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Merge "Remove MPI define for FAH" into release-4-6
2012-06-24
Christ
o
ph Junghans
Me
r
ge "Re
m
o
v
e
MPI def
i
ne for FAH" into rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-06-24
Michael Shirts
Merge
"
Fix mdp_o
p
t formatting o
f
expanded ens
e
mble
.
.
.
commit
|
commitdiff
|
tree
2012-06-23
Rolan
d
Schulz
Fix illegal
usage of MPI_Comm_c
r
e
a
te
commit
|
commitdiff
|
tree
2012-06-22
Christoph Junghans
Merge "Simple
pat
c
h f
o
r openm
m
_
wrapper
.
c
p
p" into release-4-
6
commit
|
commitdiff
|
tree
2012-06-18
Martin Hoe
f
lin
g
gmx_dyecoupl: check se
l
e
c
t
e
d groups from use
r
commit
|
commitdiff
|
tree
2012-06-01
Christoph
Ju
n
ghans
Mer
g
e "Use External BLAS/L
A
PACK by
def
a
ult" into relea
s
e
-
4
-6
commit
|
commitdiff
|
tree
2012-06-01
Christ
o
ph J
u
nghans
Me
r
ge
"
R
e
place our
f
ftpack version with Numpy'
s
versio
n
.
.
.
commit
|
commitdiff
|
tree
2012-05-29
Sa
n
der P
r
on
k
Re
m
oved dependency on windows
.
h
t
hrough commrec
.
h,
.
.
.
commit
|
commitdiff
|
tree
2012-05-29
Christop
h
Junghans
Merge "Revised g_tune
_
pme"
into
r
elease-4-6
commit
|
commitdiff
|
tree
2012-05-28
Christ
o
ph Jun
g
ha
n
s
M
e
rge
"
C
ontinu
i
ng to fix
t
hreading on Cy
g
win" into
.
.
.
commit
|
commitdiff
|
tree
2012-05-27
David van der S
p
oe
l
Merge "added explici
t
s
q
rtf t
o
the float
v
e
r
s
i
on
of
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
Ro
l
an
d
Schulz
Make loa
d
_vm
d
_library st
a
tic
commit
|
commitdiff
|
tree
2012-05-25
Roland Schulz
Made all
v
md
i
o head
e
rs priva
t
e
commit
|
commitdiff
|
tree
2012-05-25
Roland
Sch
u
lz
M
erge "fixed
[
dd] and [TT]
t
yp
o
s in documen
t
ation of
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
David v
a
n der Sp
o
e
l
M
erge "g
r
o
m
p
p n
o
w retains
the order of
b
o
n
ds c
o
nv
e
rted
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
Christoph Ju
n
ghans
Merge
"Fix
t
ha
t
sig
a
ction mask wasn't zeroed
"
int
o
.
.
.
commit
|
commitdiff
|
tree
2012-05-24
Teemu Mu
r
tol
a
Merge "
C
ode cleanup
t
o avoid n
a
me collisions" into
.
.
.
commit
|
commitdiff
|
tree
2012-05-17
Teemu Murtola
Merg
e
"Fixing
m
o
re clang warnin
g
s" int
o
r
e
lease-4-6
commit
|
commitdiff
|
tree
2012-05-09
Christoph
J
unghans
M
e
rge "Ba
c
kp
o
rting "m
o
vin
g
membed to mdrun
"
f
r
om ma
s
t
er
.
.
.
commit
|
commitdiff
|
tree
2012-05-01
Roland
S
ch
u
lz
Mer
g
e
"Disable OpenMP fo
r
llvm-gcc 4
.
2
.
x" into relea
s
e
-4-6
commit
|
commitdiff
|
tree
2012-04-29
D
a
vid van der Spoel
Merge "changed number of ia
t
o
m
s
for
F
_SETTLE
f
rom 1
.
.
