t
i
v
e selection input
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtol
a
Tests for
i
nt
e
r
a
ctive se
l
ect
i
on input
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
Fix
copy-paste b
u
g in gmx distance
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murt
o
la
Refactor for testi
n
g in
t
eract
i
ve
select
i
on i
n
put
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murto
l
a
R
emove gmx::File (except
for File::exists())
commit
|
commitdiff
|
tree
2015-07-04
T
e
e
mu Murtola
Re
p
lace
dir
e
ct
uses
o
f gmx::F
i
l
e
with streams
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murt
o
la
Bump v
a
rious versio
n
numbe
r
s
commit
|
commitdiff
|
tree
2015-07-04
Teem
u
Mur
t
ola
Make some uni
t
tests
u
se mock file outpu
t
commit
|
commitdiff
|
tree
2015-07-02
T
e
e
m
u Murtol
a
Convert
gm
x
f
i
o
to C++
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Remove st
a
t
u
s
messa
g
es about
S
phin
x
detection
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murto
l
a
Clean
u
p
gmxfio includ
e
s
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Reor
d
er code within gmxf
i
o
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
F
urther gmx
f
i
o c
l
ea
n
up re
l
ated to
xdr ha
n
dling
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Mino
r
in
c
lude sorting changes
commit
|
commitdiff
|
tree
2015-07-01
Teem
u
Murtola
Clean up unu
s
ed c
o
d
e f
r
om gmxfio
commit
|
commitdiff
|
tree
2015-06-29
Teemu Murtola
Only ac
c
e
pt
e
xact
matche
s
for
selectio
n
key
w
ords
commit
|
commitdiff
|
tree
2015-06-29
Teemu Murtola
Make some
unit tests skip file system
a
cce
s
s
commit
|
commitdiff
|
tree
2015-06-27
Teemu Mur
t
o
l
a
Document tool changes in 5
.
1
commit
|
commitdiff
|
tree
2015-06-25
Te
e
mu Murt
o
la
Move documentation o
n
tool ch
a
nges from wiki
commit
|
commitdiff
|
tree
2015-06-17
Te
e
m
u
M
u
rtola
Minor clean up for refdata
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teemu Murtola
Imp
r
ove logic fo
r
automatic
s
election names
commit
|
commitdiff
|
tree
2015-06-16
Teemu
Murto
l
a
Fix
broken links from the old fl
o
w chart
commit
|
commitdiff
|
tree
2015-06-12
T
eem
u
Murtola
Update help ou
t
put
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Improve uncrust
i
fy Jenkins buil
d
s
commit
|
commitdiff
|
tree
2015-06-12
Te
e
mu
Murto
l
a
Initial
d
ocs for Jen
k
ins i
n
tegra
t
ion
commit
|
commitdiff
|
tree
2015-06-12
Tee
m
u Mu
r
tola
I
n
i
tial build system documen
t
ati
o
n in
d
ev guide
commit
|
commitdiff
|
tree
2015-06-12
Teemu
M
urto
l
a
Impr
o
ve
J
enk
i
ns doc
s
build
commit
|
commitdiff
|
tree
2015-06-12
Teemu Mu
r
tola
Extend so
u
rce
l
a
yout description in dev
g
uide
commit
|
commitdiff
|
tree
2015-06-11
Teemu Murt
o
l
a
Script for J
e
nki
n
s
document
a
tion
b
uild
commit
|
commitdiff
|
tree
2015-06-09
Teem
u
Murt
o
la
Misc
.
improvements to docs build
syste
m
commit
|
commitdiff
|
tree
2015-06-09
Te
e
mu Mur
t
ola
A
dd description of r
e
locat
a
ble binaries
commit
|
commitdiff
|
tree
2015-06-09
Teemu Mu
r
tola
R
es
o
lve one
T
ODO for co
m
mand li
n
e help tests
commit
|
commitdiff
|
tree
2015-06-09
Tee
m
u Murtola
Im
p
r
ove
u
ser gui
d
e
t
ext for comma
n
d line in
t
er
f
a
ce
commit
|
commitdiff
|
tree
2015-06-04
Teemu M
u
rtola
Fix potential
FP
E
in selectio
n
tests
commit
|
commitdiff
|
tree
2015-06-04
Teemu Mur
t
ol
a
Ref
a
ctor rst parsing for
c
onsole o
u
tput
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Repla
c
e gromacs
.
