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Merge "Merge branch release-4-6 into release-5-0" into release-5-0
2014-02-20
Roland Schulz
Fi
x
Reference B
u
i
l
d
commit
|
commitdiff
|
tree
2014-02-20
Teemu Murto
l
a
Add documentation for
using Doxygen
commit
|
commitdiff
|
tree
2014-02-19
Mark
Abraham
Ma
k
e some va
r
iable names l
e
ss cryptic
commit
|
commitdiff
|
tree
2014-02-18
Ma
r
k Abraham
Fi
x
har
m
less b
u
g
with combination of group
a
nd twin
.
.
.
commit
|
commitdiff
|
tree
2014-02-17
Ro
l
and Schulz
Enable
m
ore warnings
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
Small en
h
ancem
e
nt of c
o
mp
u
tational electrophysi
o
logy
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Teemu Murtola
Improve man p
a
g
e
form
a
tting sl
i
g
h
t
l
y
commit
|
commitdiff
|
tree
2014-02-16
Teemu Murto
l
a
F
ix
default enum values
i
n help
o
utput
commit
|
commitdiff
|
tree
2014-02-13
M
a
g
nus Lu
n
dborg
Removed option to use
O
penMP with
the
TNG
libra
r
y
.
commit
|
commitdiff
|
tree
2014-02-12
Mark Abr
a
ham
Re-fix compiler warnings with sc
a
nner
.
cpp
commit
|
commitdiff
|
tree
2014-02-11
Mark
A
b
rah
a
m
Split genbox into '
s
olvat
e
' and 'insert-mol
e
c
ules'
commit
|
commitdiff
|
tree
2014-02-11
Dav
i
d
van der Spoe
l
Fixed another vmdio
issue
.
commit
|
commitdiff
|
tree
2014-02-11
Erik Lindahl
First part of
c
ommit
f
o
r
r
edesig
n
ed SIM
D
module - namecha
n
ges
.
commit
|
commitdiff
|
tree
2014-02-11
Magnu
s
Lundborg
A
d
de
d
i
n
for
m
ation
a
bo
u
t h
o
w to cite t
h
e
T
NG paper
.
commit
|
commitdiff
|
tree
2014-02-09
Mark Abraham
Move
orient
a
tio
n
r
estraints checks
inside init function
commit
|
commitdiff
|
tree
2014-02-09
Tee
m
u Murtola
Refac
t
or new
help formatting implementatio
n
commit
|
commitdiff
|
tree
2014-02-08
Mar
k
Abraham
Clean up
.
log file dump of inputrec
commit
|
commitdiff
|
tree
2014-02-08
Mark Abraham
I
ssue fa
t
al errors
rath
e
r than
u
se b
r
oken shell code
commit
|
commitdiff
|
tree
2014-02-08
Teemu
M
urtol
a
Fix & upd
a
te docs for GMX_
T
ES
T
_O
P
TIONS
commit
|
commitdiff
|
tree
2014-02-07
Mar
k
Abraham
Initialize inp
u
tre
c
b
e
tter in
g
e
nbox
commit
|
commitdiff
|
tree
2014-02-06
T
eemu Murtola
Fix b
u
ild o
f
share/template when insta
l
le
d
commit
|
commitdiff
|
tree
2014-02-06
Mic
h
ael Shirts
EE dhdl header
should not spe
c
ify one lambda
commit
|
commitdiff
|
tree
2014-02-06
Mark Abr
a
ham
Re
m
ove antiquated and
unu
s
ed gmx
p
ar
.
tex documen
t
ation
commit
|
commitdiff
|
tree
2014-02-06
Roland Schulz
Use rand
o
m
seeds by def
a
ul
t
commit
|
commitdiff
|
tree
2014-02-05
Mark Abraha
m
Upd
a
t
e des
c
ription
o
f g
e
nrestr
commit
|
commitdiff
|
tree
2014-02-04
Ro
l
a
n
d Schu
l
z
Fix and simpl
i
fy
r
p
ath
commit
|
commitdiff
|
tree
2014-02-03
Mark Abraha
m
Clean up genbox and associat
e
d code
commit
|
commitdiff
|
tree
2014-02-03
T
e
em
u
M
u
rt
o
la
Merge "Merge
r
e
l
ea
s
e-4-6 into mas
t
e
r
"
commit
|
commitdiff
|
tree
2014-02-03
T
eemu Murtola
Optimize
D
oxygen build
commit
|
commitdiff
|
tree
2014-02-03
Ma
r
k Ab
r
aham
Im
p
roved wallc
y
cle reporting
commit
|
commitdiff
|
tree
2014-02-02
Teemu
M
urt
o
la
Fix
s
egfault in 'gmx -
h
'
commit
|
commitdiff
|
tree
2014-02-02
T
ee
m
u Murtola
G
et
r
id of src/progra
m
s/g
m
x/
commit
|
commitdiff
|
tree
2014-02-02
T
eemu M
u
rtol
a
Sim
p
l
ify Optio
n
s
::se
t
De
s
cripti
o
n(
)
usag
e
commit
|
commitdiff
|
tree
2014-02-01
Tee
m
u Murt
o
la
Fix some is
s
u
e
s
re
p
ort
e
d by 'make depcheck d
o
ccheck'
commit
|
commitdiff
|
tree
2014-01-31
Teem
u
Mu
r
t
o
la
O
verview
d
ocs for u
n
it t
e
stin
g
commit
|
commitdiff
|
tree
2014-01-30
Roland
S
chulz
A
d
d cm
a
ke o
p
tion
for Re
f
e
r
enc
e
ke
r
nel
commit
|
commitdiff
|
tree
2014-01-30
Mark Abraham
Minor improve
m
ents
to ewald_LRcorrection
commit
|
commitdiff
|
tree
2014-01-30
Berk Hess
Mad
e
reference SIMD work again
commit
|
commitdiff
|
tree
2014-01-30
Teemu Murtola
Fix s
h
e
l
l c
o
mplet
i
ons of ffMULT
o
ptions
commit
|
commitdiff
|
tree
2014-01-30
Teemu Mu
r
tola
Ref
a
ctor Prog
r
amInfo use
commit
|
commitdiff
|
tree
2014-01-30
Ros
s
en Apostolov
Rem
o
ved ion
s
.
