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Address review comments
2020-04-17
Christian Blau
p
roposed
fix for
redmine bug #3403
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
R
e
move
d
ysfunc
t
i
o
nal QMMM interfac
e
pt4
commit
|
commitdiff
|
tree
2020-03-16
Chris
t
i
an Blau
Remove dysfuncti
o
nal
Q
MM
M
interface
pt3
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
R
emove dysfun
c
tional Q
M
MM interfac
e
pt2
commit
|
commitdiff
|
tree
2020-03-16
C
hristian Blau
Remove dys
f
unctio
n
al QMMM int
e
rf
a
ce pt1
commit
|
commitdiff
|
tree
2020-03-11
Christ
i
a
n
Bla
u
Amend
o
p
t
ional docum
e
n
tation
commit
|
commitdiff
|
tree
2020-03-05
C
hristian Bl
a
u
Add function calls t
o
Md
M
odules to sign up f
o
r notifications
commit
|
commitdiff
|
tree
2020-03-05
Chris
t
ian Blau
Spli
t
o
ff implementa
t
ion details of
MdModu
l
e
Notification
commit
|
commitdiff
|
tree
2020-03-04
Ch
r
is
t
ia
n
Blau
Save exclud
e
d non-bonded interaction
s
i
n
.
tpr file
commit
|
commitdiff
|
tree
2020-03-04
Christian
B
lau
Add cl
a
sshelper macro
to forbid copy,
m
ove and any
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Chr
i
stian Blau
Do
c
ument den
s
ity
-
fit cross
-
cor
r
elation in
.
mdp o
p
tions
commit
|
commitdiff
|
tree
2020-02-18
Christia
n
B
l
au
Sp
l
it MdModuleNotifica
t
i
ons
into topics
commit
|
commitdiff
|
tree
2020-02-12
Christian Blau
Int
r
oduce readXvgDa
t
a to read xvg dat
a
int
o
std::ve
c
tor
commit
|
commitdiff
|
tree
2020-01-31
C
h
ris
t
ian Blau
D
ocume
n
tation fix for loc
a
l
a
tom se
t
da
t
a
commit
|
commitdiff
|
tree
2019-12-20
Ch
r
ist
i
an Blau
Remove proble
m
a
t
i
c
o
utput
o
f gmx angle
commit
|
commitdiff
|
tree
2019-12-15
Christian
B
lau
Fix densityfit
t
ing st
a
lling and energies
commit
|
commitdiff
|
tree
2019-12-12
Christian
Blau
Densityfitti
n
g - enforce similar
i
ty incr
e
ase
with adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
Chan
g
e arbitrary units to count
s
in RMSD distance distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christi
a
n
Bl
a
u
Relax cross-
c
orre
l
ation test pre
c
ision
commit
|
commitdiff
|
tree
2019-12-04
Christian Blau
R
emove cutof
f
-scheme grou
p
from
default mdout
.
mdp o
u
tput
commit
|
commitdiff
|
tree
2019-12-02
Christian
B
lau
Relax tes
t
tolera
n
ce fo
r
cross correla
t
ion me
a
s
ur
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
C
hris
t
ian Bl
a
u
Fix check-p
o
inting
f
or density gu
i
ded si
m
ulations
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Fix
d
up
l
ica
t
e
CONN
E
CT records in
p
db files
commit
|
commitdiff
|
tree
2019-11-25
C
h
ristian Blau
Read mrc den
s
ity map form
a
t wit
h
all e
n
dianes
s
es
.
commit
|
commitdiff
|
tree
2019-11-25
Christ
i
an Blau
Che
c
k mrc header for
s
anity
commit
|
commitdiff
|
tree
2019-11-24
Christ
i
an Blau
I
nMemorySerializer with endianess swap
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
Stochast
i
c
dynamics -
document that nsttco
u
ple
is ignored
commit
|
commitdiff
|
tree
2019-11-01
Ch
r
ist
i
an Blau
Fix c
r
os
s
-
c
o
rre
l
a
tion cal
c
ulation instability
commit
|
commitdiff
|
tree
2019-10-22
C
h
r
ist
i
an Bla
u
Fi
x
nst in density
-
fitting
m
o
d
ule
commit
|
commitdiff
|
tree
2019-10-18
Christian
B
l
a
u
Manua
l
en
t
r
y and
.
