repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Make SD stuff private for update.cpp
2020-04-17
Chr
i
s
t
ian Blau
proposed
f
ix for r
e
dmine
bug #3
4
03
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
Remove dy
s
fu
n
cti
o
nal QMMM
i
nterface p
t
4
commit
|
commitdiff
|
tree
2020-03-16
Chri
s
tian
B
la
u
Re
m
o
v
e dysfunctional QM
M
M interface
p
t3
commit
|
commitdiff
|
tree
2020-03-16
C
hrist
i
an Blau
R
e
move dys
f
u
ncti
o
nal QMMM
interface p
t
2
commit
|
commitdiff
|
tree
2020-03-16
C
hristian B
l
au
R
emove dysfuncti
o
nal QMMM inter
f
ace pt1
commit
|
commitdiff
|
tree
2020-03-11
Christian Blau
Am
e
nd
optional
documentation
commit
|
commitdiff
|
tree
2020-03-05
Christian Blau
Add function
calls to MdModule
s
t
o
sign up f
o
r no
t
ificat
i
ons
commit
|
commitdiff
|
tree
2020-03-05
C
hri
s
tian Bl
a
u
S
p
lit off
i
m
plementa
t
ion details
o
f
M
dModuleNo
t
ification
commit
|
commitdiff
|
tree
2020-03-04
Christian B
l
a
u
Save excluded non-bond
e
d i
n
teractions in
.
tpr file
commit
|
commitdiff
|
tree
2020-03-04
Chr
i
stian Blau
Add
c
lasshelper macro to f
o
rbid copy,
m
ove and an
y
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Ch
r
isti
a
n
Blau
Docu
m
ent dens
i
ty-fit cross-
c
orr
e
latio
n
in
.
mdp options
commit
|
commitdiff
|
tree
2020-02-18
Chri
s
tian Blau
Split
MdModuleNoti
f
i
cati
o
n
s int
o
topics
commit
|
commitdiff
|
tree
2020-02-12
C
hristian B
l
au
I
n
trod
u
ce readXvgData to r
e
a
d
xvg data into
s
td::ve
c
tor
commit
|
commitdiff
|
tree
2020-01-31
C
h
rist
i
an
Blau
Doc
u
m
entation
fi
x
for local atom set data
commit
|
commitdiff
|
tree
2019-12-20
C
h
ris
t
ian Blau
Remo
v
e pr
o
blematic output of gmx angle
commit
|
commitdiff
|
tree
2019-12-15
Christ
i
an Blau
Fix density
f
itting
s
t
alli
n
g
and energ
i
es
commit
|
commitdiff
|
tree
2019-12-12
Christi
a
n Blau
Densit
y
fittin
g
- enforce similarity
i
ncrease
with adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian
B
la
u
Cha
n
g
e
ar
b
itrary u
n
it
s
to c
o
un
t
s in RMSD
d
istan
c
e distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christian Blau
Relax cross-correlation test precision
commit
|
commitdiff
|
tree
2019-12-04
Christian Bla
u
Re
m
o
ve cutoff-scheme group f
r
om default mdout
.
md
p
output
commit
|
commitdiff
|
tree
2019-12-02
C
h
r
istian Blau
Relax test toleranc
e
for
c
ross
c
orr
e
lation me
a
sure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Christian Blau
Fix
check-pointing
f
or density guided simulation
s
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Fix duplicate CONNECT
r
e
c
o
rds in
p
d
b
files
commit
|
commitdiff
|
tree
2019-11-25
Christi
a
n
Blau
Read mrc
density map for
m
at with all end
i
anesses
.
commit
|
commitdiff
|
tree
2019-11-25
C
h
risti
a
n Blau
Check mrc h
e
a
d
e
r f
o
r
s
a
n
ity
commit
|
commitdiff
|
tree
2019-11-24
Christian Blau
I
n
MemorySerializer with endiane
s
s swap
.
commit
|
commitdiff
|
tree
2019-11-07
C
h
ristian Blau
S
tochastic dynamics - document that nsttcouple is i
g
nored
commit
|
commitdiff
|
tree
2019-11-01
Chris
t
ian
B
lau
Fix cr
o
s
s
-
c
o
r
relation calcula
t
ion
instabil
i
ty
commit
|
commitdiff
|
tree
2019-10-22
Christian Blau
Fi
x
nst in density-
f
it
t
ing module
commit
|
commitdiff
|
tree
2019-10-18
C
hristian Blau
M
a
nu
a
l entry
and
.
