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GROMACS 2020 release candidate
2019-12-15
Christian Blau
Fix densi
t
yfitting
s
tal
l
ing and energies
commit
|
commitdiff
|
tree
2019-12-12
Christia
n
Blau
Densit
y
fitting - en
f
o
rc
e
similarity in
c
re
a
se wi
t
h adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christia
n
Blau
Relax cross-correlation test
p
recision
commit
|
commitdiff
|
tree
2019-12-04
Christian Blau
Remove cutoff-scheme group f
r
o
m default mdout
.
mdp ou
t
put
commit
|
commitdiff
|
tree
2019-12-02
Christian Blau
Relax te
s
t tolerance for cross co
r
re
l
ation
me
a
sure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Christian Blau
F
ix check-p
o
inting for
d
ensity
g
uid
e
d sim
u
lations
commit
|
commitdiff
|
tree
2019-11-25
Ch
r
istian Blau
Fix du
p
licate CONNECT r
e
cords
in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Christian B
l
au
R
ead mrc density map format wi
t
h all endianesses
.
commit
|
commitdiff
|
tree
2019-11-25
Christian B
l
au
Ch
e
ck mrc header for sa
n
i
t
y
commit
|
commitdiff
|
tree
2019-11-24
C
h
ristian
Blau
InMe
m
o
r
ySerializer wit
h
endian
e
ss
s
wap
.
commit
|
commitdiff
|
tree
2019-11-07
C
h
r
i
stian Blau
S
t
o
c
h
astic dynamics - d
o
c
ume
n
t that nsttcouple is ignored
commit
|
commitdiff
|
tree
2019-11-01
C
hristian
B
lau
Fix cross-corre
l
ation calcul
a
ti
o
n ins
t
abilit
y
commit
|
commitdiff
|
tree
2019-10-22
Christ
i
an
Blau
F
i
x nst i
n
density-
f
i
t
ting modul
e
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an
B
l
a
u
Manual e
n
try an
d
.
mdp op
t
ion for adaptive force s
c
ali
n
g
commit
|
commitdiff
|
tree
2019-10-18
Chri
s
tian B
l
au
g
enion
:
prohi
b
it ion place
m
ent c
l
ose t
o
non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refactoring genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Chri
s
tian Blau
Adapt
i
ve force scaling
f
or densityfitting
commit
|
commitdiff
|
tree
2019-10-16
Christian Bl
a
u
Exponential moving average
commit
|
commitdiff
|
tree
2019-09-23
Chri
s
tia
n
Bla
u
Grompp erro
r
fo
r
mismatchi
n
g n
s
t
for
e
nergy calulation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Chris
t
ian
Blau
Amendme
n
ts to
densi
t
y
f
itti
n
g ma
n
ual
sec
t
io
n
commit
|
commitdiff
|
tree
2019-09-22
C
hristian Blau
A
dd c
r
o
ss-correlatio
n
as d
e
nsit
y
si
m
lari
t
y me
a
s
u
re
commit
|
commitdiff
|
tree
2019-09-19
Christi
a
n Bla
u
Check input record
a
lso in tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consis
t
ently cha
n
ge densityfitting spre
a
d
ing
weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Ch
r
isti
a
n Bl
a
u
Add mdp option do
c
umentation for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Chris
t
ian Blau
Manual en
t
ry for
d
ensit
y
guided simul
a
tions
commit
|
commitdiff
|
tree
2019-09-12
Chri
s
tian Bl
a
u
Add release note
f
or
d
e
nsity fi
t
ting
.
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Add comments to
grompp
g
enera
t
ed
.
