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New and reorganized documentation
2014-11-26
Chris
t
oph Junghans
Merge release-5-0 into master
commit
|
commitdiff
|
tree
2014-11-21
C
h
ristoph Junghans
A
d
ded
.
t
r
avis
.
y
ml
commit
|
commitdiff
|
tree
2014-09-04
Chris
t
oph Junghans
cmake: missing quote
commit
|
commitdiff
|
tree
2014-03-11
C
h
r
i
stoph J
u
nghans
Install enums
.
h
commit
|
commitdiff
|
tree
2014-03-01
Christoph J
u
nghans
s
witc
h
ld_seed from int
t
o gmx_int64_t
commit
|
commitdiff
|
tree
2014-02-20
Christo
p
h J
u
nghans
added gmx_is
_
{
single,double
}
_prec
i
sion
commit
|
commitdiff
|
tree
2014-02-03
C
h
ristoph Jung
h
ans
cmak
e
eats slashes
commit
|
commitdiff
|
tree
2014-01-28
C
hr
i
s
toph
J
u
n
g
hans
cmake:
added FFT
W
_URL
to
a
l
low easy offline
b
uild
commit
|
commitdiff
|
tree
2013-12-29
C
h
risto
p
h Junghans
cmake: make
G
M
X
_BUI
L
D_OWN_FFTW work without fortran
.
.
.
commit
|
commitdiff
|
tree
2013-12-20
Chr
i
sto
p
h Junghans
re-a
d
d
Carsten &
m
e to
t
he copy
r
ite
commit
|
commitdiff
|
tree
2013-10-03
Christo
p
h Ju
n
ghans
Fi
x
parallel
b
uild for GMX
_
BUIL
D
_
O
WN_
F
FTW
commit
|
commitdiff
|
tree
2013-09-26
Chris
t
o
p
h Junghans
Drop md5sum check fo
r
GMX_BUILD_OWN
_
FFTW
commit
|
commitdiff
|
tree
2013-07-30
Christoph Junghans
cmake: Im
p
rove some error messages
commit
|
commitdiff
|
tree
2013-07-06
Ch
r
istoph Junghans
more
pkg-config fixes
commit
|
commitdiff
|
tree
2013-07-04
Chris
t
oph Junghans
F
i
xed
some inconsist
e
n
c
ie
s
i
n pkg-
c
onfi
g
f
ile
s
commit
|
commitdiff
|
tree
2013-05-15
Christoph Ju
n
ghans
Merge "fi
x
ed incorre
c
t scal
i
ng of c
o
s-accelerat
i
on
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Christoph Junghans
improve b
u
ild with OpenMM, sti
l
l no
t
100% f
i
xed
commit
|
commitdiff
|
tree
2013-04-29
Christo
p
h Junghans
Mer
g
e "Fix anot
h
e
r
bug
in se
l
ection sube
x
pression ha
n
dling
.
"
commit
|
commitdiff
|
tree
2013-04-29
Chr
i
stoph
J
unghans
Merge "Fix bug
i
n
selection
subexpression h
a
nd
l
ing
.
"
commit
|
commitdiff
|
tree
2013-04-26
Chris
t
o
ph Junghans
Merge "v-r
e
sca
l
e works with tau-t >= 0
"
into
release-
4
-
6
commit
|
commitdiff
|
tree
2013-04-16
Chr
i
s
t
oph Jung
h
ans
Use git snapshots of
t
he tests if are on git
commit
|
commitdiff
|
tree
2013-03-29
Christ
o
ph Junghans
Me
r
ge "Added
install guide s
e
ction for BLAS/LA
P
ACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
Christoph Junghans
Merge "Essen
t
ial dynami
c
s
: fixed
legend i
n
ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-02
Christoph Jungh
a
n
s
Merge "Un
c
rustified
c
ode changes sin
c
e 4
.
