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Added the bundled clFFT into OpenCL builds
2018-05-10
Carsten Kutzner
Intro
d
uce helpe
r
classes for f
o
rce provid
e
r input and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
C
arsten
K
u
t
zner
Fix a few typ
o
s
in SI
M
D docu
m
ent
a
tion
commit
|
commitdiff
|
tree
2017-12-20
C
ars
t
en Kutzner
De
s
truct M
D
Modu
l
es
/
fo
r
ce providers p
r
ior to calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
Carsten
Kutzn
e
r
F
i
x
electric field
.
mdp documentation
commit
|
commitdiff
|
tree
2017-08-10
Carste
n
Kutzner
Corrected
the PDF manual t
o
reflect that a
l
l tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten Kutzn
e
r
Added missing
.
m
dp file documentation for the enfo
r
ced
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten Kutzner
Add
e
d missing
.
mdp file do
c
umentation
f
or t
h
e
enforce
d
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Ca
r
sten Kutzner
Fixe
d
#2206 IMD in
t
erfa
c
e
malfunctio
n
s
commit
|
commitdiff
|
tree
2017-06-16
Carst
e
n Kutzn
e
r
Fixed a consiste
n
cy check in ma
k
e_edi fo
r
floo
d
ing
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutz
n
er
M
oved esse
n
t
ial d
y
na
m
i
c
s initi
a
lizat
i
o
n cal
l
into
d
o_md()
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutz
n
e
r
Adopt and document
i
mpleme
n
tation policy for MD module
s
commit
|
commitdiff
|
tree
2017-04-29
Carsten K
u
tzner
M
in
o
r header file
c
leanu
p
in ED, IMD and CompEL mod
u
les
commit
|
commitdiff
|
tree
2017-04-19
Ca
r
st
e
n Ku
t
zn
e
r
Re
m
ove
unused forward declaration
s
o
f
t_commrec in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
C
ars
t
en Kutzner
Remove
u
nnecessary i
n
clude
commit
|
commitdiff
|
tree
2016-11-16
Carsten Ku
t
zner
I
ncreased the
def
a
ult
r
e
s
et ste
p
t
o
1500 in gmx tune_p
m
e
commit
|
commitdiff
|
tree
2016-11-15
Carsten Kutzner
Fixed
t
ypo in
m
em
b
ed
.
c
p
p
commit
|
commitdiff
|
tree
2016-04-14
C
arsten
K
utz
n
e
r
Corrected value
of electric
c
o
nversio
n
factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
C
arsten Kutzne
r
C
lean-up cod
e
f
or
s
wapcoords
.
commit
|
commitdiff
|
tree
2016-03-18
C
a
rst
e
n
Kutzn
e
r
Clarifie
d
l
icense text in th
e
.
tex
m
anual
commit
|
commitdiff
|
tree
2016-03-17
C
a
rsten
Kutzner
Fix m
e
mbed initialization
commit
|
commitdiff
|
tree
2016-02-18
C
arsten Kutz
n
er
Small update to reference manual
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Changed
norm(
.
.
.
) > 0 condition to
nor
m
2(
.
.
.
) > 0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Im
p
rove
d
/enlarged Fig
.
4
.
9 in manual for better readability
commit
|
commitdiff
|
tree
2016-01-20
Ca
r
s
ten
K
u
t
zner
Made g_tune_pme
w
o
rk with
-
c
p
i
-deffnm combination
commit
|
commitdiff
|
tree
2015-11-17
Carst
e
n Kutzner
Fixed -npstring command li
n
e argu
m
ent in gmx tune_pme
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzn
e
r
Ion
/
water positi
o
n
s
wappin
g
fo
r
mult
i
ple ion types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Cars
t
en Kutzner
Described the computational electr
o
physiology
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
C
a
rsten Kutzner
E
xtra opt
i
ons fo
r
c
o
mputational electr
o
physiology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
C
ode
c
leanup in swapcoords
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Car
s
te
n
Kutzner
Fixed a bug in computatio
n
al ele
c
trop
h
ys
i
ology with DD
commit
|
commitdiff
|
tree
2015-07-15
Carsten Kutzner
Re
m
oved information
about obsolete
.
edo
fi
l
e format
commit
|
commitdiff
|
tree
2014-12-09
Carsten K
u
tzner
Make tune_pme understa
n
d
the "-nsteps" option
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten Ku
t
z
ner
Fixed
a t
y
po
i
n
the
m
a
nual
.
commit
|
commitdiff
|
tree
2014-11-12
Ca
r
sten
K
utzne
r
Updated some
.
m
d
p file variables to use "-" i
n
st
e
ad
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carsten Kutzne
r
Fix order of ED
/
swap blocks during checkpoint
r
eadi
n
g
.
commit
|
commitdiff
|
tree
2014-10-01
Carsten Kutzner
Allow gmx tune_pme to s
k
ip the check for command-lin
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Carsten
K
utzner
Fixed
o
u
tput of eigenvalue
s
in g_covar
.
