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minor fixes in ditribution files
2010-05-27
Teemu Murtola
Fixed a fe
w
signed/unsigned comparison warnings
.
commit
|
commitdiff
|
tree
2010-05-21
Teemu Murto
l
a
Selections compiler commen
t
s and d
e
bugging aid
s
.
commit
|
commitdiff
|
tree
2010-05-21
Tee
m
u M
u
rtola
Simplifi
e
d selection compilation, fixin
g
a bu
g
.
commit
|
commitdiff
|
tree
2010-05-20
Tee
m
u Murtola
Added gemin
a
t
e
.
c
t
o
src/tools
/
CM
a
keL
i
sts
.
txt
.
commit
|
commitdiff
|
tree
2010-05-20
Teemu Murtola
Reduced memory usa
g
e f
o
r
stat
i
c sele
c
tions
.
commit
|
commitdiff
|
tree
2010-05-20
Tee
m
u
M
urtola
Selection
compiler bug f
i
x
.
commit
|
commitdiff
|
tree
2010-05-20
Teemu Murtola
Fixed save_reallo
c
() to
not leak memory
.
commit
|
commitdiff
|
tree
2010-05-20
T
eemu Murtola
Reduced mem
o
ry us
e
for arit
h
metic in selections
.
commit
|
commitdiff
|
tree
2010-05-20
Tee
m
u Murtola
R
emoved comp
i
ler warnings
.
commit
|
commitdiff
|
tree
2010-05-19
Teemu
M
u
r
t
ol
a
Merge branch 'ma
s
ter
'
of
git@git
.
gromacs
.
org:g
r
oma
c
s
commit
|
commitdiff
|
tree
2010-05-19
Tee
m
u Murtola
Rem
o
ved obsolete sel
e
c
t
i
o
n c
o
d
e
.
commit
|
commitdiff
|
tree
2010-05-19
T
e
emu Murto
l
a
Big rework o
f
sel
e
ction
compi
l
atio
n
/e
v
aluat
i
o
n
.
commit
|
commitdiff
|
tree
2010-05-14
T
ee
m
u Murt
o
la
Restructured selec
t
i
o
n subexpression
c
ompilation
.
commit
|
commitdiff
|
tree
2010-05-14
T
e
emu Murtola
Basic selection
memory pooling
.
commit
|
commitdiff
|
tree
2010-05-14
Teemu Murtola
Simpler spe
c
ial case subexpression handling
.
commit
|
commitdiff
|
tree
2010-05-14
Teemu Murtola
Selection compi
l
er bool flags i
n
to
a
s
i
n
gle f
i
e
l
d
.
commit
|
commitdiff
|
tree
2010-05-11
Teemu Murt
o
la
Updated share/top Make
f
ile
.
am files
.
commit
|
commitdiff
|
tree
2010-05-11
Teem
u
M
urtola
G
r
id-based utility nbsearch impleme
n
tat
i
o
n
.
commit
|
commitdiff
|
tree
2010-05-11
T
eemu
M
ur
t
ola
I
m
p
rov
e
d
n
ei
g
h
b
or s
e
arching API f
o
r
analysis
.
commit
|
commitdiff
|
tree
2010-05-07
Tee
m
u Murtola
Minor improvements to
s
e
lectio
n
h
elp
.
commit
|
commitdiff
|
tree
2010-05-07
T
e
e
mu Murtola
Bas
i
c a
r
ith
m
etic e
x
pression support
i
n
s
elections
.
commit
|
commitdiff
|
tree
2010-05-06
Teemu Murtola
More memo
r
y optimizati
o
ns for se
l
e
ctions
.
commit
|
commitdiff
|
tree
2010-05-06
Teemu Murtola
Redu
c
ed peak
m
emory us
a
ge
for select
i
o
ns
.
commit
|
commitdiff
|
tree
2010-05-05
Teemu Murtola
Fixed a bug in
g
m
x
_wcma
t
ch(
)
.
commit
|
commitdiff
|
tree
2010-04-29
Teem
u
Murtola
Fi
x
ed some memory leaks
.