.
commit
|
commitdiff
|
tree
2012-04-29
D
avid
v
an der Spoel
M
erge "add
e
d support for graphs not startin
g
at 0"
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Teemu Murtola
Merge "Fix for sigaction" into
r
e
l
ease-4-6
commit
|
commitdiff
|
tree
2012-04-28
Mark Abraham
M
e
rge "Remove checks
b
a
s
ed on Genera
t
o
r" into r
e
lea
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Mark Abraham
Merge "Fix version info gene
r
ation for aut
o
co
n
f
.
" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
Merge
"Merge r
e
lease
-
4-
5
-pa
t
ches i
n
t
o r
e
le
a
se-
4
-6"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
D
avid v
a
n der Spoel
Merge
"
[
t
ools] g_sans - splited out fixes and a
d
d
e
d
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Szilá
r
d
Pál
l
Merge "fixed initial CO
M
motion rem
o
v
a
l w
i
th mul
t
i
ple
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
David
van der
S
poel
Merge "
V
arious improv
e
ments to shell co
d
e"
into re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2012-04-24
Ber
k
Hess
Merge "
a
llow -app
e
nd to
ove
r
rule unsupported fi
l
e lo
c
king
.
.
.
commit
|
commitdiff
|
tree
2012-04-23
C
h
r
i
s
toph Jung
h
ans
Merge "compiler fla
g
fixes" into release-4-6
commit
|
commitdiff
|
tree
2012-04-22
R
oland Schulz
Merge "enable command line option
c
h
e
k
i
ng in mdrun
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
Roland Schulz
M
erge "changed defa
u
l
t for
n
stxou
t
,
nstvou
t
and nstlog
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
R
o
land Schul
z
Merge
"
che
c
kpoint fil
e
s n
o
w contain a do
u
ble prec
i
si
o
n
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
Dav
i
d van der
S
po
e
l
Merg
e
"Added support for dssp2
.
X
with
the -ver
option
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
D
a
vid van der Spoel
Merge "E
x
p
anded t
h
e hel
p
te
x
t regarding the
-
r
2
and
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
S
a
nder P
r
onk
Me
r
ge "Permit th
r
ead
s
build o
n
Cyg
w
in" into release
.
.
.
commit
|
commitdiff
|
tree
2012-04-14
T
e
emu Mur
t
o
la
Me
r
ge "Clarified war
n
ing messa
g
e" into release-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-04-14
Teemu
M
urtola
M
e
rge "Clarified wa
r
n
ing
s
t
ring" into release-4-
5
-p
a
tches
commit
|
commitdiff
|
tree
2012-04-09
Ch
r
is
t
oph Junghans
Merge "Doc
u
menta
t
io
n
and error messa
g
e enhancements
.
.
.
commit
|
commitdiff
|
tree
2012-04-09
Chris
t
oph Junghans
M
e
rge "Consolid
a
ted d
o
cume
n
t
ation of
.
mdp restraint
.
.
.
commit
|
commitdiff
|
tree
2012-04-03
Roland Schulz
M
erge "Fixes problems
with g
_
msd
and g_energy"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
David v
a
n
d
e
r
S
po
e
l
Merge "Improved pdb2
g
mx error
messa
g
e
"
into r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-03-28
Ch
r
is
t
oph
J
u
n
ghan
s
Merge "Resolvi
n
g
c
lang a
n
alyzer wa
r
nings in a
n
aly
s
is
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
C
hr
i
stoph Jungha
n
s
M
e
rge "Warnings aga
i
nst equilibrating with
P-R P
-
c
o
upling
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
David va
n
der Spoel
Mer
g
e
"Fi
x
typo i
n
Clan
g
CFlags"
i
nto release-4-5-p
a
tches
commit
|
commitdiff
|
tree
2012-03-18
David van der Spoel
Merge
"
Merge rele
a
se-4-5-p
a
tches into rele
a
se-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-03-15
Christoph Jun
g
hans
M
erge "Clarified wording of documentation"
i
nto re
l
eas
e
.
.
.
commit
|
commitdiff
|
tree
2012-03-13
Roland S
c
hulz
Me
r
g
e "mdru
n
-npme
with
o
ut PME or with PD now g
e
nerates
.
