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Added more docs and tests to EnumerationArray
2020-02-18
C
hris
t
ian Bla
u
Split MdModuleNotifications in
t
o topics
commit
|
commitdiff
|
tree
2020-02-12
Chri
s
t
ian Bl
a
u
Intro
d
u
c
e
readXvgDat
a
to r
e
ad xvg dat
a
i
nto
std::vect
o
r
commit
|
commitdiff
|
tree
2020-01-31
Christian Blau
D
ocumentat
i
on fix for loc
a
l atom set data
commit
|
commitdiff
|
tree
2019-12-20
Christia
n
Blau
R
em
o
ve problematic output
of gmx
a
n
gle
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
Fix den
s
ityfitting s
t
allin
g
and energies
commit
|
commitdiff
|
tree
2019-12-12
C
hristian Blau
D
e
nsit
y
fitting - enforce si
m
il
a
rity in
c
r
e
ase
with adapti
v
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
Change
a
rbitrary units to count
s
in RMSD distance
distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christian Blau
R
elax c
r
oss-cor
r
ela
t
ion t
e
st precision
commit
|
commitdiff
|
tree
2019-12-04
C
h
ristian Blau
Remove
cutoff-scheme
gro
u
p f
r
o
m
defau
l
t
mdout
.
mdp out
p
ut
commit
|
commitdiff
|
tree
2019-12-02
C
h
rist
i
an Blau
Relax
t
est toler
a
nce for cross
c
orrelati
o
n
mea
s
ure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Chris
t
ian Blau
Fix
c
heck-pointing for de
n
si
t
y guided simulat
i
ons
commit
|
commitdiff
|
tree
2019-11-25
C
h
ristian Blau
F
ix dup
l
icate CONNECT
recor
d
s in p
d
b fi
l
es
commit
|
commitdiff
|
tree
2019-11-25
C
h
ristian
B
lau
Read
mrc density
m
ap fo
r
mat
w
ith all endia
n
esses
.
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian Bla
u
Ch
e
ck mr
c
hea
d
er for
s
anity
commit
|
commitdiff
|
tree
2019-11-24
Christian Bl
a
u
InMemo
r
y
S
erializer
with endianess swap
.
commit
|
commitdiff
|
tree
2019-11-07
Christian B
l
au
Stochastic dynamics - document that ns
t
tcou
p
l
e
i
s ignored
commit
|
commitdiff
|
tree
2019-11-01
Christi
a
n
Blau
Fix
cro
s
s-correlation calculation instabili
t
y
commit
|
commitdiff
|
tree
2019-10-22
C
h
ristian
B
lau
Fix
n
st
in density-fit
t
ing mo
d
ule
commit
|
commitdiff
|
tree
2019-10-18
Christian
Blau
M
a
nual
e
ntry and
.
mdp option
f
or adaptive
force scaling
commit
|
commitdiff
|
tree
2019-10-18
Ch
r
ist
i
a
n Blau
genio
n
: prohibit ion placeme
n
t clos
e
to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refactori
n
g
g
e
n
ion and a
d
ding tes
t
commit
|
commitdiff
|
tree
2019-10-18
C
h
ris
t
ian Blau
Adap
t
ive force s
c
aling for den
s
ityf
i
tting
commit
|
commitdiff
|
tree
2019-10-16
Christian Blau
Exponen
t
ial moving a
v
erage
commit
|
commitdiff
|
tree
2019-09-23
Christian
Blau
Grompp error for
m
i
s
matching nst for energy calulati
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Chris
t
ian B
l
au
Amend
m
ents to density fitting
manual secti
o
n
commit
|
commitdiff
|
tree
2019-09-22
Christ
i
an B
l
au
Add
cross-co
r
r
e
lation as density siml
a
rity measur
e
commit
|
commitdiff
|
tree
2019-09-19
Chr
i
stia
n
B
l
au
C
heck inp
u
t recor
d
also
i
n tests
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
Consistently change de
n
sit
y
fit
t
ing
spreading w
e
ight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christia
n
Blau
Add mdp op
t
ion documentatio
n
for density
f
itting
.
commit
|
commitdiff
|
tree
2019-09-12
Christian Bla
u
Manu
a
l entry fo
r
density guided simulations
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
A
dd rele
a
se note for density fit
t
i
ng
.
commit
|
commitdiff
|
tree
2019-09-11
Ch
r
istian Blau
A
d
d
c
omments t
o
grompp generated
.
