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Improve mdrun performance user guide
2019-12-20
Christian Blau
Remove problematic output of gmx a
n
gle
commit
|
commitdiff
|
tree
2019-12-15
Christian
Blau
Fix density
f
i
t
t
ing stallin
g
a
nd
energies
commit
|
commitdiff
|
tree
2019-12-12
Chr
i
s
t
ian Blau
Densityfitting - enforce
si
m
il
a
rity incre
a
se w
i
th adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
Change
a
r
bitrary units to
c
ounts
in RMSD
distance
distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christi
a
n Blau
Relax cross-correlation
t
es
t
precision
commit
|
commitdiff
|
tree
2019-12-04
Christian Bl
a
u
Remove c
u
toff-
s
cheme group f
r
om def
a
ult mdout
.
mdp output
commit
|
commitdiff
|
tree
2019-12-02
Chris
t
ian Blau
Rel
a
x test tolerance
for cross correlation
measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Christian Blau
Fix
check-point
i
ng f
o
r density guide
d
simulat
i
o
ns
commit
|
commitdiff
|
tree
2019-11-25
Christian
Blau
Fix duplica
t
e CONNECT records
in p
d
b
f
iles
commit
|
commitdiff
|
tree
2019-11-25
C
h
ristian Bla
u
Read mrc density
m
ap for
m
at
with a
l
l
end
i
a
n
e
s
se
s
.
commit
|
commitdiff
|
tree
2019-11-25
Christian Bl
a
u
Chec
k
m
r
c header for sanity
commit
|
commitdiff
|
tree
2019-11-24
Ch
r
i
stian Blau
I
n
Memor
y
Serialize
r
with endi
a
n
ess
s
w
a
p
.
commit
|
commitdiff
|
tree
2019-11-07
Ch
r
i
stian Blau
Stochastic dynamic
s
- document
th
a
t nst
t
couple is ignored
commit
|
commitdiff
|
tree
2019-11-01
Chris
t
ian Blau
Fix cross-correlation calculation instab
i
lity
commit
|
commitdiff
|
tree
2019-10-22
Christia
n
Blau
Fix nst
in dens
i
ty-fittin
g
module
commit
|
commitdiff
|
tree
2019-10-18
Christi
a
n B
l
au
Man
u
al entry and
.
mdp option
for adaptive
force scaling
commit
|
commitdiff
|
tree
2019-10-18
Ch
r
istian Blau
ge
n
i
o
n
:
prohibit ion p
l
a
c
ement close to
n
o
n
-
s
olvent
commit
|
commitdiff
|
tree
2019-10-18
Christian
B
lau
Basic refactoring genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Christian
B
lau
A
daptiv
e
force scaling for densityfit
t
ing
commit
|
commitdiff
|
tree
2019-10-16
Christian
Blau
Expone
n
tial
m
o
ving average
commit
|
commitdiff
|
tree
2019-09-23
Christian Bl
a
u
G
rompp error for
mismatchin
g
n
st for energy cal
u
l
a
tion
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Amendments to density fitting manual section
commit
|
commitdiff
|
tree
2019-09-22
Chr
i
stian B
l
au
Add cross-corre
l
ation as density simlari
t
y
m
easure
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian
Blau
C
h
eck input record
a
l
s
o
in
tests
commit
|
commitdiff
|
tree
2019-09-19
Chris
t
ian Blau
Consistently change densityf
i
tting spreadin
g
weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christian Blau
Add mdp op
t
ion documentation for
d
e
nsity fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Manual entry for density
guided simulatio
n
s
commit
|
commitdiff
|
tree
2019-09-12
Christian Bl
a
u
Add relea
s
e note
f
or
d
ens
i
ty
f
itting
.
commit
|
commitdiff
|
tree
2019-09-11
Christian Bla
u
Add comm
e
nts to
gromp
p
g
enerated
.