6" in
t
o release-4-6
commit
|
commitdiff
|
tree
2013-02-26
Chr
i
stoph Jungha
n
s
Merge "Merge
rel
e
ase-4-6
i
nto master"
commit
|
commitdiff
|
tree
2013-02-20
Christop
h
Junghans
Bump shared o
b
ject
v
ersi
o
n
t
o
8
commit
|
commitdiff
|
tree
2013-02-12
Christoph J
u
n
ghans
Up
d
ated FindGSL
.
c
m
a
ke to
v
ersion written by me
.
commit
|
commitdiff
|
tree
2013-02-05
Chri
s
toph Junghans
Merge "Docu
m
ented what
G
MX_CPU_ACCELERAT
I
O
N
really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph Junghans
improve set
u
p
of
multipl
e
tf
t
abl
e
s
commit
|
commitdiff
|
tree
2013-02-02
Christoph
J
unghans
Fi
x
ed flop
counting fo
r
g
e
neri
c
cg/adress ke
r
ne
l
s
commit
|
commitdiff
|
tree
2013-02-02
Christop
h
Junghans
cmake: fixed typo in templat
e
C
M
akeLi
s
ts
.
txt
commit
|
commitdiff
|
tree
2013-01-25
C
h
r
i
stoph
Ju
n
ghans
fixed copy
r
ight
o
f a
d
ress ker
n
el
commit
|
commitdiff
|
tree
2013-01-25
Christop
h
J
u
nghans
Merge "M
o
ved a
f
ew comments back into position" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-21
Chris
t
o
p
h Jung
h
ans
M
erge "S
e
t
v
ersi
o
n
info for
4
.
6
.
x
r
elease seri
e
s" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-19
Chris
t
oph
Ju
n
ghans
Re-li
c
enced Fi
n
dGR
O
M
A
C
S
.
cma
k
e (was written by me
)
commit
|
commitdiff
|
tree
2013-01-17
Christoph Jun
g
hans
Merge "Adde
d
note about make_edi and flood
i
ng
i
n ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Chri
s
toph Junghans
M
e
rge "u
s
e the compiler vers
i
on provided by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ch
r
isto
p
h
Jungha
n
s
Mer
g
e "note
t
h
e
re
a
son for auto-d
i
sabling GPU
s
upport
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph J
u
nghans
clean
u
p f
o
rtran name mangling
commit
|
commitdiff
|
tree
2013-01-16
Ch
r
istoph
J
unghan
s
Rem
o
v
e
debug statme
n
t
commit
|
commitdiff
|
tree
2013-01-15
Christoph Jung
h
ans
Merge "A
d
ded fatal error for constraints
+ L
-
BFGS minimiz
e
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
C
h
ri
s
toph Junghans
M
erge "di
s
able OpenMP with all OS
X gcc 4
.
2-b
a
s
ed compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Christoph
J
unghans
Me
r
ge
"Remove unused bf
u
nc
.
h
.
" i
n
to re
l
e
a
se-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph
J
u
nghans
Merge "Clarifi
e
d some comments & warnings ab
o
ut thread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
C
h
ristoph Junghans
Merge "Ma
n
a
ge BlueGene/Q configuration" into r
e
lease
-
4
-6
commit
|
commitdiff
|
tree
2013-01-13
C
hristoph Junghans
Merge
"Re-organ
i
ze Blue
G
ene toolchain files
"
into release
-
4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Jung
h
ans
M
e
r
ge "Changed def
a
u
l
ts for
building shar
e
d
l
i
b
rari
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Ch
r
istoph Junghans
Me
r
ge "Added missi
n
g export
"
into
relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-01-11
C
h
r
istoph
Junghans
Merge "
c
onsole an
d
log output i
m
p
r
o
vements
"
i
nto relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
i
stoph Jun
g
hans
Merge "Fix CU
D
A
being quiet and m
a
rk all CUDA_* a
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Chris
t
oph
Junghans
Merge
"Remove incor
r
ect assert a
d
d
e
d b
y
05f9a7
4
0" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Christoph Junghans
cmake: re
m
ove dou
b
le-
n
egative quotes
l
ogic
commit
|
commitdiff
|
tree
2013-01-07
Christop
h
Jung
h
ans
Merge "Make gmx_cp
u
id
.
h
s
e
lf-standing
.