mdp output for dens
i
t
yfitting
commit
|
commitdiff
|
tree
2019-09-11
C
hri
s
tian Blau
E
n
d to end test for density
f
itting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
D
e
nsityfitting write int64_t
indice
s
instead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Use the current mass
i
nstead of massA in
d
ensi
t
y
fitt
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christi
a
n
Blau
Acc
o
unt for reference de
n
s
i
t
y
origin shift in
pb
c
c
or
r
ect
i
on
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relative entropy
a
s densi
t
y similarity mea
s
ure
commit
|
commitdiff
|
tree
2019-09-09
Christ
i
an Blau
Add
o
ptio
n
to normalize densitie
s
pr
i
or
t
o
d
ensity
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
C
hrist
i
an Blau
A
d
d
i
ng
every N-steps
opti
o
n to
d
ensityfitting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
A
d
d
i
ng energy output field for density fitting
commit
|
commitdiff
|
tree
2019-09-06
C
h
r
i
stian Blau
Per
i
odic bou
n
dary correction for density
fitting
commit
|
commitdiff
|
tree
2019-09-05
Ch
r
is
t
ian
Blau
Add
reference density file o
p
ti
o
n to densityfi
t
ti
n
g
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Fix
double overload in
LocalAtomSet c
o
de when gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christia
n
Blau
Read mrc file
u
sing f
i
le n
a
me
commit
|
commitdiff
|
tree
2019-09-01
C
h
ristian Blau
Add ch
e
c
kp
o
inting
f
or MdM
o
d
ules
commit
|
commitdiff
|
tree
2019-08-30
C
hristian Blau
Construc
t
ing local atom sets for
d
ensity
f
itti
n
g
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
stia
n
Bla
u
LocalAtomSet
construction with v
e
c
t
ors of gmx::ind
e
x
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
stian Blau
Implementing
the density fitting f
o
rce provider
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n
B
lau
Add
d
ensity fi
t
tin
g
parameters
commit
|
commitdiff
|
tree
2019-08-27
C
h
ristia
n
Blau
Acce
s
s
to
Gauss
T
ransform3D data
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add index group option
to densi
t
y fi
t
t
i
ng
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activation of density fitting and move of m
o
d
ule notif
i
ca
t
ions
commit
|
commitdiff
|
tree
2019-08-25
C
h
rist
i
an
B
lau
I
n
dex groups for Md
M
o
d
ules f
r
om grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian Blau
F
ix s
e
gfault with old tprs proces
s
i
ng internal p
a
ramet
e
rs
commit
|
commitdiff
|
tree
2019-08-15
Christian
Blau
Move
d
ensityfitting options an
d
o
u
tput
into seperat
e
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
ristian Blau
Info class
t
o
name and generate th
e
d
ensityfi
t
t
ing
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Ch
r
istian Bla
u
Internal para
m
eter
s
t
orage for IMDModul
e
s
commit
|
commitdiff
|
tree
2019-08-08
Christi
a
n Bla
u
Harmon
i
ze mrc de
n
sity
format extents with rest of co
d
e
.
commit
|
commitdiff
|
tree
2019-08-08
Christian
Blau
Provide callb
a
cks/notifications for MDModules
commit
|
commitdiff
|
tree
2019-07-26
C
hrist
i
an Blau
Fix fai
l
ing check-source t
a
rget on py
t
hon3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Christian Blau
Fix HTML
source d
o
cumenation er
r
or ca
u
sed by GaussTra
n
sform3D
commit
|
commitdiff
|
tree
2019-06-28
Christian
Blau
A
d
d
c
opy a
n
d move
o
peratio
n
s to density simi
l
arity
commit
|
commitdiff
|
tree
2019-06-28
Christ
i
a
n
Blau
Add
class
t
o l
o
ok up density fitting amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Christian
Blau
Add coordinate scali
n
g class and e
x
tend
T
rans
l
ateAn
d
Scal
e
commit
|
commitdiff
|
tree
2019-06-20
C
h
r
istia
n
Bla
u
A
llow
n
on-uni
f
orm G
a
uss
i
ans
commit
|
commitdiff
|
tree
2019-06-20
Christi
a
n Blau
Add
B
a
sicVector sc
a
ling, m
a
x, min and toIvec
commit
|
commitdiff
|
tree
2019-06-18
Christi
a
n
B
lau
Mr
c
f
ormat heade
r
to latt
i
ce coordinate tr
a
nsform
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
D
e
nsity similarity measure
a
nd
g
radient
commit
|
commitdiff
|
tree
2019-04-27
Christian
Blau
mrc densi
t
y map re
a
ding/writing
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
Three dimensional c
o
ordiante tra
n
s
f
ormation
.
