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Convert nbnxn_search to C++
2018-05-10
Carsten Kutzne
r
I
ntroduce
h
elpe
r
class
e
s for f
o
r
ce
prov
i
der in
p
ut and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carsten Kutzner
Fix a few
t
ypo
s
in
S
I
M
D d
o
c
umentation
commit
|
commitdiff
|
tree
2017-12-20
Carsten K
u
tzner
Destruct MDMod
u
les/force providers p
r
ior to calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
C
a
rsten K
u
t
zner
Fix electr
i
c
field
.
mdp doc
u
mentation
commit
|
commitdiff
|
tree
2017-08-10
C
a
rst
e
n Ku
t
zner
C
o
rrected the PDF
manual to
refl
e
ct
tha
t
all tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten Kutzn
e
r
Added mis
s
ing
.
mdp file documentat
i
o
n
for t
h
e
enf
o
rc
e
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten Kutzner
Add
e
d missing
.
m
d
p f
i
le documentation for
t
he
enf
o
r
c
ed
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carsten K
u
tzner
Fixed #2206 I
M
D interface mal
f
unctions
commit
|
commitdiff
|
tree
2017-06-16
Carste
n
Ku
t
zner
Fixed a co
n
s
i
stency chec
k
in
m
ake_ed
i
for flood
i
ng
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kut
z
ner
Moved es
s
en
t
ial dyna
m
ics initializat
i
on call into do_md()
commit
|
commitdiff
|
tree
2017-06-09
C
ars
t
en Kut
z
ner
Adopt and document implementation policy for MD modules
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kutzner
Minor h
e
ader file cleanup in
ED, IM
D
and Com
p
E
L modules
commit
|
commitdiff
|
tree
2017-04-19
C
a
rsten K
u
tz
n
er
R
e
move unused forward decla
r
ations of t_co
m
mrec in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Cars
t
en Kut
z
ner
Re
m
ove unnec
e
ssary incl
u
de
commit
|
commitdiff
|
tree
2016-11-16
Cars
t
en Ku
t
zner
Increas
e
d the de
f
au
l
t reset step to 15
0
0 in gmx
tu
n
e_pme
commit
|
commitdiff
|
tree
2016-11-15
Carsten
Kutzner
Fixed ty
p
o
in
m
e
mbed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Carsten Kut
z
ner
Corrected value of
ele
c
tr
i
c co
n
versio
n
fac
t
o
r
f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutz
n
er
Clean-up code for swa
p
coords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten Kut
z
ne
r
Clar
i
f
i
ed
l
icen
s
e text in t
h
e
.
tex m
a
nual
commit
|
commitdiff
|
tree
2016-03-17
Carste
n
Kutzner
F
i
x membed initializati
o
n
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutzn
e
r
Small update to r
e
ference man
u
al
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzne
r
Changed
n
or
m
(
.
.
.
) > 0
c
ond
i
tion to norm2(
.
.
.
) > 0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzne
r
Imp
r
o
ved/enlarge
d
Fig
.
4
.
9
in ma
n
ua
l
f
o
r better readability
commit
|
commitdiff
|
tree
2016-01-20
Carsten
K
utzner
Made g_tu
n
e_pme wor
k
w
ith
-
cpi -deffnm combinat
i
on
commit
|
commitdiff
|
tree
2015-11-17
C
arsten Ku
t
z
ner
Fixe
d
-npstr
i
ng
command line
a
r
g
u
ment in gm
x
tune_pme
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzner
Ion/wa
t
er position swapping for multip
l
e
i
on type
s
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
C
arsten Kutzner
Described t
h
e
c
o
m
putatio
n
al electrophysiology
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Cars
t
en
K
utzner
Extra options for
computationa
l
electrophysio
l
ogy
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten
K
u
t
z
ne
r
Code cle
a
nup in swa
p
coord
s
.
cp
p
commit
|
commitdiff
|
tree
2015-10-02
C
a
rste
n
Kutzn
e
r
F
ixed a bu
g
in comp
u
tational electrophysiology
w
ith DD
commit
|
commitdiff
|
tree
2015-07-15
Ca
r
st
e
n Kutzner
Rem
o
ved in
f
ormation a
b
ou
t
obsolete
.
edo fi
l
e format
commit
|
commitdiff
|
tree
2014-12-09
Carst
e
n Kut
z
ner
M
a
ke
t
une_p
m
e un
d
ers
t
and the "-nsteps" o
p
tion
.