m
d
p opt
i
o
n
f
or
a
dapt
i
v
e force scal
i
ng
commit
|
commitdiff
|
tree
2019-10-18
Ch
r
i
sti
a
n Bla
u
genion: prohibit ion p
l
acement
c
lose to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Chris
t
ian Blau
Bas
i
c
refact
o
ring
gen
i
o
n and adding test
commit
|
commitdiff
|
tree
2019-10-18
Christian
B
lau
A
dap
t
i
v
e force sca
l
in
g
for densityfi
t
t
ing
commit
|
commitdiff
|
tree
2019-10-16
C
h
rist
i
an Bla
u
Exponential m
o
v
i
ng averag
e
commit
|
commitdiff
|
tree
2019-09-23
Christian
B
lau
Grompp e
r
ror
for mismatchi
n
g nst
for energy cal
u
lati
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
C
h
ristian
B
lau
Amendments to den
s
ity
f
i
t
ting
m
anual
sectio
n
commit
|
commitdiff
|
tree
2019-09-22
C
hristian Blau
Add cross-corre
l
ation as density
simlar
i
ty measur
e
commit
|
commitdiff
|
tree
2019-09-19
Chr
i
st
i
an B
l
au
Check input record
a
lso in t
e
s
t
s
commit
|
commitdiff
|
tree
2019-09-19
C
h
ri
s
tian Blau
Consistently chang
e
d
e
nsityfitting spreadi
n
g weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christian Bl
a
u
Ad
d
m
dp op
t
ion do
c
umentat
i
on
for density fitting
.
commit
|
commitdiff
|
tree
2019-09-12
C
h
ris
t
i
an Bl
a
u
Ma
n
ua
l
en
t
ry
for density gu
i
ded
s
imulations
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Add release note fo
r
d
e
ns
i
ty fittin
g
.
commit
|
commitdiff
|
tree
2019-09-11
C
h
r
i
stian Blau
Add comments to grompp g
e
nerat
e
d
.
mdp output for densi
t
yfi
t
ting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
E
nd to end
t
e
st
for density fitting
commit
|
commitdiff
|
tree
2019-09-11
Christia
n
Blau
Densityfitt
i
n
g
write int64_
t
i
ndic
e
s instead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Use the current mas
s
instead of m
a
ssA
i
n
densi
t
y fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian
B
l
a
u
Ac
c
ount
for re
f
e
re
n
ce den
s
ity origin shift in pbc correction
commit
|
commitdiff
|
tree
2019-09-09
Christian Bl
a
u
Relative
entropy as density
s
imilarity me
a
sure
commit
|
commitdiff
|
tree
2019-09-09
Christian
B
lau
Add option
t
o normalize densities prior to d
e
nsity
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian
Blau
Adding e
v
ery N-steps option to densityfitting
commit
|
commitdiff
|
tree
2019-09-06
C
h
ristian Bla
u
Adding energy o
u
tput field for density fitting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
P
e
r
i
o
dic bounda
r
y c
o
r
r
ection for d
e
ns
i
ty fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian
B
lau
Add reference
d
ensity
file opt
i
on to den
s
i
t
yfitt
i
ng
commit
|
commitdiff
|
tree
2019-09-04
Christian
Blau
F
ix d
o
uble overload in LocalAtomSet code
w
h
e
n
gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christ
i
an Bla
u
Read m
r
c file
using file name
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
Add checkpointing for MdM
o
d
u
les
commit
|
commitdiff
|
tree
2019-08-30
Christ
i
a
n
Blau
Co
n
structing lo
c
al atom sets for dens
i
ty fitt
i
ng
commit
|
commitdiff
|
tree
2019-08-30
Chri
s
tian
B
lau
LocalAtomSet cons
t
ruction w
i
th
vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Implementin
g
the density
f
itting force
p
rovider
commit
|
commitdiff
|
tree
2019-08-27
Christ
i
an
Bl
a
u
Ad
d
densit
y
fitting pa
r
ame
t
ers
commit
|
commitdiff
|
tree
2019-08-27
C
h
ris
t
i
an Blau
Access to
G
aussTr
a
nsf
o
rm3D d
a
ta
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n Blau
Add
i
n
dex group opt
i
on to
de
n
sity fitting
commit
|
commitdiff
|
tree
2019-08-26
Chr
i
stian
Blau
A
c
tivation o
f
densi
t
y
fitting and move o
f
module notific
a
tions
commit
|
commitdiff
|
tree
2019-08-25
Christia
n
Blau
Index
g
roups for
M
d
Modules from grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian
Blau
Fix segfault with
o
ld tprs proce
s
s
ing inter
n
al par
a
m
eters
commit
|
commitdiff
|
tree
2019-08-15
C
h
ri
s
tian B
l
au
Move d
e
nsityfitting options and outpu
t
into seper
a
te
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Christian
B
lau
Inf
o
class to n
a
me
and
g
e
nerate the den
s
i
t
y
f
ittin
g
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
ris
t
ian Blau
Intern
a
l parameter storage for
I
MD
M
odules
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Harmonize mrc density
form
a
t extents
w
ith rest o
f
code
.
