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Simplify PME GPU constants
2020-03-16
Ch
r
i
stian Blau
Remove dysfu
n
ctional QMMM
i
nterfa
c
e
p
t
4
commit
|
commitdiff
|
tree
2020-03-16
Christi
a
n Blau
Remove dysfunc
t
i
o
n
al Q
M
MM i
n
terface pt3
commit
|
commitdiff
|
tree
2020-03-16
Christia
n
Blau
Re
m
ove dysfunctional
Q
MMM i
n
terface pt2
commit
|
commitdiff
|
tree
2020-03-16
Christ
i
an Blau
Remove dy
s
functional QMM
M
interface pt1
commit
|
commitdiff
|
tree
2020-03-11
Christian Blau
Am
e
nd option
a
l documentat
i
o
n
commit
|
commitdiff
|
tree
2020-03-05
Ch
r
istian
B
l
au
A
d
d function calls to M
d
Modu
l
es to si
g
n up
fo
r
notif
i
cations
commit
|
commitdiff
|
tree
2020-03-05
Christian Blau
Spl
i
t off implementa
t
ion
d
e
t
ails of MdModu
l
e
N
o
t
if
i
cation
commit
|
commitdiff
|
tree
2020-03-04
Christian
B
lau
S
a
v
e ex
c
luded
non-bonded int
e
r
a
ctions in
.
tpr file
commit
|
commitdiff
|
tree
2020-03-04
Christian Blau
A
d
d
classhelper macro to forbid copy, move and any
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Christian B
l
a
u
Do
c
umen
t
den
s
i
t
y
-
fit cross-correlatio
n
i
n
.
m
dp opt
i
o
n
s
commit
|
commitdiff
|
tree
2020-02-18
Chris
t
ian Blau
Spli
t
M
dMo
d
uleNotifi
c
ations into topics
commit
|
commitdiff
|
tree
2020-02-12
Christian Blau
I
ntroduce readXvgData to
read xvg dat
a
i
n
to std::vector
commit
|
commitdiff
|
tree
2020-01-31
Christian Blau
Doc
u
m
en
t
ation fix for local
atom set data
commit
|
commitdiff
|
tree
2019-12-20
Christi
a
n B
l
au
Remove pro
b
lemat
i
c output
of gmx angle
commit
|
commitdiff
|
tree
2019-12-15
Chr
i
stian Bla
u
Fix
densityfi
t
ting stalling an
d
energies
commit
|
commitdiff
|
tree
2019-12-12
Ch
r
istian Blau
Density
f
it
t
in
g
- enfor
c
e similarity
i
n
c
rease
w
ith adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
C
h
ange arbitrary uni
t
s to count
s
i
n RMSD distance distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
C
h
ri
s
tia
n
Blau
Re
l
a
x cross-correlat
i
on test precision
commit
|
commitdiff
|
tree
2019-12-04
C
h
ristian Blau
R
e
m
o
ve cutoff-sche
m
e gro
u
p from def
a
ult
mdo
u
t
.
mdp out
p
u
t
commit
|
commitdiff
|
tree
2019-12-02
Chr
i
stian Blau
R
elax
test tolerance for cross
correlati
o
n
measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Chris
t
ian Blau
F
i
x check-pointin
g
for dens
i
ty gui
d
ed simulati
o
n
s
commit
|
commitdiff
|
tree
2019-11-25
Christ
i
an Bla
u
Fix duplicate CONNECT records in pdb
f
i
l
es
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Re
a
d
mrc
density map for
m
at wit
h
all e
n
d
ianesses
.
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Check
m
r
c
header for sanity
commit
|
commitdiff
|
tree
2019-11-24
Christi
a
n
Blau
InMemorySerialize
r
with endianess
s
wap
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
Stochastic d
y
n
amics
-
docu
m
ent that nsttcouple
is ignored
commit
|
commitdiff
|
tree
2019-11-01
Chris
t
i
an Blau
Fix cr
o
s
s
-correlation calc
u
lation i
n
stabil
i
ty
commit
|
commitdiff
|
tree
2019-10-22
Chri
s
t
i
a
n Blau
F
i
x nst in den
s
ity-fitting modul
e
commit
|
commitdiff
|
tree
2019-10-18
C
hristian Blau
Man
u
al en
t
ry and
.