i
tp from
GMX/share/top directo
r
y
.
commit
|
commitdiff
|
tree
2014-01-30
Teemu Murtola
Move
command listing to 'gm
x
hel
p
command
s
'
commit
|
commitdiff
|
tree
2014-01-30
R
o
land Schulz
Allo
c
ate me
m
ory
f
or MD5 on heap
commit
|
commitdiff
|
tree
2014-01-29
Ma
r
k Abraha
m
Improv
e
d depe
n
dencies on maths inc
l
udes
commit
|
commitdiff
|
tree
2014-01-29
Teemu Murtola
Fixes to filename s
h
ell c
o
m
p
letions
commit
|
commitdiff
|
tree
2014-01-29
Ro
l
and Schulz
Uncrusti
f
y all files
commit
|
commitdiff
|
tree
2014-01-29
Be
r
k Hess
Automated Ve
r
l
et rlist
f
or NVE sim
u
lations
commit
|
commitdiff
|
tree
2014-01-29
Teemu
M
urto
l
a
Merge
"
M
e
rge br
a
nch
'release-
4
-6'"
commit
|
commitdiff
|
tree
2014-01-28
D
avid van der Spoel
Moved r
a
n
d
om number
g
enerator code
t
o s
e
parat
e
dir
.
commit
|
commitdiff
|
tree
2014-01-28
Car
s
ten Kutz
n
er
Al
l
ow for "computational elect
r
ophysiology" s
i
mulation
s
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Christoph
Jun
g
han
s
c
m
ak
e
: added FF
T
W_URL to allow e
a
sy offline b
u
ild
commit
|
commitdiff
|
tree
2014-01-28
Rossen Apostolov
Bump own fftw bu
i
ld t
o
version 3
.
3
.
3
commit
|
commitdiff
|
tree
2014-01-28
Mark Abraham
R
em
o
ve "gmx tr
j
conv -app"
commit
|
commitdiff
|
tree
2014-01-28
Teemu Murtola
Shell compl
e
tion export from the wrapper bina
r
y
commit
|
commitdiff
|
tree
2014-01-28
Mark A
b
raham
Unify logic for timing counts
commit
|
commitdiff
|
tree
2014-01-28
Szilárd Páll
clar
i
fied OpenMP-rel
a
ted things i
n
mdrun help/man
commit
|
commitdiff
|
tree
2014-01-28
Tee
m
u
Mur
t
ol
a
Extend
version
inf
o
r
ma
t
ion ou
t
put
commit
|
commitdiff
|
tree
2014-01-27
Teemu Murtola
Simpli
f
y ProgramInfo
commit
|
commitdiff
|
tree
2014-01-23
Mark Abraham
Break dependency of fileio on t
o
ols
commit
|
commitdiff
|
tree
2014-01-22
Mark Abraham
Update libxml2 CMake
d
e
tectio
n
commit
|
commitdiff
|
tree
2014-01-21
Rosse
n
Apostolov
Fi
x
ed wrong messa
g
e when buil
d
i
ng own FFTW
.
commit
|
commitdiff
|
tree
2014-01-21
Rol
a
nd Sch
u
lz
F
i
x race
c
ondi
t
ions
commit
|
commitdiff
|
tree
2014-01-21
Mark Abra
h
am
Ensu
r
e we don'
t
#
d
efine const
a
nts before
s
ystem headers
commit
|
commitdiff
|
tree
2014-01-21
Justin Lemkul
Added ASPP and G
L
UP
t
o
r
esi
d
ue
t
ypes
.
dat
.
commit
|
commitdiff
|
tree
2014-01-21
Teemu Murtola
Imp
r
ove
f
ile na
m
e
o
p
t
i
on h
e
lp
commit
|
commitdiff
|
tree
2014-01-20
Te
e
mu Murtola
Rewri
t
e
help output from
O
pt
i
ons
commit
|
commitdiff
|
tree
2014-01-20
Mark Abraham
Fix
.
giti
g
nore of
s
ome files
commit
|
commitdiff
|
tree
2014-01-19
Teemu Murt
o
l
a
Fix installe
d
headers
commit
|
commitdiff
|
tree
2014-01-19
T
eem
u
Mur
t
ola
Move md5
.
