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Split espresso I/O routines from confio.cpp
2015-07-23
Tee
m
u Murt
o
la
Spl
i
t espre
s
so
I
/O routines from confio
.
cpp
commit
|
commitdiff
|
tree
2015-07-22
Tee
m
u Murtola
S
plit gr
o
I/O routin
e
s
f
rom
c
onfio
.
cpp
commit
|
commitdiff
|
tree
2015-07-22
T
eemu Mu
r
tola
Spli
t
g96 I/O routines fro
m
confio
.
cp
p
commit
|
commitdiff
|
tree
2015-07-22
Teemu M
u
rtola
Mo
v
e read_tps_conf(
)
to
confio
.
h
commit
|
commitdiff
|
tree
2015-07-22
Teem
u
Murtol
a
Add b
a
sic t
e
s
t
s for re
a
ding/writ
i
ng structure files
commit
|
commitdiff
|
tree
2015-07-18
Teemu Murtola
Move Op
t
io
n
s::setDescription()
el
s
ew
h
ere
commit
|
commitdiff
|
tree
2015-07-18
Teemu Murtola
C
han
g
e n
a
mi
n
g con
v
ention for C
+
+ interfaces
commit
|
commitdiff
|
tree
2015-07-10
Teemu Mu
r
t
o
la
More gmx
f
io sim
p
li
f
i
c
ation
commit
|
commitdiff
|
tree
2015-07-07
T
e
e
m
u Mur
t
ola
W
r
ap uses of thread_mpi/mutex
.
h
commit
|
commitdiff
|
tree
2015-07-05
Teem
u
Murtola
Improve g
m
x help -expor
t
S
phinx rebuild behavio
r
commit
|
commitdiff
|
tree
2015-07-04
Teemu
M
u
rtola
Fix erro
r
wr
a
p
p
ing in interactive sel
e
ction input
commit
|
commitdiff
|
tree
2015-07-04
Teemu M
u
rtola
Tests for interactive selection input
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
Fix copy-paste bug in g
m
x dis
t
ance
commit
|
commitdiff
|
tree
2015-07-04
T
eemu Murto
l
a
Refactor for testing
interactive selection
input
commit
|
commitdiff
|
tree
2015-07-04
Tee
m
u M
u
r
tola
Remove gmx::File
(except for F
i
le:
:
exists()
)
commit
|
commitdiff
|
tree
2015-07-04
Teemu M
u
rtola
Re
p
lace d
i
rect uses of gmx::File w
i
th stream
s
commit
|
commitdiff
|
tree
2015-07-04
Teemu M
u
rtola
Bump various version numbers
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murto
l
a
Make som
e
unit te
s
t
s
use mock file ou
t
p
u
t
commit
|
commitdiff
|
tree
2015-07-02
Tee
m
u Murtola
Conve
r
t gm
x
f
i
o
to C++
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Remove status messa
g
es about Sphinx detecti
o
n
commit
|
commitdiff
|
tree
2015-07-02
T
e
e
mu Murtola
Clean
u
p g
m
xfio in
c
lud
e
s
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Reo
r
der code within gmx
f
io
commit
|
commitdiff
|
tree
2015-07-02
T
e
em
u
M
urtola
Further gmxfio cl
e
anup
related to xdr
handling
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murt
o
l
a
Minor include sorting changes
commit
|
commitdiff
|
tree
2015-07-01
Teemu
M
urto
l
a
Cl
e
an up
unused code from gm
x
fio
commit
|
commitdiff
|
tree
2015-06-29
Teemu Mur
t
ola
O
n
l
y accept exact matches fo
r
sele
c
tion keywords
commit
|
commitdiff
|
tree
2015-06-29
Teemu Murtola
Make some unit tests skip f
i
le
s
ystem access
commit
|
commitdiff
|
tree
2015-06-27
Te
e
mu Murtola
Document to
o
l ch
a
ng
e
s in 5
.
1
commit
|
commitdiff
|
tree
2015-06-25
T
eemu Murtol
a
Mov
e
docum
e
ntation on tool changes from
wiki
commit
|
commitdiff
|
tree
2015-06-17
Teemu
M
urtola
M
inor c
l
ean up for r
e
fdata
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teemu Murto
l
a
Impro
v
e
logic f
o
r automatic selection na
m
es
commit
|
commitdiff
|
tree
2015-06-16
T
e
emu Mu
r
t
o
la
Fi
x
broken
links f
r
om th
e
old flow ch
a
r
t
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Update help output
commit
|
commitdiff
|
tree
2015-06-12
T
e
e
m
u Murt
o
la
Improve un
c
rustify Jenk
i
ns
b
uilds
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Init
i
al doc
s
f
or Jenkins integration
commit
|
commitdiff
|
tree
2015-06-12
T
eemu Murtola
Initi
a
l
buil
d
sy
s
tem docum
e
ntation in dev gu
i
de
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murto
l
a
Improve Jenkins docs build
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Extend source lay
o
u
t
descript
i
on in dev gu
i
de
commit
|
commitdiff
|
tree
2015-06-11
Teemu Murt
o
la
Script f
o
r Jenki
n
s docum
e
n
t
a
t
ion
build
commit
|
commitdiff
|
tree
2015-06-09
T
ee
m
u Murt
o
la
M
i
s
c
.
