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Added more docs and tests to EnumerationArray
2020-02-18
Ma
r
k Abrah
a
m
Added more
docs
a
n
d te
s
ts to Enumerati
o
nAr
r
ay
commit
|
commitdiff
|
tree
2020-02-18
Chr
i
stian Blau
S
p
li
t
MdModuleNotific
a
tions into
topics
commit
|
commitdiff
|
tree
2020-01-31
Paul Bauer
Start us
i
ng MDL
o
gger in gmxpreprocess
commit
|
commitdiff
|
tree
2020-01-20
Artem
Z
hmu
r
ov
Rename LincsCu
d
a into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zh
m
urov
Rename LeapFrogCuda t
o
LeapF
r
ogGpu
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use s
t
d::
v
ector in shellfc
commit
|
commitdiff
|
tree
2020-01-13
A
rte
m
Zhmurov
Report if update i
s
running on the GPU or
o
n the
CPU
commit
|
commitdiff
|
tree
2020-01-10
P
aul Bauer
Fi
x
co
m
piler warnings o
n
windows
commit
|
commitdiff
|
tree
2019-12-17
Paul Bauer
Fix formatt
i
ng er
r
or
commit
|
commitdiff
|
tree
2019-12-16
Pau
l
Bauer
Fix to
r
sion
angle calculation
commit
|
commitdiff
|
tree
2019-12-12
B
erk Hess
Add
cl
a
ss List
O
fLists
commit
|
commitdiff
|
tree
2019-12-12
Christi
a
n Blau
Dens
i
tyfitting - enfor
c
e s
i
milarity increase wit
h
adaptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
C
h
ristian Blau
R
e
l
ax test toleranc
e
for cross co
r
rel
a
tion measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-07
C
hristian Blau
Stochastic dynamics
-
document that nstt
c
ouple
i
s ignored
commit
|
commitdiff
|
tree
2019-10-22
Christian B
l
au
Fix nst in densi
t
y-fitting module
commit
|
commitdiff
|
tree
2019-10-18
Christian
Blau
Basic refactoring genion an
d
adding t
e
st
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an Blau
A
dapti
v
e force scaling for den
s
i
t
yfit
t
ing
commit
|
commitdiff
|
tree
2019-09-22
Christian B
l
au
Add cros
s
-
correla
t
ion as density siml
a
rity
m
eas
u
re
commit
|
commitdiff
|
tree
2019-09-13
Paul
B
a
u
er
Fix nightly
failures
commit
|
commitdiff
|
tree
2019-09-13
C
h
risto
p
h
Junghans
c
make: ad
d
o
p
t
ion to install
legacy headers
commit
|
commitdiff
|
tree
2019-09-11
Christi
a
n Bl
a
u
Add comm
e
nts to grompp gen
e
rated
.
mdp
outp
u
t for densityfitting
commit
|
commitdiff
|
tree
2019-09-11
Christ
i
an Blau
End to end
tes
t
for den
s
ity fitti
n
g
commit
|
commitdiff
|
tree
2019-09-11
C
h
ri
s
t
i
an Bla
u
Densityf
i
tt
i
ng
write int64_t indices inst
e
ad
of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian
Blau
Use the current
m
ass i
n
st
e
ad
o
f massA in densi
t
y fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christ
i
an Bl
a
u
Accou
n
t for
refe
r
ence density origin shift
in pbc correction
commit
|
commitdiff
|
tree
2019-09-09
Christi
a
n Blau
Add option to
normalize densiti
e
s prior
to densi
t
y
.
.
.
commit
|
commitdiff
|
tree
2019-09-06
Ch
r
istia
n
Blau
Periodic
boundary correction for den
s
ity fitt
i
ng
commit
|
commitdiff
|
tree
2019-09-04
Ch
r
i
s
tian Blau
Fix double overload
in LocalAtomSet code when gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Chris
t
ian Blau
I
n
dex
groups for MdModule
s
from grompp
commit
|
commitdiff
|
tree
2019-08-15
Chr
i
stian Blau
Move de
n
sityfitting
o
ptions an
d
outp
u
t into s
e
p
erate
.
.
.
