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Use std::vector in nbnxn_search_t
2018-05-10
C
a
rsten Kutzner
Introduce helper
classes for force p
r
ovider inp
u
t and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carsten Kut
z
ner
F
i
x a f
e
w typos in SIMD docu
m
en
t
a
t
ion
commit
|
commitdiff
|
tree
2017-12-20
Cars
t
en K
u
tzner
Destr
u
ct
M
DModules/
f
o
rce provid
e
rs
prio
r
t
o
calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
Carsten Kutzner
Fi
x
ele
c
tric
f
i
e
ld
.
mdp documenta
t
i
on
commit
|
commitdiff
|
tree
2017-08-10
Carsten
Kutzner
Corrected
the
P
DF manu
a
l
to reflect th
a
t all tool
s
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten
Ku
t
zner
Added missing
.
mdp file docum
e
ntat
i
on for the
e
n
f
o
rce
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten Kutzner
A
dded mis
s
ing
.
m
d
p
file do
c
umentation for th
e
e
n
forced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carste
n
Kutzne
r
F
ixed #2
2
06 IMD interface malfunctions
commit
|
commitdiff
|
tree
2017-06-16
Carsten
K
utzne
r
Fixed a
consistency check in make_
e
di for floodin
g
commit
|
commitdiff
|
tree
2017-06-09
Carst
e
n Kutz
n
e
r
Moved essent
i
al
d
ynamics initializati
o
n call into do_md()
commit
|
commitdiff
|
tree
2017-06-09
C
a
rsten Kutzner
Ad
o
p
t and
d
oc
u
ment implementation policy
f
or MD mod
u
les
commit
|
commitdiff
|
tree
2017-04-29
Carst
e
n Kut
z
ner
Minor heade
r
fil
e
cleanup in ED,
IMD and CompEL modules
commit
|
commitdiff
|
tree
2017-04-19
Carst
e
n Kutzner
Remove unuse
d
forwa
r
d declarations o
f
t_commrec in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Carsten
Kutz
n
e
r
Remove
u
nneces
s
ary include
commit
|
commitdiff
|
tree
2016-11-16
Carsten Ku
t
zne
r
Increased the default res
e
t step to
1
500 in
g
mx
tu
n
e
_pme
commit
|
commitdiff
|
tree
2016-11-15
Carsten Kutz
n
er
F
i
xed typo in
m
embed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Cars
t
en Kut
z
ner
Corre
c
t
e
d val
u
e of
e
lectric c
o
n
version factor
f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten
K
u
t
z
n
er
Clean-up code for s
w
apcoords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten Kutzner
Clarified li
c
ense text
in the
.
tex manual
commit
|
commitdiff
|
tree
2016-03-17
Carsten Kutzn
e
r
Fix
membed init
i
alizati
o
n
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutzner
Small updat
e
to
r
eference manual
commit
|
commitdiff
|
tree
2016-02-16
Carsten Ku
t
zne
r
Changed norm(
.
.
.
) >
0
co
n
dition t
o
norm
2
(
.
.
.
) > 0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Car
s
ten Ku
t
zner
Improved
/
enlarged Fig
.
4
.
9
in manual for bett
e
r r
e
adability
commit
|
commitdiff
|
tree
2016-01-20
Carsten Kutz
n
er
Made g_tune_pme
work with -cpi -deffnm combinatio
n
commit
|
commitdiff
|
tree
2015-11-17
Carst
e
n
Kutzner
Fixe
d
-n
p
s
t
ring command line argument in gmx
tune_pme
commit
|
commitdiff
|
tree
2015-11-13
C
arsten
K
utzn
e
r
Ion/wa
t
er position swa
p
ping for multip
l
e ion
types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutzner
Describe
d
th
e
comput
a
tional ele
c
trophysiol
o
gy
.
m
dp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten
Kutzne
r
Extra o
p
tions
fo
r
computationa
l
electrophy
s
iology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Cod
e
cleanup in s
w
apcoords
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Carsten Kutzner
Fixed a bug in compu
t
ational electrophysiology with DD
commit
|
commitdiff
|
tree
2015-07-15
Car
s
ten K
u
tzn
e
r
Removed inform
a
t
i
on abou
t
o
b
so
l
e
t
e
.
edo f
i
le format
commit
|
commitdiff
|
tree
2014-12-09
Carsten Kut
z
n
e
r
Make
tune_p
m
e under
s
tand the "-nst
e
ps" op
t
ion
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Car
s
t
en Ku
t
zner
Fixed a
typo in the manual
.
commit
|
commitdiff
|
tree
2014-11-12
Car
s
ten Kutzner
Updated some
.
mdp file
v
ariables
to use "-
"
instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
C
a
rsten Kutzn
e
r
Fix order of ED/swap
b
locks during check
p
oint reading
.
commit
|
commitdiff
|
tree
2014-10-01
Cars
t
en Kutzner
Allow
g
m
x tune
_
pm
e
t
o
skip the c
h
eck for
c
o
m
m
and-lin
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Car
s
t
en
Kutzner
Fixed output of eigen
v
alues in g
_
c
o
v
ar
.
