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Support for portable hardware locality (hwloc)
2016-02-01
Teemu Murt
o
la
Handle pdb
i
nfo i
n
AtomsBuilde
r
commit
|
commitdiff
|
tree
2016-01-28
Teemu
M
ur
t
ola
U
p
date build scripts
t
o rele
n
g
changes
commit
|
commitdiff
|
tree
2016-01-24
T
e
emu Murtola
D
ocument limitations
on
3
2-
b
it Li
n
ux
commit
|
commitdiff
|
tree
2016-01-12
Tee
m
u M
u
rtola
Mak
e
GM
X
_MPI always defined to 0
/
1
commit
|
commitdiff
|
tree
2016-01-12
Teemu M
u
rtola
Move fla
g
s o
u
t of t_tr
x
fr
a
me
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Remove hist
o
rical times from t_trxframe
commit
|
commitdiff
|
tree
2016-01-12
Teemu
M
urto
l
a
S
u
pport passing
t
arbal
l
MD5 fo
r
webpage bu
i
ld
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
R
e
move
v
mdplu
g
in from t
_
tr
x
frame
commit
|
commitdiff
|
tree
2016-01-11
Tee
m
u
Murtola
Convert more confi
g
.
h defines
to
0/1
commit
|
commitdiff
|
tree
2016-01-10
Teemu
M
ur
t
ola
Support trajectory a
n
alysis with any
atom s
u
bs
e
t
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu Murtola
Support frames w
i
th ato
m
su
b
s
e
t
s in selections
commit
|
commitdiff
|
tree
2016-01-10
Teemu
M
urtola
Support ar
b
itrar
y
subset trajector
i
es in p
o
scalc
.
*
commit
|
commitdiff
|
tree
2016-01-10
T
ee
m
u Murtola
Make file names in fatal error mes
s
a
g
es mor
e
robust
commit
|
commitdiff
|
tree
2016-01-10
Teemu
M
u
r
tola
Do not warn abou
t
mis
s
ing OpenMP with GMX_GPU=O
F
F
commit
|
commitdiff
|
tree
2016-01-10
T
e
emu Murtola
More config
.
h macr
o
s to 0/1
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Conve
r
t some config
.
h ma
c
ro
s
to use 0/1
commit
|
commitdiff
|
tree
2016-01-05
Teemu Mu
r
tola
U
p
d
ate pac
k
agi
n
g build
commit
|
commitdiff
|
tree
2015-12-31
Teemu Murto
l
a
Report used defines i
n
c
h
e
ck
-
source
commit
|
commitdiff
|
tree
2015-12-29
T
e
em
u
M
u
r
t
ola
Packaging build
s
c
rip
t
for we
b
site
commit
|
commitdiff
|
tree
2015-12-29
Teemu Mur
t
ola
Reduce
inputrec
.
h depe
n
dencie
s
commit
|
commitdiff
|
tree
2015-12-27
Teemu Mu
r
to
l
a
Impro
v
e te
x
t writing i
n
hel
p
output
commit
|
commitdiff
|
tree
2015-12-27
Teemu Murto
l
a
Source
p
ackaging with n
e
w rele
n
g
commit
|
commitdiff
|
tree
2015-12-27
Teemu M
u
rtol
a
Further v
e
c
.
h c
l
ea
n
up
commit
|
commitdiff
|
tree
2015-12-26
Teemu Mur
t
ola
Clean up vec
.
h
commit
|
commitdiff
|
tree
2015-12-24
T
e
emu M
u
rtola
Add functional
i
ty to T
e
xtWr
i
te
r
commit
|
commitdiff
|
tree
2015-12-20
Teem
u
Mur
t
ola
Fix most
w
a
r
nings
w
i
th Doxyg
e
n 1
.
8
.
10
commit
|
commitdiff
|
tree
2015-12-19
Teemu M
u
rtola
Update versioning for new scheme
commit
|
commitdiff
|
tree
2015-12-16
T
e
e
m
u
Murtola
Move calcgrid
.
* to fft/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Mur
t
ola
Mov
e
main
.
*
, splitter
.
*
,
gmx_om
p
_nthr
e
ads
.
*
t
o
m
dli
b
commit
|
commitdiff
|
tree
2015-12-15
T
eemu Murtola
Mo
v
e readinp
.
* and
w
arninp
.
* to filei
o
/
commit
|
commitdiff
|
tree
2015-12-15
T
e
e
mu Murtola
Move hardware detection to hardw
a
re/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move s
o
m
e
mdrun
c
ode
o
u
t
o
f
gmxlib/
commit
|
commitdiff
|
tree
2015-12-15
T
e
emu Mu
r
tola
Move g
p
u_uti
l
s et
c
.
out of gmxlib
commit
|
commitdiff
|
tree
2015-12-14
Teemu Murtola
I
nstall b
a
s
e
v
ersion
.
h
commit
|
commitdiff
|
tree
2015-12-12
Teemu M
u
rto
l
a
Cre
a
te
se
p
a
r
ate modu
l
e for trajectory d
a
t
a
commit
|
commitdiff
|
tree
2015-12-12
Teemu M
u
r
t
o
l
a
Move
disre
.