mdp option
for ad
a
ptive force scaling
commit
|
commitdiff
|
tree
2019-10-18
C
h
r
istian Bl
a
u
g
e
nion:
p
r
o
hibit io
n
placement cl
o
se to no
n
-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refactoring
geni
o
n and adding tes
t
commit
|
commitdiff
|
tree
2019-10-18
Christian Bla
u
Ad
a
pti
v
e force sc
a
ling
for densityfitting
commit
|
commitdiff
|
tree
2019-10-16
Christian Blau
Exp
o
ne
n
tial moving a
v
er
a
g
e
commit
|
commitdiff
|
tree
2019-09-23
Christi
a
n Blau
Grompp e
r
r
or for misma
t
ching nst f
o
r energy calul
a
tion
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Chris
t
i
a
n
B
lau
Amend
m
ents to density fitting m
a
nual
s
e
ct
i
on
commit
|
commitdiff
|
tree
2019-09-22
C
hristian Blau
Add c
r
oss-c
o
rrelation as density s
i
mlar
i
ty measure
commit
|
commitdiff
|
tree
2019-09-19
Christian
Blau
Check in
p
ut
r
ecord also
i
n
tests
commit
|
commitdiff
|
tree
2019-09-19
Christ
i
an Bl
a
u
Consistently cha
n
ge densityfitting spreading
w
eight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Chr
i
stian Blau
Add mdp o
p
tion document
a
tion
f
o
r
densit
y
fitting
.
commit
|
commitdiff
|
tree
2019-09-12
C
h
r
i
sti
a
n Blau
Manual entry f
o
r dens
i
ty g
u
ided simul
a
tion
s
commit
|
commitdiff
|
tree
2019-09-12
Christ
i
an B
l
au
Add re
l
ease note
for
density fitting
.
commit
|
commitdiff
|
tree
2019-09-11
Chri
s
t
i
an Blau
Add comments
to grompp generated
.
mdp outpu
t
fo
r
densityfitting
commit
|
commitdiff
|
tree
2019-09-11
Chr
i
stian Blau
En
d
to end test for densi
t
y f
i
tting
commit
|
commitdiff
|
tree
2019-09-11
Christian B
l
au
Densityfitting wr
i
te in
t
64_t indices instead
o
f gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
C
hris
t
ian
B
lau
Use
t
he curren
t
mass instead of
massA in
d
ensity fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Ch
r
istian Blau
Account for reference den
s
ity origin s
h
ift in pbc correction
commit
|
commitdiff
|
tree
2019-09-09
Christ
i
an Blau
Relative entro
p
y as den
s
ity sim
i
larity
m
easure
commit
|
commitdiff
|
tree
2019-09-09
Christian
B
lau
Add o
p
tio
n
t
o normalize densities p
r
ior to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christi
a
n
B
lau
Adding every
N
-steps
option to den
s
ityfitting
commit
|
commitdiff
|
tree
2019-09-06
C
hri
s
t
ian Blau
Addi
n
g
e
nergy
o
utput field for density f
i
tting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
Periodic boundary co
r
rection f
o
r density fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian Blau
Add re
f
er
e
n
ce
densit
y
file option
t
o densi
t
yfi
t
t
ing
commit
|
commitdiff
|
tree
2019-09-04
Christian Bla
u
F
i
x doub
l
e
ove
r
load in L
o
calA
t
o
mSet code whe
n
gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Chri
s
ti
a
n Blau
Read mrc file us
i
ng file
name
commit
|
commitdiff
|
tree
2019-09-01
Chr
i
stian Blau
Add checkpointin
g
for
M
dMo
d
ules
commit
|
commitdiff
|
tree
2019-08-30
Christ
i
a
n Blau
Const
r
uct
i
ng local atom sets for d
e
nsity fi
t
ting
commit
|
commitdiff
|
tree
2019-08-30
Christian B
l
a
u
LocalAtomSet
c
onstruction wit
h
vectors of gmx::
i
ndex
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
i
stian
B
lau
Implementing
the density fitting
f
orc
e
provide
r
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add density fitting
parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian B
l
au
A
c
cess to GaussTra
n
sfor
m
3
D
data
commit
|
commitdiff
|
tree
2019-08-27
Christian Bl
a
u
Add index group o
p
tion
t
o de
n
sity
fitting
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activati
o
n of density fitting and mo
v
e
of module n
o
t
ificat
i
ons
commit
|
commitdiff
|
tree
2019-08-25
Christian B
l
au
I
ndex
g
roups for
M
dModules
f
r
om gr
o
mpp
commit
|
commitdiff
|
tree
2019-08-17
Christi
a
n Bl
a
u
Fix seg
f
au
l
t with
o
ld tprs pr
o
cessing int
e
rnal p
a
rameters
commit
|
commitdiff
|
tree
2019-08-15
Christia
n
Blau
Move densit
y
fitting options and output into sepe
r
ate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info
c
lass to n
a
me and generate the dens
i
tyfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christ
i
an B
l
a
u
Internal paramete
r
storage for IMDMod
u
les
commit
|
commitdiff
|
tree
2019-08-08
Chri
s
t
i
an Blau
Harmoniz
e
mrc density format extents with r
e
st of code
.
commit
|
commitdiff
|
tree
2019-08-08
Christian Bla
u
P
rovide callbacks/notif
i
ca
t
ion
s
for MDModules
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing
c
heck-source
tar
g
et o
n
py
t
hon3
.