Fixes #1575
commit
|
commitdiff
|
tree
2014-06-27
Carsten Kutzner
Remove obsol
e
te pull-geometry op
t
ion 'positio
n
' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten
K
utz
n
er
R
e
-use gmx_wit
h
in_tol from
m
ath
/
utilities ins
t
e
a
d of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carste
n
K
u
tzner
F
i
x documentation of swap/e
n
u
ms
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten
K
utzner
Fi
x
document
a
tion issues for i
n
teractive
MD m
o
dule
.
commit
|
commitdiff
|
tree
2014-03-26
Carsten Ku
t
zn
e
r
Docum
e
ntation house-k
e
eping in file sw
a
pcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
Cars
t
e
n Kutzner
Avoid
cross product with
zero vect
o
r in rot
a
t
i
o
nal
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kutzner
The van der Waa
l
s rad
i
u
s
must equa
l
the Coul
o
mb radi
u
s
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
C
arsten Kutzner
Small enhan
c
emen
t
of computational
e
lectro
p
hysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten
Kutzner
A
l
low f
o
r "compu
t
at
i
on
a
l electrophysiolo
g
y" simulatio
n
s
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carste
n
K
u
t
z
ner
Move pu
l
l co
d
e to separate subdir
e
ctory
commit
|
commitdiff
|
tree
2014-01-11
Carste
n
Kutzner
Move essential dy
n
amics / floodin
g
c
ode to separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten
K
utzner
Rea
d
essential dynamics data from checkpoint at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Ca
r
sten Kut
z
ner
Removed a
f
ew typos in three German
quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carst
e
n Kutzner
Pa
s
s on default value of radstep
i
n make_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten Kutzner
Ess
e
ntial dy
n
amics: m
o
ve bNeedD
o
Edsam evaluati
o
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Carsten
K
utzner
Fixed essential dyna
m
i
c
s
(ED) co
n
tinuation
from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Car
s
ten Kutzner
Prope
r
ly finali
z
e MPI on mdrun -
v
e
rsion
.
F
ixes #
1
31
3
commit
|
commitdiff
|
tree
2013-06-26
Cars
t
en Kutzne
r
Fixed -npstring command line argument
i
n g_tu
n
e_pme
commit
|
commitdiff
|
tree
2013-05-28
C
a
rsten K
u
tzner
Fixed calculatio
n
of slab buff
e
r si
z
e for fle
x
ibl
e
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
F
i
x
for a rare condi
t
io
n
in
f
lexible rotation potent
i
als
.
commit
|
commitdiff
|
tree
2013-05-27
C
a
rsten Ku
t
zner
Co
d
e clea
n
up in en
f
orced rotation
m
odule, r
e
move warnings
.
commit
|
commitdiff
|
tree
2013-05-16
Cars
t
en Kutzner
C
h
oose the
P
B
C
image of each ro
t
ation gr
o
up ato
m
depending
commit
|
commitdiff
|
tree
2013-04-29
Carsten Ku
t
zne
r
Eva
l
uate enf
o
rced
r
o
tation potenial with Verl
e
t, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Cars
t
en Kutzner
E
s
s
ential
d
yn
a
mics: fixed
l
e
gend in
E
D
.
xvg output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Cars
t
en
Kutzner
M
a
de
g_
t
une_pme work wi
t
h 4
.
6 if
user sets "-p" comma
n
d
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
a
rsten Kutz
n
er
Fixed the MPI recognitio
n
string in g
_
tune_p
m
e
commit
|
commitdiff
|
tree
2013-01-22
Ca
r
sten Kutzner
Mov
e
d a few comments back in
t
o po
s
itio
n
commit
|
commitdiff
|
tree
2013-01-17
Carsten
Kutzner
Added note abou
t
make_ed
i
and flooding in ED paragr
a
ph
commit
|
commitdiff
|
tree
2013-01-16
Ca
r
ste
n
K
u
tzner
Made g_tune_pm
e
work corr
e
ctly a
g
ain with thr
e
ad
-
MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten
Ku
t
zne
r
Ess
e
nt
i
al dynamics output fi
l
e
n
ow
i
n
.
xvg format
commit
|
commitdiff
|
tree
2012-12-20
Car
s
ten
K
utzne
r
Small
f
ix for g_tune
_
pme
commit
|
commitdiff
|
tree
2012-12-20
Ca
r
ste
n
Kutzner
Essential dynamics: fixed restart
s
when ED g
r
oup has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carst
e
n Kutzner
Made g_tune_
p
me
wo
r
k correctly
wh
e
n ir->
i
n
i
t_step > 0
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
M
a
de g_tune_pme read (n
s
/day) from 4
.
