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Fixes some memory leaks associated with testing applied forces
2016-10-14
Teemu Murtola
U
s
e gmx_mtop_t i
n
selections, par
t
3
commit
|
commitdiff
|
tree
2016-10-14
Tee
m
u Murtola
U
s
e gmx_
m
top_t in selections,
p
art 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Use gmx_mtop_t in se
l
ections, part
2
commit
|
commitdiff
|
tree
2016-10-13
T
e
e
mu Murtola
Ad
d
back-map
p
ing to Ke
y
ValueTreeTransfor
m
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
Up
d
ate
b
und
l
e
d TNG
commit
|
commitdiff
|
tree
2016-10-13
Tee
m
u Mu
r
tola
Getter
f
or mappe
d
pa
t
h
s from Key
V
alueTree
T
rans
f
o
r
m
commit
|
commitdiff
|
tree
2016-10-12
T
eemu Murto
l
a
Use gmx_mtop_t i
n
selec
t
ions, par
t
1
commit
|
commitdiff
|
tree
2016-10-12
Tee
m
u M
u
rtola
Wrap
sel
.
metho
d
evaluation par
a
m
e
t
e
rs to struc
t
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murtola
Support con
c
urrent t_topolo
g
y and gmx_mtop_t us
e
commit
|
commitdiff
|
tree
2016-10-11
Teemu Mu
r
tola
Check atom m
a
ss availab
i
li
t
y
in selec
t
ions
commit
|
commitdiff
|
tree
2016-10-05
T
e
emu
Murtola
Su
p
port different key match
i
ng in K
e
yValueTree
T
ransfor
m
commit
|
commitdiff
|
tree
2016-10-05
T
ee
m
u
M
u
rtola
Merg
e
"Mer
g
e
b
ranch r
e
le
a
se-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Teemu Murtola
Fix
d
efaul
t
n
i
c
e
level i
n
mdrun-on
l
y build
commit
|
commitdiff
|
tree
2016-09-12
Teemu Mu
r
to
l
a
F
i
x
v
a
rious memory leaks
commit
|
commitdiff
|
tree
2016-09-07
Tee
m
u
Murtola
Clean up
CTest test management
commit
|
commitdiff
|
tree
2016-08-30
Teemu Mu
r
tola
B
a
s
i
c support for transfor
m
ing
K
eyValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
S
uppor
t
K
e
yVa
l
ueTree objects in refd
a
t
a
commit
|
commitdiff
|
tree
2016-08-18
T
e
emu Murto
l
a
C
h
eck fo
r
unuse
d
r
efdata va
l
ues
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Generic
structu
r
ed key-value tree for opt
i
ons
commit
|
commitdiff
|
tree
2016-08-18
Teemu Mu
r
tola
Support
f
or
no
n
-string
o
pt
i
on val
u
e assig
n
ment
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Bas
i
c suppo
r
t
f
or array-of-s
t
ructs in options
commit
|
commitdiff
|
tree
2016-08-17
Te
e
m
u Murtola
Generalize and sim
p
li
f
y op
t
ion value storage
commit
|
commitdiff
|
tree
2016-08-17
Tee
m
u Murtola
General
i
z
e
option
section in
t
er
n
a
l
s
commit
|
commitdiff
|
tree
2016-08-17
T
eemu Murtola
Reimplement
s
u
bsecti
o
ns in Options
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murto
l
a
Fix/improve doc lin
k
s i
n
template/README
commit
|
commitdiff
|
tree
2016-08-01
Teemu
Murtola
Fu
n
c
t
ion to split delimited strings
commit
|
commitdiff
|
tree
2016-07-14
Teemu Mur
t
o
l
a
Us
e
newer gcc
for c
o
verage
commit
|
commitdiff
|
tree
2016-07-07
Teemu
M
urto
l
a
C
hange
h
a
n
dli
n
g for missing rele
n
g docs
commit
|
commitdiff
|
tree
2016-06-30
T
e
emu Murtola
Extra
c
t string
p
arsing routines to utility
commit
|
commitdiff
|
tree
2016-06-28
Teemu Murtola
Split up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Murtola
F
a
ctory
f
or creating t_inputrec
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murtola
Use C
+
+ replacement for
m
d_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu M
u
r
t
o
la
Basic
C
++ logging in
t
erf
a
ce
commit
|
commitdiff
|
tree
2016-05-31
Teemu Mur
t
ola
Improve
m
ake
_
ndx help text
commit
|
commitdiff
|
tree
2016-05-25
Teemu Mur
t
ola
S
u
p
port
f
o
r
real MPI
u
n
i
t
t
e
sts
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murt
o
l
a
Te
s
ts for single-rank thread affinity s
e
ttin
g
commit
|
commitdiff
|
tree
