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Fix warnings with clang 9
2020-04-17
Christi
a
n Blau
p
roposed fi
x
for redmine
b
ug
#34
0
3
commit
|
commitdiff
|
tree
2020-03-16
Chr
i
st
i
an Bla
u
R
emove dysfunctional QMMM interface
pt
4
commit
|
commitdiff
|
tree
2020-03-16
C
hristia
n
Blau
Remov
e
d
y
s
functio
n
al QMMM inter
f
ace pt3
commit
|
commitdiff
|
tree
2020-03-16
Christi
a
n Blau
Remo
v
e dysfu
n
ctional QM
M
M interface pt2
commit
|
commitdiff
|
tree
2020-03-16
Christi
a
n Bl
a
u
Remove dysfun
c
tional QMMM interface pt1
commit
|
commitdiff
|
tree
2020-03-11
Ch
r
istian
B
lau
Am
e
nd optiona
l
d
o
cumentatio
n
commit
|
commitdiff
|
tree
2020-03-05
Christ
i
an Bl
a
u
Add fu
n
ction c
a
lls to MdM
o
dule
s
t
o sign up for
notific
a
tions
commit
|
commitdiff
|
tree
2020-03-05
Christi
a
n Blau
Split off impl
e
mentati
o
n d
e
tail
s
of MdModuleNotifica
t
ion
commit
|
commitdiff
|
tree
2020-03-04
Ch
r
istian Bl
a
u
S
ave excluded
non-bo
n
ded inter
a
ction
s
in
.
tpr file
commit
|
commitdiff
|
tree
2020-03-04
Ch
r
i
stian Blau
Add cla
s
shelpe
r
macro to
forbid copy, m
o
ve and any
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Chr
i
stia
n
Blau
Doc
u
ment densit
y
-fit c
r
o
s
s-correla
t
i
on i
n
.
mdp options
commit
|
commitdiff
|
tree
2020-02-18
Christian
B
l
a
u
Split MdModuleNotifications into topics
commit
|
commitdiff
|
tree
2020-02-12
Chr
i
sti
a
n Blau
Introduce readXvgData to rea
d
x
vg data into std:
:
vector
commit
|
commitdiff
|
tree
2020-01-31
Christi
a
n
Blau
D
ocumentat
i
on fix for
local atom set data
commit
|
commitdiff
|
tree
2019-12-20
C
h
rist
i
an Bl
a
u
Remove problematic output of gmx ang
l
e
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
F
i
x density
f
ittin
g
stalling and energi
e
s
commit
|
commitdiff
|
tree
2019-12-12
Christian Bl
a
u
Densityfitt
i
ng - enforce similarity increase with adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Chris
t
ian Blau
Change arbitrary uni
t
s
to co
u
nt
s
in RMS
D
d
istance dis
t
ributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
C
hristian Blau
Relax cross-correla
t
ion
t
est pr
e
cisi
o
n
commit
|
commitdiff
|
tree
2019-12-04
C
hr
i
stian Blau
Remove
c
utoff-scheme group f
r
om
d
efau
l
t
mdout
.
mdp output
commit
|
commitdiff
|
tree
2019-12-02
Chri
s
tian Blau
Re
l
ax test tolerance for cr
o
ss
c
orrel
a
tion measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Christian
B
lau
F
ix
check-pointing
f
or density guid
e
d si
m
u
l
ation
s
commit
|
commitdiff
|
tree
2019-11-25
C
hristi
a
n Bl
a
u
Fix duplicate CONNECT
records i
n
p
d
b files
commit
|
commitdiff
|
tree
2019-11-25
Ch
r
istian Blau
R
ead mrc density
map format
w
ith
all endianesses
.
commit
|
commitdiff
|
tree
2019-11-25
C
hris
t
ia
n
Blau
Che
c
k mrc head
e
r for sa
n
ity
commit
|
commitdiff
|
tree
2019-11-24
Chri
s
tian
B
lau
InMemorySeriali
z
er with
e
ndianess swap
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
S
t
ochast
i
c dyn
a
mics - docu
m
ent t
h
at nsttcoup
l
e is ignored
commit
|
commitdiff
|
tree
2019-11-01
Christian Blau
Fix cross
-
correlation calcula
t
ion
i
nstabilit
y
commit
|
commitdiff
|
tree
2019-10-22
Christian B
l
au
Fi
x
ns
t
in den
s
ity-fitting
module
commit
|
commitdiff
|
tree
2019-10-18
C
hrist
i
an Blau
Manual en
t
ry and
.
