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Modernize naming in GPU buffer ops kernels
2019-11-07
Christian Blau
Stoc
h
astic d
y
n
am
i
c
s
- document
that
nsttcouple is ignored
commit
|
commitdiff
|
tree
2019-11-01
Christian
B
lau
Fix cross-c
o
rre
l
at
i
o
n c
a
l
c
ul
a
tion instabili
t
y
commit
|
commitdiff
|
tree
2019-10-22
Christian Blau
Fix nst
in de
n
si
t
y-fitting module
commit
|
commitdiff
|
tree
2019-10-18
Christian B
l
au
Man
u
al entr
y
a
nd
.
mdp option for
a
d
aptive
f
o
rce scaling
commit
|
commitdiff
|
tree
2019-10-18
Christian Bla
u
genion: prohib
i
t ion p
l
acement c
l
ose to non-so
l
vent
commit
|
commitdiff
|
tree
2019-10-18
Christian
Blau
Basic r
e
factorin
g
genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Chr
i
st
i
an Blau
Adapti
v
e force sc
a
ling for densityfitting
commit
|
commitdiff
|
tree
2019-10-16
Christian B
l
au
E
xpone
n
t
ial moving average
commit
|
commitdiff
|
tree
2019-09-23
C
hri
s
tian Bl
a
u
Gr
o
m
pp error for mismatch
i
ng nst f
o
r
ene
r
g
y
calulation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Amend
m
ents to density fitting manu
a
l secti
o
n
commit
|
commitdiff
|
tree
2019-09-22
Christia
n
Blau
Add cross-correl
a
tion as density si
m
l
arit
y
measure
commit
|
commitdiff
|
tree
2019-09-19
Chri
s
tian Bla
u
Check
i
n
p
ut record
also in tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
C
onsistentl
y
cha
n
ge
d
ensityfitting spre
a
ding weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Ch
r
i
stian Blau
Add mdp o
p
ti
o
n documentation fo
r
density f
i
tt
i
ng
.
commit
|
commitdiff
|
tree
2019-09-12
Christ
i
an Blau
M
a
nu
a
l
entry fo
r
density guided simulations
commit
|
commitdiff
|
tree
2019-09-12
C
h
ristian Blau
Ad
d
rel
e
ase note
f
o
r
d
e
nsity
fitting
.
commit
|
commitdiff
|
tree
2019-09-11
Chris
t
ian Blau
Add com
m
ents t
o
grompp generated
.
mdp output for den
s
ityfitting
commit
|
commitdiff
|
tree
2019-09-11
C
hr
i
stian Blau
End to end test for d
e
nsity fittin
g
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
De
n
sityfittin
g
wri
t
e int64_t indices inst
e
ad
of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
C
hristian Blau
Use t
h
e cur
r
ent ma
s
s ins
t
ead of massA in densit
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
A
c
count for reference
de
n
sity origin shif
t
in
p
bc correction
commit
|
commitdiff
|
tree
2019-09-09
Ch
r
istia
n
Blau
Relat
i
v
e
entro
p
y as den
s
it
y
simil
a
r
ity measure
commit
|
commitdiff
|
tree
2019-09-09
Chri
s
ti
a
n Blau
Add opt
i
on to normal
i
ze densit
i
es pri
o
r to density
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian B
l
a
u
A
ddi
n
g
every N-s
t
eps
option to densityfitt
i
n
g
commit
|
commitdiff
|
tree
2019-09-06
Ch
r
istian Blau
Adding energy output
f
i
eld
f
or density fittin
g
commit
|
commitdiff
|
tree
2019-09-06
Christia
n
Blau
P
e
riodic
b
oundary c
o
r
r
ec
t
ion for
d
ens
i
ty
f
itting
commit
|
commitdiff
|
tree
2019-09-05
C
h
risti
a
n
Blau
Add
ref
e
rence den
s
ity file opt
i
o
n to densit
y
fitting
commit
|
commitdiff
|
tree
2019-09-04
Chri
s
tian Blau
Fi
x
d
ouble ove
r
l
oad in
LocalAtomSet
c
ode when
g
mx
:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
C
hristian Blau
Read mr
c
f
ile
using file n
a
me
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