6
commit
|
commitdiff
|
tree
2019-07-24
C
h
rist
i
an Blau
Fix HTML source doc
u
menation err
o
r caused by Gaus
s
Trans
f
orm
3
D
commit
|
commitdiff
|
tree
2019-06-28
C
h
ristia
n
Blau
A
dd copy and move operations to
d
e
nsit
y
similarity
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add clas
s
to
l
ook up dens
i
ty
f
i
tting
a
mplitude
s
commit
|
commitdiff
|
tree
2019-06-20
Christ
i
an Blau
Add coord
i
n
a
t
e
sca
l
ing clas
s
and e
x
tend TranslateAn
d
Scale
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
A
llow non-uniform Gau
s
sians
commit
|
commitdiff
|
tree
2019-06-20
Christian
B
lau
Add Ba
s
icV
e
ctor sca
l
ing, max,
m
in and t
o
Ivec
commit
|
commitdiff
|
tree
2019-06-18
C
hristian B
l
au
Mrc format he
a
de
r
to lattice co
o
rdinate tra
n
sfor
m
commit
|
commitdiff
|
tree
2019-06-18
Ch
r
isti
a
n Bl
a
u
Density similarity mea
s
ure
a
n
d
grad
i
ent
commit
|
commitdiff
|
tree
2019-04-27
Christia
n
Blau
mrc densit
y
map reading
/
writing
commit
|
commitdiff
|
tree
2019-04-27
C
hristian B
l
au
Thre
e
di
m
ensional c
o
ordiante
t
ran
s
f
ormation
.
commit
|
commitdiff
|
tree
2019-04-25
Ch
r
istian Blau
densi
t
y fitting f
o
rces
commit
|
commitdiff
|
tree
2019-04-22
Christ
i
a
n
Blau
Three dime
n
sion
a
l gauss transform
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
O
ne
d
imen
s
i
onal Gaussian function on lattice
.
commit
|
commitdiff
|
tree
2019-04-05
C
hristian Bla
u
densi
t
yfitting - MDModule d
e
clar
a
t
i
o
n
commit
|
commitdiff
|
tree
2019-03-22
C
h
ris
t
ian Blau
den
s
i
ty
f
i
tting -
s
eriali
z
er for
m
rc h
e
ad
e
r data
.
commit
|
commitdiff
|
tree
2019-03-19
Christian Bla
u
densi
t
yfi
t
t
i
ng - density fi
l
e
format (mrc) hea
d
er
.
commit
|
commitdiff
|
tree
2019-02-12
Christian Blau
3x3 matri
c
es
commit
|
commitdiff
|
tree
2019-02-11
Chr
i
stian Blau
view on M
u
ltiDi
m
Array
commit
|
commitdiff
|
tree
2019-02-07
Chris
t
ian Blau
mds
p
an -
a
dd bracket operator slicin
g
commit
|
commitdiff
|
tree
2019-02-04
Christi
a
n Blau
mdspa
n
- free b
e
gi
n
and end functi
o
ns
commit
|
commitdiff
|
tree
2019-02-04
Christi
a
n Bla
u
multidime
n
s
i
onal array
-
b
u
gfix
s
wap
commit
|
commitdiff
|
tree
2019-01-24
Chris
t
ian Bla
u
Remove extra semicolons causing clang warnings
.
commit
|
commitdiff
|
tree
2019-01-23
Christian Blau
M
u
lti
d
imensional da
t
a in c
a
n
onical layout
.
commit
|
commitdiff
|
tree
2018-12-26
Christian
B
lau
mdspa
n
-
bas
i
c_mdspan and md
s
pan declarati
o
n
commit
|
commitdiff
|
tree
2018-12-20
C
hristian
B
lau
mdspan - ba
s
ic accessor poli
c
y
commit
|
commitdiff
|
tree
2018-12-20
Christ
i
an B
l
au
mdspan - ma
p
p
ing
f
or r
i
g
h
t
layout
commit
|
commitdiff
|
tree
2018-12-04
C
h
r
istian
B
la
u
mdspan - ex
t
ents o
f
multid
i
mens
i
onal arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Chris
t
i
a
n Blau
md
s
pan - basic infrastructure
commit
|
commitdiff
|
tree
2018-08-30
Christian Blau
Convert esse
n
t
i
al
d
yna
m
ics
C
-st
r
ucts to C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
Christian Blau
Store es
s
entia
l
d
ynami
c
s
p
arameter
s
as vectors instead
.
.
.
commit
|
commitdiff
|
tree
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