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Misc. Doxygen build system improvements
2014-02-26
Teem
u
Murt
o
la
Misc
.
Do
x
ygen build system i
m
provements
commit
|
commitdiff
|
tree
2014-02-26
Erik Linda
h
l
A
d
ded message to warn that gro
u
p ke
r
nel
s
are deprec
a
ted
.
commit
|
commitdiff
|
tree
2014-02-26
Mic
h
ael Sh
i
rts
Updati
n
g an
d
im
p
r
o
ving Anderse
n
t
h
er
m
ostat documentation
commit
|
commitdiff
|
tree
2014-02-26
Roland Schulz
I
CC aliasing optimization fla
g
s
commit
|
commitdiff
|
tree
2014-02-26
Rol
a
nd Schulz
Rep
l
ace
a
ll
m
drun rngs with cycle based rng
commit
|
commitdiff
|
tree
2014-02-26
Mark Abraha
m
Add
T
hreadSaniti
z
e
r
bui
l
d
type
commit
|
commitdiff
|
tree
2014-02-25
B
e
r
k Hess
Fixes sepe
r
ate PME
nodes wit
h
out LJ-PME
commit
|
commitdiff
|
tree
2014-02-24
Ber
k
Hess
Fixed bug with LJ po
t
-
swi
t
ch in
4
xN kernels
commit
|
commitdiff
|
tree
2014-02-24
Mark Abraha
m
Sup
p
ress icc warning f
o
r
Boost 1
.
55 use of #pragma
.
.
.
commit
|
commitdiff
|
tree
2014-02-23
Rosse
n
Aposto
l
o
v
Removed deprecate
d
Encad
FF
.
commit
|
commitdiff
|
tree
2014-02-21
R
oland Sch
u
lz
Fix load_lj_p
a
i
r_params2 for MIC
commit
|
commitdiff
|
tree
2014-02-21
Roland Sc
h
ul
z
Updated
Boo
s
t to la
t
est
1
.
55
.
0
commit
|
commitdiff
|
tree
2014-02-21
R
o
land Schulz
Me
r
ge "Merge release-4-
6
into master"
commit
|
commitdiff
|
tree
2014-02-20
M
a
rk Abraha
m
Remove pa
r
ticle decompositio
n
commit
|
commitdiff
|
tree
2014-02-20
Christoph J
u
n
g
hans
added gmx_is_{si
n
gl
e
,d
o
uble}_precision
commit
|
commitdiff
|
tree
2014-02-20
R
oland S
c
hulz
Fix aligned store to unaligned memo
r
y
commit
|
commitdiff
|
tree
2014-02-20
Mark Abraham
avoid md
r
u
n
crash when rdtscp i
s
not supported
commit
|
commitdiff
|
tree
2014-02-20
Mar
k
A
b
raham
Ad
d
integr
a
tion tests for rep
l
ica exchange
commit
|
commitdiff
|
tree
2014-02-20
R
ol
a
nd Schulz
Fix Reference Build
commit
|
commitdiff
|
tree
2014-02-20
Teemu
Murtola
A
dd document
a
tion for usi
n
g Doxygen
commit
|
commitdiff
|
tree
2014-02-19
Ma
r
k Abr
a
ham
Make
s
o
m
e
v
a
riable names less cryptic
commit
|
commitdiff
|
tree
2014-02-18
Mark Abra
h
am
Fix harm
l
ess
bug with combinatio
n
of
group and twin
.
.