* and orires
.
* t
o
listed
-
forces/
commit
|
commitdiff
|
tree
2015-12-12
Tee
m
u Murtola
Move ifunc
.
* to topol
o
gy/
commit
|
commitdiff
|
tree
2015-12-12
Teemu M
u
rtola
Mo
v
e
p
ut_atoms_in_box_omp(
)
to sim_u
t
il
.
*
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
R
e
move topolog
y
-> fileio d
e
pendency
commit
|
commitdiff
|
tree
2015-12-11
Teemu Murt
o
la
Merge "Merge bran
c
h
'origin/r
e
l
e
ase-5-1'"
commit
|
commitdiff
|
tree
2015-12-09
Tee
m
u
M
urto
l
a
Split txtdump
.
*, part 2
commit
|
commitdiff
|
tree
2015-12-09
Teemu Mur
t
ola
Split tx
t
dump
.
*, part
1
commit
|
commitdiff
|
tree
2015-12-03
Teemu Murtola
Move strdb
.
*
t
o
util
i
ty/
commit
|
commitdiff
|
tree
2015-12-03
Teemu Murtola
Move filenm
.
* to com
m
a
n
dline
commit
|
commitdiff
|
tree
2015-12-02
Tee
m
u M
u
rt
o
la
Sp
l
i
t
filenm
.
*
commit
|
commitdiff
|
tree
2015-11-30
Tee
m
u Murtol
a
Remove topology -> m
d
type
s
dependency
commit
|
commitdiff
|
tree
2015-11-30
Teemu
M
urtola
Rem
o
v
e obsolete ref
e
r
e
nces to legacyheaders
/
commit
|
commitdiff
|
tree
2015-11-30
Teemu Mu
r
t
o
la
Merge r
e
maining legac
y
headers/t
y
pes/
t
o mdtyp
e
s/
commit
|
commitdiff
|
tree
2015-11-30
Teemu Murtola
Mov
e
ifu
n
c
.
h t
o
gmxlib
commit
|
commitdiff
|
tree
2015-11-30
Teemu Murtola
Move f
o
rce_flags
.
h
t
o
m
dlib
/
commit
|
commitdiff
|
tree
2015-11-30
T
ee
m
u
M
urt
o
l
a
libgroma
c
s CMake sourc
e
file m
a
n
agem
e
nt
c
lea
n
up
commit
|
commitdiff
|
tree
2015-11-30
T
eemu Murtola
Move
h
ardwar
e
info structs to hardware/
commit
|
commitdiff
|
tree
2015-11-30
Te
e
m
u
M
u
rtola
Cl
e
a
n
up s
o
me
selection cod
e
commit
|
commitdiff
|
tree
2015-11-23
T
e
e
m
u Murtola
Move pre
c
ision detection symbols to bas
e
version
.
*
commit
|
commitdiff
|
tree
2015-11-22
Teemu Mur
t
ola
Remove correlatio
n
functions -> mdtype
s
d
e
pendency
commit
|
commitdiff
|
tree
2015-11-21
Te
e
mu Murtola
Use v
.
data() ins
t
ead of &v[0] for C intero
p
commit
|
commitdiff
|
tree
2015-11-15
Te
e
mu Murtol
a
Add E
n
u
m
Option with sup
p
ort f
o
r
p
roper enum types
commit
|
commitdiff
|
tree
2015-11-15
Teemu M
u
rto
l
a
F
i
x r
e
por
t
ing of unused cycle suppre
s
sions
commit
|
commitdiff
|
tree
2015-11-14
Teemu Murtola
Move
n
etw
o
rk
.
h to gmxlib/
commit
|
commitdiff
|
tree
2015-11-14
Teemu
M
urtola
Mov
e
gmx_ga2la
.
h to d
o
mde
c
/
commit
|
commitdiff
|
tree
2015-11-13
Teemu Murtola
R
e
move t_commre
c
dep
e
nd
e
ncy from cmdlineinit
.
cpp
commit
|
commitdiff
|
tree
2015-11-13
Te
e
mu Murt
o
la
M
o
ve g
m
x
_detect_hardware
.
h to gmxlib/
commit
|
commitdiff
|
tree
2015-11-13
T
eemu Murt
o
la
Move
n
o
n
bonded
.
h
t
o gm
x
li
b
/nonbonded/
commit
|
commitdiff
|
tree
2015-11-13
T
eemu Murtola
Le
t
users b
u
ild wit
h
o
ut compiler warnin
g
s
commit
|
commitdiff
|
tree
2015-11-13
Teemu Murtola
M
e
rge types/nsgr
i
d
.
h into
nsgrid
.
h
commit
|
commitdiff
|
tree
2015-11-13
Teemu M
u
rtola
Report unused cycl
e
supp
r
e
ssi
o
ns
commit
|
commitdiff
|
tree
2015-11-11
Teemu Murtola
Support inspec
t
ing expected erro
r
me
s
sag
e
s in tests
commit
|
commitdiff
|
tree
2015-11-11
Teemu Mur
t
ola
Remove b
u
i
l
d system f
o
r boost
commit
|
commitdiff
|
tree
2015-11-10
Teem
u
Mur
t
ola
Remove r
e
maini
n
g boos
t
de
p
end
e
ncies
commit
|
commitdiff
|
tree
2015-11-07
T
eemu Murto
l
a
Remove
m
i
s
c
.
copyr
i
te
.
h functions
commit
|
commitdiff
|
tree
2015-11-07
Tee
m
u Murtola
Move gmx_omp_
n
threa
d
s
.
h and
g
mx_thread_affinit
y
.
h t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-06
Teem
u
Murt
o
la
Move PBC
enums to pbc
.