md
p
output
f
or densityfi
t
ting
commit
|
commitdiff
|
tree
2019-09-11
Chri
s
tia
n
Blau
E
n
d to end test for
d
ens
i
ty fitt
i
ng
commit
|
commitdiff
|
tree
2019-09-11
Chri
s
tian Blau
Densityfit
t
i
ng write int64_
t
indices i
n
stead
of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Use the current m
a
ss instead of massA in dens
i
t
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
A
c
co
u
n
t for reference de
n
sity origin shif
t
i
n
p
bc
c
o
r
r
ection
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relative en
t
ro
p
y as dens
i
ty similarit
y
measur
e
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Add o
p
tion to nor
m
alize densities
prior to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christia
n
B
lau
A
ddi
n
g every N-ste
p
s option to den
s
ityfitting
commit
|
commitdiff
|
tree
2019-09-06
C
h
ris
t
ia
n
Bl
a
u
Adding energy output fiel
d
for density fitting
commit
|
commitdiff
|
tree
2019-09-06
Christ
i
an Blau
Periodic boundary correction for density fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian B
l
au
A
d
d reference d
e
nsity file option to de
n
s
ityfitting
commit
|
commitdiff
|
tree
2019-09-04
Christian B
l
au
Fix double overload
in
L
ocalAtomSet co
d
e whe
n
gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Chri
s
tian Blau
Read
mrc
file u
s
i
ng fi
l
e name
commit
|
commitdiff
|
tree
2019-09-01
C
h
ristian Blau
Add checkpointing fo
r
MdM
o
dules
commit
|
commitdiff
|
tree
2019-08-30
C
h
rist
i
an Bla
u
Constructing
l
ocal atom sets for den
s
ity fitting
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian B
l
au
LocalAtomSet co
n
st
r
ucti
o
n with vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Impl
e
menting the
d
ensity fitting
force pr
o
v
ider
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Add density fitting parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian Bla
u
Ac
c
e
ss t
o
Gau
s
sTransform3D da
t
a
commit
|
commitdiff
|
tree
2019-08-27
Chri
s
ti
a
n Blau
A
dd index g
r
oup option to densit
y
f
i
t
tin
g
commit
|
commitdiff
|
tree
2019-08-26
Christian B
l
a
u
Activation of density fit
t
ing
a
nd
move o
f
module notifications
commit
|
commitdiff
|
tree
2019-08-25
Christia
n
B
l
au
Index
groups for
M
dMo
d
ules
from
g
ro
m
pp
commit
|
commitdiff
|
tree
2019-08-17
Christian
Blau
Fix segfault with
o
ld tprs processing internal parameters
commit
|
commitdiff
|
tree
2019-08-15
Christian Blau
Move densityfitting opt
i
ons an
d
output into
seperate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
I
nfo class to name and generate
t
h
e densityfittin
g
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Chri
s
tian Bla
u
Internal
param
e
t
er stor
a
ge for IMDModules
commit
|
commitdiff
|
tree
2019-08-08
C
h
ris
t
ian Blau
Harmonize mrc density forma
t
ex
t
ent
s
w
i
th rest of code
.
commit
|
commitdiff
|
tree
2019-08-08
Christian
B
l
a
u
P
rovide callback
s
/notifications
fo
r
MDModules
commit
|
commitdiff
|
tree
2019-07-26
Christian
Bl
a
u
Fix
failing check-sourc
e
target on python3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Ch
r
i
stian Blau
Fix HT
M
L source documenati
o
n er
r
or caused by GaussTransform3D
commit
|
commitdiff
|
tree
2019-06-28
C
h
r
ist
i
an Bla
u
A
dd c
o
py a
n
d mov
e
operations to density similarity
commit
|
commitdiff
|
tree
2019-06-28
C
h
r
i
st
i
an Blau
Add class to look up
den
s
i
t
y
f
itti
n
g amplitude
s
commit
|
commitdiff
|
tree
2019-06-20
C
hristi
a
n Blau
Add coordinate s
c
aling clas
s
and
exten
d
TranslateA
n
dSc
a
le
commit
|
commitdiff
|
tree
2019-06-20
C
hr
i
stian Blau
A
l
l
o
w non-uniform G
a
uss
i
ans
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
sti
a
n
Blau
Add
B
asicVector
scaling, ma
x
,
m
in and to
I
vec
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Mr
c
f
o
rmat header to latti
c
e coo
r
dina
t
e transform
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Density similarity mea
s
ur
e
and gradi
e
nt
commit
|
commitdiff
|
tree
2019-04-27
Christi
a
n
Blau
mrc de
n
sity map rea
d
ing/writing
commit
|
commitdiff
|
tree
2019-04-27
Chri
s
t
ian Bl
a
u
Three dime
n
si
o
nal coordiante transfor
m
atio
n
.