.
commit
|
commitdiff
|
tree
2014-02-17
Rola
n
d Schulz
Enable m
o
r
e
warn
i
ngs
commit
|
commitdiff
|
tree
2014-02-16
Ca
r
sten Kutzn
e
r
Small enhancement of c
o
mputa
t
ional
e
lectrophysiology
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
T
eemu Murtola
Improve ma
n
page formatting slight
l
y
commit
|
commitdiff
|
tree
2014-02-16
Teemu Mu
r
tola
Fi
x
d
e
fault enum val
u
es in h
e
lp
o
u
tput
commit
|
commitdiff
|
tree
2014-02-13
M
agnus
L
u
ndborg
Remo
v
ed option
t
o use
Open
M
P with
t
he TN
G
libr
a
ry
.
commit
|
commitdiff
|
tree
2014-02-12
M
a
r
k
Abraham
Re
-
fix
compiler wa
r
nings
w
ith scanner
.
cpp
commit
|
commitdiff
|
tree
2014-02-11
Mark
Abrah
a
m
Split genbo
x
into 'solv
a
t
e' an
d
'insert-molecules'
commit
|
commitdiff
|
tree
2014-02-11
Dav
i
d
v
a
n der
S
p
oel
Fixed another vmdio
issue
.
commit
|
commitdiff
|
tree
2014-02-11
E
rik L
i
ndahl
First part of commit f
o
r red
e
sig
n
ed SIMD mod
u
le - namecha
n
ges
.
commit
|
commitdiff
|
tree
2014-02-11
Magnus Lundborg
Added informati
o
n
a
bout how
t
o cit
e
the TNG paper
.
commit
|
commitdiff
|
tree
2014-02-09
Ma
r
k Abraham
Move orie
n
tation
r
estr
a
ints
checks inside
i
ni
t
func
t
ion
commit
|
commitdiff
|
tree
2014-02-09
Teemu Mu
r
t
ola
Refac
t
or new help f
o
rmatting impl
e
mentation
commit
|
commitdiff
|
tree
2014-02-08
Mark Abraham
Clean
u
p
.
log file dump
o
f
i
nputrec
commit
|
commitdiff
|
tree
2014-02-08
Mark Abr
a
ham
I
ssue fatal
e
rrors r
a
th
e
r than use b
r
oken shell
c
ode
commit
|
commitdiff
|
tree
2014-02-08
Teemu Murtola
Fix &
u
pdate
docs for GMX_
T
EST_OPTIO
N
S
commit
|
commitdiff
|
tree
2014-02-07
Mark Abra
h
am
I
n
it
i
alize inputrec better in
genbox
commit
|
commitdiff
|
tree
2014-02-06
Teemu Murtola
F
ix build of sh
a
re/
t
empl
a
te when
i
nstall
e
d
commit
|
commitdiff
|
tree
2014-02-06
Micha
e
l
S
hir
t
s
EE dhdl
h
eader should not specify
one l
a
mbda
commit
|
commitdiff
|
tree
2014-02-06
Mark Abraham
R
e
m
ove antiquated and
u
nused gmxpar
.
tex documentation
commit
|
commitdiff
|
tree
2014-02-06
Roland Sc
h
ulz
Use random seeds b
y
default
commit
|
commitdiff
|
tree
2014-02-05
Mark Ab
r
aham
Update descriptio
n
of genres
t
r
commit
|
commitdiff
|
tree
2014-02-04
Roland Sc
h
ulz
Fix
a
nd simplify rpath
commit
|
commitdiff
|
tree
2014-02-03
M
ark A
b
raham
C
lean up genbox an
d
as
s
o
ci
a
ted c
o
de
commit
|
commitdiff
|
tree
2014-02-03
Teem
u
M
ur
t
ola
M
erge "Merge release-4-6
i
n
t
o master
"
commit
|
commitdiff
|
tree
2014-02-03
T
eemu Mur
t
o
l
a
Opt
i
m
i
z
e Doxygen
b
u
ild
commit
|
commitdiff
|
tree
2014-02-03
Mark Abraha
m
Im
p
r
o
ved wallc
y
cle report
i
ng
commit
|
commitdiff
|
tree
2014-02-02
Teem
u
M
urtola
Fix se
g
fault
i
n
'
gmx
-
h
'
commit
|
commitdiff
|
tree
2014-02-02
Teemu Murtola
G
et rid of
src/programs/gmx/
commit
|
commitdiff
|
tree
2014-02-02