7 man page with gm
x
.
1
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
D
o
c
umen
t
cu
r
rent help forma
t
ting
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Basic support for
titles within to
o
l
help
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Support rst tables in
t
ool help
t
exts
commit
|
commitdiff
|
tree
2015-05-28
Teemu Murtola
I
m
prove lists
i
n user guide for se
l
ec
t
i
ons
commit
|
commitdiff
|
tree
2015-05-28
T
e
emu Murtol
a
Additional selection examples
commit
|
commitdiff
|
tree
2015-05-25
Teemu M
u
rtola
Overview docs
f
or
analysis nbsearc
h
commit
|
commitdiff
|
tree
2015-05-24
Teemu M
u
rtola
In
c
l
ude selection ke
y
word deta
i
l
s in
u
ser guide
commit
|
commitdiff
|
tree
2015-05-22
Tee
m
u Murtola
Al
l
ow a
n
y orde
r
for sections in
'gmx help -e
x
port'
commit
|
commitdiff
|
tree
2015-05-22
Teemu
Murtola
Bas
e
to get all '
g
mx help' contents to user g
u
ide
commit
|
commitdiff
|
tree
2015-05-22
Teem
u
Mu
r
tola
Mer
g
e rel
e
ase-5-0
int
o
master
commit
|
commitdiff
|
tree
2015-05-22
Teem
u
Murt
o
la
Avo
i
d crash
with
empty reference for 'same as' selection
commit
|
commitdiff
|
tree
2015-05-22
T
eem
u
Mu
r
t
o
l
a
Add sub
s
e
c
t
ion dept
h
to Hel
p
WriterCont
e
xt
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murt
o
la
Add note ab
o
ut ato
m
o
r
d
e
r
in
selections
commit
|
commitdiff
|
tree
2015-05-21
Teemu Murtola
Restr
u
ctu
r
e C
o
mmandLineModuleManager tests
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtola
Fix han
d
li
n
g
of real-va
l
ued 'to' selection ranges
commit
|
commitdiff
|
tree
2015-05-20
Te
e
mu Murtola
Fix dependencies for regression tes
t
custom
t
a
rget
commit
|
commitdiff
|
tree
2015-05-20
T
eemu Murtola
Some tests
for 'gm
x
help -expo
r
t rs
t
'
commit
|
commitdiff
|
tree
2015-05-18
Teemu Murto
l
a
Mer
g
e "Mer
g
e branch origin/rel
e
ase-5-0"
commit
|
commitdiff
|
tree
2015-05-17
T
e
emu Murtola
Move a fe
w
defines
to b
u
i
ldinf
o
.
h
commit
|
commitdiff
|
tree
2015-05-13
Teemu
M
ur
t
ol
a
Remove remainin
g
old-html content
commit
|
commitdiff
|
tree
2015-05-11
T
e
e
mu Murtola
Use
s
i
n
gl
e
varia
b
le
for exp
e
cted Doxygen versi
o
n
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtol
a
Mov
e
some testutils and ov
e
rvie
w
d
ocs t
o
dev guide
commit
|
commitdiff
|
tree
2015-05-10
Tee
m
u Murtola
Print co
r
r
e
ct order for inclu
d
e or
d
e
r/
s
ty
l
e
iss
u
e
s
commit
|
commitdiff
|
tree
2015-05-10
T
e
emu Murtola
I
mprove
b
uild system for Sphinx
commit
|
commitdiff
|
tree
2015-05-10
Teemu
M
urtola
Convert dev
e
loper manual to r
s
t
commit
|
commitdiff
|
tree
2015-05-05
Teemu Murtola
Avoid rounding
er
r
or
s
affecti
n
g results i
n
one test
commit
|
commitdiff
|
tree
2015-04-24
T
e
emu Murt
o
l
a
Ad
d
section on n
a
ming
co
n
vent
i
ons to de
v
manual
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
R
eplace m
o
re [B
R
]
with
r
s
t bulle
t
l
ists
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Replace som
