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Relax cross-correlation test precision
2019-12-05
Christian Blau
Relax cros
s
-co
r
relation te
s
t
prec
i
s
i
on
commit
|
commitdiff
|
tree
2019-12-04
Christian Blau
Remov
e
cu
t
off-sc
h
eme gr
o
up
fr
o
m default
m
d
ou
t
.
mdp output
commit
|
commitdiff
|
tree
2019-12-02
C
h
ristian
B
lau
Rel
a
x test t
o
le
r
an
c
e for cross correlation
m
easure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Christian B
l
au
Fix check-pointing for
d
ens
i
ty guided simulations
commit
|
commitdiff
|
tree
2019-11-25
Christ
i
an Blau
Fi
x
duplicate CONNECT records in pd
b
files
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
R
e
a
d
m
r
c den
s
ity map f
o
rmat with a
l
l
e
ndianesse
s
.
commit
|
commitdiff
|
tree
2019-11-25
C
hr
i
stian Blau
Check mrc
header for sani
t
y
commit
|
commitdiff
|
tree
2019-11-24
C
h
r
i
stian Bla
u
InMemorySerializ
e
r
with endi
a
ness s
w
a
p
.
commit
|
commitdiff
|
tree
2019-11-07
Chris
t
ian Blau
Stochastic dynamics - documen
t
tha
t
n
s
ttcouple is ig
n
ored
commit
|
commitdiff
|
tree
2019-11-01
Ch
r
istian Blau
Fix cross-
c
orre
l
ation cal
c
ulation instabi
l
ity
commit
|
commitdiff
|
tree
2019-10-22
Christian B
l
au
F
i
x nst in density-fitting module
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Manu
a
l
e
ntry and
.
m
d
p
o
ption for adaptive
f
orce scaling
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
geni
o
n: prohibit ion placeme
n
t close t
o
n
o
n-sol
v
ent
commit
|
commitdiff
|
tree
2019-10-18
C
h
ristian
B
la
u
Bas
i
c ref
a
ctorin
g
g
e
nion
an
d
adding tes
t
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Adaptiv
e
force
s
caling for densityfitting
commit
|
commitdiff
|
tree
2019-10-16
C
h
ristian
B
la
u
Expon
e
ntial moving
average
commit
|
commitdiff
|
tree
2019-09-23
Christi
a
n B
l
a
u
Grompp err
o
r for m
i
s
m
atching nst for e
n
ergy calulatio
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christ
i
an Blau
Amend
m
en
t
s t
o
dens
i
ty fit
t
in
g
manual section
commit
|
commitdiff
|
tree
2019-09-22
Chri
s
tian
B
lau
A
dd cr
o
ss-c
o
rre
l
ati
o
n
a
s
density
si
m
larity measur
e
commit
|
commitdiff
|
tree
2019-09-19
C
hrist
i
an Bl
a
u
C
h
eck inp
u
t re
c
ord also in
t
ests
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
C
onsis
t
ently ch
a
nge
d
ensit
y
fitti
n
g spreading weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christian
B
lau
A
dd mdp op
t
ion
documentation for d
e
nsity fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Christian
Blau
M
a
nual entry f
o
r density guided simulations
commit
|
commitdiff
|
tree
2019-09-12
Chr
i
st
i
an
Bl
a
u
Add
release no
t
e fo
r
de
n
sity fi
t
ting
.
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Add comments to grompp g
e
nerate
d
.