Fix
e
s
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Ca
r
sten K
u
tzner
F
ixed a
typo in t
h
e manual
.
commit
|
commitdiff
|
tree
2014-11-12
C
a
r
sten Kutzner
Updated some
.
mdp file variabl
e
s to
u
se "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
C
arsten K
u
tzner
Fix
order of
ED/swap blocks dur
i
ng
checkpoint
read
i
ng
.
commit
|
commitdiff
|
tree
2014-10-01
Ca
r
sten Kutzner
A
l
low gmx tune_p
m
e to ski
p
the check for co
m
mand-line
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Carsten Kutzner
Fi
x
ed
o
utpu
t
of eigen
v
alues in g_covar
.
Fix
e
s #
1
575
commit
|
commitdiff
|
tree
2014-06-27
Carste
n
K
u
tz
n
er
Remove ob
s
olete pull-geometry
option 'positi
o
n' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
C
arsten Kutzner
R
e-use gmx_with
i
n_t
o
l from math
/
utilities instead of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carsten K
u
tzne
r
Fix documentation of swa
p
/en
u
ms
.
h
commit
|
commitdiff
|
tree
2014-03-28
Car
s
ten
Kutzner
Fix doc
u
m
e
nt
a
tion issues f
o
r intera
c
tive MD m
o
d
ule
.
commit
|
commitdiff
|
tree
2014-03-26
Car
s
t
en
K
utzner
Docum
e
ntation
h
ouse-keeping in file
swapcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
Carsten
Kutzn
e
r
Avoi
d
cross pr
o
duct with z
e
ro vect
o
r
in
rotatio
n
al
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
C
arsten Kut
z
ner
The van
d
er Waa
l
s
radius mu
s
t equa
l
t
he
C
oulomb
r
adius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Ca
r
sten K
u
tzner
Sma
l
l en
h
anceme
n
t
o
f
computa
t
ional ele
c
trophysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Ca
r
sten Kutzner
Allow for "computational electrophysiol
o
gy" simulati
o
ns
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten Kutzner
M
o
v
e pull code to separat
e
s
u
bdirectory
commit
|
commitdiff
|
tree
2014-01-11
Carst
e
n K
u
tzner
Mo
v
e essential dynam
i
cs / flooding c
o
de
t
o separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carste
n
Kutzner
Read
e
ssential dynamics d
a
t
a f
r
om
c
heckpoint at corre
c
t
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
Removed a few
t
ypos in thre
e
German quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten
Kutzner
Pass
o
n default value of radstep in make_
e
di
commit
|
commitdiff
|
tree
2013-12-25
Car
s
ten K
u
tz
n
er
Es
s
ential dy
n
amics: move bNeedDoEdsam e
v
alua
t
ion
to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Carsten Kutzner
Fixed essen
t
ial dynamics
(
ED) c
o
nt
i
nuation
fr
o
m
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
C
a
rsten
K
utzner
Properl
y
finalize MP
I
on mdrun -versio
n
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-06-26
C
a
rste
n
Ku
t
zner
Fi
x
ed -npst
r
in
g
c
ommand lin
e
argumen
t
in g_tune_pme
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
Fixed calculation
o
f s
l
a
b buffer size for
flexib
l
e
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten K
u
tzne
r
F
ix for
a
rare cond
i
t
i
on in flexible
ro
t
ation potenti
a
ls
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten K
u
tzner
Co
d
e cleanup in enforced rotation mo
d
ule, remove warnings
.
commit
|
commitdiff
|
tree
2013-05-16
Ca
r
sten Ku
t
zn
e
r
Choose the PBC
ima
g
e o
f
e
ach
r
o
tation
g
roup atom depending
commit
|
commitdiff
|
tree
2013-04-29
C
arste
n
Kutzner
Evaluate enforc
e
d r
o
t
a
tion p
o
t
enial wi
t
h V
e
r
let, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Cars
t
en Kutzner
Essent
i
al d
y
n
amic
s
: fixed legend in ED
.
x
v
g o
u
tput
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzn
e
r
Made g_t
u
ne_pme w
o
rk with 4
.
