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grompp: fix the -ref <file> option
2020-03-11
C
hri
s
tian Bl
a
u
Amend opti
o
n
a
l docum
e
nta
t
i
o
n
commit
|
commitdiff
|
tree
2020-03-05
Chris
t
ian Blau
A
d
d functio
n
c
alls to
MdM
o
dule
s
t
o sign
u
p
f
o
r no
t
i
f
ic
a
tions
commit
|
commitdiff
|
tree
2020-03-05
Chr
i
stian Blau
S
plit
o
ff implement
a
tion
details of Md
M
o
d
uleNotification
commit
|
commitdiff
|
tree
2020-03-04
Christian Blau
S
ave
e
xc
l
uded
n
on-bonded i
n
teractions in
.
tpr file
commit
|
commitdiff
|
tree
2020-03-04
Christian Blau
Add classhelper ma
c
ro to
forbid copy, move
a
n
d any
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Christi
a
n Blau
Do
c
ument
d
ensity-f
i
t cross
-
correlation in
.
mdp o
p
tions
commit
|
commitdiff
|
tree
2020-02-18
Chr
i
st
i
an Blau
Spli
t
MdModuleNotifications
i
nto top
i
cs
commit
|
commitdiff
|
tree
2020-02-12
Ch
r
istian Blau
Introduc
e
readXvgData
to read xvg data into std::vector
commit
|
commitdiff
|
tree
2020-01-31
Chris
t
ian
B
l
au
Documentation fix
f
o
r local atom set dat
a
commit
|
commitdiff
|
tree
2019-12-20
Christian Blau
Remo
v
e probl
e
matic output o
f
gmx angle
commit
|
commitdiff
|
tree
2019-12-15
C
h
ristian Blau
Fix densi
t
yfit
t
ing stalling
a
nd
ener
g
ies
commit
|
commitdiff
|
tree
2019-12-12
Chri
s
tian Blau
Densityfitt
i
ng
-
enforce similarity inc
r
ease with ad
a
pti
v
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Chris
t
ia
n
Blau
Change a
r
bitrary units to
counts
in
R
M
S
D distance distrib
u
ti
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
C
h
r
istia
n
Blau
Relax cr
o
ss-cor
r
elat
i
on
t
est pr
e
cision
commit
|
commitdiff
|
tree
2019-12-04
Chri
s
tian Blau
R
e
move c
u
toff-scheme group from de
f
ault mdout
.
m
d
p o
u
tput
commit
|
commitdiff
|
tree
2019-12-02
Christian
B
l
a
u
Relax te
s
t
t
olerance for cros
s
correlation me
a
sure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
C
h
ristian Blau
Fix check
-
point
i
ng for density g
u
i
d
ed
s
imula
t
ions
commit
|
commitdiff
|
tree
2019-11-25
Ch
r
istian Blau
Fix
d
u
p
l
ica
t
e
C
ON
N
ECT re
c
ords in pd
b
files
commit
|
commitdiff
|
tree
2019-11-25
C
hristian Blau
Rea
d
mrc d
e
nsity map for
m
at with al
l
end
i
a
nesses
.
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
C
heck mrc header
for sanity
commit
|
commitdiff
|
tree
2019-11-24
C
h
ristian B
l
au
InMe
m
orySeriali
z
er w
i
th endianes
s
swap
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
Sto
c
hastic dynamics - document t
h
a
t
nsttc
o
uple
i
s ignored
commit
|
commitdiff
|
tree
2019-11-01
Chri
s
tian B
l
au
F
ix cros
s
-correlatio
n
calculation insta
b
ility
commit
|
commitdiff
|
tree
2019-10-22
Chr
i
st
i
an Blau
Fix nst in
den
s
ity-fittin
g
m
odule
commit
|
commitdiff
|
tree
2019-10-18
Christian B
l
au
Manua
l
e
n
try and
.
mdp option for a
d
aptiv
e
force scaling
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
g
enio
n
:
p
rohibit ion placement clos
e
to no
n
-s
o
lv
e
nt
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an Blau
Ba
s
ic refac
t
oring genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
C
h
ris
t
ian
Blau
Adaptive force scaling for
density
f
i
t
ting
commit
|
commitdiff
|
tree
2019-10-16
Christi
a
n Bla
u
Exponential
m
oving ave
r
age
commit
|
commitdiff
|
tree
2019-09-23
Ch
r
i
s
tian
B
lau
Grompp err
o
r
for
mi
s
m
atching nst
f
or e
n
ergy
c
alu
l
ation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Amendments to densit
y
fitti
n
g manual
s
ection
commit
|
commitdiff
|
tree
2019-09-22
Christian
B
lau
A
dd cro
s
s-
c
orre
l
ation as density
s
i
mlarity mea
s
ure
commit
|
commitdiff
|
tree
2019-09-19
Christian
Bl
a
u
Check input record als
o
in
t
ests
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
Consist
e
ntl
y
change densityfitting
s
p
r
eading
weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Chri
s
tian Blau
Add mdp op
t
i
on document
a
tion for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
Christ
i
an Blau
Man
u
al en
t
ry fo
r
density
g
uided simulations
commit
|
commitdiff
|
tree
2019-09-12
C
hr
i
stian Bl
a
u
Add release note
for densit
y
fitting
.