Te
e
mu
M
urtola
Simplify
Options::setDescription() usage
commit
|
commitdiff
|
tree
2014-02-01
Teemu
M
urto
l
a
Fix some issue
s
r
e
ported
by 'ma
k
e d
e
pc
h
ec
k
docche
c
k'
commit
|
commitdiff
|
tree
2014-01-31
T
e
e
m
u
M
urtola
Ov
e
rview docs f
o
r unit t
e
sting
commit
|
commitdiff
|
tree
2014-01-30
Roland Schulz
Add cmake option for Referenc
e
kernel
commit
|
commitdiff
|
tree
2014-01-30
Mark Abrah
a
m
Minor impr
o
veme
n
ts to e
w
a
l
d
_
LRcorr
e
ction
commit
|
commitdiff
|
tree
2014-01-30
Be
r
k
Hess
Made refe
r
ence SIM
D
w
ork again
commit
|
commitdiff
|
tree
2014-01-30
Tee
m
u Mur
t
ola
Fix shell c
o
m
p
l
eti
o
ns of
f
fMUL
T
o
ptions
commit
|
commitdiff
|
tree
2014-01-30
T
e
emu Murtol
a
Refactor ProgramInfo use
commit
|
commitdiff
|
tree
2014-01-30
Rossen Apostolov
Re
m
o
v
ed ions
.
itp
f
ro
m
G
MX/share/top directo
r
y
.
commit
|
commitdiff
|
tree
2014-01-30
Teemu Murtola
Move command lis
t
i
ng t
o
'g
m
x
hel
p
commands'
commit
|
commitdiff
|
tree
2014-01-30
Roland Sc
h
ulz
Allocate memor
y
for M
D
5 o
n
heap
commit
|
commitdiff
|
tree
2014-01-29
Mark Abraham
Improved depe
n
dencies on maths
includes
commit
|
commitdiff
|
tree
2014-01-29
T
eemu Murto
l
a
Fixes to filename shell completion
s
commit
|
commitdiff
|
tree
2014-01-29
Rolan
d
S
chulz
Un
c
r
us
t
ify all files
commit
|
commitdiff
|
tree
2014-01-29
Berk Hess
Automated Verlet rlist for NVE si
m
ulati
o
ns
commit
|
commitdiff
|
tree
2014-01-29
Teemu Murtola
M
erge "Merge branch '
r
elea
s
e-4-6'"
commit
|
commitdiff
|
tree
2014-01-28
David va
n
der S
p
o
e
l
Mo
v
ed rando
m
number gen
e
rato
r
code to separate dir
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten Ku
t
zn
e
r
Allow for "co
m
putatio
n
a
l
electrop
h
ysiol
o
gy" simulations
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
C
hristoph Junghan
s
c
m
ake
:
added FF
T
W_URL to
allow easy offline build
commit
|
commitdiff
|
tree
2014-01-28
Rossen Apostolov
Bum
p
own fft
w
build t
o
v
ersion 3
.
3
.
3
commit
|
commitdiff
|
tree
2014-01-28
Mark Abrah
a
m
Remo
v
e "gmx
t
rjconv
-app"
commit
|
commitdiff
|
tree
2014-01-28
Teemu
Murtola
Shell com
p
l
e
t
ion expor
t
from the wrapper
b
inary
commit
|
commitdiff
|
tree
2014-01-28
Ma
r
k
Abraham
Unify logic for tim
i
ng count
s
commit
|
commitdiff
|
tree
2014-01-28
Szil
á
rd
P
á
ll
clarifi
e
d
Op
e
nMP-related things in mdrun help/m
a
n
commit
|
commitdiff
|
tree
2014-01-28
Teemu M
u
r
t
ola
Exte
n
d
version information output
commit
|
commitdiff
|
tree
2014-01-27
Teemu Murtola
Sim
p
lify
ProgramI
n
fo
commit
|
commitdiff
|
tree
2014-01-23
M
a
rk Abraham
B
r
e
ak dependency of fil
e
io on
t
o
ols
commit
|
commitdiff
|
tree
2014-01-22
M
a
rk Abraha
m
Updat
e
libxm
l
2 CM
a
ke det
e
ction
commit
|
commitdiff
|
tree
2014-01-21
Rossen
A
po
s
tolov
Fixe
d
wrong message
when
b
u
i
lding
own F
F
TW
.
