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Set buffers appropriately so .xpm files can be read.
2020-02-25
Chris
t
ian Bla
u
Docum
e
nt de
n
sity-f
i
t cross-correlation in
.
mdp options
commit
|
commitdiff
|
tree
2019-12-20
C
hr
i
s
tian Blau
R
e
m
ove proble
m
atic output of gmx
angle
commit
|
commitdiff
|
tree
2019-12-15
Christian B
l
a
u
Fix dens
i
tyfitt
i
n
g
s
t
allin
g
a
nd ene
r
gi
e
s
commit
|
commitdiff
|
tree
2019-12-12
Ch
r
isti
a
n Blau
Densityfittin
g
- enforce similarity in
c
rease with
adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Bl
a
u
Chan
g
e arbit
r
ary units to
coun
t
s in RMSD
distance distr
i
bu
t
i
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
C
h
ristian Blau
Re
l
ax
c
ro
s
s
-corre
l
ation test precision
commit
|
commitdiff
|
tree
2019-12-04
Christian
B
lau
Rem
o
ve
cutoff-scheme g
r
ou
p
f
rom default
m
dou
t
.
mdp out
p
ut
commit
|
commitdiff
|
tree
2019-12-02
Christian Blau
Rel
a
x
t
e
st tolerance for cross corr
e
lation mea
s
ure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
C
h
ri
s
t
i
an B
l
au
Fix check-po
i
n
ti
n
g for densit
y
guided si
m
ulations
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian Blau
Fix duplicate CONNECT
r
ecords in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Ch
r
i
stian Blau
Read mrc d
e
nsity
ma
p
format w
i
th all endiane
s
ses
.
commit
|
commitdiff
|
tree
2019-11-25
Chri
s
tian B
l
au
Check
m
r
c h
e
ader for sanity
commit
|
commitdiff
|
tree
2019-11-24
Chri
s
tian Blau
InMe
m
o
r
ySeria
l
izer with endianess swap
.
commit
|
commitdiff
|
tree
2019-11-07
Chr
i
stian Blau
Sto
c
hast
i
c dynamics - document that nsttc
o
u
ple is ignored
commit
|
commitdiff
|
tree
2019-11-01
C
hristian Blau
Fix cross-correla
t
ion
c
alcu
l
ation instability
commit
|
commitdiff
|
tree
2019-10-22
Chr
i
stian Blau
Fix nst in den
s
it
y
-fitting m
o
dule
commit
|
commitdiff
|
tree
2019-10-18
Christian B
l
au
Manual ent
r
y
and
.
mdp option for adaptive
f
o
r
ce scaling
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
ge
n
ion: prohibit ion pl
a
cement c
l
ose to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Chri
s
tian B
l
au
Basic refactoring genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Christi
a
n Bl
a
u
Adaptive forc
e
scali
n
g for density
f
itting
commit
|
commitdiff
|
tree
2019-10-16
Christian Bla
u
Expo
n
ential moving average
commit
|
commitdiff
|
tree
2019-09-23
Christian
B
lau
Grompp error for
mismatching nst for energy calulation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
C
h
r
ist
i
an Blau
A
mendm
e
nts to
density fitting manual section
commit
|
commitdiff
|
tree
2019-09-22
Christian
B
l
a
u
Add cr
o
ss-correlation as density simlarity m
e
asure
commit
|
commitdiff
|
tree
2019-09-19
Chri
s
tian Blau
Ch
e
ck
i
nput
record a
l
so in tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consistently change density
f
it
t
ing spreading weig
h
t
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Chr
i
stian Blau
Add
m
d
p
o
pt
i
o
n
d
o
c
umentation
for densi
t
y
f
i
t
t
i
n
g
.
commit
|
commitdiff
|
tree
2019-09-12
Christi
a
n
B
lau
Manual entry for d
e
nsity guided simulations
commit
|
commitdiff
|
tree
2019-09-12
Christia
n
Blau
A
d
d rel
e
ase note
for density fitting
.
commit
|
commitdiff
|
tree
2019-09-11
C
hris
t
ian Blau
Add
c
om
m
e
n
ts to gro
m
pp gener
a
ted
.