Fi
x
e
s #1575
commit
|
commitdiff
|
tree
2014-06-27
Car
s
ten Kutzner
Remove o
b
solete pull-geo
m
etry opt
i
on 'posi
t
ion' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
C
arsten
K
u
t
zner
Re-u
s
e gmx_within_tol from
math/u
t
ilit
i
e
s
instead
o
f
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Car
s
t
e
n Kut
z
n
e
r
F
ix document
a
tion of
swap/
e
nums
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten Kutzner
Fix docu
m
entation issues for inter
a
ctive MD
module
.
commit
|
commitdiff
|
tree
2014-03-26
Carsten Kutzner
Doc
u
mentati
o
n house-keeping in file
s
wa
p
coords
.
c
commit
|
commitdiff
|
tree
2014-03-14
Carsten
Ku
t
zner
A
void cross product with zero vector in rotat
i
onal
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carst
e
n Kut
z
ner
T
h
e van der W
a
als radius must e
q
u
a
l
the Coulomb rad
i
us
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
C
a
r
sten K
u
tzner
Sm
a
ll enh
a
n
c
e
ment
of
c
o
m
p
u
tational electrophysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carste
n
K
utzner
Allow for "computational elect
r
ophysio
l
ogy" simu
l
a
t
ions
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten Kutzner
Move
pull c
o
de to separate subdirectory
commit
|
commitdiff
|
tree
2014-01-11
Ca
r
sten Kutzner
Move essential dynam
i
cs /
f
l
o
o
ding code t
o
separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
C
arsten Kutzner
R
e
ad essentia
l
dy
n
a
mic
s
d
ata from checkpo
i
n
t
at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Ca
r
ste
n
Kutz
n
er
Removed
a
f
ew typos
in three G
e
rma
n
quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten
Kutzn
e
r
Pass on def
a
ult value of radstep in make_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten Ku
t
zner
Essential dyna
m
ics: move
b
N
eedDoE
d
sam evaluati
o
n t
o
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Carsten Kutzn
e
r
F
ixed
e
s
s
enti
a
l dyn
a
mi
c
s
(ED) continua
t
i
on from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
C
arsten Kutzner
Properly
finalize MPI
o
n
m
drun -v
e
rs
i
on
.
Fixes #131
3
commit
|
commitdiff
|
tree
2013-06-26
Carsten K
u
t
z
n
er
Fixed -npstring c
o
m
m
and lin
e
a
r
g
u
ment in g_tune_
p
m
e
commit
|
commitdiff
|
tree
2013-05-28
Carsten
K
utzner
Fixed c
a
lculation of slab buffe
r
size for
f
lexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten Ku
t
z
n
e
r
Fix for a rare condition
i
n flexib
l
e rotation potentials
.
commit
|
commitdiff
|
tree
2013-05-27
Cars
t
en Kutzner
C
od
e
c
l
eanup in enforced
ro
t
a
t
i
o
n
mo
d
ule, remove warnings
.
commit
|
commitdiff
|
tree
2013-05-16
Carsten Kutzner
Choo
s
e the PBC image of each rota
t
i
on gr
o
u
p atom dependin
g
commit
|
commitdiff
|
tree
2013-04-29
Carsten Kutzner
E
v
alua
t
e enforced
r
otation po
t
e
n
ial with Verl
e
t,
f
ixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Car
s
ten
K
utzner
Essential
d
y
n
a
mi
c
s: fixed legend in ED
.
xvg
output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten
K
u
t
zner
Made
g
_tune_pme
w
ork with 4
.