improvements to d
o
cs build sy
s
tem
commit
|
commitdiff
|
tree
2015-06-09
T
e
emu Murtola
A
d
d d
e
scription of relo
c
a
t
abl
e
bina
r
i
es
commit
|
commitdiff
|
tree
2015-06-09
Teemu Mu
r
to
l
a
Resolve one TODO for comm
a
n
d
li
n
e h
e
lp t
e
sts
commit
|
commitdiff
|
tree
2015-06-09
Tee
m
u Murtola
I
mprove user guide text for com
m
a
n
d line interface
commit
|
commitdiff
|
tree
2015-06-04
Te
e
mu Murtola
Fix potential FPE in selection
tests
commit
|
commitdiff
|
tree
2015-06-04
Teem
u
Murto
l
a
Refact
o
r rs
t
par
s
ing for cons
o
le output
commit
|
commitdiff
|
tree
2015-06-04
Teemu M
u
rtola
R
e
place gromacs
.
7
m
an
p
age with gmx
.
1
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Document curr
e
nt hel
p
for
m
atting
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murto
l
a
Basic support
f
o
r title
s
wit
h
in tool h
e
lp
commit
|
commitdiff
|
tree
2015-06-04
Teemu Mur
t
ola
S
u
p
po
r
t rst tables in to
o
l help text
s
commit
|
commitdiff
|
tree
2015-05-28
T
eemu Murtola
Im
p
rove
lists in
user gu
i
de
f
o
r
selections
commit
|
commitdiff
|
tree
2015-05-28
Teemu
M
urtola
Ad
d
i
t
i
onal selection examples
commit
|
commitdiff
|
tree
2015-05-25
Teemu Murto
l
a
O
v
e
r
view
docs for analysis n
b
sear
c
h
commit
|
commitdiff
|
tree
2015-05-24
Teemu Murtola
In
c
lude se
l
ection
k
e
y
word details in user guide
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
A
l
lo
w
a
n
y order for sec
t
ions in 'gmx help
-
e
x
p
ort'
commit
|
commitdiff
|
tree
2015-05-22
T
e
emu Murtola
B
ase to get all
'gmx help' c
o
ntents to user g
u
id
e
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murto
l
a
M
e
rge release-5-0
into master
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Avo
i
d crash with empty reference fo
r
'same
a
s' sel
e
c
t
io
n
commit
|
commitdiff
|
tree
2015-05-22
Teem
u
Mur
t
ol
a
Add subsection
depth to He
l
pWrit
e
rContext
commit
|
commitdiff
|
tree
2015-05-22
Teemu
Murtola
Add not
e
about atom ord
e
r
in
s
elect
i
ons
commit
|
commitdiff
|
tree
2015-05-21
Teemu
Murt
o
la
R
estructure Command
L
ineModuleManager te
s
ts
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtol
a
Fix ha
n
dling of real-
v
alu
e
d 'to' se
l
ection ranges
commit
|
commitdiff
|
tree
2015-05-20
Teemu M
u
rtola
Fix dependencies f
o
r reg
r
ession test custom target
commit
|
commitdiff
|
tree
2015-05-20
Teem
u
Murtol
a
Som
e
tests for 'gmx help -export r
s
t'
commit
|
commitdiff
|
tree
2015-05-18
Teemu Murtola
Merge
"
Mer
g
e
branch origi
n
/rel
e
ase-
5
-
0
"
commit
|
commitdiff
|
tree
2015-05-17
T
e
emu M
u
rtol
a
Move a few
d
efi
n
es to
b
uildinfo
.