mdp option for adap
t
ive for
c
e
scaling
commit
|
commitdiff
|
tree
2019-10-18
Ch
r
i
stian Blau
ge
n
io
n
: prohibit ion
plac
e
ment close to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refacto
r
ing genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Chris
t
ian Blau
Adaptive
f
orce scalin
g
for densi
t
yfitti
n
g
commit
|
commitdiff
|
tree
2019-10-16
Chr
i
stian Blau
Ex
p
onenti
a
l
m
ovin
g
ave
r
ag
e
commit
|
commitdiff
|
tree
2019-09-23
C
h
ristian Blau
G
r
omp
p
error for
m
i
s
matching nst for
e
n
ergy calulation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Chris
t
ian Blau
Amendme
n
ts to density fitti
n
g manual section
commit
|
commitdiff
|
tree
2019-09-22
C
h
rist
i
an Blau
Add cross-correlation as
density si
m
larity measure
commit
|
commitdiff
|
tree
2019-09-19
C
hr
i
stian
Bl
a
u
C
h
eck in
p
ut record also
in test
s
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
Cons
i
stently change densityfitting spreading weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
C
h
rist
i
an Bl
a
u
A
dd m
d
p option documentat
i
on fo
r
density
fitt
i
n
g
.
commit
|
commitdiff
|
tree
2019-09-12
C
h
ri
s
t
i
an Blau
Manual
entry
fo
r
densi
t
y guided si
m
ulations
commit
|
commitdiff
|
tree
2019-09-12
Christian
Blau
Add rele
a
se note for
d
e
nsity fitting
.
commit
|
commitdiff
|
tree
2019-09-11
Chri
s
t
i
a
n
Blau
Add comments to grompp ge
n
era
t
ed
.
md
p
o
u
t
p
u
t for dens
i
tyfitti
n
g
commit
|
commitdiff
|
tree
2019-09-11
Christi
a
n
Blau
End to end test for
d
ensity fitting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
D
e
n
sityf
i
t
ting wr
i
te int64_
t
indices inste
a
d of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian
Bl
a
u
Use
the current mass instead of massA in d
e
ns
i
t
y
f
i
t
tin
g
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Ch
r
istian
Blau
Acco
u
n
t
f
o
r reference d
e
nsity
o
rigin shift in
p
bc c
o
r
r
e
c
tion
commit
|
commitdiff
|
tree
2019-09-09
Ch
r
istian Blau
Relative entropy
as density similarity
m
easur
e
commit
|
commitdiff
|
tree
2019-09-09
Chr
i
s
t
ian Blau
Ad
d
o
pti
o
n
t
o norm
a
lize densi
t
ies prior to dens
i
ty
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Bla
u
Addi
n
g every N-step
s
option
to densityfitti
n
g
commit
|
commitdiff
|
tree
2019-09-06
C
hristian Blau
Addin
g
energy output field for de
n
sity fitti
n
g
commit
|
commitdiff
|
tree
2019-09-06
C
hris
t
ia
n
Bl
a
u
Peri
o
dic
b
o
undary corre
c
tion for de
n
sity f
i
tting
commit
|
commitdiff
|
tree
2019-09-05
Christia
n
Blau
Add r
e
ference density f
i
le
option to densi
t
yfitting
commit
|
commitdiff
|
tree
2019-09-04
C
hristian Blau
F
i
x double over
l
oad in
L
ocalAt
o
mSet code w
h
en gmx
:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christian
B
lau
Read m
r
c
file
u
s
ing file name
commit
|
commitdiff
|
tree
2019-09-01
Chri
s
tian Blau
Add
ch
e
ckp
o
intin
g
for MdModules
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian Blau
Constructin
g
local at
o
m s
e
ts
for de
n
sity fitting
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
LocalA
t
o
mSet construction with v
e
ctors of
gmx::ind
e
x
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Implementing the density fitting
f
orce provider
commit
|
commitdiff
|
tree
2019-08-27
Chris
t
ian Blau
Add density fitt
i
n
g
parameters
commit
|
commitdiff
|
tree
2019-08-27
C
h
ristian Blau
Access to GaussTransfor
m
3D
data
commit
|
commitdiff
|
tree
2019-08-27
Christ
i
an
Blau
Add in
d
ex group option to
d
ensity fitting
commit
|
commitdiff
|
tree
2019-08-26
Christian B
l
au
A
ctivation of
d
ensit
y
fitting and m
o
ve of modul
e
notifications
commit
|
commitdiff
|
tree
2019-08-25
Ch
r
istian Bl
a
u
Index groups for MdModules from grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian Blau
Fix s
e
gfault with o
l
d
tpr
s
pr
o
cessi
n
g internal
p
arameters
commit
|
commitdiff
|
tree
2019-08-15
Christian B
l
au
Move densi
t
yfitting o
p
tion
s
an
d
output
i
nto
s
eperat
e
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Chri
s
tian
B
l
a
u
Info class to
n
ame and generate the
d
ensit
y
f
itting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
ristian Blau
Internal paramet
e
r stora
g
e for IM
D
M
o
d
ules
commit
|
commitdiff
|
tree
2019-08-08
Ch
r
istian Blau
Ha
r
m
o
nize
mrc den
s
ity format extents with
rest of cod
e
.
