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Fix segfault in gmx genrestr.
2020-07-03
Kevi
n
Boyd
Fix segfault
in gmx
gen
r
estr
.
commit
|
commitdiff
|
tree
2020-06-12
Paul Bauer
F
i
x
false initialization values in gmx hbond
commit
|
commitdiff
|
tree
2020-02-25
Christian Bl
a
u
D
oc
u
ment density-fit cr
o
ss-correlation in
.
md
p
options
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix chec
k
N
u
mb
e
rOfBondedInte
r
act
i
o
n
s bug
commit
|
commitdiff
|
tree
2020-01-13
Artem
Zhmu
r
ov
Rep
o
r
t
if up
d
ate is running
on the
GPU or on the CPU
commit
|
commitdiff
|
tree
2019-12-17
P
a
ul Bauer
Fix formatting
e
rror
commit
|
commitdiff
|
tree
2019-12-16
Paul Bauer
Fix t
o
r
s
ion
a
ngle
calcula
t
ion
commit
|
commitdiff
|
tree
2019-12-12
Christian Blau
Densityf
i
tt
i
n
g
- enforce similar
i
ty increase
w
ith adap
t
ive
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Christian
B
la
u
Relax test tolerance for cr
o
ss correl
a
ti
o
n
measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
Stochastic dynamics -
d
ocument
t
ha
t
nsttcouple
i
s ignored
commit
|
commitdiff
|
tree
2019-10-22
C
h
r
i
s
tian Blau
Fix
nst in
de
n
si
t
y-f
i
t
ting module
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an B
l
au
Basic
r
efactoring
genion
a
nd addin
g
te
s
t
commit
|
commitdiff
|
tree
2019-10-18
Chri
s
tian Blau
Adaptive force scali
n
g for
de
n
s
ity
f
itt
i
ng
commit
|
commitdiff
|
tree
2019-09-22
Christian Blau
Add c
r
o
s
s-correlation
a
s dens
i
t
y
simlarity
mea
s
u
re
commit
|
commitdiff
|
tree
2019-09-13
Paul Bauer
Fi
x
nightly fai
l
ures
commit
|
commitdiff
|
tree
2019-09-13
Ch
r
ist
o
ph
J
unghans
cmake:
add option
t
o in
s
tall legac
y
heade
r
s
commit
|
commitdiff
|
tree
2019-09-11
C
hristian Blau
Add comments to g
r
ompp generated
.
mdp out
p
ut f
o
r densit
y
fitting
commit
|
commitdiff
|
tree
2019-09-11
Christ
i
an Blau
End to end test for density
fi
t
ting
commit
|
commitdiff
|
tree
2019-09-11
Christian Bla
u
Densit
y
fitting write int64_t indices i
n
stead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christi
a
n B
l
au
U
se the current
m
ass instead of
mas
s
A i
n
density fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christ
i
an Blau
Account f
o
r
reference den
s
i
t
y
origin
shift i
n
pbc c
o
rrectio
n
commit
|
commitdiff
|
tree
2019-09-09
C
hrist
i
a
n
B
lau
Add
option to normali
z
e dens
i
ties p
r
ior to den
s
it
y
.
.
.
commit
|
commitdiff
|
tree
2019-09-06
Christian Bla
u
Periodic boundary correction for d
e
nsity fittin
g
commit
|
commitdiff
|
tree
2019-09-04
Christ
i
a
n
B
l
au
Fix double
o
verl
o
ad in LocalAtom
S
et
c
od
e
w
h
en gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
C
h
ristia
n
B
la
u
Index
grou
p
s for
M
d
M
odules fro
m
gr
o
mpp
commit
|
commitdiff
|
tree
2019-08-15
C
hristian Blau
Move densityfittin
g
options an
d
output into seperate
.
.