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
T
e
m
plate b
o
nded interactions on k
e
rnel flavor
commit
|
commitdiff
|
tree
2019-08-13
A
rtem
Z
hm
u
rov
M
ake use o
f
refe
r
ence data in integrator t
e
sts
commit
|
commitdiff
|
tree
2019-08-13
Ar
t
em Zhm
u
r
ov
Make use of reference d
a
t
a in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Paul Bauer
Add conversion from legacy to modern matrix type
commit
|
commitdiff
|
tree
2019-08-08
Christ
i
an Blau
P
ro
v
id
e
callbac
k
s/notifi
c
ations for MD
M
odu
l
e
s
commit
|
commitdiff
|
tree
2019-08-06
Artem Zh
m
urov
Re
m
ove PImpl s
c
af
f
o
l
d
i
ng fro
m
CUDA ver
s
i
o
n of
L
eap
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
Ber
k
Hess
Add ForceWithShiftFo
r
ces class
commit
|
commitdiff
|
tree
2019-08-06
Berk He
s
s
Fix
l
at
e
x formula
i
n r
e
f
e
rence
ma
n
u
al
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irr
g
an
g
R
e
solve
a
compile
r
warning f
o
r the gmxapi Pyth
o
n package
.
commit
|
commitdiff
|
tree
2019-08-05
Ma
r
k
Abraham
Add quote
commit
|
commitdiff
|
tree
2019-08-05
Berk
H
ess
M
a
ke b
o
x
const in do_force(
)
commit
|
commitdiff
|
tree
2019-08-05
Pa
u
l Bauer
Add replacements for pbc enum
e
rations
commit
|
commitdiff
|
tree
2019-08-05
Paul Bauer
A
d
d free
f
u
nc
t
ion to
convert matr
i
x type
commit
|
commitdiff
|
tree
2019-07-25
K
e
vin B
o
yd
Add
t
ranspose operation to Mat
r
ix3x3
commit
|
commitdiff
|
tree
2019-07-24
Chri
s
tia
n
Blau
F
i
x
HTML
s
o
u
rce doc
u
m
ena
t
ion error caus
e
d by G
a
ussTran
s
form3D
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
ric Irrgang
Begi
n
new
sample_rest
r
aint d
e
velopme
n
t
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric Irrgang
Improve some docume
n
t
a
t
ion formatting
a
nd spellin
g
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric
Irrgang
Remo
v
e
extran
e
o
us fi
l
e
.
commit
|
commitdiff
|
tree
2019-07-18
Paul
B
auer
Extend
MDLogger leve
l
s
commit
|
commitdiff
|
tree
2019-07-17
Paul Bauer
Move methods out
f
rom trjcon
v
commit
|
commitdiff
|
tree
2019-07-03
Mark
A
braham
Reor
d
e
r op
t
ions
commit
|
commitdiff
|
tree
2019-06-28
C
hristian Blau
Add class to loo
k
up density fitting amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
Add coordina
t
e sca
l
ing cl
a
ss a
n
d ex
t
end Tran
s
lateAndScal
e
commit
|
commitdiff
|
tree
2019-06-20
C
h
risti
a
n Blau
Allow non
-
uniform Gauss
i
a
n
s
commit
|
commitdiff
|
tree
2019-06-18
Paul Bau
e
r
Ext
e
nd
I
Serializer
f
unctionality
commit
|
commitdiff
|
tree
2019-05-08
Mark Ab
r
aham
Pro
v
ide hook for forks of
GROMACS
t
o describe the
m
s
e
lves
commit
|
commitdiff
|
tree
2019-04-22
C
h
ristian Blau
T
h
ree dimens
i
onal gauss transform
commit
|
commitdiff
|
tree
2019-04-22
Christ
i
an Blau
One dimensio
n
a
l
Ga
u
s
sian function on latt
i
c
e
.
commit
|
commitdiff
|
tree
2019-03-25
Mark Ab
r
aham
S
upport ArrayRef of Enumeration
A
rray
commit
|
commitdiff
|
tree
2019-03-25
M
.
Eric Irrgang
Remove uses of std::iterator mix-i
n
.
commit
|
commitdiff
|
tree
2019-03-22
Paul Ba
u
er
Ad
d
simp
l
e
t
e
sts for symbol t
a
ble
commit
|
commitdiff
|
tree
2019-03-20
Paul Bauer
Add simp
l
e test
to
p
reprocess bo
n
d atom type
commit
|
commitdiff
|
tree
2019-03-20
P
a
ul Bauer
Add test for
s
tring
com
p
a
rison
commit
|
commitdiff
|
tree
2019-03-19
Mark
A
braham
Add sup
p
o
r
t
f
or serializ
i
ng 32-bit
i
n
tege
r
s
commit
|
commitdiff
|
tree
2019-03-19
Chri
s
tian Blau
densityf
i
t
t
ing - densi
t
y file f
o
r
m
at (mrc)
h
eader
.