m
dp output
f
o
r d
e
nsityf
i
tting
commit
|
commitdiff
|
tree
2019-09-11
Chri
s
tian Blau
E
nd to end test
f
or density fit
t
ing
commit
|
commitdiff
|
tree
2019-09-11
Christian Bla
u
Density
f
i
tting writ
e
int64
_
t i
n
dices in
s
t
e
a
d
o
f
gm
x
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
U
se the current mass i
n
stead of massA in densi
t
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christia
n
Blau
Acc
o
unt fo
r
re
f
erence density origin shif
t
in
pbc correcti
o
n
commit
|
commitdiff
|
tree
2019-09-09
Chris
t
i
a
n Blau
R
e
l
ative entropy as density sim
i
la
r
ity
m
easure
commit
|
commitdiff
|
tree
2019-09-09
Christian Bla
u
A
dd option to normalize densit
i
es prior to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christ
i
a
n Blau
Adding every
N
-steps option to densi
t
yfitting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
A
dding energy outpu
t
fi
e
ld for density fitting
commit
|
commitdiff
|
tree
2019-09-06
Christi
a
n Blau
Periodic
b
o
u
ndar
y
correct
i
on for den
s
i
t
y fitting
commit
|
commitdiff
|
tree
2019-09-05
Ch
r
i
s
t
i
a
n Blau
Add reference d
e
nsit
y
file option to densityfitt
i
ng
commit
|
commitdiff
|
tree
2019-09-04
C
h
ristian Bl
a
u
Fix do
u
ble ov
e
rload in LocalAtomSet code
when gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christian
Blau
Re
a
d mrc file using file name
commit
|
commitdiff
|
tree
2019-09-01
Christian Bl
a
u
Add checkpointing for MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christ
i
a
n Blau
Constr
u
cting loc
a
l atom s
e
ts for density
f
itting
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
stian
B
lau
LocalAtomSet
c
o
nstructi
o
n with vectors o
f
gmx
:
:index
commit
|
commitdiff
|
tree
2019-08-30
Christian
B
l
a
u
Implementing t
h
e density
fi
t
ting f
o
r
ce provider
commit
|
commitdiff
|
tree
2019-08-27
C
h
ris
t
i
a
n Blau
Add density fitt
i
ng
p
aramet
e
rs
commit
|
commitdiff
|
tree
2019-08-27
C
h
r
istia
n
Blau
Access to
GaussTransform3D data
commit
|
commitdiff
|
tree
2019-08-27
Christia
n
Blau
Add index group option to d
e
ns
i
ty fitti
n
g
commit
|
commitdiff
|
tree
2019-08-26
Chr
i
s
t
ian Blau
A
cti
v
at
i
on
o
f density fitting and move of module
n
o
t
i
f
icati
o
ns
commit
|
commitdiff
|
tree
2019-08-25
C
h
ristian Blau
Index
g
r
oups
f
o
r MdModules
from
grompp
commit
|
commitdiff
|
tree
2019-08-17
Christi
a
n Blau
Fix segfault with old tprs proce
s
sing
i
n
t
ernal paramete
r
s
commit
|
commitdiff
|
tree
2019-08-15
Christian Bl
a
u
Move densi
t
yfitting
opt
i
ons and outp
u
t into seperate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christia
n
Blau
Info cla
s
s to name and generate the densityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
r
i
st
i
an
B
lau
Internal
pa
r
a
m
e
ter sto
r
age f
o
r IMD
M
odu
l
es
commit
|
commitdiff
|
tree
2019-08-08
Christian
B
lau
H
a
rmonize mrc
d
ensity for
m
at extents with rest of code
.
commit
|
commitdiff
|
tree
2019-08-08
C
hristian
B
lau
Provi
d
e callbacks/notifications for MDModules
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing check
-
so
u
rce t
a
rge
t
on python
3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Chr
i
stian B
l
au
Fix HT
M
L source docume
n
ation er
r
or caused by
G
aussT
r
ansform
3
D
commit
|
commitdiff
|
tree
2019-06-28
Christian
B
lau
Add copy and
move op
e
rations to den
s
ity similar
i
ty
commit
|
commitdiff
|
tree
2019-06-28
Ch
r
istian
Blau
Add class to look up density fittin
g
a
m
plit
u
d
es
commit
|
commitdiff
|
tree
2019-06-20
Christian B
l
au
A
dd coordinate s
c
alin
g
cl
a
ss and extend Translate
A
n
dScale
commit
|
commitdiff
|
tree
2019-06-20
Christi
a
n Blau
Allow
non-uniform Gaussians
commit
|
commitdiff
|
tree
2019-06-20
Christ
i
an Bl
a
u
Add
BasicVect
o
r s
c
aling, max, m
i
n and toI
v
ec
commit
|
commitdiff
|
tree
2019-06-18
C
h
ristian Blau
Mrc format he
a
der
t
o
l
a
ttice coordi
n
at
e
trans
f
orm
commit
|
commitdiff
|
tree
2019-06-18
C
hristian Blau
Den
s
ity simila
r
i
t
y m
e
asure an
d
gradient
commit
|
commitdiff
|
tree
2019-04-27
Chri
s
ti
a
n Blau
m
rc de
n
sity m
a
p rea
d
ing/writ
i
n
g
commit
|
commitdiff
|
tree
2019-04-27
Ch
r
istian Bl
a
u
Three dimensional coordiante
transformation
.