commit
|
commitdiff
|
tree
2019-04-25
Christ
i
an Blau
density fi
t
ting forces
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
T
h
ree di
m
ensional g
a
u
ss transf
o
rm
commit
|
commitdiff
|
tree
2019-04-22
Christi
a
n
Blau
O
ne dim
e
n
sional Ga
u
s
sian function
o
n lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
dens
i
ty
f
itting
-
M
D
Modu
l
e declaratio
n
commit
|
commitdiff
|
tree
2019-03-22
Christian Blau
dens
i
tyfitting - s
e
rializer fo
r
mrc
header
d
ata
.
commit
|
commitdiff
|
tree
2019-03-19
Christ
i
an Blau
d
e
ns
i
tyfitting -
den
s
ity
f
ile format (mrc)
header
.
commit
|
commitdiff
|
tree
2019-02-12
Chri
s
tian
Bl
a
u
3x3 mat
r
ices
commit
|
commitdiff
|
tree
2019-02-11
Christia
n
Blau
vie
w
on MultiDimArray
commit
|
commitdiff
|
tree
2019-02-07
Christian
B
lau
m
d
span - add bracket
operator slicing
commit
|
commitdiff
|
tree
2019-02-04
Chr
i
stian Blau
mdspan - free begi
n
and
e
nd func
t
ions
commit
|
commitdiff
|
tree
2019-02-04
Chr
i
sti
a
n Blau
multi
d
i
mensio
n
a
l arr
a
y
- bugfix swap
commit
|
commitdiff
|
tree
2019-01-24
Chri
s
t
ia
n
B
lau
R
e
move ex
t
ra semicol
o
ns
cau
s
ing clang wa
r
nings
.
commit
|
commitdiff
|
tree
2019-01-23
Christian Blau
Multidime
n
sional data in
canonical layout
.
commit
|
commitdiff
|
tree
2018-12-26
Christian B
l
au
m
dspan - ba
s
ic_mdspan
and mdspan d
e
clarati
o
n
commit
|
commitdiff
|
tree
2018-12-20
C
h
r
i
st
i
an Blau
mdspan - basic a
c
cessor policy
commit
|
commitdiff
|
tree
2018-12-20
Christian Blau
m
dspan - mapp
i
ng for right layou
t
commit
|
commitdiff
|
tree
2018-12-04
Christia
n
Bla
u
mdspan - extents of m
u
ltidimen
s
ional
a
rrays
.
commit
|
commitdiff
|
tree
2018-11-22
Chr
i
stian Bl
a
u
mdspan - bas
i
c infrastructu
r
e
commit
|
commitdiff
|
tree
2018-08-30
C
h
r
i
s
t
ian Bla
u
Convert esse
n
t
i
al dynamics C-structs to
C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
Ch
r
istian Bla
u
S
tor
e
ess
e
ntia
l
dynamics
param
e
ters as vectors instead
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
C
h
ristian
Bl
a
u
Add
test for structural simi
l
arity measures rms
d
and
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
Christ
i
an Bla
u
Remove Debug Helpers from Essenti
a
l
D
ynamics
c
ode
.
commit
|
commitdiff
|
tree
2018-08-08
Ch
r
istian Blau
L
oca
l
atom sets in rota
t
iona
l
p
u
lling
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Essenti
a
l dynamic
s
fu
n
ctions use cons
t
-
ref f
o
r input
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Split essential dynamics eigenve
c
tor reading
.
commit
|
commitdiff
|
tree
2018-08-08
Ch
r
istian Blau
Make
e
ssential dynamics a C++ t
y
p
e
.
commit
|
commitdiff
|
tree
2018-08-07
Chri
s
tian Blau
Local atom sets in compEL / io
n
sw
a
p
ping code
.
commit
|
commitdiff
|
tree
2018-08-04
Christian Blau
S
p
lit essential
d
y
n
amics reading r
o
ut
i
ne
commit
|
commitdiff
|
tree
2018-07-17
Christia
n
B
lau
Loc
a
l atom set
h
andling dur
i
ng simulat
i
o
n
s
.
commit
|
commitdiff
|
tree
2018-07-16
Christian Blau
Add Local
A
tomSet for hand
l
i
n
g atom indi
c
es
.
commit
|
commitdiff
|
tree