.
.
commit
|
commitdiff
|
tree
2012-03-13
Ch
r
i
stoph
J
u
ng
h
ans
Merge "Vibration
s
pect
r
a
from vel
o
city ACF
or No
r
m
al
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
Christoph Junghans
Merge "
M
o
r
e
editoria
l
fixe
s
to tool doc
u
m
entation"
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
Teem
u
Murtola
Merg
e
"
M
ade
d
es
c
ripti
o
n string for g_select
-selec
t
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
Roland Schul
z
Merg
e
"
Improve Fi
n
dF
F
TW" in
t
o rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-03-09
D
a
vid van der
S
poel
Merge "
I
mpro
v
ed cryptic error me
s
s
ag
e
" into rel
e
a
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
Carsten
Kutzner
Merge "Impr
o
v
ed wa
r
ning note with DD
an
d
per
i
odic mole
c
ules
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
David van
de
r
Spoel
Merge "Minimal support f
o
r
C
l
ang
"
i
nto rel
e
ase-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
David
v
an de
r
Spoel
Merge "Minor forma
t
ting
f
ixes to
.
md
p
o
ption
d
ocumentati
o
n
.
.
.
commit
|
commitdiff
|
tree
2012-02-21
Teemu Murtola
M
erge "
U
s
e Gi
t
server
(
mirror) to avoid fe
t
ching problems
.
.
.
commit
|
commitdiff
|
tree
2012-02-21
Christoph
Jun
g
h
ans
Me
r
ge "changed def
a
ult eps
i
lon-rf
value to 0" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-19
Berk Hess
Merge "Generate warnings for QMMM usage" into release-4-6
commit
|
commitdiff
|
tree
2012-02-15
Rola
n
d
S
chulz
Merge "Cmake: unite FindFFTW3* int
o
on
e
file" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-11
Szilárd Páll
Merge c
h
anges
I
f0
c
2f9d9,Ic2a
8
ad82 into release-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-10
Chri
s
t
o
ph
J
unghan
s
Merge "Fixed b
u
g
w
i
t
h
C
OM motio
n
r
e
moval on p
a
rt of
.
.
.
commit
|
commitdiff
|
tree
2012-02-08
Chr
i
s
t
oph Junghans
M
erge
"
fixed confusin
g
nonbonded kernel pointer initializati
.
.
.
commit
|
commitdiff
|
tree
2012-02-03
David
v
a
n
der Spoe
l
Merg
e
"Improved the
accuracy of the sd1
i
n
te
g
r
ator
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Szilárd Páll
Merge "Append all ICC Performance fla
g
s
o
nly to R
e
le
a
se
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Szilárd Páll
Merge
"
M
erges in threading br
a
nc
h
as o
n
e squashed c
o
mmit
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Teemu Mu
r
tola
M
erge "Rev
e
rt "Fix ICC on
W
i
n
dows Build"" i
n
to r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David
v
an der Spoel
Merg
e
"g_san
s
-
t
ool to comp
u
te SANS
s
pectra" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van
der Spoe
l
M
erge "Fixed erro
r
message to
i
de
n
tif
y
t
he correct
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
M
e
rge "F
i
x
e
d
trj
c
onv -s
u
b
"
into rele
a
se
-
4-5-patches
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
Merge "Improved
error
m
e
ssage" into re
l
ease-4-
5
-patc
h
es
commit
|
commitdiff
|
tree
2012-02-01
Chri
s
toph Junghans
Merg
e
"Fix signed/unsig
n
ed war
n
ings" into
re
l
ease-4
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Roland
S
ch
u
lz
R
e
ver
t
"
F
i
x
ICC
o
n Windows
B
u
i
ld"
commit
|
commitdiff
|
tree
2012-01-31
David van d
e
r Spoel
M
e
rge
"
Fix I
C
C on Windows B
u
ild" into re
l
ease-4-5-patches
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abr
a
ham
Merge "Correcte
d
use of
?