commit
|
commitdiff
|
tree
2019-04-25
Christian
B
l
a
u
density fitti
n
g f
o
rc
e
s
commit
|
commitdiff
|
tree
2019-04-22
Chri
s
tia
n
Blau
Three d
i
mensi
o
nal gauss t
r
ansform
commit
|
commitdiff
|
tree
2019-04-22
Christ
i
a
n Blau
One dimensional G
a
ussian function
o
n lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
dens
i
tyf
i
tting
-
M
D
M
o
dule de
c
la
r
ation
commit
|
commitdiff
|
tree
2019-03-22
Christian Blau
densityfitti
n
g
-
s
e
rialize
r
for mrc header data
.
commit
|
commitdiff
|
tree
2019-03-19
Christian Blau
densityfitt
i
ng - density file format (mrc) he
a
der
.
commit
|
commitdiff
|
tree
2019-02-12
Christian Blau
3x3 matrices
commit
|
commitdiff
|
tree
2019-02-11
Chri
s
tian Bla
u
view o
n
Mul
t
iDimArray
commit
|
commitdiff
|
tree
2019-02-07
Christian Bl
a
u
mdspan - ad
d
bracke
t
op
e
rat
o
r sl
i
c
i
ng
commit
|
commitdiff
|
tree
2019-02-04
Christian
B
lau
m
d
span
- fr
e
e b
e
gin
a
nd end f
u
nctions
commit
|
commitdiff
|
tree
2019-02-04
Christian Blau
multidimensional array
-
bugfix s
w
ap
commit
|
commitdiff
|
tree
2019-01-24
Chris
t
i
a
n Bla
u
Remove extra se
m
i
c
o
lo
n
s causing c
l
ang warnings
.
commit
|
commitdiff
|
tree
2019-01-23
C
h
ristian Bl
a
u
Multidimensi
o
nal da
t
a in
c
anonical layout
.
commit
|
commitdiff
|
tree
2018-12-26
Christian Blau
mdspan
- basic_mdspan and mdspan decl
a
ration
commit
|
commitdiff
|
tree
2018-12-20
Chr
i
stian Blau
mdsp
a
n
- basic accessor
p
ol
i
cy
commit
|
commitdiff
|
tree
2018-12-20
Chris
t
i
a
n Blau
mdspan
-
m
ap
p
ing
f
or right lay
o
ut
commit
|
commitdiff
|
tree
2018-12-04
Christian Blau
mdspan -
e
xtents of
m
ultidi
m
ensional
arra
y
s
.
commit
|
commitdiff
|
tree
2018-11-22
Ch
r
ist
i
a
n
B
l
a
u
mdspan
-
basic infrastructure
commit
|
commitdiff
|
tree
2018-08-30
Christian
B
lau
Conv
e
rt esse
n
tial dynamics C-structs to C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
Christ
i
an Bl
a
u
Store
e
s
s
ential dynamics p
a
r
a
meters as vectors inst
e
a
d
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
Christi
a
n Blau
A
d
d test for
s
t
r
uctur
a
l sim
i
l
a
rity measures rmsd a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
C
h
ristian Blau
Remo
v
e Debug He
l
pers f
r
om Essential Dynamics cod
e
.
commit
|
commitdiff
|
tree
2018-08-08
Christian
B
lau
Local atom
s
e
t
s
i
n
r
otational pulling
.
commit
|
commitdiff
|
tree
2018-08-08
C
h
r
istian Blau
Essential dynamic
s
func
t
i
ons use const-re
f
f
o
r
inpu
t
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
S
plit essen
t
ial
d
y
namics
e
ig
e
nvect
o
r r
e
a
din
g
.
commit
|
commitdiff
|
tree
2018-08-08
Chri
s
t
i
an B
l
au
M
a
ke
e
ssential dynamics a C++
type
.
commit
|
commitdiff
|
tree
2018-08-07
Chris
t
i
a
n Blau
Loc
a
l atom set
s
i
n
compEL / ion swapping code
.
commit
|
commitdiff
|
tree
2018-08-04
Chri
s
tian Blau
Split essential dynami
c
s
r
eading routine
commit
|
commitdiff
|
tree
2018-07-17
Christian Blau
Loca
l
atom set handlin
g
d
u
ring simulatio
n
s
.
commit
|
commitdiff
|
tree
2018-07-16
Christian Blau
A
dd
Lo
c
alAt
o
m
S
et for handli
n
g at
o
m indices
.
commit
|
commitdiff
|
tree