mdp output for densityfittin
g
commit
|
commitdiff
|
tree
2019-09-11
Christia
n
Blau
End to e
n
d
t
est for density fitting
commit
|
commitdiff
|
tree
2019-09-11
Christian
B
l
au
De
n
sityfitting
w
rite int64_t indices instead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
C
hristian Bl
a
u
Use t
h
e cu
r
rent m
a
ss i
n
s
tead of massA in density fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian
Bl
a
u
Acc
o
unt for reference density
o
rigin shift in pbc co
r
rection
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Re
l
a
tive entropy as density sim
i
larity measure
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
A
dd option
to normal
i
ze densit
i
es p
r
ior to d
e
nsity
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Chris
t
ian Blau
Adding
e
v
ery N
-
steps option to d
e
ns
i
tyfitting
commit
|
commitdiff
|
tree
2019-09-06
Christia
n
B
lau
Adding e
n
e
rgy output fiel
d
for density fitting
commit
|
commitdiff
|
tree
2019-09-06
C
h
ristian
B
lau
Periodic bou
n
dary
c
orrection f
o
r density
f
itting
commit
|
commitdiff
|
tree
2019-09-05
Ch
r
istian
Bl
a
u
Ad
d
reference densi
t
y file option
to densityf
i
t
ti
n
g
commit
|
commitdiff
|
tree
2019-09-04
Chr
i
stian
B
lau
Fix dou
b
le overlo
a
d in LocalAtomSet code w
h
en
g
mx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Chri
s
tian Blau
Re
a
d
mrc file
usi
n
g fil
e
n
a
me
commit
|
commitdiff
|
tree
2019-09-01
Chris
t
ian Blau
Add c
h
eckpointin
g
f
or MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n Blau
Cons
t
r
u
cting local atom sets
for d
e
nsity fitting
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Lo
c
a
lAtomS
e
t construction w
i
th vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n Blau
Implemen
t
ing the dens
i
ty fit
t
i
ng force
p
rovider
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add d
e
ns
i
ty
f
i
t
ting p
a
rameters
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Access to
G
aussTransform3D data
commit
|
commitdiff
|
tree
2019-08-27
Christian Bla
u
Add index group opt
i
on t
o
density fi
t
ti
n
g
commit
|
commitdiff
|
tree
2019-08-26
C
h
risti
a
n Blau
Ac
t
iva
t
ion of de
n
s
i
ty fitting
a
nd move
o
f module
no
t
ifi
c
ations
commit
|
commitdiff
|
tree
2019-08-25
Christian Blau
Index groups for MdModul
e
s from grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian Blau
Fix se
g
fault with old tprs processing inte
r
nal pa
r
ameters
commit
|
commitdiff
|
tree
2019-08-15
Christian
Blau
Mo
v
e densityf
i
tting opt
i
ons and ou
t
put into sepe
r
ate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian B
l
au
Info class to name and generat
e
t
h
e
densityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Inter
n
al param
e
ter storage for IMDModules
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
sti
a
n Blau
Harmonize m
r
c de
n
sity form
a
t
e
xtents
with rest
o
f
c
ode
.
commit
|
commitdiff
|
tree
2019-08-08
Chri
s
t
ian Blau
P
r
ovide callbacks
/
n
o
t
i
fi
c
ati
o
ns
f
or MDModules
commit
|
commitdiff
|
tree
2019-07-26
Chri
s
tian Blau
F
i
x failing che
c
k-
s
ource target o
n
p
ython3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Christian
B
lau
Fix HTML s
o
urce documenation e
r
r
or caused b
y
G
a
us
s
Transfo
r
m
3
D
commit
|
commitdiff
|
tree
2019-06-28
Chr
i
st
i
an
B
lau
Add copy and
m
ove operations to density simi
l
ar
i
ty
commit
|
commitdiff
|
tree
2019-06-28
Chr
i
stian Bl
a
u
Add clas
s
to l
o
ok up density f
i
tting
amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
stian Blau
Add coordina
t
e sca
l
i
ng class and extend Tran
s
l
a
teAndScale
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
A
llow non-uniform Gaus
s
i
ans
commit
|
commitdiff
|
tree
2019-06-20
C
h
ristian
Blau
Add BasicVector scal
i
ng
,
max, min
a
nd toIvec
commit
|
commitdiff
|
tree
2019-06-18
Chris
t
ian Blau
Mrc
f
o
rmat header
to l
a
ttice co
o
rdinate t
r
ansform
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
D
e
n
sity sim
i
larity
m
ea
s
ure and
gradient
commit
|
commitdiff
|
tree
2019-04-27
Christi
a
n
B
lau
mrc density map reading/wr
i
ting
commit
|
commitdiff
|
tree
2019-04-27
Ch
r
istian
Blau
Th
r
e
e
dim
e
ns
i
onal coordian
t
e trans
f
ormation
.