mdp output
f
o
r
d
ensityfitting
commit
|
commitdiff
|
tree
2019-09-11
C
hristian Blau
End
t
o end test
for
d
ensity fitti
n
g
commit
|
commitdiff
|
tree
2019-09-11
Chris
t
ia
n
Blau
D
e
nsityfitting write int
6
4_t indic
e
s
i
nstead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Ch
r
istian Blau
U
s
e the curr
e
n
t mass instead of mas
s
A
in density
f
i
tting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
C
hristi
a
n Blau
Accoun
t
for refere
n
ce densit
y
origin shift in
pbc correction
commit
|
commitdiff
|
tree
2019-09-09
Chris
t
ian B
l
au
Relative
e
ntropy as d
e
nsity simi
l
arity measure
commit
|
commitdiff
|
tree
2019-09-09
C
h
ristian Blau
Add opt
i
on to
normalize
d
e
nsities prio
r
to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian B
l
a
u
A
dding
e
very N-step
s
option to
densityfitting
commit
|
commitdiff
|
tree
2019-09-06
Christ
i
an Blau
A
d
ding energy
output field for density fi
t
ti
n
g
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
Per
i
o
di
c
bounda
r
y cor
r
e
c
tion for density
fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian B
l
au
A
d
d referen
c
e density
f
ile option to densityfitting
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Fix double
o
verload in L
o
calAtomSet code when gm
x
:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Read mrc
f
i
le
using fil
e
name
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
Ad
d
c
he
c
kpointing
for Md
M
odules
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian Blau
Con
s
tructing loca
l
ato
m
sets for de
n
sity fitting
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian
B
l
au
Local
A
tomSet co
n
s
truction with
v
ectors of
g
m
x:
:
i
ndex
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian Bla
u
Implementi
n
g the densit
y
fittin
g
force provi
d
er
commit
|
commitdiff
|
tree
2019-08-27
Chri
s
tian Bla
u
A
dd de
n
sity f
i
tting par
a
mete
r
s
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Acce
s
s to GaussTransfo
r
m3D
d
ata
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Add i
n
d
ex group op
t
io
n
to dens
i
ty fitting
commit
|
commitdiff
|
tree
2019-08-26
Ch
r
istian Blau
Activation of
d
en
s
i
t
y
f
i
tting and move of modul
e
notifications
commit
|
commitdiff
|
tree
2019-08-25
Ch
r
istian Blau
I
n
d
ex gro
u
ps for MdMod
u
les from grompp
commit
|
commitdiff
|
tree
2019-08-17
C
hristian B
l
au
Fix se
g
faul
t
w
ith old
tprs processing internal p
a
ra
m
eters
commit
|
commitdiff
|
tree
2019-08-15
Christian
B
lau
Move
d
ensityfitting options and out
p
ut
into seperate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christia
n
Blau
Info c
l
a
ss t
o
name and g
e
nerate the densityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian
Blau
Inte
r
nal para
m
eter storage for I
M
DMo
d
ules
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Har
m
onize mrc density
f
o
r
mat ext
e
nts with re
s
t of
c
ode
.
commit
|
commitdiff
|
tree
2019-08-08
Ch
r
istian Bla
u
P
r
ovide c
a
ll
b
a
cks/notifications for MDM
o
d
u
les
commit
|
commitdiff
|
tree
2019-07-26
Christ
i
an Bla
u
Fix fai
l
ing c
h
eck
-
source
target o
n
python3
.
6
commit
|
commitdiff
|
tree
2019-07-24
C
hris
t
ian Bl
a
u
Fix HTML so
u
rce documenation er
r
or caused by Gau
s
sTr
a
nsform3D
commit
|
commitdiff
|
tree
2019-06-28
C
h
ristian Blau
Add copy and move
o
p
erat
i
ons to density
similarity
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Ad
d
clas
s
to look up density fi
t
t
i
ng amplitu
d
es
commit
|
commitdiff
|
tree
2019-06-20
C
h
ristian
Blau
Add coordinate scaling cla
s
s and
e
xtend
T
ranslateAn
d
Scale
commit
|
commitdiff
|
tree
2019-06-20
C
h
r
i
stian Blau
All
o
w non-uniform Gaussians
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
stian Blau
Add
BasicVec
t
o
r scaling
,
max, min and
t
o
Ivec
commit
|
commitdiff
|
tree
2019-06-18
Chris
t
i
a
n Blau
Mrc format header to lattice co
o
rdinate
transform
commit
|
commitdiff
|
tree
2019-06-18
Ch
r
isti
a
n Blau
D
e
nsity
simila
r
ity
m
easure and
gradient
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
mrc den
s
ity m
a
p
readi
n
g
/wr
i
t
ing
commit
|
commitdiff
|
tree
2019-04-27
Chr
i
stian Blau
Three dime
n
sional co
o
r
d
ian
t
e t
r
a
nsformation
.