" into r
e
l
e
a
s
e
-4-6
commit
|
commitdiff
|
tree
2013-01-03
Chri
s
toph
J
ung
h
ans
add
an opti
o
n to n
o
t build
t
he temp
l
a
te
commit
|
commitdiff
|
tree
2013-01-03
Christoph Junghans
A
dd missing def
i
nes to PKG_
C
FLAGS
commit
|
commitdiff
|
tree
2013-01-03
Christoph Ju
n
ghans
Merge "R
e
move non-functional
P
owerP
C
invsqrt
.
"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Christop
h
Junghans
cm
a
k
e: add option to inst
a
ll libmd as
l
ibgmxmd
commit
|
commitdiff
|
tree
2012-12-22
Christo
p
h Jung
h
ans
cmake: mark F
F
TW_
H
AVE_{
S
IMD,A
V
X} as
a
dvanced
commit
|
commitdiff
|
tree
2012-12-21
Chris
t
oph
J
unghan
s
Me
r
ge
"Remove non-fu
n
ctional compiler override
for
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
C
hristoph Junghans
Merge "F
i
x
e
d AVX256 double-precision kernels
for gcc
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Christoph J
u
n
g
hans
cmake: added
option to disable quotes
commit
|
commitdiff
|
tree
2012-12-18
Christoph Ju
n
g
h
ans
Merge
"Fixes redmine i
s
su
e
#
1
071
"
in
t
o release-4
-
6
commit
|
commitdiff
|
tree
2012-12-17
C
h
r
i
stoph J
u
nghans
Remove
t
he rest of t
h
e for
t
ran/po
w
er6 acceleration
commit
|
commitdiff
|
tree
2012-12-13
Chr
i
s
t
oph
J
unghans
Merge "Extende
d
genbox to inse
r
t
mo
l
ecu
l
es at given
.
.
.
commit
|
commitdiff
|
tree
2012-12-13
Christoph J
u
nghan
s
Al
w
ays build template
program
commit
|
commitdiff
|
tree
2012-12-11
Christo
p
h Jungha
n
s
Merge "Fix c
o
mpilation wi
t
h
P
GI" into
r
elease-4-6
commit
|
commitdiff
|
tree
2012-12-10
C
h
r
i
stoph Jungh
a
ns
M
erge "force C++ li
n
king of
the gpu_utils" in
t
o release-4-6
commit
|
commitdiff
|
tree
2012-12-05
C
hristoph Junghans
fixed obsolete gm
x
_fatal in OpenMM b
u
ild
commit
|
commitdiff
|
tree
2012-11-29
Christoph Junghans
Merge "Print error if
n
o
th
r
ead support i
s
a
v
ail
a
ble
.
.
.
commit
|
commitdiff
|
tree
2012-11-28
Christ
o
ph
J
un
g
han
s
Merge "Fix
cpa
c
k src i
g
n
ore
rule" into releas
e
-
4
-6
commit
|
commitdiff
|
tree
2012-11-28
Chri
s
toph Junghans
Add option to inter
n
ally buil
d
F
F
TW if select
e
d
commit
|
commitdiff
|
tree
2012-11-22
C
h
risto
p
h Junghans
improve FindGROM
A
CS
.
cmak
e
commit
|
commitdiff
|
tree
2012-11-20
Christoph Jung
h
ans
Mer
g
e "Fix
g
_msd -mol"
into releas
e
-
4
-
6
commit
|
commitdiff
|
tree
2012-11-20
Christoph
Jung
h
ans
Merge "Fi
x
es bug in
g_hb
o
n
d th
a
t
m
akes
i
t
produce fatal
.
.
.
commit
|
commitdiff
|
tree
2012-11-16
Chris
t
o
p
h
Junghans
R
emove rest o
f
t
h
e xm
l
suppor
t
commit
|
commitdiff
|
tree
2012-11-15
Christoph Junghans
Me
r
ge
"
Test
t
hat compiling
a
nd link
i
n
g
o
f AVX works
.
.
.
commit
|
commitdiff
|
tree
2012-11-12
Chris
t
o
ph Junghans
Me
r
ge "Option to create symli
n
ks to g_ana
.