commit
|
commitdiff
|
tree
2019-08-08
Christia
n
Blau
Pr
o
vide cal
l
bac
k
s/notifications for
M
DModules
commit
|
commitdiff
|
tree
2019-07-26
C
h
ristian
B
l
a
u
Fix fai
l
ing check-source target on py
t
hon3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Ch
r
istian B
l
au
Fix
H
TML source do
c
ume
n
a
t
io
n
e
r
r
o
r caused by Gau
s
sT
r
ans
f
o
r
m3D
commit
|
commitdiff
|
tree
2019-06-28
C
h
rist
i
an Blau
Add
c
opy and move operations to density similarity
commit
|
commitdiff
|
tree
2019-06-28
Chr
i
stian Blau
A
d
d class to look
up de
n
s
ity fitting amplit
u
des
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
Add co
o
rdinat
e
scaling cl
a
ss
and
e
xtend TranslateAndScale
commit
|
commitdiff
|
tree
2019-06-20
Ch
r
istian Blau
Allow non-u
n
ifo
r
m
Gauss
i
ans
commit
|
commitdiff
|
tree
2019-06-20
Chri
s
tian Bl
a
u
Add BasicVector sc
a
ling, max, min
a
nd toIvec
commit
|
commitdiff
|
tree
2019-06-18
C
hristian Blau
Mrc forma
t
header to latti
c
e c
o
ordin
a
te trans
f
orm
commit
|
commitdiff
|
tree
2019-06-18
C
h
rist
i
an Blau
D
e
nsity simil
a
rity measure and gr
a
dient
commit
|
commitdiff
|
tree
2019-04-27
Chris
t
ian
B
l
au
mrc density map
r
eadin
g
/writi
n
g
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
Three d
i
mensional co
o
rdiante
t
ransformation
.
commit
|
commitdiff
|
tree
2019-04-25
Christian Blau
density
f
itti
n
g force
s
commit
|
commitdiff
|
tree
2019-04-22
Chris
t
ian
B
lau
Three dim
e
nsional
gauss
t
ransform
commit
|
commitdiff
|
tree
2019-04-22
Ch
r
istia
n
Bla
u
One
dim
e
nsional Gaussian func
t
i
o
n
o
n lattice
.
commit
|
commitdiff
|
tree
2019-04-05
Chri
s
tian Blau
densityfitti
n
g - MDModule dec
l
ara
t
i
on
commit
|
commitdiff
|
tree
2019-03-22
Christian Blau
densityfittin
g
-
serializer for
m
rc header d
a
ta
.
commit
|
commitdiff
|
tree
2019-03-19
Chris
t
ian
Blau
densit
y
fitt
i
n
g - densit
y
file form
a
t (mrc) h
e
ader
.
commit
|
commitdiff
|
tree
2019-02-12
Christ
i
an Blau
3x3 matrices
commit
|
commitdiff
|
tree
2019-02-11
C
hri
s
tian B
l
au
vi
e
w
on MultiDimA
r
ray
commit
|
commitdiff
|
tree
2019-02-07
C
h
ris
t
ian Blau
m
dspan - add brack
e
t
oper
a
t
o
r sli
c
ing
commit
|
commitdiff
|
tree
2019-02-04
C
h
r
istian Blau
mdspa
n
- free be
g
i
n and en
d
funct
i
ons
commit
|
commitdiff
|
tree
2019-02-04
Ch
r
ist
i
an
B
lau
m
ultidimensiona
l
array
-
bug
f
ix swap
commit
|
commitdiff
|
tree
2019-01-24
Christian Bl
a
u
Remove
extr
a
semicolons causing clang warnings
.
commit
|
commitdiff
|
tree
2019-01-23
Chr
i
st
i
an Blau
Mult
i
dimens
i
onal d
a
ta i
n
canonical layo
u
t
.
commit
|
commitdiff
|
tree
2018-12-26
C
hristian Blau
mdspan
-
b
as
i
c
_mdspan and m
d
span decl
a
ration
commit
|
commitdiff
|
tree
2018-12-20
C
hrist
i
an Blau
mdspan
-
bas
i
c
a
c
c
esso
r
policy
commit
|
commitdiff
|
tree
2018-12-20
Christian
B
l
au
mdspan - mapping for
r
i
gh
t
l
a
yout
commit
|
commitdiff
|
tree
2018-12-04
Christian
Blau
m
dspan -
e
xtents of multidimensiona
l
arrays
.
commit
|
commitdiff
|
tree
2018-11-22
Christian Blau
mdsp
a
n - basic infra
s
t
ructure
commit
|
commitdiff
|
tree
2018-08-30
Chris
t
ian
B
lau
Convert essent
i
al dynamics C-
s
tructs t
o
C
+
+ pt1
.
commit
|
commitdiff
|
tree
next