commit
|
commitdiff
|
tree
2019-09-11
Chr
i
s
tia
n
B
lau
Add comments to grompp ge
n
erate
d
.
mdp output for
d
ensityfi
t
ting
commit
|
commitdiff
|
tree
2019-09-11
Ch
r
istian Blau
End to end test for
d
e
n
sity fi
t
t
ing
commit
|
commitdiff
|
tree
2019-09-11
Chris
t
ian
Blau
D
e
ns
i
tyfitting
write int64_
t
indices
inst
e
ad of
g
mx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Chris
t
ian Blau
U
se the cu
r
rent
m
as
s
instead of mas
s
A in de
n
sit
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Ac
c
ount for
reference den
s
ity origin shift
in pbc cor
r
ection
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relati
v
e
e
n
tropy as density similarity m
e
asu
r
e
commit
|
commitdiff
|
tree
2019-09-09
Christ
i
an Bl
a
u
Add op
t
io
n
t
o
normalize densities prior to d
e
nsity
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Chr
i
stian Blau
Ad
d
ing
every
N-steps o
p
tion to de
n
sit
y
fi
t
ting
commit
|
commitdiff
|
tree
2019-09-06
Chri
s
tian
B
lau
Adding energy
o
utp
u
t field for density
fitting
commit
|
commitdiff
|
tree
2019-09-06
Christian B
l
au
P
eriod
i
c boundary correctio
n
for density fitting
commit
|
commitdiff
|
tree
2019-09-05
C
h
ristian
B
lau
A
dd re
f
eren
c
e
d
e
ns
i
t
y
fi
l
e opti
o
n to densityfitting
commit
|
commitdiff
|
tree
2019-09-04
C
h
ristian Blau
Fix doubl
e
overload in L
o
calAt
o
mSet code whe
n
gmx
:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Read mrc file u
s
i
ng
f
ile name
commit
|
commitdiff
|
tree
2019-09-01
C
hristian Blau
Add c
h
eck
p
ointing for MdModules
commit
|
commitdiff
|
tree
2019-08-30
C
h
ristian B
l
au
Con
s
truct
i
n
g
loc
a
l atom
s
ets
for density fitting
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
st
i
an Bl
a
u
LocalAtom
S
et
co
n
structi
o
n with vecto
r
s o
f
g
m
x
::index
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
stia
n
Blau
Implementing the densit
y
fitting force
p
rovider
commit
|
commitdiff
|
tree
2019-08-27
Christian
Blau
Add density
f
itt
i
ng parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian
Bl
a
u
Ac
c
e
ss to GaussTr
a
n
s
form3D d
a
t
a
commit
|
commitdiff
|
tree
2019-08-27
C
hristian Bla
u
Ad
d
index group
o
ption to den
s
ity fitting
commit
|
commitdiff
|
tree
2019-08-26
C
h
ristian Blau
Activ
a
tion of densit
y
fitting and move of
module not
i
ficati
o
ns
commit
|
commitdiff
|
tree
2019-08-25
C
h
ristian Blau
Index gr
o
ups for MdM
o
dules f
r
om grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian Blau
Fix segfault with old tp
r
s
p
rocess
i
ng i
n
ternal p
a
rameters
commit
|
commitdiff
|
tree
2019-08-15
Christian B
l
au
M
o
ve
dens
i
tyfitting optio
n
s
and output into seperate
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info class to na
m
e and ge
n
er
a
t
e t
h
e den
s
ityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
hrist
i
a
n
Blau
Internal par
a
meter
s
torag
e
f
o
r IMDModules
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
st
i
a
n
Blau
H
a
rmonize mr
c
d
ensity form
a
t
e
xtents w
i
th re
s
t of
co
d
e
.