commit
|
commitdiff
|
tree
2014-01-21
Roland Schulz
Fix race
con
d
iti
o
ns
commit
|
commitdiff
|
tree
2014-01-21
Mark Abraham
E
n
s
u
re we don't #define
c
onstants befo
r
e system headers
commit
|
commitdiff
|
tree
2014-01-21
Jus
t
in Lemkul
Added ASP
P
and
G
LU
P
to residuetypes
.
da
t
.
commit
|
commitdiff
|
tree
2014-01-21
T
e
em
u
Murtola
Improve file nam
e
option help
commit
|
commitdiff
|
tree
2014-01-20
Teemu Murtola
R
e
write help output fro
m
Optio
n
s
commit
|
commitdiff
|
tree
2014-01-20
M
a
rk Ab
r
ah
a
m
F
i
x
.
gitignore of some
f
iles
commit
|
commitdiff
|
tree
2014-01-19
Te
e
m
u
Murtola
F
i
x insta
l
l
e
d
hea
d
ers
commit
|
commitdiff
|
tree
2014-01-19
Teemu
M
urtola
Move md5
.
* to fi
l
eio/
commit
|
commitdiff
|
tree
2014-01-19
Teemu Murtola
M
o
ve s
t
rdb
.
* to src/g
r
o
m
acs/fileio/
commit
|
commitdiff
|
tree
2014-01-19
Ma
r
k
Abraham
M
o
v
e
dump, check an
d
tpb
c
onv utilit
i
es
commit
|
commitdiff
|
tree
2014-01-19
Roland Schulz
Fix that
c
heck_library_ex
i
st is r
e
run for FFTW
commit
|
commitdiff
|
tree
2014-01-18
Da
v
id van der
S
p
o
el
Thi
s
patch
mo
v
es the statistics l
i
brary to
it
s
o
w
n
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
M
ark
A
braham
Fix, simplify and tes
t
XTC
w
r
i
ting
commit
|
commitdiff
|
tree
2014-01-17
Da
v
id van der Sp
o
el
T
his patch mov
e
s pre
p
rocessi
n
g
h
eaders to
gm
x
preproce
s
s
commit
|
commitdiff
|
tree
2014-01-17
Roland
S
c
h
ulz
D
e
fine
MPI_INT64
_
T if no
t
d
efined by mpi
commit
|
commitdiff
|
tree
2014-01-17
Mark Abraham
Clean
u
p
inputrec r
e
ading
commit
|
commitdiff
|
tree
2014-01-16
Teemu Murtola
Fi
x
build
w
ith G
M
X
_BUILD
_
UNIT
T
ESTS=O
F
F
commit
|
commitdiff
|
tree
2014-01-15
Teemu Murtola
Suppo
r
t
f
or 64
-
bit int an
d
re
a
l valued Opt
i
ons
commit
|
commitdiff
|
tree
2014-01-15
Teemu Murtola
Remove unused PCA_KEEP_A
R
G
S
commit
|
commitdiff
|
tree
2014-01-15
Ro
l
and Schulz
Add nb
n
x
n
tree forc
e
reduc
t
ion
commit
|
commitdiff
|
tree
2014-01-15
T
e
emu Murtola
Si
m
plify C array handling
in C++ code
commit
|
commitdiff
|
tree
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