commit
|
commitdiff
|
tree
2010-04-29
Teemu Murtola
Fix for
trj
c
on
v
-e option (bu
g
#305)
.
commit
|
commitdiff
|
tree
2010-04-28
Teemu Murt
o
l
a
Fixe
d
g_
w
ham error mess
a
ge (bug
z
il
l
a #39
7
)
.
commit
|
commitdiff
|
tree
2010-04-28
Teemu Murto
l
a
Added a
f
ew functions for freeing
memory
.
commit
|
commitdiff
|
tree
2010-04-28
Teemu Murtola
Se
l
ecti
o
n based o
n
molecu
l
e numbe
r
s
.
commit
|
commitdiff
|
tree
2010-04-28
Teemu Murtola
Fixed a memory
l
eak in selection code
.
commit
|
commitdiff
|
tree
2010-04-27
Teem
u
Murtola
"same
"
selections
w
ith stri
n
g
keywords
.
commit
|
commitdiff
|
tree
2010-04-27
Teemu Murtol
a
Suppo
r
t for selectio
n
string keywords
a
s params
.
commit
|
commitdiff
|
tree
2010-04-27
T
e
emu Murtola
Fix
e
d a me
m
o
ry leak in parse_common_ar
g
s
.
commit
|
commitdiff
|
tree
2010-04-27
Teemu Murt
o
l
a
Re
m
ov
e
d in
c
orrect make mdrun cmds in Makefile
.
a
m
.
commit
|
commitdiff
|
tree
2010-04-26
Teemu Murtola
Merge br
a
nch 'master' o
f
git@
g
it
.
gromacs
.
org:
g
rom
a
cs
commit
|
commitdiff
|
tree
2010-04-26
T
eemu Mur
t
ola
Improved se
l
ectio
n
k
e
yword "sam
e
"
.
commit
|
commitdiff
|
tree
2010-04-26
T
eemu Murto
l
a
Added som
e
s
y
n
o
nyms for
c
ommon sele
c
tio
n
keywords
.
commit
|
commitdiff
|
tree
2010-04-26
T
e
emu Mur
t
o
la
Fix
e
d minor
m
emory leak on
some se
l
ect
i
on errors
.
commit
|
commitdiff
|
tree
2010-04-26
Tee
m
u Murtola
Im
p
rov
e
ment to co
m
mit 67311e
3
.
commit
|
commitdiff
|
tree
2010-04-26
Teemu Murtol
a
I
mproved sel
e
ction
s
ubexp
r
ession compilatio
n
.
commit
|
commitdiff
|
tree
2010-04-22
Teem
u
Murtola
S
epa
r
ate
method
fo
r
freeing selection method
d
ata
.
commit
|
commitdiff
|
tree
2010-04-22
Te
e
mu Murtola
Ma
d
e two selection parser functi
o
ns non-static
.
commit
|
commitdiff
|
tree
2010-04-22
T
e
emu Murtola
Selection compi
l
er memory allocat
i
on bug fix
.
commit
|
commitdiff
|
tree
2010-04-22
Teemu
Murtola
Suppor
t
i
nit_fr
a
me in static selection methods
.
commit
|
commitdiff
|
tree
2010-04-20
Teemu
M
urtola
Ad
d
ed
g
_select to pr
o
grams
.
txt
.
commit
|
commitdiff
|
tree
2010-04-20
Teemu Murtola
More
robust l
i
bto
o
l
p
refi
x
s
tr
i
pping
.
commit
|
commitdiff
|
tree
2010-04-12
T
e
emu Murto
l
a
C++
f
ixes for snew() a
n
d frie
n
d
s
.
commit
|
commitdiff
|
tree
2010-04-08
Teemu Murt
o
la
Autoconf
checks for ve
r
sion info generat
i
o
n
.
commit
|
commitdiff
|
tree
2010-03-24
Teemu Murtola
Fixed genver
s
ion
.
sh on Macs
.
commit
|
commitdiff
|
tree
2010-03-11
Teemu Mu
r
tola
Minor version str
i
ng up
d
ate
.
commit
|
commitdiff
|
tree
2010-03-05
Teemu Murtola
Improve
d
v
e
rsion
strings
.