* to fileio/
commit
|
commitdiff
|
tree
2014-01-19
T
eemu Murtola
Mov
e
strdb
.
* to
src/gromacs/fileio/
commit
|
commitdiff
|
tree
2014-01-19
M
a
rk Abrah
a
m
Move dum
p
,
check and
t
p
bconv utili
t
ies
commit
|
commitdiff
|
tree
2014-01-19
Roland Schulz
Fi
x
that check_l
i
brar
y
_
e
xist is rerun
f
o
r
FF
T
W
commit
|
commitdiff
|
tree
2014-01-18
D
avid v
a
n der Spo
e
l
T
h
is p
a
tch moves the
s
tatistics lib
r
a
r
y
t
o its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
Mark Abra
h
a
m
Fix,
simplify
and test XTC wr
i
ti
n
g
commit
|
commitdiff
|
tree
2014-01-17
David van der
S
poel
Thi
s
patch moves p
r
eprocessing hea
d
e
r
s
to gmx
p
reprocess
commit
|
commitdiff
|
tree
2014-01-17
R
ola
n
d Sc
h
ulz
Defi
n
e MPI_I
N
T64_T if not d
e
fi
n
ed
b
y mp
i
commit
|
commitdiff
|
tree
2014-01-17
Mark
Abraham
C
l
ean up inp
u
trec reading
commit
|
commitdiff
|
tree
2014-01-16
Teemu M
u
rtola
Fix bui
l
d
w
ith GMX_BUILD_UNITTESTS=OFF
commit
|
commitdiff
|
tree
2014-01-15
Teemu M
u
rtola
Support for 64-bit int and real va
l
ued Options
commit
|
commitdiff
|
tree
2014-01-15
Teemu M
u
rt
o
la
R
emove unused PC
A
_K
E
EP
_
ARGS
commit
|
commitdiff
|
tree
2014-01-15
Roland Schulz
Add nbnxn
t
r
ee force reduct
i
on
commit
|
commitdiff
|
tree
2014-01-15
Teemu Murtola
S
i
mplify
C
array handling in C++
c
ode
commit
|
commitdiff
|
tree
2014-01-15
D
a
v
id
v
a
n
d
er Sp
o
el
This
p
atch m
o
v
e
s the nrama
.
[ch] to the g
m
xana
d
ir
.
commit
|
commitdiff
|
tree
2014-01-15
T
e
em
u
Murtola
Reo
r
g
a
n
i
ze shared unit test code
commit
|
commitdiff
|
tree
2014-01-14
Ma
r
k Abraham
Stop doing
cppche
c
k on
src/external
commit
|
commitdiff
|
tree
2014-01-14
Teem
u
Murtola
Don't in
s
t
a
ll li
n
ks
.
d
a
t
commit
|
commitdiff
|
tree
2014-01-14
Teemu Mur
t
ola
Split
CommandLineHelpModule in
t
o a
se
p
arate file
commit
|
commitdiff
|
tree
2014-01-14
Teemu Murtola
Fix line wrapping for long options
commit
|
commitdiff
|
tree
2014-01-14
Mark Abra
h
am
Remo
v
e
usel
e
s
s
trj
c
at -prec
o
pti
o
n
commit
|
commitdiff
|
tree
2014-01-13
Ca
r
sten Ku
t
z
n
er
M
o
ve pul
l
c
ode to separate subdirectory
commit
|
commitdiff
|
tree
2014-01-13
T
e
e
mu Murtola
Move wr
i
tep
s
.
* into
fileio/
commit
|
commitdiff
|
tree
2014-01-13
Teemu Mur
t
ola
Move gmxcomplex
.
h
to gromac
s
/math/
commit
|
commitdiff
|
tree
2014-01-13
Mark Ab
r
aham
Fix
m
drun in
t
egration tests
commit
|
commitdiff
|
tree
2014-01-13
Teemu Murtola
Fix i
n
stallation of HTML man
u
al
commit
|
commitdiff
|
tree
2014-01-13
David van der Spoel
Cl
e
aned u
p
list of GROMACS author
s
commit
|
commitdiff
|
tree
2014-01-11
Car
s
ten Kutzner
M
ove essential dynamics / fl
o
od
i
n
g code t
o
s
e
para
t
e
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten K
u
tzner
Read
e
ssent
i
al dyna
m
i
c
s data from checkpoin
t
at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-09
Jochen H
u
b
Fixed n
o
n-working flat-bottom
posres c
o
d
e
.
commit
|
commitdiff
|
tree
2014-01-09
David van der Spoel
Fixed preci
s
i
on in therm
a
l expan
s
ion coefficien
t
c
a
l
c
.
commit
|
commitdiff
|
tree
2014-01-09
Roland Schulz
Add SIMD support for Intel MIC
commit
|
commitdiff
|
tree
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