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Reduce rounding errors in SETTLE
2016-08-18
Teemu Murtola
C
h
e
ck
f
or unuse
d
ref
d
ata va
l
u
e
s
commit
|
commitdiff
|
tree
2016-08-18
T
e
em
u
Mur
t
ola
G
e
neric s
t
ructured key-value tree for opti
o
ns
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Support f
o
r n
o
n-
s
tring option value a
s
signment
commit
|
commitdiff
|
tree
2016-08-17
Teemu Mu
r
tola
Basic support for array-of-str
u
c
ts
in opti
o
n
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
G
e
neralize an
d
simplify option val
u
e storage
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Generalize optio
n
secti
o
n
i
nterna
l
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtol
a
Reimplement subs
e
ctions in
Options
commit
|
commitdiff
|
tree
2016-08-04
T
e
emu Murtola
Fix/improve doc l
i
nks in temp
l
ate/REA
D
ME
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtola
Fu
n
cti
o
n to split delimit
e
d strings
commit
|
commitdiff
|
tree
2016-07-14
Teemu Murtol
a
Use newer gcc for co
v
erage
commit
|
commitdiff
|
tree
2016-07-07
Teemu M
u
rtola
Change
h
andling for
m
issing
r
e
leng
d
oc
s
commit
|
commitdiff
|
tree
2016-06-30
Teemu Murtola
Extract string parsi
n
g
routines to util
i
ty
commit
|
commitdiff
|
tree
2016-06-28
T
e
emu Murtola
Spl
i
t up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Murtola
Factory for
creatin
g
t_inputre
c
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murto
l
a
Use C++ replacemen
t
for md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Murt
o
la
Basic C
+
+
l
ogging interface
commit
|
commitdiff
|
tree
2016-05-31
Teemu Murtola
Improve make_ndx help text
commit
|
commitdiff
|
tree
2016-05-25
Teemu Murto
l
a
Supp
o
rt for r
e
al MP
I
unit te
s
t
s
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
T
est
s
fo
r
s
i
n
gl
e
-r
a
nk thread affinity sett
i
ng
commit
|
commitdiff
|
tree
2016-05-21
T
e
emu Murtola
Pass number of loca
l
threa
d
s to thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu M
u
rtola
Allow creatin
g
mock HardwareTo
p
ology
objects
commit
|
commitdiff
|
tree
2016-05-21
T
e
em
u
Murtol
a
Use only
HardwareTop
o
logy for thread
affinity
commit
|
commitdiff
|
tree
2016-05-21
Tee
m
u
Murtol
a
Merge branch re
l
ea
s
e-2016
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu Murtol
a
B
u
mp version number
s
for 2017 developm
e
nt
commit
|
commitdiff
|
tree
2016-05-17
Tee
m
u Mu
r
tol
a
Fix some thread affinity cases
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtol
a
A
d
ditional
Jenkins documentation
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
I
n
c
l
u
de releng
d
ocumentati
o
n to de
v
eloper guide
commit
|
commitdiff
|
tree
2016-05-08
Teemu Murt
o
la
S
u
p
por
t
for OpenCL CI builds
commit
|
commitdiff
|
tree
2016-05-05
Teemu Murtola
Merge br
a
nch rele
a
se-5
-
1
commit
|
commitdiff
|
tree
2016-05-05
T
eemu Murtola
Make Sphi
n
x bui
l
d sile
n
t for
version 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Teemu Murtola
M
a
rk
optional input/output files in gmx order
commit
|
commitdiff
|
tree
2016-04-28
Teemu
M
u
rtola
Use Hardw
a
r
e
Topolo
g
y to
s
et nthrea
d
s_hw_a
v
ail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Remove gmx_hw_inf
o
_t
:
:
n
c
o
re
commit
|
commitdiff
|
tree
2016-04-27
T
e
e
mu Murtol
a
Imp
r
ove release workflow testing
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Disable multiple
r
a
n
ks
f
or non-MPI unit tests
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix iss
u
es with fa
i
ling thread a
f
finity setting
commit
|
commitdiff
|
tree
2016-04-27
Te
e
mu Mur
t
ola
Merge
"
Merge b
r
an
c
h release-5-1"
commit
|
commitdiff
|
tree
2016-04-18
Teemu Murtola
Make thread affini
t
y
failures always end
up in log
commit
|
commitdiff
|
tree
2016-03-30
T
eemu M
u
rtola
M
a
ke in
c
l
u
desor
t
er
.