e
[BR
]
in
h
elp
texts with rst lit
e
rals
commit
|
commitdiff
|
tree
2015-02-13
T
e
e
m
u
Murtola
Move flow
c
hart from old
-
html to
S
p
h
inx
commit
|
commitdiff
|
tree
2015-02-13
T
e
emu Mur
t
o
la
Make (m
o
s
t
)
HT
M
L
li
n
k
s to file form
a
t
s work again
commit
|
commitdiff
|
tree
2015-02-13
Teem
u
Murt
o
la
C
o
n
v
ert file f
o
rmat description
s
t
o rst
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Generate m
a
n
pages t
h
rou
g
h
S
p
h
inx
commit
|
commitdiff
|
tree
2015-02-13
T
eem
u
Murtola
Rep
l
ace tool HT
M
L
help wi
t
h Sp
h
inx-generated
d
ocs
commit
|
commitdiff
|
tree
2015-02-07
T
eemu Murtola
Suppo
r
t
more c
o
mplex fixed p
o
sition selections
commit
|
commitdiff
|
tree
2015-01-29
T
eemu Mu
r
tola
Add input fil
e
option
s
th
a
t accept missing
f
i
l
e
s
commit
|
commitdiff
|
tree
2015-01-24
Teemu Murtola
Remove ol
d
selectio
n
p
a
rser erro
r
h
a
ndling code
commit
|
commitdiff
|
tree
2015-01-24
T
e
emu Murtola
I
m
p
rove selection error messages (us
e
exceptions)
commit
|
commitdiff
|
tree
2015-01-23
Teemu Murtola
Igno
r
e
test-
o
nly dependency
cycles
commit
|
commitdiff
|
tree
2015-01-20
Teemu Mur
t
ola
Mak
e
data file path sear
c
h mo
r
e reu
s
a
b
le
commit
|
commitdiff
|
tree
2015-01-20
Teemu M
u
rtol
a
Conv
e
rt f
o
rcefiel
d
sear
c
h to
C
+
+
commit
|
commitdiff
|
tree
2015-01-19
Teem
u
Mur
t
ol
a
R
e
move AnalysisNeighborhood::setUseBoundingBox
(
)
commit
|
commitdiff
|
tree
2015-01-17
Teemu Mur
t
ola
M
e
rge "Merge branc
h
release-5-0"
commit
|
commitdiff
|
tree
2015-01-08
Teemu Murt
o
l
a
Ref
a
cto
r
logic for finding share/t
o
p/ fil
e
s
commit
|
commitdiff
|
tree
2015-01-08
Teemu Mu
r
tola
C
losed some
.
xvg files t
h
at were being left open
commit
|
commitdiff
|
tree
2015-01-07
T
e
emu Murtola
C
usto
m
program
c
ontext for unit tests
commit
|
commitdiff
|
tree
2015-01-07
Tee
m
u Murtola
Split unit test ini
t
from testo
p
tions
.
cpp
commit
|
commitdiff
|
tree
2015-01-06
Teemu
M
urtola
Use analysis n
b
s
e
a
r
ch for surfa
c
e area cal
c
ul
a
tion
commit
|
commitdiff
|
tree
2015-01-06
Teemu M
u
rtola
Us
e
xvgrcl
o
se() for files
opened with
xvgropen()
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Support
s
ubset of rvec a
r
r
a
y as input for analysi
s
.
.
.
commit
|
commitdiff
|
tree
2015-01-05
Te
e
mu M
u
rtola
Minimal
C++
r
ep
l
a
cement for rvec
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Clari
f
y GMX_MPI management
commit
|
commitdiff
|
tree
2015-01-03
T
e
e
mu Mu
r
tola
Mino
r
selection
c
larifi
c
ations
commit
|
commitdiff
|
tree
2015-01-03
Teemu Murto
l
a
Fix cras
h
w
i
th '
z
of
.
.
.
' with
i
n
a
n e
x
pression
commit
|
commitdiff
|
tree
2015-01-02
Te
e
mu
Mu
r
tola
Update co
p
yright y
e
ar in cop
y
r
i
te
.
cp
p
commit
|
commitdiff
|
tree
2014-12-28
Teemu Mu
r
tola
C
o
nvert
gmx-ins
e
rt-molecu
l
es
i
nto proper C++ modu
l
e
commit
|
commitdiff
|
tree
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