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Prov
i
de callbacks/notif
i
cations
f
or
M
DModules
commit
|
commitdiff
|
tree
2019-07-26
Christian
B
lau
Fix fai
l
i
n
g chec
k
-
s
o
urce
target on
p
y
t
h
on3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Christian Blau
Fix HTML s
o
urce documenati
o
n error caused by GaussTransfo
r
m3D
commit
|
commitdiff
|
tree
2019-06-28
C
h
r
is
t
i
a
n Blau
Add
cop
y
and
m
ove ope
r
at
i
ons to
density simil
a
rity
commit
|
commitdiff
|
tree
2019-06-28
Chr
i
st
i
an
B
lau
Add class to look up den
s
ity fitting amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
sti
a
n Bl
a
u
A
d
d c
o
ordinate scal
i
ng class and extend
T
ranslateAndScal
e
commit
|
commitdiff
|
tree
2019-06-20
C
hristian Blau
Allow
n
on-uniform Gau
s
sians
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
Add Ba
s
icVect
o
r s
c
aling, max, min a
n
d
t
oIvec
commit
|
commitdiff
|
tree
2019-06-18
Chri
s
tian
B
lau
Mrc format header to lattice co
o
rdinate transform
commit
|
commitdiff
|
tree
2019-06-18
C
hristian Blau
Den
s
i
ty similarity measure and gradient
commit
|
commitdiff
|
tree
2019-04-27
Christian Bla
u
mrc density map reading/wr
i
tin
g
commit
|
commitdiff
|
tree
2019-04-27
Ch
r
isti
a
n Blau
Three dimensio
n
al co
o
rdiant
e
t
r
ansformati
o
n
.
commit
|
commitdiff
|
tree
2019-04-25
Christian
Blau
d
e
nsit
y
f
i
tting forces
commit
|
commitdiff
|
tree
2019-04-22
Christian
B
lau
Th
r
ee dimensional gauss t
r
ansform
commit
|
commitdiff
|
tree
2019-04-22
Chris
t
i
an Blau
O
ne dimensi
o
nal Gaus
s
ian function on lat
t
i
ce
.
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
densi
t
yfitting - MDMod
u
le
declar
a
tion
commit
|
commitdiff
|
tree
2019-03-22
Ch
r
i
s
t
i
a
n
B
l
au
d
ensity
f
it
t
ing
-
ser
i
al
i
zer for mrc header da
t
a
.
commit
|
commitdiff
|
tree
2019-03-19
C
h
r
istian
B
lau
dens
i
t
y
fitting - den
s
ity file
f
orm
a
t (m
r
c) heade
r
.
commit
|
commitdiff
|
tree
2019-02-12
Christi
a
n Blau
3x3 matrice
s
commit
|
commitdiff
|
tree
2019-02-11
Christian Blau
view on MultiDimArra
y
commit
|
commitdiff
|
tree
2019-02-07
Christian
B
l
au
mdspan - add bracke
t
operator
s
licing
commit
|
commitdiff
|
tree
2019-02-04
Christian
B
lau
mdspan - free begin and end f
u
nction
s
commit
|
commitdiff
|
tree
2019-02-04
Chri
s
tian Blau
multid
i
me
n
sional array -
b
ugfix swa
p
commit
|
commitdiff
|
tree
2019-01-24
Ch
r
ist
i
an Blau
R
e
m
o
v
e
e
xtr
a
se
m
ic
o
lons causing c
l
ang warn
i
ngs
.
commit
|
commitdiff
|
tree
2019-01-23
Chri
s
t
i
a
n
Blau
Multidi
m
ensional data in
c
anonic
a
l layout
.
commit
|
commitdiff
|
tree
2018-12-26
C
h
ristian Blau
mdspan
-
basic_md
s
p
an and
m
d
span
d
eclaration
commit
|
commitdiff
|
tree
2018-12-20
Chris
t
ian Blau
mdspan - basic
accessor poli
c
y
commit
|
commitdiff
|
tree
2018-12-20
C
h
ristia
n
Blau
mdspan
- m
a
pping
f
or rig
h
t lay
o
ut
commit
|
commitdiff
|
tree
2018-12-04
C
h
ristian Blau
mdspan
-
extents of mu
l
tidimensional arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian Blau
m
dspan - basic infrastruc
t
u
re
commit
|
commitdiff
|
tree
2018-08-30
Chri
s
tian Blau
Convert essential dynami
c
s C-s
t
r
u
c
ts to
C+
+
pt1
.
commit
|
commitdiff
|
tree
2018-08-30
C
h
risti
a
n Blau
Store essent
i
al dynamics para
m
eters
as vectors instead
.
.
.
commit
|
commitdiff
|
tree
2018-08-21
Christi
a
n B
l
a
u
A
dd test for structural similarity measures r
m
sd a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-08-09
C
h
ristian
B
lau
Remove D
e
b
u
g Helpers from Essential Dynami
c
s
code
.
commit
|
commitdiff
|
tree
2018-08-08
Chris
t
ian Bla
u
Local a
t
om sets
i
n rotational
p
ulli
n
g
.
commit
|
commitdiff
|
tree
2018-08-08
Chr
i
stian Blau
Essential dynam
i
c
s functions use const-re
f
for
i
npu
t
.
.
.
commit
|
commitdiff
|
tree
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