2016-05-21
T
eem
u
M
u
rtola
Pa
s
s nu
m
ber
o
f local threads
t
o
thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Mur
t
ola
A
llo
w
cre
a
tin
g
m
o
ck H
a
rdw
a
reTopology objects
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
ur
t
ola
Use only
H
a
rd
w
areT
o
pology for thread
a
ff
i
nity
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Murtola
Merge branch release-2016
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Bump version
number
s
for 201
7
dev
e
lopment
commit
|
commitdiff
|
tree
2016-05-17
Teemu Murt
o
l
a
Fix some thread affinity cases
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu Murtola
Additiona
l
Jenkins documentation
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Include
r
elen
g
documentation to d
e
veloper guide
commit
|
commitdiff
|
tree
2016-05-08
Teemu Mur
t
ola
S
upport for OpenCL CI builds
commit
|
commitdiff
|
tree
2016-05-05
Teemu
M
u
rtola
Merg
e
branch r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-05-05
Teemu
M
urtola
Mak
e
Sphinx build silent f
o
r version 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Tee
m
u Murtola
Mark optional input/output files in gmx orde
r
commit
|
commitdiff
|
tree
2016-04-28
Te
e
mu Murtola
Use Hardwa
r
eTopology to set nthreads_h
w
_avail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Remove g
m
x
_
h
w_inf
o
_t::ncore
commit
|
commitdiff
|
tree
2016-04-27
Te
e
mu
M
urtol
a
Im
p
r
ov
e
rele
a
s
e workfl
o
w t
e
sti
n
g
commit
|
commitdiff
|
tree
2016-04-27
Teemu Mur
t
ola
Disable multiple r
a
nks for non-MPI unit
t
e
sts
commit
|
commitdiff
|
tree
2016-04-27
Teemu M
u
rtola
Fix is
s
ues wi
t
h
f
a
i
ling
t
hrea
d
af
f
in
i
ty sett
i
ng
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Me
r
ge "Merge branch release-5-1"
commit
|
commitdiff
|
tree
2016-04-18
Teemu M
u
rtola
Make thre
a
d affinity failures al
w
ays end
u
p in
l
og
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Make include
s
orter
.
p
y
work with Doxygen 1
.
8
.
1
0
+
commit
|
commitdiff
|
tree
2016-03-30
T
e
emu Murtola
Fix error reporting for docu
m
entati
o
n build
commit
|
commitdiff
|
tree
2016-03-28
Teemu Murto
l
a
More support for release workfl
o
w
commit
|
commitdiff
|
tree
2016-03-26
Te
e
m
u
Mur
t
ola
Ignore emp
t
y GMXLIB
commit
|
commitdiff
|
tree
2016-03-14
T
eemu Murtola
Add
t
est
s
f
or empty
s
t
r
i
ngs in ref
d
ata
commit
|
commitdiff
|
tree
2016-03-13
Tee
m
u Murtola
S
u
pport replacing
s
olve
n
t in insert-molecules
commit
|
commitdiff
|
tree
2016-02-01
Te
e
mu Murtola
Handl
e
pdbinfo in AtomsBui
l
der
commit
|
commitdiff
|
tree
2016-01-28
Teemu Murtola
Update
b
u
i
ld scri
p
ts to
r
e
le
n
g changes
commit
|
commitdiff
|
tree
2016-01-24
Teemu Murtola
D
o
cument limitati
o
ns on 32-bi
t
Linux
commit
|
commitdiff
|
tree
2016-01-12
Teemu
Murtola
Make GMX_MPI always
d
ef
i
n
e
d to 0/
1
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Move flags out of
t
_trxframe
commit
|
commitdiff
|
tree
2016-01-12
T
ee
m
u
M
u
r
tola
Remo
v
e
historical
t
i
mes from t_tr
x
f
rame
commit
|
commitdiff
|
tree
2016-01-12
Teemu Mu
r
tol
a
S
u
pport passing tar
b
all MD
5
for webpage bui
l
d
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Remo
v
e
vmdplugin from t_trxframe
commit
|
commitdiff
|
tree
2016-01-11
T
e
em
u
Murtola
Convert m
o
re config
.
h
de
f
i
n
es to 0
/
1
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murto
l
a
Suppo
r
t
trajectory
anal
y
sis with any atom s
u
b
set
commit
|
commitdiff
|
tree
2016-01-10
T
eemu Murto
l
a
Support frames
w
i
th atom
s
ubsets in
s
elections
commit
|
commitdiff
|
tree
2016-01-10
T
e
emu Murtol
a
Sup
p
o
rt arb
i
t
rary subset trajec
t
o
r
ie
s
i
n
poscalc
.