A
dd checkpointi
n
g
fo
r
MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christ
i
an Blau
Constructing loca
l
a
tom sets for density fi
t
ting
commit
|
commitdiff
|
tree
2019-08-30
C
h
ristian Blau
LocalAtomSet construc
t
io
n
with v
e
c
tors of
gmx::ind
e
x
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n
Blau
Impleme
n
ting the den
s
ity fittin
g
force
p
rovider
commit
|
commitdiff
|
tree
2019-08-27
Chr
i
stian Blau
Add
d
e
n
s
ity fittin
g
parameters
commit
|
commitdiff
|
tree
2019-08-27
C
hr
i
stian Blau
Acces
s
to GaussTransform3D d
a
ta
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n
Blau
Add index gro
u
p option to
d
ensity
f
itting
commit
|
commitdiff
|
tree
2019-08-26
Christ
i
an Blau
Activation
of densi
t
y
f
itt
i
ng and move of module notificati
o
ns
commit
|
commitdiff
|
tree
2019-08-25
Ch
r
i
s
tian Blau
In
d
ex gro
u
ps
for MdModul
e
s from gr
o
mpp
commit
|
commitdiff
|
tree
2019-08-17
Christia
n
B
l
au
Fix segfault
w
ith
old t
p
rs
p
rocessing internal parameters
commit
|
commitdiff
|
tree
2019-08-15
C
hr
i
stian
Blau
Move densityfitting
options and
o
utput into seper
a
te
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Chr
i
stian Blau
Info class
t
o na
m
e and
g
e
n
erate the de
n
s
ityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christia
n
Bl
a
u
Internal
parameter stora
g
e for IMDMo
d
u
l
es
commit
|
commitdiff
|
tree
2019-08-08
Ch
r
isti
a
n B
l
au
Ha
r
monize mrc d
e
nsity f
o
rmat
e
xtents with rest
o
f co
d
e
.
commit
|
commitdiff
|
tree
2019-08-08
C
hristian
Blau
Provi
d
e
c
allbacks/no
t
ifications for MDModules
commit
|
commitdiff
|
tree
2019-07-26
C
h
risti
a
n Blau
F
ix
f
ai
l
in
g
check
-
so
u
rc
e
t
arget on python3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Chri
s
tian Blau
Fix
HTML source docu
m
enati
o
n error c
a
u
se
d
by Gauss
T
ra
n
s
f
orm3D
commit
|
commitdiff
|
tree
2019-06-28
Chri
s
tia
n
Blau
Add copy and
move
o
perations to density simila
r
ity
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add class to look u
p
density fi
t
t
ing amplitud
e
s
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
Add co
o
rdi
n
ate scaling class
a
n
d extend Translate
A
ndScale
commit
|
commitdiff
|
tree
2019-06-20
Christian
Bl
a
u
Allow non-unif
o
rm
G
a
ussia
n
s
commit
|
commitdiff
|
tree
2019-06-20
Christian
Blau
Add
B
asicVector s
c
al
i
n
g,
m
a
x, min and toIvec
commit
|
commitdiff
|
tree
2019-06-18
C
h
risti
a
n Bl
a
u
M
rc format header to lattice coordinate trans
f
o
rm
commit
|
commitdiff
|
tree
2019-06-18
Christian Bla
u
Density simila
r
ity mea
s
ure
a
nd gr
a
d
ient
commit
|
commitdiff
|
tree
2019-04-27
C
hristian
Blau
mrc
d
ensity map re
a
d
i
n
g
/writing
commit
|
commitdiff
|
tree
2019-04-27
C
h
ris
t
ian Blau
Three di
m
ensio
n
a
l
coordiante tr
a
nsformation
.
commit
|
commitdiff
|
tree
2019-04-25
C
h
ristian Blau
d
e
nsity fittin
g
forces
commit
|
commitdiff
|
tree
2019-04-22
C
hris
t
ia
n
Blau
Three
d
i
mensional gauss transform
commit
|
commitdiff
|
tree
2019-04-22
Chri
s
tian
B
lau
On
e
dimen
s
ional Gaussian
f
u
nction on
lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Christian
B
lau
densit
y
fit
t
ing - MD
M
odule declaration
commit
|
commitdiff
|
tree
2019-03-22
Chri
s
tian B
l
au
densityfitting - serializer
for mr
c
header dat
a
.