py work with Do
x
yge
n
1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Te
e
mu
M
urto
l
a
Fix error reporting fo
r
documen
t
ation build
commit
|
commitdiff
|
tree
2016-03-28
Teemu M
u
r
tola
More support
for r
e
le
a
se work
f
l
o
w
commit
|
commitdiff
|
tree
2016-03-26
Teemu Murtola
I
g
nore empty GMXLIB
commit
|
commitdiff
|
tree
2016-03-14
Teemu Murtola
Ad
d
t
e
s
ts for empty strings in re
f
d
ata
commit
|
commitdiff
|
tree
2016-03-13
Teemu Mur
t
ola
Suppor
t
replacing s
o
lv
e
nt in inser
t
-molecu
l
e
s
commit
|
commitdiff
|
tree
2016-02-01
T
e
emu Murtola
Ha
n
dle
p
dbinfo in AtomsBuilder
commit
|
commitdiff
|
tree
2016-01-28
Tee
m
u Murtola
Upda
t
e buil
d
scri
p
ts to rele
n
g changes
commit
|
commitdiff
|
tree
2016-01-24
Teemu Mu
r
tola
D
oc
u
me
n
t limi
t
ations o
n
32-bit Linux
commit
|
commitdiff
|
tree
2016-01-12
Teemu M
u
rtola
Make GMX_MPI al
w
a
y
s d
e
fined to 0
/
1
commit
|
commitdiff
|
tree
2016-01-12
Teem
u
Murtola
M
o
ve flags out of t_trxf
r
a
m
e
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Re
m
ove histor
i
cal times
f
rom t_trxfra
m
e
commit
|
commitdiff
|
tree
2016-01-12
T
e
e
m
u Murtola
Support passing
t
a
r
ball MD5 for webp
a
ge bui
l
d
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Remove vm
d
plugi
n
from
t_trxframe
commit
|
commitdiff
|
tree
2016-01-11
Teemu
Murto
l
a
Convert more con
f
ig
.
h
defines to 0/1
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Suppor
t
traje
c
t
ory
a
na
l
y
sis with any atom
s
ubset
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murt
o
l
a
Sup
p
ort
fram
e
s
w
i
t
h ato
m
subsets in selections
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Support
arbit
r
ary subset trajectories in poscalc
.
*
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murt
o
la
Make file
names in fata
l
error
messa
g
es more robust
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu Mur
t
ol
a
Do n
o
t warn about missin
g
Ope
n
MP
w
i
t
h GMX_
G
PU=OFF
commit
|
commitdiff
|
tree
2016-01-10
Tee
m
u
Murtola
M
o
re
config
.
h macros
t
o 0/1
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu M
u
rtola
C
onvert som
e
c
o
n
fig
.
h macros to use 0/1
commit
|
commitdiff
|
tree
2016-01-05
Teemu Murtola
U
p
date packaging
b
uild
commit
|
commitdiff
|
tree
2015-12-31
Tee
m
u Murtola
Report used defines in check-s
o
urce
commit
|
commitdiff
|
tree
2015-12-29
Teemu M
u
rtola
Packaging build
s
cript
for
w
eb site
commit
|
commitdiff
|
tree
2015-12-29
Teemu
Murto
l
a
Redu
c
e inputrec
.
h depen
d
encies
commit
|
commitdiff
|
tree
2015-12-27
Teemu Mu
r
tola
Improve text wr
i
ti
n
g
i
n help
o
u
tput
commit
|
commitdiff
|
tree
2015-12-27
Te
e
mu Murto
l
a
S
o
urce pack
a
g
i
ng
with new relen
g
commit
|
commitdiff
|
tree
2015-12-27
Teemu Murtola
Furth
e
r ve
c
.
h cleanup
commit
|
commitdiff
|
tree
2015-12-26
T
eemu Murtola
Clean up vec
.
h
commit
|
commitdiff
|
tree
2015-12-24
Teemu Murtola
Add functionality
to TextWri
t
er
commit
|
commitdiff
|
tree
2015-12-20
Teemu M
u
r
tola
Fix m
o
s
t
warnin
g
s
with D
o
xygen 1
.
8
.