commit
|
commitdiff
|
tree
2019-04-25
Christian Blau
density fitt
i
ng f
o
rces
commit
|
commitdiff
|
tree
2019-04-22
C
h
ristian Blau
T
h
ree
d
imen
s
ional
g
auss transform
commit
|
commitdiff
|
tree
2019-04-22
Chris
t
ian B
l
au
On
e
d
im
e
n
s
i
o
nal Ga
u
ssian func
t
i
o
n on la
t
tice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
density
f
itting
-
M
DModule declaration
commit
|
commitdiff
|
tree
2019-03-22
Christi
a
n Blau
de
n
sityfitting - serializer fo
r
mrc header d
a
ta
.
commit
|
commitdiff
|
tree
2019-03-19
Christian B
l
au
densityfi
t
ting
-
density file
format
(mrc) he
a
der
.
commit
|
commitdiff
|
tree
2019-02-12
Chr
i
stian
Bla
u
3x3
matrices
commit
|
commitdiff
|
tree
2019-02-11
Ch
r
istia
n
Bl
a
u
view o
n
Mul
t
iDimArra
y
commit
|
commitdiff
|
tree
2019-02-07
Christian Blau
mdsp
a
n - add bracket operator sl
i
cing
commit
|
commitdiff
|
tree
2019-02-04
Ch
r
istian Blau
m
dspan - free be
g
in and end fun
c
tions
commit
|
commitdiff
|
tree
2019-02-04
Christian Blau
multidimens
i
ona
l
array - bugfix swap
commit
|
commitdiff
|
tree
2019-01-24
Christia
n
Blau
Remo
v
e
ext
r
a
semicol
o
n
s causing clan
g
w
a
rnings
.
commit
|
commitdiff
|
tree
2019-01-23
Christian Blau
M
ultidimensional data in canoni
c
a
l
layout
.
commit
|
commitdiff
|
tree
2018-12-26
C
h
ristian Blau
mdspan - ba
s
ic_mdspan and mdsp
a
n
d
ecl
a
ration
commit
|
commitdiff
|
tree
2018-12-20
C
h
risti
a
n Blau
mdsp
a
n - ba
s
i
c accessor policy
commit
|
commitdiff
|
tree
2018-12-20
C
h
ristian Blau
mdspan - mapping
f
or r
i
g
h
t layou
t
commit
|
commitdiff
|
tree
2018-12-04
Christian Blau
m
dspan - e
x
tents
of m
u
lt
i
dimen
s
ional arr
a
ys
.
commit
|
commitdiff
|
tree
2018-11-22
Christia
n
Blau
mdspan - basic inf
r
a
s
t
ru
c
t
ure
commit
|
commitdiff
|
tree
2018-08-30
Chris
t
ian Blau
Convert e
s
sential dy
n
amics C-st
r
uc
t
s to
C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
C
hristian Blau
S
t
ore
essential dynami
c
s
parameters as vector
s
in
s
tead
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
Christian Blau
Add test
f
or structural
similarity measures r
m
sd and
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
C
hristia
n
Blau
Remov
e
Debug
Helpers from E
s
sential Dynamics code
.
commit
|
commitdiff
|
tree
2018-08-08
C
h
ristian Blau
Lo
c
al ato
m
s
e
t
s in
rotational pull
i
ng
.
commit
|
commitdiff
|
tree
2018-08-08
Christian
B
l
au
E
s
senti
a
l d
y
n
a
mics functions use const-ref fo
r
input
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Split essential dynamics
eigenve
c
tor
reading
.
commit
|
commitdiff
|
tree
2018-08-08
C
h
ri
s
t
i
an Blau
Make essent
i
a
l d
y
namics
a
C++ typ
e
.
commit
|
commitdiff
|
tree
2018-08-07
Ch
r
istian
B
l
au
Local atom sets in comp
E
L /
i
o
n
s
w
apping co
d
e
.
commit
|
commitdiff
|
tree
2018-08-04
Chris
t
ian Blau
Split essential dynamics reading routine
commit
|
commitdiff
|
tree
2018-07-17
C
h
ristian Blau
Local atom se
t
ha
n
dling during simulati
o
ns
.
commit
|
commitdiff
|
tree
2018-07-16
Christian Blau
Add Loc
a
lAtomSet for handling a
t
o
m indi
c
es
.
commit
|
commitdiff
|
tree