*
commit
|
commitdiff
|
tree
2016-01-10
Teem
u
Murtola
Mak
e
file names
i
n fatal erro
r
mess
a
ge
s
more r
o
b
u
st
commit
|
commitdiff
|
tree
2016-01-10
T
eemu Murtola
Do
not warn about missin
g
O
penMP with GMX_GPU=OFF
commit
|
commitdiff
|
tree
2016-01-10
T
e
emu Murto
l
a
More con
f
ig
.
h
macros
to 0/1
commit
|
commitdiff
|
tree
2016-01-10
T
eemu
M
urtola
Convert some co
n
fig
.
h macros
t
o use 0/1
commit
|
commitdiff
|
tree
2016-01-05
Teemu
Murtol
a
Upd
a
te pac
k
aging buil
d
commit
|
commitdiff
|
tree
2015-12-31
Teemu Murtola
Report us
e
d
d
efine
s
in check-
s
ource
commit
|
commitdiff
|
tree
2015-12-29
T
e
emu
M
urtola
Pa
c
kaging bu
i
ld script for
web site
commit
|
commitdiff
|
tree
2015-12-29
Te
e
mu Murtola
Re
d
uce
inputrec
.
h dependencies
commit
|
commitdiff
|
tree
2015-12-27
Teemu Mur
t
o
la
Improve text wr
i
ting in hel
p
output
commit
|
commitdiff
|
tree
2015-12-27
Teemu
Mu
r
tola
Source packaging with
n
ew releng
commit
|
commitdiff
|
tree
2015-12-27
Teemu Mu
r
tola
Further vec
.
h cl
e
a
n
up
commit
|
commitdiff
|
tree
2015-12-26
Teemu Murtola
C
l
ean up vec
.
h
commit
|
commitdiff
|
tree
2015-12-24
Te
e
mu
Murtola
Add functional
i
ty to Te
x
t
W
riter
commit
|
commitdiff
|
tree
2015-12-20
Teem
u
Murt
o
la
F
i
x most warnings
with Doxygen 1
.
8
.
10
commit
|
commitdiff
|
tree
2015-12-19
Teemu Murtola
Update
versi
o
ning for ne
w
sch
e
m
e
commit
|
commitdiff
|
tree
2015-12-16
Tee
m
u
Murtol
a
Move ca
l
cgrid
.
* to fft/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move main
.
*
, spli
t
t
er
.
*,
g
mx
_
omp_nthreads
.
* to mdl
i
b
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move readinp
.
* and war
n
in
p
.
* to f
i
leio/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Mur
t
ola
Mo
v
e hardware det
e
ction
t
o h
a
rdware/
commit
|
commitdiff
|
tree
2015-12-15
T
eemu
M
urtola
Move some mdrun co
d
e out of gm
x
lib/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
M
ove gp
u
_utils
e
tc
.
o
u
t of gmxli
b
commit
|
commitdiff
|
tree
2015-12-14
Teemu
M
urtola
Install baseversion
.
h
commit
|
commitdiff
|
tree
2015-12-12
Teemu
Mur
t
o
l
a
Create sepa
r
ate mod
u
le
for trajectory data
commit
|
commitdiff
|
tree
2015-12-12
Teemu
M
urtola
Move d
i
sre
.
*
and orir
e
s
.
* to listed
-
forc
e
s/
commit
|
commitdiff
|
tree
2015-12-12
Teem
u
M
u
rtola
Move ifu
n
c
.
* to t
o
p
olog
y
/
commit
|
commitdiff
|
tree
2015-12-12
Teemu Mu
r
tola
Move put
_
atoms_i
n
_box_omp() to sim_util
.
*
commit
|
commitdiff
|
tree
2015-12-12
T
e
emu Mur
t
o
la
R
e
move topology
-> fileio
d
e
p
e
nde
n
cy
commit
|
commitdiff
|
tree
next