commit
|
commitdiff
|
tree
2019-03-19
Christian B
l
a
u
densityfitting - de
n
sit
y
file f
o
rmat
(
mrc) h
e
a
d
er
.
commit
|
commitdiff
|
tree
2019-02-12
Christian Blau
3x3 matri
c
es
commit
|
commitdiff
|
tree
2019-02-11
Ch
r
istian Bl
a
u
view on MultiDimArray
commit
|
commitdiff
|
tree
2019-02-07
Chr
i
s
t
ian Blau
mdspan - add br
a
cket op
e
rator
s
l
icing
commit
|
commitdiff
|
tree
2019-02-04
C
hris
t
ian Blau
mds
p
an -
f
r
e
e b
e
gin an
d
end functions
commit
|
commitdiff
|
tree
2019-02-04
Chr
i
stia
n
Blau
multidi
m
ensiona
l
arra
y
-
bugfix swap
commit
|
commitdiff
|
tree
2019-01-24
Ch
r
isti
a
n Bla
u
Remov
e
extra semicolons caus
i
ng clang warning
s
.
commit
|
commitdiff
|
tree
2019-01-23
C
hris
t
ian
Blau
Multidimensi
o
nal data in can
o
nical layout
.
commit
|
commitdiff
|
tree
2018-12-26
Christi
a
n Blau
mdspan
- basic_mdspan an
d
mdspan decl
a
ration
commit
|
commitdiff
|
tree
2018-12-20
Christian
B
lau
mdspan -
b
a
s
ic a
c
c
essor poli
c
y
commit
|
commitdiff
|
tree
2018-12-20
Chr
i
s
t
i
a
n Blau
md
s
p
an - mappi
n
g for rig
h
t layout
commit
|
commitdiff
|
tree
2018-12-04
Christia
n
Blau
mdspan - exten
t
s of m
u
lti
d
ime
n
sio
n
al
a
rra
y
s
.
commit
|
commitdiff
|
tree
2018-11-22
C
hristian Blau
mdspan - basic in
f
rastructure
commit
|
commitdiff
|
tree
2018-08-30
Christian
Blau
Convert essential dynamics C-structs to C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-30
Chri
s
t
i
an Blau
Stor
e
es
s
entia
l
d
y
namics par
a
meters a
s
v
ector
s
instead
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
Chr
i
stian B
l
au
A
d
d
test for str
u
ctural s
i
milarity mea
s
ure
s
rmsd and
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
C
hrist
i
an Bla
u
Rem
o
ve D
e
bug Helper
s
from Esse
n
t
i
al Dynamics co
d
e
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Local atom sets in rotational
p
ulling
.
commit
|
commitdiff
|
tree
2018-08-08
Ch
r
istian Bl
a
u
E
s
s
e
ntial dynamics func
t
ions use c
o
nst-
r
ef fo
r
input
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Chri
s
tian
B
l
a
u
Split e
s
sential
d
ynamics eigenvector rea
d
ing
.
commit
|
commitdiff
|
tree
2018-08-08
Christia
n
Blau
Make
e
ssential d
y
namics
a
C+
+
t
y
pe
.
commit
|
commitdiff
|
tree
2018-08-07
C
hrist
i
an B
l
au
Local a
t
om sets
in compEL /
i
on
s
wapping
c
o
de
.
commit
|
commitdiff
|
tree
2018-08-04
Christian Bl
a
u
Split
essential dynamics readin
g
rout
i
ne
commit
|
commitdiff
|
tree
2018-07-17
Christia
n
Blau
Lo
c
al ato
m
set
h
andlin
g
during simulations
.
commit
|
commitdiff
|
tree
2018-07-16
Chr
i
st
i
an Bla
u
Ad
d
LocalA
t
omSet for handling atom i
n
dice
s
.
commit
|
commitdiff
|
tree