"
commit
|
commitdiff
|
tree
2012-11-12
Christoph J
u
nghans
M
e
r
ge "Alw
a
ys
use relative install pat
h
s
.
"
commit
|
commitdiff
|
tree
2012-11-08
Ch
r
i
s
t
oph
J
unghan
s
Merge "auto-
s
e
t nvcc hos
t
compil
e
r with FindMPI
det
e
ction
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
C
h
r
i
stoph Junghans
Me
r
g
e
"Relo
c
ated logic of simple-vs-GPU Ewald table
.
.
.
commit
|
commitdiff
|
tree
2012-11-07
C
h
ristop
h
Jung
h
ans
O
bey
DSO s
t
andar
d
commit
|
commitdiff
|
tree
2012-11-03
Chr
i
st
o
ph Junghans
R
e
w
o
rked version of c
m
ake FFTW dete
c
t
i
on
commit
|
commitdiff
|
tree
2012-11-01
Christo
p
h Jung
h
ans
Act
u
ally di
s
able
GPU when compiling in double
commit
|
commitdiff
|
tree
2012-10-27
Christoph Junghans
Mer
g
e
"Fix la
r
ge file supp
o
rt" into
release-4-
5
-pa
t
ches
commit
|
commitdiff
|
tree
2012-10-26
Christoph Jung
h
a
n
s
Merge "enabl
e
GMX_
P
R
EFER_
S
TATIC_LIBS CMake option on
.
.
.
commit
|
commitdiff
|
tree
2012-10-26
Christoph
J
u
ngha
n
s
M
e
r
ge
"
fix false posi
t
ive gcc 4
.
7 warning
in libx
d
rf
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Ch
r
i
stoph
J
u
ngha
n
s
f
i
xed header for
3rd par
t
y apps
commit
|
commitdiff
|
tree
2012-10-02
Christop
h
Ju
n
ghans
Merge "Merge
r
elease-4-6 int
o
master"
commit
|
commitdiff
|
tree
2012-09-27
Christ
o
ph
J
u
nghans
Merge "
F
ixed an off-
b
y
-one
error
in at
o
m cou
n
tin
g
in
.
.
.
commit
|
commitdiff
|
tree
2012-09-25
Christoph J
u
nghan
s
Mer
g
e
"Fix
REMD use of gmx_large_int_t
f
or
#
steps variable
.
.
.
commit
|
commitdiff
|
tree
2012-09-14
Ch
r
istoph Jung
h
ans
Merge
"
fixed rec
e
nt bug with grompp check for
P
-R
P
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Christo
p
h Junghans
updated references
commit
|
commitdiff
|
tree
2012-09-10
C
hrist
o
ph Junghans
Merge "Al
l
o
w
'atomname' and 'atomtype' in
s
elections
.
"
commit
|
commitdiff
|
tree
2012-09-07
Christoph Ju
n
gha
n
s
Mer
g
e
"Fix
VMD plugi
n
s on
W
indows" into r
e
lease
-
4-6
commit
|
commitdiff
|
tree
2012-09-07
Christoph Junghans
M
e
rge "Check
th
a
t
gm
x
_de
t
ectcpu
r
uns correc
t
l
y
" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-09-04
Christop
h
Junghans
Merge "Fixes too many backup f
i
les for *
.
nroff fil
e
s
.
.
.
commit
|
commitdiff
|
tree
2012-09-04
Christoph Jungha
n
s
Merge "Reorga
n
ize Comm
a
ndLi
n
eHelp
W
riter im
p
lemen
t
ation
.
"
commit
|
commitdiff
|
tree
2012-09-04
C
hri
s
toph
Jung
h
a
ns
Merg
e
"Fix SelectionParse
r
Par
a
m
e
ter move const
r
uctor
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Christop
h
Jungh
a
ns
Merge "Fixing of t
h
i
n
gs associa
t
e
d
with aminoa
c
id
.
rtp
.
.
.
commit
|
commitdiff
|
tree
2012-08-20
Christoph Ju
n
ghan
s
Me
r
ge "Clean up
s
ome var
i
a
ble na
m
ing for e
i
gensolvin
g
.
.
.
commit
|
commitdiff
|
tree
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