*
commit
|
commitdiff
|
tree
2015-11-06
Teemu Murto
l
a
Move ns
.
h and nsgr
i
d
.
h to mdlib/
commit
|
commitdiff
|
tree
2015-11-06
Teemu Murtola
Move force
.
h and
vsi
t
e
.
h i
n
to mdlib/
commit
|
commitdiff
|
tree
2015-11-05
Te
e
m
u
Murtola
Move typ
e
s/rgb
.
h to fileio/
commit
|
commitdiff
|
tree
2015-11-04
Teemu Murtola
M
e
r
g
e "
M
e
rge b
r
a
n
ch r
e
leas
e
-
5-1"
commit
|
commitdiff
|
tree
2015-11-03
Teemu M
u
rtola
Update
b
uild sc
r
ipts to match releng refactor
i
ng
commit
|
commitdiff
|
tree
2015-11-02
Teemu
M
urt
o
la
R
e
pl
a
ce boost::exception_
p
tr with st
d
::e
x
c
ept
i
on
_
pt
r
commit
|
commitdiff
|
tree
2015-11-01
Teemu M
u
rtola
Re
m
ove
r
emaining scop
e
d_ptrs
commit
|
commitdiff
|
tree
2015-11-01
Teemu Murtola
Remove
m
ore s
c
oped_
p
tr uses
commit
|
commitdiff
|
tree
2015-10-28
Teemu Murtola
Rem
o
ve unus
e
d TrajectoryAnalysis
M
o
d
ule code
commit
|
commitdiff
|
tree
2015-10-27
Teemu Murtola
Addi
t
ional checks
f
or
selec
t
ion i
n
put
commit
|
commitdiff
|
tree
2015-10-26
Tee
m
u
Mur
t
ola
Rem
o
ve some boost::scoped
_
ptr
u
s
e
s
commit
|
commitdiff
|
tree
2015-10-25
Teemu Murtola
Fix missing help
text for traj
e
c
t
ory analysis tools
commit
|
commitdiff
|
tree
2015-10-24
Teemu
Murtola
Change
some sh
a
red_ptrs
back to u
n
i
q
ue_ptr
commit
|
commitdiff
|
tree
2015-10-22
Te
e
mu
Murtola
Addi
t
i
ona
l
n
o
r
malization options for
gmx rdf
commit
|
commitdiff
|
tree
2015-10-22
Teemu Murtola
Use include_direc
t
orie
s
(SYSTEM
.
.
.
) consistently
commit
|
commitdiff
|
tree
2015-10-22
Teemu Murtola
Clean up
a
nd im
p
rove f
a
tal error handl
i
n
g
commit
|
commitdiff
|
tree
2015-10-19
T
e
emu Murto
l
a
S
plit EnumI
n
t
Option
f
rom
StringOpti
o
n
commit
|
commitdiff
|
tree
2015-10-14
Te
e
mu Murtola
M
ake
bash
complet
i
o
ns w
o
rk with ba
s
h
--posix
commit
|
commitdiff
|
tree
2015-10-13
Teemu Murtola
Improve docu
m
entation and
test
s
for
refd
a
ta
commit
|
commitdiff
|
tree
2015-10-12
Teem
u
Murtola
H
ide implementat
i
on details from cmdlinerunner
.
h
commit
|
commitdiff
|
tree
2015-10-12
Teemu Murto
l
a
Imp
r
ove
g
mx sasa tests
a
nd
c
lean
u
p -
o
r handling
commit
|
commitdiff
|
tree
2015-10-11
Teemu Murtola
R
e
move
o
b
sole
t
e build scripts
commit
|
commitdiff
|
tree
2015-10-08
Teemu Murt
o
l
a
Remove unused error handling code
commit
|
commitdiff
|
tree
2015-10-05
Teemu Murtola
Ma
k
e using C++ type wit
h
snew() a compiler error
commit
|
commitdiff
|
tree
2015-10-05
Te
e
mu
Murtola
Mo
r
e deta
i
led error message for missing file
s
commit
|
commitdiff
|
tree
2015-10-03
Teemu Murtola
Silence Python detec
t
ion on CMake
r
erun
commit
|
commitdiff
|
tree
2015-10-03
Teemu Murtola
Merge branch
rele
a
se-5-
1
into
m
a
ster
commit
|
commitdiff
|
tree
2015-10-03
Teemu M
u
rt
o
l
a
M
i
nor
c
leanup in gmx i
n
ser
t
-molecules
commit
|
commitdiff
|
tree
next