mdp opt
i
on for adaptive f
o
r
c
e scaling
commit
|
commitdiff
|
tree
2019-10-18
C
h
ris
t
ian Blau
genion: prohi
b
it ion placement close
t
o no
n
-
s
olv
e
n
t
commit
|
commitdiff
|
tree
2019-10-18
C
hrist
i
an Bl
a
u
Basic refactor
i
ng genion a
n
d adding test
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Adapt
i
ve force scalin
g
for d
e
nsityfitting
commit
|
commitdiff
|
tree
2019-10-16
Christ
i
an
Bla
u
Exponentia
l
movi
n
g av
e
rage
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Gr
o
mpp
e
rror for
m
i
smatchin
g
nst for ene
r
g
y
calu
l
a
t
ion
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Chr
i
stian Blau
Amendments to density fitti
n
g manua
l
section
commit
|
commitdiff
|
tree
2019-09-22
C
h
ristian Bla
u
Add cross-
c
orrelation
a
s d
e
nsity simla
r
ity meas
u
re
commit
|
commitdiff
|
tree
2019-09-19
Christian
Blau
C
h
eck i
n
pu
t
record also in tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Cons
i
s
ten
t
ly ch
a
nge densit
y
fitting spreading
w
eight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christi
a
n Blau
Add
m
dp optio
n
documentation for density fittin
g
.
commit
|
commitdiff
|
tree
2019-09-12
Chri
s
ti
a
n Blau
M
a
n
ua
l
entry for density g
u
i
de
d
simulations
commit
|
commitdiff
|
tree
2019-09-12
Ch
r
istian Blau
A
dd
r
ele
a
se
note for density fitting
.
commit
|
commitdiff
|
tree
2019-09-11
C
h
r
i
stian Blau
Add comm
e
nts to grompp generate
d
.
m
d
p output for densi
t
yfitt
i
ng
commit
|
commitdiff
|
tree
2019-09-11
Christia
n
Bl
a
u
End to end test for density fitti
n
g
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Densityfitting write int64_t indices instead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian
B
l
a
u
Use the current
mass instead of massA i
n
densit
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Chr
i
s
tian B
l
au
Account
f
or
reference density origin shi
f
t in pbc
c
orrecti
o
n
commit
|
commitdiff
|
tree
2019-09-09
C
h
ristian B
l
au
Relative entropy as density sim
i
lar
i
ty m
e
asure
commit
|
commitdiff
|
tree
2019-09-09
Christ
i
an Blau
Ad
d
option to n
o
rmaliz
e
densiti
e
s
pr
i
or to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Bla
u
A
d
d
i
ng
e
very N-steps
o
ption to
densityfitt
i
ng
commit
|
commitdiff
|
tree
2019-09-06
Ch
r
isti
a
n
Bl
a
u
Adding ene
r
gy out
p
u
t
field for de
n
s
i
t
y fittin
g
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
P
e
riodic bou
n
da
r
y correction for d
e
nsit
y
fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian Bl
a
u
Add refere
n
c
e
den
s
ity fi
l
e option to densi
t
yfit
t
ing
commit
|
commitdiff
|
tree
2019-09-04
Christ
i
an Bla
u
Fix d
o
u
ble overl
o
ad in Lo
c
alAtomSet
code when gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Ch
r
i
stian Blau
Read
mrc file usin
g
file name
commit
|
commitdiff
|
tree
2019-09-01
Christian Bl
a
u
Add checkpointing for MdMo
d
u
les
commit
|
commitdiff
|
tree
2019-08-30
Christian Bl
a
u
Constructing local atom se
t
s for density
f
itt
i
n
g
commit
|
commitdiff
|
tree
2019-08-30
Christia
n
Blau
Lo
c
alAto
m
Set construction with vect
o
rs of gmx::in
d
ex
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n Blau
I
m
p
l
ement
i
n
g t
h
e
density fitt
i
ng fo
r
ce
p
ro
v
id
e
r
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Add
d
ensity fit
t
ing parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Ac
c
ess to GaussTrans
f
o
r
m3D
d
at
a
commit
|
commitdiff
|
tree
2019-08-27
C
h
rist
i
a
n
Blau
A
dd
i
ndex group option to density fittin
g
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activation of
d
e
n
sity
fitting and
m
ove of
m
odule notifications
commit
|
commitdiff
|
tree
2019-08-25
Christian Blau
Index g
r
ou
p
s for MdModules from grompp
commit
|
commitdiff
|
tree
2019-08-17
Ch
r
istian Bl
a
u
Fix segfa
u
l
t
with
o
l
d tprs proce
s
sing intern
a
l
par
a
meters
commit
|
commitdiff
|
tree
2019-08-15
C
h
rist
i
an Blau
Move
d
ensityfitting options and output into sepe
r
a
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
hristian Blau
In
f
o class
t
o nam
e
a
n
d generat
e
the densityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
rist
i
a
n Bla
u
Int
e
rnal
p
a
r
ameter s
t
o
r
a
ge for IMDM
o
dules
commit
|
commitdiff
|
tree
2019-08-08
Ch
r
istian Blau
Har
m
oniz
e
mrc density for
m
at
e
xtents with
rest
o
f code
.