.
commit
|
commitdiff
|
tree
2019-08-15
B
erk Hess
Tem
p
l
a
te bon
d
ed interactions on ker
n
el fl
a
vor
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmu
r
ov
Make u
s
e of referenc
e
dat
a
in inte
g
r
a
tor tests
commit
|
commitdiff
|
tree
2019-08-13
Artem
Zhm
u
rov
Ma
k
e
use of reference data in SE
T
T
LE te
s
t
s
commit
|
commitdiff
|
tree
2019-08-09
Paul Bauer
Add
c
o
nversion from lega
c
y to modern matri
x
type
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
stia
n
B
lau
Provid
e
callbacks/notifications f
o
r MDModules
commit
|
commitdiff
|
tree
2019-08-06
Art
e
m Zhmurov
Remove PImpl scaffolding from CUDA version of
L
eap
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
Berk
H
e
s
s
A
d
d ForceWithShiftFor
c
es class
commit
|
commitdiff
|
tree
2019-08-06
Berk H
e
ss
F
ix latex formu
l
a in
r
eference
manual
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irr
g
ang
Re
s
olve a compiler warni
n
g for th
e
gm
x
api
Pyt
h
on
pac
k
age
.
commit
|
commitdiff
|
tree
2019-08-05
Mark Abrah
a
m
A
d
d quote
commit
|
commitdiff
|
tree
2019-08-05
Berk
Hess
Make box const in do
_
force()
commit
|
commitdiff
|
tree
2019-08-05
Pa
u
l Bauer
Add replace
m
ents
for p
b
c en
u
mer
a
tio
n
s
commit
|
commitdiff
|
tree
2019-08-05
Paul Bauer
Add f
r
ee func
t
ion to
c
o
n
v
e
rt
m
atrix ty
p
e
commit
|
commitdiff
|
tree
2019-07-25
Kevin Boyd
Add transpose operation to Matrix
3
x3
commit
|
commitdiff
|
tree
2019-07-24
Chr
i
stian Blau
Fix
H
TM
L
source d
o
cumenation error caus
e
d by GaussTransform
3
D
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric
I
rrga
n
g
Beg
i
n n
e
w sample_
r
estra
i
n
t
development
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eri
c
Irrgang
Impro
v
e so
m
e d
o
cume
n
ta
t
i
o
n format
t
ing
and s
p
elling
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric Irrgang
Remove extraneo
u
s file
.
commit
|
commitdiff
|
tree
2019-07-18
Paul B
a
uer
Extend M
D
L
o
gger l
e
vels
commit
|
commitdiff
|
tree
2019-07-17
Paul Bauer
M
o
v
e methods out from trjconv
commit
|
commitdiff
|
tree
2019-07-03
Mark
A
braham
Reorder options
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
A
dd cla
s
s
t
o
look up densit
y
fitting amplitudes
commit
|
commitdiff
|
tree
2019-06-20
C
h
ristian Blau
Ad
d
coord
i
nate s
c
ali
n
g cl
a
ss and extend
TranslateAndSc
a
le
commit
|
commitdiff
|
tree
2019-06-20
C
h
ristian Blau
A
l
low n
o
n-unifor
m
Gaus
s
ians
commit
|
commitdiff
|
tree
2019-06-18
Paul Bauer
Ex
t
end ISerializer
f
unctionalit
y
commit
|
commitdiff
|
tree
2019-05-08
Mark Abra
h
am
Provide hook for forks of
G
R
OMACS to
desc
r
ibe th
e
mselves
commit
|
commitdiff
|
tree
2019-04-22
Christian Bla
u
Three d
i
mensional
gauss transfor
m
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
One di
m
ensional Gau
s
s
ian function on
l
a
tti
c
e
.
commit
|
commitdiff
|
tree
2019-03-25
Mar
k
A
braham
Support A
r
rayRef
of Enumeration
A
rra
y
commit
|
commitdiff
|
tree
2019-03-25
M
.
Eric
Irrgang
Remove
u
ses of
s
td
:
:i
t
erator mix-i
n
.
commit
|
commitdiff
|
tree
2019-03-22
P
a
ul Ba
u
er
A
d
d si
m
ple tests
f
or symbol
table
commit
|
commitdiff
|
tree
2019-03-20
Paul Bauer
Ad
d
si
m
ple test to
p
rep
r
ocess bon
d
atom type
commit
|
commitdiff
|
tree
2019-03-20
Paul Baue
r
A
d
d test for strin
g
com
p
arison
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
aham
Add support for serializing 32
-
bit i
n
tegers
commit
|
commitdiff
|
tree
2019-03-19
C
hristian Blau
densityfi
t
ting -
density
f
i
l
e
f
o
r
m
a
t
(
mrc)
h
eader
.