6 if
u
ser sets
"
-p" command
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
arsten Kutzner
Fix
e
d the MPI recogniti
o
n
st
r
ing in g_tune_pme
commit
|
commitdiff
|
tree
2013-01-22
Cars
t
e
n Kutz
n
er
Mov
e
d a few
c
o
mments bac
k
i
nto positio
n
commit
|
commitdiff
|
tree
2013-01-17
Carsten Kutzner
Added not
e
about make_edi and fl
o
oding in ED
p
aragrap
h
commit
|
commitdiff
|
tree
2013-01-16
Ca
r
sten
Kutzn
e
r
Made g
_
tune_pme wo
r
k corre
c
tly
again wit
h
thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
C
arsten Ku
t
zner
Essential dy
n
a
m
ics output
f
ile now
in
.
xvg format
commit
|
commitdiff
|
tree
2012-12-20
Carsten
Kutzn
e
r
Small
f
ix f
o
r g_tune_pme
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzne
r
Essenti
a
l dyna
m
ics:
f
ix
e
d re
s
tar
t
s when ED group
has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kutzner
Made g_tune
_
p
m
e work correctly when ir-
>
init_ste
p
> 0
commit
|
commitdiff
|
tree
2012-10-16
Carste
n
Kutzner
Made
g_tune
_
pme read
(ns
/
day) from 4
.
6
md
.
log output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten
K
utz
n
er
R
e
moved obsolete hint in error
m
essage
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten Kutzn
e
r
Fixed essential dynamics / flo
o
d
ing g
r
oup P
B
C se
r
ial
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kutzner
Fixed
c
alculation of projection for STAR a
n
d
/or SORI
commit
|
commitdiff
|
tree
2012-08-06
Carst
e
n
Ku
t
zner
Add
e
d
commen
t
in get_str
u
ctur
e
about which stru
c
tures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
Fixed segv i
n
essential dynam
i
cs module
commit
|
commitdiff
|
tree
2012-07-06
Carst
e
n Kutz
n
e
r
Enforced rotat
i
on: PBC/res
t
a
r
t
fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten
K
u
t
zner
Small fi
x
f
o
r g
_
tun
e
_pme
commit
|
commitdiff
|
tree
2012-05-23
Carsten
K
utzner
Revised g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
C
a
rst
e
n Kutzner
Merge "Imp
r
ove
d
war
n
ing n
o
te
w
ith DD and periodic
m
olecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten Kutz
n
er
New
tool that extracts
d
y
e dy
n
amics from
t
r
ajectories
commit
|
commitdiff
|
tree
2011-12-20
Carst
e
n
Kut
z
ner
Added -d
h
d
l
t
o tp
r
file lis
t
, fixes #855
commit
|
commitdiff
|
tree
2011-12-19
Ca
r
sten Kutzner
E
n
for
c
ed rotation
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutzner
Act
u
ally -cp
i
and -b
c
p
o
must n
o
t
be id
e
nti
c
al
commit
|
commitdiff
|
tree
2011-10-31
Ca
r
sten Kutzner
Fixed bug #830 (segv in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Carsten
K
u
tzner
Rem
o
ve segv i
n
x
pm2ps
,
fixe
s
#611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kut
z
ne
r
Remove segv in xpm2ps
,
f
i
x
e
s
#611
commit
|
commitdiff
|
tree
2011-08-25
Carsten Kutzner
In
s
t
e
a
d of a
segv,
m
drun
n
o
w gives an error msg
i
f
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten Kutzner
T
y
po
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten Kutzner
Fi
x
ed
c
a
l
c
u
l
ation of max an
d
min num
b
er of
P
ME-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Car
s
t
e
n
Kutzner
Removed old-
f
a
s
h
ioned
MPE lo
g
ging code
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutzner
Added two miss
i
ng headers
commit
|
commitdiff
|
tree
2011-07-06
Carsten K
u
tzner
Added globsig
.
h to inc
l
ude/types/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Kutzne
r
Flooding as harm
.
r
es
t
rai
n
t
:
Abort when origin position
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Checks f
o
r zero
-
mass atoms in ED
,
be
t
ter orde
r
ing of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Car
s
t
en Kutzner
Fixed wron
g
error
m
essage when using flooding
c
o
d
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Carsten
K
u
tzner
Fixed bug #714: deprecated structure in gettimeofday
commit
|
commitdiff
|
tree
2011-02-25
Carste
n
Kutz
n
er
Corrected output of a warning message
.
commit
|
commitdiff
|
tree
2011-02-25
Ca
r
s
t
en
K
u
t
zner
Added the -fix option t
o
g_tu
n
e_p
m
e for tuning of
r
coulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
Carsten Kutz
n
e
r
Enforced
rota
t
ion: fix
c
o
m
piler
w
arning
commit
|
commitdiff
|
tree
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