commit
|
commitdiff
|
tree
2010-03-04
Te
e
m
u
Murto
l
a
Added selection
examples
.
commit
|
commitdiff
|
tree
2010-03-01
Teemu Murto
l
a
Fi
x
e
d
a bug cau
s
ing incorrect empty se
l
ections
.
commit
|
commitdiff
|
tree
2010-02-26
Teemu
Murtola
Improved version f
o
r bui
l
ds f
r
om m
o
dified
t
rees
.
commit
|
commitdiff
|
tree
2010-02-22
Tee
m
u
M
u
r
t
ola
Ba
c
kport
e
d git sh
a
1 version string (b
u
gzilla #393)
.
commit
|
commitdiff
|
tree
2010-02-18
T
e
emu Murtola
A m
o
re intuitive fix
t
o c
o
pyr
i
t
e
.
c
d
ependency
.
commit
|
commitdiff
|
tree
2010-02-18
T
eemu
M
u
r
tola
Show
g
it sh
a
1 ha
s
h in version string (bug #
3
93)
.
commit
|
commitdiff
|
tree
2009-12-19
Teemu Mu
r
t
ola
F
ixed interacti
v
e sel
e
ction
h
elp
.
commit
|
commitdiff
|
tree
2009-12-17
Teemu Murtola
Ve
l
ocitie
s
and forces
for
s
election
s
.
commit
|
commitdiff
|
tree
2009-12-16
Teemu M
u
rtola
U
se read_stdin
_
line()
f
o
r s
e
lecti
o
ns from
a pipe
.
commit
|
commitdiff
|
tree
2009-12-14
Teemu Murtola
B
e
t
ter select
i
on std
i
n handling
.
commit
|
commitdiff
|
tree
2009-11-11
Te
e
m
u
Murtol
a
Fi
x
e
d segfaults with empty
selections
.
commit
|
commitdiff
|
tree
2009-11-11
Tee
m
u Murtola
More g
e
neral sel
e
cti
o
n p
a
r
ser gr
a
mmar
.
commit
|
commitdiff
|
tree
2009-11-10
T
ee
m
u Murt
o
la
gmxcpp fixes (bug #360 plus other fix
e
s)
.
commit
|
commitdiff
|
tree
2009-11-10
Teemu Murto
l
a
gmxcpp fixes (bug #360 plus o
t
her fixes)
.
commit
|
commitdiff
|
tree
2009-11-10
Teemu
M
urtola
Added a
g
mx
d
ump -p
option to prepr
o
ce
s
s top
o
logy
.
commit
|
commitdiff
|
tree
2009-11-09
T
eemu Murtola
S
o
me simple m
e
mory leak fixes
.
commit
|
commitdiff
|
tree
2009-11-09
Teem
u
M
u
r
t
ola
Add
e
d
a
r
e
sind selection keyword
.
commit
|
commitdiff
|
tree
2009-11-06
Teemu Murtola
Selection merge
now wor
k
s with constant positions
.
commit
|
commitdiff
|
tree
2009-11-06
Teemu Murtola
A
b
it more modular selection position handling
.
commit
|
commitdiff
|
tree
2009-11-06
Teemu Murtola
Better
g_
e
n
e
rgy -nmol
b
ehavior (b
u
g #3
6
5)
.
commit
|
commitdiff
|
tree
2009-11-06
Teemu Murtola
B
e
tter
g_energy -nmol beh
a
vio
r
(bug #365)
.
commit
|
commitdiff
|
tree
2009-11-05
Teemu Mu
r
tola
Mor
e
mod
u
lar po
s
ition hand
l
ing
.
commit
|
commitdiff
|
tree
2009-11-05
Tee
m
u Mur
t
ola
More fle
x
ible
s
el
e
ction merging
.
commit
|
commitdiff
|
tree
2009-11-05
T
e
emu
M
u
r
to
l
a
S
elect
i
o
n
merge keyw
o
rd fixes
.
commit
|
commitdiff
|
tree
2009-11-05
Teemu
M
u
rtola
A
d
ded a mi
s
sing
ret
u
rn in gmx_fio_get_fil
e
_md5()
.