h
commit
|
commitdiff
|
tree
2015-05-13
Teemu Murtola
R
emove remai
n
ing old-html c
o
ntent
commit
|
commitdiff
|
tree
2015-05-11
Teemu
M
urtola
Use
s
i
n
gle variable
f
o
r
expe
c
te
d
Doxygen version
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtola
M
ove s
o
me
testutils and overv
i
ew docs to dev guide
commit
|
commitdiff
|
tree
2015-05-10
Teemu Mur
t
ola
Pri
n
t correct ord
e
r for in
c
lude order/styl
e
issu
e
s
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtola
Improv
e
build system for
S
phinx
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtola
C
o
nvert developer
manual to rst
commit
|
commitdiff
|
tree
2015-05-05
Teemu Mur
t
ola
A
v
oid
r
o
u
nd
i
ng error
s
affecting results i
n
o
n
e test
commit
|
commitdiff
|
tree
2015-04-24
Teemu Murtola
Add
s
ection on naming co
n
v
ention
s
to de
v
manual
commit
|
commitdiff
|
tree
2015-02-13
T
eemu Murtola
Re
p
l
a
c
e
more [BR] with rst bullet list
s
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Repl
a
ce s
o
me
[
BR] in help texts
w
ith rst literals
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
M
ove flow ch
a
rt fr
o
m old-h
t
ml
t
o Sphinx
commit
|
commitdiff
|
tree
2015-02-13
Te
e
mu Murtola
Make (most) H
T
M
L
link
s
to f
i
le forma
t
s
work again
commit
|
commitdiff
|
tree
2015-02-13
Teemu
Mu
r
tola
C
o
n
vert
f
ile forma
t
d
escri
p
tions to rst
commit
|
commitdiff
|
tree
2015-02-13
Teem
u
M
u
r
tola
G
e
ner
a
te ma
n
pages
t
hrough Sphinx
commit
|
commitdiff
|
tree
2015-02-13
T
eemu Murtol
a
R
e
place too
l
H
TML help with Sphin
x
-g
e
ne
r
ated docs
commit
|
commitdiff
|
tree
2015-02-07
Teemu Mu
r
tola
Supp
o
rt
more co
m
plex fixed
p
osition selections
commit
|
commitdiff
|
tree
2015-01-29
Teem
u
Murtola
Add input fil
e
o
p
tio
n
s that accept mis
s
i
n
g
f
i
les
commit
|
commitdiff
|
tree
2015-01-24
Teemu Murtola
R
e
move o
l
d
s
election
p
a
rser err
o
r hand
l
ing
c
ode
commit
|
commitdiff
|
tree
2015-01-24
Teemu Murtola
Improve
selection err
o
r
messages (u
s
e
exceptions)
commit
|
commitdiff
|
tree
2015-01-23
T
eemu
Mu
r
tola
Ignore t
e
s
t-only
d
e
pendency c
y
cles
commit
|
commitdiff
|
tree
2015-01-20
T
eem
u
Mu
r
t
ola
Make data fi
l
e
path search mor
e
reusable
commit
|
commitdiff
|
tree
2015-01-20
Tee
m
u Murtol
a
Convert forcefield
s
e
arch
t
o C++
commit
|
commitdiff
|
tree
2015-01-19
Teemu Murtola
Re
m
ove
A
nalysisNeighbo
r
hood::setU
s
eBoundingB
o
x()
commit
|
commitdiff
|
tree
2015-01-17
Teemu
M
urtola
Merge "
M
e
rge branch release
-
5
-0
"
commit
|
commitdiff
|
tree
2015-01-08
Teemu Murtola
Refa
c
t
o
r log
i
c
for
f
inding share/t
o
p/ files
commit
|
commitdiff
|
tree
2015-01-08
Teemu Murtola
Closed som
e
.
xvg file
s
th
a
t
w
ere being le
f
t o
p
en
commit
|
commitdiff
|
tree
2015-01-07
Te
e
mu M
u
rtola
Custom
program context
f
or unit
t
ests
commit
|
commitdiff
|
tree
2015-01-07
Teem
u
Murtola
Spli
t
unit test
in
i
t from test
o
ptions
.
cpp
commit
|
commitdiff
|
tree
2015-01-06
Teemu Murtola
U
s
e
analysis
n
bsearch for su
r
face area calc
u
lation
commit
|
commitdiff
|
tree
2015-01-06
Teemu Murtol
a
Use xvgrclose() for file
s
opene
d
with xvgrope
n
(
)
commit
|
commitdiff
|
tree
2015-01-05
T
e
emu M
u
rtol
a
Support subset of
rvec arra
y
as input for
analysis
.
.
.
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murt
o
la
Minimal C++ repla
c
ement
for rv
e
c
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murt
o
l
a
Clarify GMX_MPI manage
m
e
n
t
commit
|
commitdiff
|
tree
2015-01-03
T
e
emu Mu
r
tola
M
i
n
or selection c
l
arifications
commit
|
commitdiff
|
tree
2015-01-03
T
eem
u
Murto
l
a
Fix crash with 'z
of
.
.
.
'
wit
h
in an e
x
pre
s
s
ion
commit
|
commitdiff
|
tree
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