commit
|
commitdiff
|
tree
2019-04-25
Christian Blau
density fitting forces
commit
|
commitdiff
|
tree
2019-04-22
Chris
t
i
a
n Bl
a
u
Three dimensional
g
auss transform
commit
|
commitdiff
|
tree
2019-04-22
Christian
B
lau
One
dimensional Gauss
i
an function on lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Chri
s
t
i
an Blau
densityfitting
-
MDM
o
dule
declaration
commit
|
commitdiff
|
tree
2019-03-22
Christ
i
an Blau
d
ens
i
tyfitti
n
g - seri
a
l
i
zer for
m
rc
heade
r
data
.
commit
|
commitdiff
|
tree
2019-03-19
Ch
r
istian
B
lau
densityfitting - density file format
(mrc) header
.
commit
|
commitdiff
|
tree
2019-02-12
C
hristian
B
lau
3x3 matri
c
e
s
commit
|
commitdiff
|
tree
2019-02-11
C
h
r
is
t
ian Blau
view on MultiDim
A
rray
commit
|
commitdiff
|
tree
2019-02-07
Christi
a
n Blau
md
s
pan -
a
dd bracket oper
a
to
r
s
l
icing
commit
|
commitdiff
|
tree
2019-02-04
Chr
i
stian Blau
mdspan - free begin an
d
en
d
functio
n
s
commit
|
commitdiff
|
tree
2019-02-04
Christian
B
lau
mult
i
dimens
i
o
n
al
array
-
bugfix s
w
a
p
commit
|
commitdiff
|
tree
2019-01-24
Ch
r
istian Blau
Remove e
x
tra semicolons ca
u
sing cl
a
ng
w
arn
i
ngs
.
commit
|
commitdiff
|
tree
2019-01-23
Chri
s
tian Blau
Mult
i
d
i
mensional data in ca
n
onic
a
l layout
.
commit
|
commitdiff
|
tree
2018-12-26
Christian Blau
mdspan - basic_
m
dsp
a
n
and mdspan declar
a
t
i
on
commit
|
commitdiff
|
tree
2018-12-20
Chris
t
ian B
l
au
mdsp
a
n
-
ba
s
ic acce
s
sor
policy
commit
|
commitdiff
|
tree
2018-12-20
Chr
i
stian
B
lau
mdspan
-
map
p
ing for right l
a
you
t
commit
|
commitdiff
|
tree
2018-12-04
C
hr
i
s
t
i
an Blau
mdspan - extents of multidimensional arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian Blau
mdspan -
b
asi
c
i
n
frastructure
commit
|
commitdiff
|
tree
2018-08-30
Chr
i
stia
n
B
l
au
Conve
r
t es
s
e
ntia
l
dyna
m
ics
C-stru
c
ts to C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
C
hr
i
stian
Bl
a
u
Store essential dyna
m
ics parameters as vecto
r
s instead
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
Christian
B
la
u
Ad
d
t
e
s
t for
s
tructural s
i
m
i
larity measures rm
s
d and
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
Chris
t
i
a
n
B
lau
Remov
e
D
ebug H
e
l
pers
f
rom Essent
i
al Dy
n
amics code
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Loca
l
a
tom sets in rotational p
u
lling
.
commit
|
commitdiff
|
tree
2018-08-08
Chr
i
sti
a
n Blau
Essential dynamics fun
c
tions
use const-
r
ef for inpu
t
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Split essential dynam
i
cs e
i
ge
n
vecto
r
readin
g
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Make
e
s
s
ential dyna
m
ics a
C++
t
ype
.
commit
|
commitdiff
|
tree
2018-08-07
Ch
r
istian Blau
Local atom sets in compEL / ion
swapping code
.
commit
|
commitdiff
|
tree
2018-08-04
Christian Blau
Spl
i
t esse
n
tial dynamics rea
d
i
ng rou
t
ine
commit
|
commitdiff
|
tree
2018-07-17
Chr
i
stian Bl
a
u
Lo
c
al atom set handling
d
uring simulation
s
.
commit
|
commitdiff
|
tree
2018-07-16
Chr
i
stian
Bla
u
Add
LocalAtomSet for han
d
ling
atom
indices
.
commit
|
commitdiff
|
tree