commit
|
commitdiff
|
tree
2009-11-04
Teemu Mur
t
ola
Addit
i
ona
l
s
elec
t
ion keyword
s
(plus
and
m
e
rge)
.
commit
|
commitdiff
|
tree
2009-11-02
Teemu Mur
t
o
l
a
Im
p
r
o
ved Doxy
g
en d
o
cs for select
i
on i
n
t
ernals
.
commit
|
commitdiff
|
tree
2009-10-29
Teemu Mur
t
ola
I
mproved i
n
tera
c
t
i
ve
s
election inp
u
t
.
commit
|
commitdiff
|
tree
2009-10-28
Teemu M
u
rto
l
a
U
pdated
s
electio
n
documentation
.
commit
|
commitdiff
|
tree
2009-10-27
T
e
e
mu Murtola
Selection
parser
c
l
e
anu
p
.
commit
|
commitdiff
|
tree
2009-10-26
Teem
u
Murtola
Analysis lib
.
can now
a
nalyze
j
ust a topology
.
commit
|
commitdiff
|
tree
2009-10-26
Teemu Murtola
Fixed se
l
ections
i
ntr
o
d
u
ced in commit 82ecf01
.
.
.
commit
|
commitdiff
|
tree
2009-10-26
Teemu
Murtola
Fixed a segfault
i
n
s
e
lection
lib
.
commit
|
commitdiff
|
tree
2009-10-21
Teemu Murtola
Fourier dihedrals (
d
ih
.
type
5
)
should now w
o
rk
.
commit
|
commitdiff
|
tree
2009-10-21
Teemu Murtola
Fourie
r
dihed
r
a
l
s (dih
.
type 5) s
h
o
ul
d
now work
.
commit
|
commitdiff
|
tree
2009-10-09
Teemu Mur
t
ol
a
Implem
e
nted se
l
ection
s
li
k
e "occu
p
a
n
cy
0
.
5 to
1
"
.
commit
|
commitdiff
|
tree
2009-10-09
Teemu Murtola
Mo
r
e fl
e
xible selection par
s
er syntax
.
commit
|
commitdiff
|
tree
2009-10-08
T
eemu
Murtola
Better er
r
or handling
i
n s
e
l
ection pa
r
sing
.
commit
|
commitdiff
|
tree
2009-10-08
Teemu Murt
o
la
Reorgan
i
zation of
sel
e
ct
i
on
parse
r
.
commit
|
commitdiff
|
tree
2009-10-08
T
eemu Murtola
Fixed/bet
t
er
sel
e
ction n
a
me init
i
alization
.
commit
|
commitdiff
|
tree
2009-10-08
Teemu Murtola
Selection outp
u
t to xv
g
r files is
n
o
w cleaner
.
commit
|
commitdiff
|
tree
2009-10-07
Te
e
mu
Murt
o
la
Renamed
I
NT to IN
T
EGER in selec
t
ion parser
.
commit
|
commitdiff
|
tree
2009-10-07
Teemu Murtola
CM
a
ke check
s
fo
r
r
egular expressio
n
sup
p
or
t
.
commit
|
commitdiff
|
tree
2009-10-07
T
e
em
u
M
urtola
C
M
ake b
u
ild for
s
electi
o
n library
.
commit
|
commitdiff
|
tree
2009-10-07
Teemu Murtola
Fixed some Win
d
ows build issues with selecti
o
ns
.
commit
|
commitdiff
|
tree
2009-10-06
Teem
u
Murtola
Autocon
f
c
h
ecks
for regular
expres
s
ion support
.
commit
|
commitdiff
|
tree
2009-10-06
Teemu Murtola
D
on't
u
se
P
OSIX fnmatch() fo
r
pa
t
te
r
n ma
t
chin
g
.
commit
|
commitdiff
|
tree
2009-10-05
Teemu Murtola
Merge branch 'master' of g
i
t@g
i
t
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2009-10-05
Tee
m
u M
u
rtol
a
Fixed memory handling issues
i
n se
l
ec
t
ions
.
commit
|
commitdiff
|
tree
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