6
md
.
log output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
C
a
rste
n
Kutzn
e
r
Rem
o
ve
d
obsolete hint in error
m
essage
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten
K
utzner
Fixed essential dynamic
s
/ flooding gr
o
u
p
PBC serial
commit
|
commitdiff
|
tree
2012-08-06
Carsten K
u
tzn
e
r
Fixed calculat
i
on of proje
c
tion
fo
r
STAR
and/or SORI
commit
|
commitdiff
|
tree
2012-08-06
Ca
r
sten Kutzner
Added comme
n
t
in get_stru
c
ture ab
o
ut which structure
s
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten K
u
tzner
Fixed s
e
g
v in esse
n
tial
d
ynami
c
s module
commit
|
commitdiff
|
tree
2012-07-06
Carste
n
Kutzner
Enforced rotation
:
P
BC/restart fix
commit
|
commitdiff
|
tree
2012-06-11
Carste
n
Kutzner
Small f
i
x fo
r
g_tune_pme
commit
|
commitdiff
|
tree
2012-05-23
Ca
r
sten Kutzner
Revised g_t
u
ne_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten Ku
t
zn
e
r
Merge "Improved w
a
rn
i
ng
n
ote with DD and
p
eriodic mo
l
ecu
l
es
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Ca
r
s
ten Ku
t
zner
N
ew
tool that
e
xtracts
d
ye dy
n
amics fr
o
m t
r
ajectories
commit
|
commitdiff
|
tree
2011-12-20
C
arste
n
Kutzner
A
d
ded -dh
d
l
t
o
t
p
r
fi
l
e list, fix
e
s
#
85
5
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kut
z
ne
r
Enforced rotat
i
on
commit
|
commitdiff
|
tree
2011-11-22
C
arsten Kutzner
Actually
-cpi and -bcpo must
n
ot b
e
identical
commit
|
commitdiff
|
tree
2011-10-31
C
arsten Kutzner
F
i
xed bug
#830
(
segv
in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Carsten
K
ut
z
n
er
Remov
e
segv
in xpm2p
s
, fix
e
s
#
611
commit
|
commitdiff
|
tree
2011-08-26
C
a
rsten Ku
t
zner
Remove segv in xp
m
2p
s
, fixe
s
#61
1
commit
|
commitdiff
|
tree
2011-08-25
Carsten
K
utzner
Inst
e
ad of a segv
,
mdrun now gives
an er
r
or msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten Kutzn
e
r
T
y
po
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten K
u
tzner
Fixed calc
u
lation of max and min numbe
r
o
f P
M
E-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carste
n
Kutzner
Removed old-fashioned MPE
l
oggi
n
g c
o
de
commit
|
commitdiff
|
tree
2011-07-11
Carsten
K
u
t
zner
Added two m
i
ss
i
ng headers
commit
|
commitdiff
|
tree
2011-07-06
C
arste
n
Kutzner
A
d
ded globsig
.
h to inc
l
ude/types/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
C
a
rsten Kutzner
F
l
o
oding as harm
.
restraint: Abort when or
i
gin position
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Ca
r
sten
Kutzner
Ch
e
cks for zero-mass atoms in
ED, bett
e
r ordering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
C
a
rst
e
n Kutz
n
er
Fixed wrong
er
r
or message when using floodi
n
g
code
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Carsten K
u
tzner
Fixed bug #7
1
4: deprecat
e
d
structure in
g
ett
i
meofday
commit
|
commitdiff
|
tree
2011-02-25
Carste
n
Kutzner
Corre
c
ted
o
utput
of
a
wa
r
ning messag
e
.
commit
|
commitdiff
|
tree
2011-02-25
Car
s
ten Kutzner
A
dd
e
d
the
-
fix
op
t
ion to g_
t
un
e
_pme for t
u
ning of rcoulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
Carsten Kutzner
Enforce
d
r
otation: fix co
m
pile
r
warning
commit
|
commitdiff
|
tree
next