6 if
user
s
ets "-p
"
c
o
mmand
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
a
rst
e
n K
u
tzner
Fixed the MP
I
recog
n
ition string
i
n g_tune_p
m
e
commit
|
commitdiff
|
tree
2013-01-22
C
arsten Kutzner
Move
d
a few comments back into
p
o
sition
commit
|
commitdiff
|
tree
2013-01-17
Carsten K
u
tzner
Added note ab
o
u
t
make_edi and fl
o
oding in
E
D paragraph
commit
|
commitdiff
|
tree
2013-01-16
C
a
rsten Kutz
n
er
Made g_tune_pme
w
ork corr
e
c
tly again with thr
e
ad-MP
I
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
C
arsten Kutz
n
e
r
Ess
e
ntial dy
n
amics
o
utput file
n
ow i
n
.
x
vg format
commit
|
commitdiff
|
tree
2012-12-20
Carst
e
n
Kutzner
Small
fix
f
or g_t
u
ne_pme
commit
|
commitdiff
|
tree
2012-12-20
Carsten K
u
tzn
e
r
Essential
dynamics: fixed
r
estarts whe
n
ED g
r
o
up
has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kutzner
Made
g
_tune
_
p
me
wor
k
cor
r
e
c
tly when ir->
i
nit_step > 0
commit
|
commitdiff
|
tree
2012-10-16
Carste
n
K
u
tzner
M
ade g_tun
e
_
p
me r
e
ad (ns/da
y
) from 4
.
6
md
.
log output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten
Kut
z
ner
Removed
o
bsolete h
i
nt in erro
r
mess
a
ge
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten Kutzner
F
i
x
e
d
essent
i
al dynamics / fl
o
oding g
r
oup PBC serial
commit
|
commitdiff
|
tree
2012-08-06
Carsten
K
utz
n
er
Fixed ca
l
culat
i
on of projecti
o
n
f
or ST
A
R and/or
SO
R
I
commit
|
commitdiff
|
tree
2012-08-06
Carst
e
n Ku
t
zner
Added comment in get_structure about
which
s
tructures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
Fixed
s
egv
in e
s
sential dynamics modu
l
e
commit
|
commitdiff
|
tree
2012-07-06
Carsten
K
utzner
Enforce
d
rotation: PBC/resta
r
t fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Kutz
n
er
S
m
all f
i
x
for
g
_tun
e
_pme
commit
|
commitdiff
|
tree
2012-05-23
Carsten Kut
z
ner
Revised g_t
u
ne_
p
me
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kutzner
Merge "Improved w
a
rning note with
DD and peri
o
dic molecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carste
n
Kutzner
New
t
ool that extracts dye dynamics fro
m
trajectories
commit
|
commitdiff
|
tree
2011-12-20
Carsten
K
utzner
A
d
ded -d
h
dl to tp
r
f
i
le list, fixes
#
8
5
5
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kutzner
E
nf
o
rced rotat
i
on
commit
|
commitdiff
|
tree
2011-11-22
C
a
rs
t
en Kutzner
Actual
l
y -
c
pi
and
-
b
c
po
must not be identical
commit
|
commitdiff
|
tree
2011-10-31
Carst
e
n
Kutzn
e
r
Fixed bug #83
0
(segv in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
C
a
rsten Kutzne
r
R
e
move segv in xpm2ps, fixes
#
6
1
1
commit
|
commitdiff
|
tree
2011-08-26
Car
s
ten Kutzner
R
e
move
segv in xp
m
2ps, fix
e
s #6
1
1
commit
|
commitdiff
|
tree
2011-08-25
C
a
rsten Kutzner
Instead of a
s
egv, m
d
run n
o
w
gives an err
o
r m
s
g if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten
K
utzner
Typo
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten
K
u
tzne
r
Fixe
d
calcul
a
tion of max and m
i
n num
b
er of PME-
o
nly
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Ca
r
s
t
e
n Kutzner
R
e
mov
e
d old-f
a
shioned MPE logging code
commit
|
commitdiff
|
tree
2011-07-11
Carsten
K
utzner
Added
t
wo m
i
ssing headers
commit
|
commitdiff
|
tree
2011-07-06
Carst
e
n Kutzner
Add
e
d
g
l
obsig
.
h to in
c
lude
/
ty
p
es/
M
akefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Kutzne
r
Flooding as harm
.
restraint: Abort when origin p
o
s
i
tion
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carst
e
n Kut
z
n
er
C
h
ecks
for zero-mass atoms in ED, better ordering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten Kutzner
Fixed wron
g
error message w
h
en usi
n
g flooding co
d
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Cars
t
en Kutzner
Fi
x
ed
bug #7
1
4: dep
r
ecated structure in
g
et
t
i
meo
f
day
commit
|
commitdiff
|
tree
2011-02-25
Carsten Kut
z
ner
Cor
r
ected
output of a warni
n
g message
.
commit
|
commitdiff
|
tree
2011-02-25
Carsten K
u
tz
n
er
Added the -fix option t
o
g_
t
un
e
_p
m
e
f
or t
u
ning of rcoulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
C
arsten
K
u
tzne
r
Enf
o
rced
rotat
i
on:
fix co
m
piler warn
i
n
g
commit
|
commitdiff
|
tree
next