commit
|
commitdiff
|
tree
2019-04-25
C
h
ris
t
ian
B
lau
den
s
ity fitting forces
commit
|
commitdiff
|
tree
2019-04-22
C
h
risti
a
n Blau
Th
r
ee dimensional
gau
s
s
tran
s
form
commit
|
commitdiff
|
tree
2019-04-22
C
hristian
Blau
One di
m
e
nsional Gauss
i
an f
u
nct
i
o
n
on lat
t
i
ce
.
commit
|
commitdiff
|
tree
2019-04-05
C
h
ristian B
l
a
u
d
e
n
s
i
t
y
fitting - MDM
o
d
u
l
e declar
a
tion
commit
|
commitdiff
|
tree
2019-03-22
Ch
r
istian Blau
densityfit
t
ing - serializer for m
r
c
h
e
a
der data
.
commit
|
commitdiff
|
tree
2019-03-19
C
h
ristian
B
la
u
de
n
sity
f
itting - den
s
ity
f
ile fo
r
mat (
m
rc) header
.
commit
|
commitdiff
|
tree
2019-02-12
C
h
ristian
B
lau
3x3 matrices
commit
|
commitdiff
|
tree
2019-02-11
Chris
t
i
a
n
Blau
view on M
u
ltiDimA
r
ray
commit
|
commitdiff
|
tree
2019-02-07
Chri
s
tian Bla
u
mdsp
a
n
- add brac
k
et operat
o
r slicing
commit
|
commitdiff
|
tree
2019-02-04
Christ
i
a
n Blau
mdspan -
f
r
ee beg
i
n an
d
end f
u
nctions
commit
|
commitdiff
|
tree
2019-02-04
Christi
a
n Blau
multidi
m
ens
i
onal array
- bugf
i
x swap
commit
|
commitdiff
|
tree
2019-01-24
Chri
s
tian Blau
Remov
e
extra semic
o
lons causing c
l
a
ng warnings
.
commit
|
commitdiff
|
tree
2019-01-23
C
h
r
ist
i
an
B
la
u
Multidimens
i
onal
d
ata
i
n canoni
c
a
l layo
u
t
.
commit
|
commitdiff
|
tree
2018-12-26
Christi
a
n Blau
mdspan - basic_mdspan an
d
mdspa
n
d
eclaration
commit
|
commitdiff
|
tree
2018-12-20
Ch
r
istian B
l
a
u
mdspan - basic accessor policy
commit
|
commitdiff
|
tree
2018-12-20
C
h
r
istian Blau
mdspan - mapping for right
layout
commit
|
commitdiff
|
tree
2018-12-04
Chr
i
stian Blau
mdspan - extents of mult
i
d
i
m
ensional
arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian B
l
au
md
s
p
a
n - basi
c
infrastruct
u
re
commit
|
commitdiff
|
tree
2018-08-30
Christian Bl
a
u
Convert essential dy
n
am
i
cs C-s
t
ructs to C
+
+ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
Christian Bla
u
Stor
e
es
s
enti
a
l dyna
m
i
c
s p
a
ramete
r
s a
s
vector
s
instea
d
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
C
h
ristian Blau
Ad
d
test f
o
r structur
a
l similar
i
ty measu
r
es
r
m
sd a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
C
h
ristian Bl
a
u
Remove Debug Hel
p
ers f
r
om Essen
t
ial Dynami
c
s code
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Local
a
tom sets in rotati
o
n
a
l
pulling
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Essential dynamics fu
n
ctions use const-ref for input
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Spl
i
t essential dynamics eigenvector
r
e
a
ding
.
commit
|
commitdiff
|
tree
2018-08-08
C
hristian Blau
Make
ess
e
nti
a
l dynamics a C++ t
y
pe
.
commit
|
commitdiff
|
tree
2018-08-07
Chr
i
stia
n
Blau
Loca
l
atom se
t
s
i
n compEL / ion swapping
c
o
de
.
commit
|
commitdiff
|
tree
2018-08-04
Christian Blau
S
p
lit ess
e
nti
a
l dy
n
a
mics reading
r
ou
t
ine
commit
|
commitdiff
|
tree
2018-07-17
Christ
i
a
n Blau
Local atom
s
et
h
and
l
i
n
g durin
g
s
imula
t
i
ons
.
commit
|
commitdiff
|
tree
2018-07-16
C
hristian Bl
a
u
Add LocalAtomSet for handli
n
g atom
i
ndices
.
commit
|
commitdiff
|
tree