commit
|
commitdiff
|
tree
2019-03-19
P
a
ul Bauer
F
i
x
case in
s
e
nsitive s
t
ring comparis
o
n
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraham
Fix clang warning
commit
|
commitdiff
|
tree
2019-03-19
Mark Abr
a
ham
Updat
e
Electric
F
ield module
commit
|
commitdiff
|
tree
2019-03-13
Paul Bau
e
r
Add
t
ests
for pre
p
roce
s
s
atom typ
e
s
commit
|
commitdiff
|
tree
2019-03-13
Pau
l
Bauer
Refactor t_param
t
o
InteractionType
commit
|
commitdiff
|
tree
2019-03-08
Paul Bauer
Refactor preprocessi
n
g at
o
m types
.
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
New tests for pdb2gmx and e
d
itconf
commit
|
commitdiff
|
tree
2019-03-06
P
a
ul Bauer
Add error when ma
n
ual
cann
o
t be built
commit
|
commitdiff
|
tree
2019-02-27
Mark Abraham
Keep niche
C
Make
v
a
riables
as advan
c
ed
commit
|
commitdiff
|
tree
2019-02-25
Mark
Abraha
m
Move code out of sim_util
.
cpp
commit
|
commitdiff
|
tree
2019-02-15
Paul B
a
uer
Fix memory leaks in editc
o
nf
commit
|
commitdiff
|
tree
2019-02-14
Mark A
b
raham
Fix use
of
sel
e
c
tions referring t
o
ind
e
x grou
p
s
commit
|
commitdiff
|
tree
2019-02-14
Mar
k
Abraham
Revert changes
t
o implementation of i
n
sert-molecules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Paul Bauer
Re
f
actor rtp renami
n
g
commit
|
commitdiff
|
tree
2019-02-13
Mark Abr
a
ham
M
a
k
e EnergyOutput wr
a
pper class
commit
|
commitdiff
|
tree
2019-02-08
M
ark Abraham
Re
m
ove co
p
y
_
e
nergy f
r
om energy-writ
i
ng ste
p
s
commit
|
commitdiff
|
tree
2019-02-07
R
o
lan
d
Schul
z
Add ssize an
d
re
m
o
v
e static_cast
s
commit
|
commitdiff
|
tree
2019-01-25
Mark Abraham
Unify regex implementation
commit
|
commitdiff
|
tree
2019-01-24
Chr
i
stian
Blau
R
e
move extra se
m
icolons
c
ausing clang warnings
.
commit
|
commitdiff
|
tree
2019-01-18
Kevin
B
o
yd
Add t
e
s
ts for gmx
mindist
commit
|
commitdiff
|
tree
2018-12-20
David van
d
e
r Spoel
Removed t_topology fro
m
gmx
msd
commit
|
commitdiff
|
tree
2018-12-12
Szilá
r
d
P
áll
Imp
r
ove DLB re
p
ort/not
e
commit
|
commitdiff
|
tree
2018-12-10
Pau
l
Bauer
Use more const ref
e
ren
c
es i
n
topology
c
o
d
e
commit
|
commitdiff
|
tree
2018-12-06
boristim
Updates to do_dssp
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
Ba
s
ic m
o
dern
i
za
t
i
on of md
5
handling
commit
|
commitdiff
|
tree
2018-08-30
Christian Blau
C
o
nver
t
essential
dynamics
C
-stru
c
ts
to C+
+
pt1
.
commit
|
commitdiff
|
tree
2018-08-20
Berk He
s
s
Make
g
mx_ga2la
_
t a proper class
commit
|
commitdiff
|
tree
2018-08-17
Berk He
s
s
Make pu
l
l pbc atom use LocalAtomSet
commit
|
commitdiff
|
tree
2018-08-14
Roland Schul
z
Remove B
a
si
c
Vector
.
as_v
e
c
commit
|
commitdiff
|
tree
2018-08-10
K
e
vin Boyd
Ad
d
e
d
physical
v
alida
t
ion d
o
cument to
the dev manual
.
commit
|
commitdiff
|
tree
2018-08-09
Christ
i
an B
l
a
u
R
emove
Debug He
l
pers from Es
s
ential Dyn
a
mics code
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Essen
t
ial dynamics function
s
use c
o
n
st-ref for input
.
.
.
commit
|
commitdiff
|
tree
2018-08-08
Christian Blau
Split esse
n
tial dynamics eigenvector reading
.
commit
|
commitdiff
|
tree
2018-08-08
Christ
i
an Bla
u
Make
e
ssential dyn
a
mics a
C++ t
y
pe
.
commit
|
commitdiff
|
tree