commit
|
commitdiff
|
tree
2019-03-19
P
aul Bauer
Fix case i
n
sensitive string comparison
commit
|
commitdiff
|
tree
2019-03-19
Mar
k
A
b
rah
a
m
Fix clang warning
commit
|
commitdiff
|
tree
2019-03-19
Mark A
b
r
aham
Update E
l
ec
t
ri
c
Field m
o
dule
commit
|
commitdiff
|
tree
2019-03-13
Paul Ba
u
er
Ad
d
tests fo
r
pre
p
roces
s
atom types
commit
|
commitdiff
|
tree
2019-03-13
P
a
u
l Bauer
R
e
factor t
_
param to InteractionType
commit
|
commitdiff
|
tree
2019-03-08
P
a
u
l B
a
uer
Refactor
preproc
e
ss
i
ng
atom types
.
commit
|
commitdiff
|
tree
2019-03-07
Mark Abr
a
ham
New t
e
sts f
o
r pdb2gmx and editconf
commit
|
commitdiff
|
tree
2019-03-06
Paul
Baue
r
A
dd er
r
or when manual canno
t
be
built
commit
|
commitdiff
|
tree
2019-02-27
Mark A
b
r
a
ham
Keep ni
c
he CMake variables as advanc
e
d
commit
|
commitdiff
|
tree
2019-02-25
Mark
Abr
a
ham
Move cod
e
o
ut
of sim_util
.
cpp
commit
|
commitdiff
|
tree
2019-02-15
P
aul Bauer
Fix memory
leaks
i
n editc
o
nf
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
Fix
u
s
e
of selections refe
r
ri
n
g to index groups
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
Reve
r
t c
h
anges to implementation of insert-molecules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Paul Bauer
Refactor rtp renamin
g
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraham
Make Ener
g
yOutput
w
r
apper class
commit
|
commitdiff
|
tree
2019-02-08
Mark Abraham
Remo
v
e
c
o
py_energy f
r
om energy-writin
g
steps
commit
|
commitdiff
|
tree
2019-02-07
Roland Schulz
Add
ssize and
rem
o
ve s
t
atic_ca
s
ts
commit
|
commitdiff
|
tree
2019-01-25
Mar
k
Abraham
U
n
ify regex
i
m
plementatio
n
commit
|
commitdiff
|
tree
2019-01-24
Christian Blau
R
e
m
o
ve extra semicolons causi
n
g clan
g
warnings
.
commit
|
commitdiff
|
tree
2019-01-18
K
evin Boyd
Add tests f
o
r g
m
x mindist
commit
|
commitdiff
|
tree
2018-12-20
David van der Spoel
Remove
d
t_to
p
o
l
o
gy fro
m
g
m
x msd
commit
|
commitdiff
|
tree
2018-12-12
Szilárd Páll
I
m
prove DLB repor
t
/note
commit
|
commitdiff
|
tree
2018-12-10
Paul
B
auer
Us
e
more const r
e
ferences in topology code
commit
|
commitdiff
|
tree
2018-12-06
b
o
ristim
Updates
t
o d
o
_dssp
commit
|
commitdiff
|
tree
2018-10-03
Mark
Abraham
Bas
i
c mo
d
erniza
t
ion of
md5 han
d
ling
commit
|
commitdiff
|
tree
2018-08-30
Chris
t
ian
B
lau
Convert essential dy
n
amics C-str
u
c
ts to C++ pt1
.
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Make gmx_ga2
l
a_t a prop
e
r
c
las
s
commit
|
commitdiff
|
tree
2018-08-17
B
erk Hess
M
a
ke pull pb
c
atom use L
o
calAtomSe
t
commit
|
commitdiff
|
tree
2018-08-14
R
o
land
Sc
h
u
l
z
Remove
BasicVe
c
to
r
.
as_vec
commit
|
commitdiff
|
tree
2018-08-10
K
e
vin Boyd
A
d
ded physical val
i
dation d
o
cument to t
h
e de
v
manual
.
commit
|
commitdiff
|
tree
2018-08-09
Chr
i
stian Bl
a
u
Remove Debug Helper
s
from Essen
t
ial Dyna
m
ics code
.
commit
|
commitdiff
|
tree
2018-08-08
Ch
r
istian Blau
Essential dyn
a
mics functions use const-ref for
inp
u
t
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
C
hristi
a
n Blau
Split essential dy
n
amics e
i
genvector
reading
.
commit
|
commitdiff
|
tree
2018-08-08
C
hri
s
tian Blau
Make essential
d
ynamics
a
C+
+
type
.
commit
|
commitdiff
|
tree