:
in cond
i
tion
a
l
"
into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Rola
n
d
Schulz
Merge "Merge release-4-5-patches in
t
o releas
e
-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Roland Sc
h
u
lz
Merge
"New appro
a
ch for
G
erritBuild script" i
n
to r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Ber
k
H
ess
Merge
"
Added two new bonded functions
.
" into release-4-6
commit
|
commitdiff
|
tree
2012-01-24
Sebasti
a
n
Fri
t
s
c
h
Merge "document AdR
e
sS mdp
o
ption
s
" into release-4
-
6
commit
|
commitdiff
|
tree
2012-01-20
Da
v
i
d van de
r
Spoel
Mer
g
e "Fix
e
d t
i
ming measurements
.
" into rele
a
se-4
-
5
.
.
.
commit
|
commitdiff
|
tree
2012-01-18
Rol
a
nd Schulz
Revert "Replace stder
r
by std
o
ut in editconf terminal
.
.
.
commit
|
commitdiff
|
tree
2012-01-15
Christop
h
Jung
h
ans
Merge "Added CMake
To
o
lc
h
ain file for BlueGene/P" into
.
.
.
commit
|
commitdiff
|
tree
2012-01-14
Mar
k
Abra
h
a
m
Me
r
ge "Remove u
s
e o
f
FindMPI
.
cmake" into
r
elease
-
4-6
commit
|
commitdiff
|
tree
2012-01-14
Mark
Abraham
Merge "Removing o
u
tdat
e
d vsite comment" into
rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-01-13
Ro
l
and Schulz
Merge "
F
ixed M
S
VC c
o
mpilin
g
with plug-in support"
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
Ch
r
is
t
oph Junghans
Merge "Documen
t
ed the function of g_cluster -cl -noav
.
.
.
commit
|
commitdiff
|
tree
2011-12-27
Roland S
c
hulz
Merge "A
d
ded -dhdl to tpr file list, fixes
#855" into
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Ro
l
and Sc
h
ulz
M
e
rge
"
U
s
ing
MinSizeRel
c
onfigura
t
ion and Release target
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Roland Schulz
Merge changes I
a
f4
c
56b7,Ibabed87f into release-4-5
.
.
.
commit
|
commitdiff
|
tree
2011-12-14
Rol
a
nd Schu
l
z
Merge "Re-fix
e
d static linking of
m
aths libra
r
ies
under
.
.
.
commit
|
commitdiff
|
tree
2011-12-13
Roland Schulz
Merge "Converted macro usage for readabil
i
ty" into
.
.
.
commit
|
commitdiff
|
tree
2011-12-13
R
oland Schulz
Mer
g
e "R
e
l
a
xe
d
so
m
e assum
p
t
ions about traject
o
r
y
tim
e
s
.
.
.
commit
|
commitdiff
|
tree
2011-12-11
R
o
land Sc
h
ulz
Merg
e
"Set -DMPI
o
nly if c
o
mpi
l
ed for FAH" in
t
o release
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Rolan
d
Schulz
Merge "Adde
d
an option to
e
asily
c
ompile
contr
i
b programs
.
.
.
commit
|
commitdiff
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tree
2011-12-08
Roland Schulz
M
e
rge "
F
ix
s
e
l
e
ction parsing
i
n double precision
.
"
.
.
.
commit
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commitdiff
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tree
2011-12-08
Roland Schulz
Merge "A
v
oid
p
ossible w
a
r
nings if HUGE_VAL != infinity
.
.
.
commit
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commitdiff
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tree
2011-11-30
Roland Schulz
Merg
e
"M
e
rge remote-tr
a
c
king b
r
anc
h
'ge
r
rit/release
.
.
.
commit
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commitdiff
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tree
2011-11-27
R
oland Sc
h
ulz
Merge "Fixes
i
nconsistent
spelli
n
g of Git cmake varia
b
les
.
.
.
commit
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commitdiff
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tree
2011-11-27
Roland Schulz
Merg
e
"Repl
a
ce '_
'
in
a
ll mdp options
t
o '-'"
i
nto
.
.
.
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