commit
|
commitdiff
|
tree
2019-08-08
Ch
r
istian Blau
Provide call
b
acks/notificati
o
ns for M
D
Modules
commit
|
commitdiff
|
tree
2019-07-26
Ch
r
i
stian B
l
a
u
Fix failing check-so
u
rce target on python3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Christian
B
l
au
Fix HTML sour
c
e
d
ocum
e
nation error caused by GaussT
r
ans
f
o
r
m3D
commit
|
commitdiff
|
tree
2019-06-28
Christian B
l
au
Add c
o
py and move operations to
de
n
s
it
y
simi
l
arity
commit
|
commitdiff
|
tree
2019-06-28
Ch
r
istian Blau
Add
class to look u
p
densit
y
fitting
amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
A
d
d coordi
n
ate
s
caling
class
a
nd
e
xte
n
d TranslateAndScale
commit
|
commitdiff
|
tree
2019-06-20
C
hristian
B
l
a
u
Allow
n
o
n-unif
o
r
m
G
a
ussi
a
ns
commit
|
commitdiff
|
tree
2019-06-20
Christian
Blau
Add
BasicVe
c
tor
scaling, max, min
a
n
d toIvec
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Mrc form
a
t header to lat
t
ic
e
coordinate transform
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Density
similarity measure and gradient
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
mrc densi
t
y map reading/writing
commit
|
commitdiff
|
tree
2019-04-27
Ch
r
istian Blau
Three di
m
ensio
n
al c
o
o
r
diante transforma
t
ion
.
commit
|
commitdiff
|
tree
2019-04-25
Christi
a
n Blau
density f
i
tting fo
r
ces
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
Three d
i
mensional gauss tran
s
form
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
One dimensio
n
al
Gaussian
f
unction
o
n lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian
Bla
u
d
e
nsityfitting - MDModule declaration
commit
|
commitdiff
|
tree
2019-03-22
C
hristian B
l
au
densityfitting - serializer for mrc header data
.
commit
|
commitdiff
|
tree
2019-03-19
Christian Blau
densityfitting - density file format (mrc) header
.
commit
|
commitdiff
|
tree
2019-02-12
C
h
ristian Blau
3
x
3 matrices
commit
|
commitdiff
|
tree
2019-02-11
Christia
n
Blau
v
i
e
w on Mul
t
iDimArr
a
y
commit
|
commitdiff
|
tree
2019-02-07
Chri
s
tia
n
B
l
au
m
d
s
pan
- add br
a
cket operator
slicing
commit
|
commitdiff
|
tree
2019-02-04
Christian B
l
au
mdspan - free
b
egin a
n
d e
n
d
funct
i
ons
commit
|
commitdiff
|
tree
2019-02-04
Christian
Blau
multid
i
m
ensiona
l
array
- bugfix s
w
ap
commit
|
commitdiff
|
tree
2019-01-24
Christian Blau
Rem
o
ve extr
a
semicolo
n
s causing clang warnings
.
commit
|
commitdiff
|
tree
2019-01-23
Chris
t
i
a
n Bl
a
u
M
u
ltidimensi
o
na
l
d
ata
i
n canonical l
a
you
t
.
commit
|
commitdiff
|
tree
2018-12-26
Christia
n
Bl
a
u
mdspan - bas
i
c_mdspan
an
d
mdsp
a
n
declaration
commit
|
commitdiff
|
tree
2018-12-20
Christ
i
an Blau
m
ds
p
a
n
- basic accessor policy
commit
|
commitdiff
|
tree
2018-12-20
C
hrist
i
an Blau
m
d
s
p
a
n
- mapp
i
ng for r
i
gh
t
layout
commit
|
commitdiff
|
tree
2018-12-04
Christian
Blau
mds
p
an -
extents of mu
l
t
i
dim
e
n
sional arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian B
l
au
m
d
span
- basic i
n
frastru
c
ture
commit
|
commitdiff
|
tree
2018-08-30
Christ
i
an Blau
Convert e
s
senti
a
l dynami
c
s C-structs to C++ pt1
.
commit
|
commitdiff
|
tree
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