commit
|
commitdiff
|
tree
2019-08-08
Christia
n
Blau
Pro
v
ide callbacks/not
i
fications f
o
r
MDModules
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing check-sou
r
ce targ
e
t on
p
ython3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Chri
s
tian Bla
u
Fix HTML sourc
e
doc
u
men
a
t
i
on err
o
r
ca
u
sed
by
G
aus
s
T
r
ansform3D
commit
|
commitdiff
|
tree
2019-06-28
Chris
t
i
a
n
Blau
Add copy and move operati
o
n
s
to density s
i
m
ilari
t
y
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add
c
lass to look
u
p densit
y
fitt
i
ng a
m
plit
u
des
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
A
dd coordinate
s
caling class and ext
e
nd TranslateAndScale
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
stian Blau
Al
l
ow non-uniform Gaussi
a
ns
commit
|
commitdiff
|
tree
2019-06-20
Chris
t
ian Blau
Add Basic
V
e
ctor scaling, max, mi
n
and toIvec
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Mrc format header to lattice
coordina
t
e transform
commit
|
commitdiff
|
tree
2019-06-18
Christian Bl
a
u
Density
similarity
mea
s
ure and grad
i
ent
commit
|
commitdiff
|
tree
2019-04-27
Chris
t
ian Blau
mrc density map reading/writi
n
g
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
Three
dimensional
c
oordiante transf
o
rma
t
ion
.
commit
|
commitdiff
|
tree
2019-04-25
Christi
a
n Bla
u
den
s
i
t
y fitting forces
commit
|
commitdiff
|
tree
2019-04-22
Ch
r
istian
Blau
Three dimensi
o
nal gauss tran
s
fo
r
m
commit
|
commitdiff
|
tree
2019-04-22
Christian
Bla
u
O
n
e
dime
n
s
i
onal Gaussian func
t
io
n
o
n
l
attice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian
Blau
dens
i
tyfit
t
ing -
M
DModu
l
e declaratio
n
commit
|
commitdiff
|
tree
2019-03-22
Christ
i
an Blau
densityfittin
g
-
s
erializer for
m
r
c h
e
ader da
t
a
.
commit
|
commitdiff
|
tree
2019-03-19
Chris
t
ia
n
B
lau
densityfitting -
d
e
ns
i
t
y
file
f
or
m
at (mrc) header
.
commit
|
commitdiff
|
tree
2019-02-12
C
h
r
i
stia
n
Blau
3x3 matric
e
s
commit
|
commitdiff
|
tree
2019-02-11
Christian Blau
view on M
u
l
tiDimArray
commit
|
commitdiff
|
tree
2019-02-07
Chr
i
s
t
ian
Blau
mdspan
-
add
b
racket operator slicin
g
commit
|
commitdiff
|
tree
2019-02-04
Christian Bl
a
u
md
s
pan - fre
e
begi
n
and
en
d
f
unctio
n
s
commit
|
commitdiff
|
tree
2019-02-04
Christian Bla
u
multidimensional array - bugfix swap
commit
|
commitdiff
|
tree
2019-01-24
Christ
i
an Blau
Remove extra
semi
c
olons cau
s
ing clang warnings
.
commit
|
commitdiff
|
tree
2019-01-23
C
hristian Blau
Multidimensional data
in ca
n
oni
c
al layout
.
commit
|
commitdiff
|
tree
2018-12-26
Chr
i
stia
n
Blau
mdspan -
b
asi
c
_mdspan
a
nd mdspan declaration
commit
|
commitdiff
|
tree
2018-12-20
Chri
s
tian Blau
m
dspan - basic ac
c
esso
r
p
o
l
i
c
y
commit
|
commitdiff
|
tree
2018-12-20
Christian Blau
mdspan -
mapp
i
n
g
for
r
i
ght l
a
yout
commit
|
commitdiff
|
tree
2018-12-04
Christian Bl
a
u
mdspan - extents of multidimens
i
onal arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian Blau
mds
p
an - basic infrastruc
t
ure
commit
|
commitdiff
|
tree
2018-08-30
Christia
n
Blau
Convert
e
ssent
i
al dyna
m
ics C-stru
c
ts to
C
+
+ pt1
.
commit
|
commitdiff
|
tree
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