10
commit
|
commitdiff
|
tree
2015-12-19
Te
e
mu Murtola
Update version
i
ng
f
or new
s
cheme
commit
|
commitdiff
|
tree
2015-12-16
T
e
e
m
u Murtola
Mo
v
e calc
g
rid
.
* to fft/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
M
ove
main
.
*, splitter
.
*, gmx_
o
mp_nt
h
reads
.
*
to m
d
lib
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move readi
n
p
.
*
and warn
i
n
p
.
* t
o
fileio/
commit
|
commitdiff
|
tree
2015-12-15
Teem
u
Murt
o
la
Move hardwa
r
e dete
c
tion
t
o h
a
rdwa
r
e/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move some m
d
run code out of g
m
xlib/
commit
|
commitdiff
|
tree
2015-12-15
Teemu
Murtola
Move gpu_util
s
etc
.
ou
t
of gmxlib
commit
|
commitdiff
|
tree
2015-12-14
Teemu Murtola
Install baseversio
n
.
h
commit
|
commitdiff
|
tree
2015-12-12
Teemu
M
u
rtola
Create separate m
o
d
ule f
o
r trajectory data
commit
|
commitdiff
|
tree
2015-12-12
Teem
u
Murtola
Move disre
.
*
and o
r
ires
.
* to l
i
s
t
ed-forces
/
commit
|
commitdiff
|
tree
2015-12-12
Teemu
Murtola
Move ifunc
.
* to topology/
commit
|
commitdiff
|
tree
2015-12-12
T
eemu Murtola
Mov
e
pu
t
_
a
toms
_
in_box_omp() to sim_util
.
*
commit
|
commitdiff
|
tree
2015-12-12
Teemu
M
u
rtola
Remove
t
opology -> fileio dependency
commit
|
commitdiff
|
tree
2015-12-11
Teemu Murtola
Merge "M
e
rge bran
c
h 'origin/rele
a
se-5-1'"
commit
|
commitdiff
|
tree
2015-12-09
Teemu Murtola
Split t
x
t
dump
.
*, part
2
commit
|
commitdiff
|
tree
2015-12-09
Teemu M
u
rtol
a
Split txtdum
p
.
*, part 1
commit
|
commitdiff
|
tree
2015-12-03
Teemu Murtol
a
Move str
d
b
.
* to utility/
commit
|
commitdiff
|
tree
2015-12-03
T
eemu Mur
t
ola
Mov
e
f
i
lenm
.
*
to commandline
commit
|
commitdiff
|
tree
2015-12-02
Teemu Mur
t
ola
Split filenm
.
*
commit
|
commitdiff
|
tree
2015-11-30
Teemu
M
urtola
Remove
topology -> mdtypes dep
e
ndency
commit
|
commitdiff
|
tree
2015-11-30
T
eemu Murtola
Remove obsolete ref
e
ren
c
es to legacyheaders/
commit
|
commitdiff
|
tree
2015-11-30
Tee
m
u Mur
t
o
l
a
Merge re
m
a
ining legacyhe
a
d
e
rs/types/ to m
d
types/
commit
|
commitdiff
|
tree
2015-11-30
Teemu Murt
o
la
Move
i
fun
c
.
h to gmxlib
commit
|
commitdiff
|
tree
2015-11-30
Teemu M
u
r
t
o
la
Move force_flags
.
h to mdlib/
commit
|
commitdiff
|
tree
2015-11-30
Teem
u
Murtola
l
i
b
g
rom
a
cs
C
Make
s
ource file management cleanup
commit
|
commitdiff
|
tree
2015-11-30
T
e
emu Murtola
Mov
e
hardwar
e
info
s
truct
s
to
h
ard
w
are/
commit
|
commitdiff
|
tree
2015-11-30
T
e
em
u
Murtola
Clea
n
up som
e
select
i
on
cod
e
commit
|
commitdiff
|
tree
2015-11-23
Teem
u
Murtola
Move precis
i
on dete
c
tion
sym
b
ols to
baseversi
o
n
.
*
commit
|
commitdiff
|
tree
2015-11-22
T
e
emu
M
u
rtola
Re
m
ove co
r
rel
a
t
i
o
nfunctions -> mdtypes dependency
commit
|
commitdiff
|
tree
2015-11-21
Teemu
Murtola
Use v
.
data() in
s
tead o
f
&
v
[0]
f
or
C
interop
commit
|
commitdiff
|
tree
next