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Use signed arithmetic in enumeration helper
2020-07-08
Kevin
Boyd
Use signed ar
i
thmeti
c
in e
n
umer
a
tion
helper
commit
|
commitdiff
|
tree
2020-07-08
Kevin Boy
d
Enforce u
n
s
igned type in flags
.
commit
|
commitdiff
|
tree
2020-07-07
Artem Zhmurov
Make cl
_
nbparam in
t
o a
s
t
ruct
commit
|
commitdiff
|
tree
2020-07-06
B
er
k
Hess
Move
f
o
reign po
t
e
ntial energy accumulation
commit
|
commitdiff
|
tree
2020-07-06
Roland Schulz
Modernize STL
u
sage
commit
|
commitdiff
|
tree
2020-07-06
Kevin Boyd
A
void overflow in R
N
G
commit
|
commitdiff
|
tree
2020-07-01
Chri
s
tian Blau
Updated t
h
e chan
g
e mana
g
ement documenta
t
ion
commit
|
commitdiff
|
tree
2020-06-22
Berk Hess
Move s
o
ft-core parameters
to i
n
teraction_
c
o
n
s
t_
t
commit
|
commitdiff
|
tree
2020-06-18
Paul B
a
ue
r
Fix mis
s
ing #i
n
clude <str
i
ng
>
commit
|
commitdiff
|
tree
2020-06-09
Paul Baue
r
Ext
r
act
C
OM
handling from trj
c
onv
commit
|
commitdiff
|
tree
2020-03-20
Berk Hess
Re
n
ame cla
s
s Gr
i
d t
o
BiasGrid
i
n A
W
H
module
commit
|
commitdiff
|
tree
2020-03-20
Artem
Z
hmurov
S
mal
l
f
i
x
e
s to
the DeviceStre
a
m
commit
|
commitdiff
|
tree
2020-03-19
Artem Zhmurov
Store Devi
c
eInfo
r
mation insid
e
the
D
eviceContext cl
a
ss
commit
|
commitdiff
|
tree
2020-03-17
Berk H
e
s
s
Convert t_
g
ra
p
h to C++
commit
|
commitdiff
|
tree
2020-03-16
C
h
ristian
B
lau
Remove
dysfunctional QMMM
i
nterface pt4
commit
|
commitdiff
|
tree
2020-03-16
C
hristian B
l
au
Remove d
y
sfunctional QMMM
i
n
t
erfa
c
e pt3
commit
|
commitdiff
|
tree
2020-03-16
C
h
rist
i
an Blau
Remove dysfunc
t
io
n
al QMMM interface pt2
commit
|
commitdiff
|
tree
2020-03-16
C
hristian Blau
Re
m
ove dys
f
un
c
t
i
onal
QMMM interface pt1
commit
|
commitdiff
|
tree
2020-03-11
A
rtem Zhmurov
Take ov
e
r mana
g
eme
n
t of O
p
enCL context from PME an
d
.
.
.
commit
|
commitdiff
|
tree
2020-03-11
B
erk Hes
s
A
dd tests for graph
commit
|
commitdiff
|
tree
2020-03-09
Artem Z
h
murov
Make DeviceC
o
ntext into a pr
o
per cl
a
ss
commit
|
commitdiff
|
tree
2020-03-05
Christian
B
lau
A
d
d fun
c
tion
c
alls to MdModules
t
o sign up
for notificat
i
ons
commit
|
commitdiff
|
tree
2020-03-05
C
hristian
B
lau
Sp
l
it off im
p
lemen
t
ation deta
i
ls of MdModuleN
o
t
i
fication
commit
|
commitdiff
|
tree
2020-03-04
Ar
t
em Z
h
muro
v
Do not
count
PME only ra
n
k wh
e
n
init
i
ali
z
i
n
g NB
N
XM
commit
|
commitdiff
|
tree
2020-02-25
Chri
s
tia
n
B
l
au
Document density-fit cros
s
-
correla
t
ion in
.
mdp options
commit
|
commitdiff
|
tree
2020-02-23
Mark Abraham
Remo
v
ed unused
PME gather
fun
c
t
ionali
t
y
commit
|
commitdiff
|
tree
2020-02-18
Mark Ab
r
aham
A
d
ded more d
o
cs an
d
tests to Enu
m
e
r
atio
n
Array
commit
|
commitdiff
|
tree
2020-02-18
Chri
s
tian Blau
Split MdMod
u
leNotifica
t
i
o
n
s into topic
s
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix checkNumberOfBond
e
dInteractio
n
s bu
g
commit
|
commitdiff
|
tree
2020-01-31
Paul Baue
r
St
a
rt
u
sing MDL
o
gger i
n
g
mxpreprocess
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Re
n
ame
L
incsCu
d
a into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
A
rtem Zhmurov
Rename
L
eapFrogCuda to L
e
apFr
o
gGpu
commit
|
commitdiff
|
tree
2020-01-20
Berk H
e
ss
Use
s
t
d
::ve
c
tor in shellfc
commit
|
commitdiff
|
tree
2020-01-13
Ar
t
em Zh
m
u
r
ov
Re
p
ort
if
u
p
date
i
s run
n
ing on the
GPU or
o
n
the CPU
commit
|
commitdiff
|
tree
2020-01-10
P
a
ul Bauer
Fix compiler
warning
s
on wi
n
do
w
s
commit
|
commitdiff
|
tree
2019-12-17
Paul Bauer
Fix formatting er
r
or
commit
|
commitdiff
|
tree
2019-12-16
P
a
ul Bauer
Fix torsi
o
n angle calculati
o
n
commit
|
commitdiff
|
tree
2019-12-12
B
erk
Hess
A
d
d c
l
ass
L
ist
O
f
List
s
commit
|
commitdiff
|
tree
2019-12-12
Christian Bl
a
u
Densityfitting -
enforce simil
a
r
i
t
y increase with a
d
apt
i
ve
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Chr
i
stian B
l
au
Relax te
s
t tolerance for cross correlat
i
o
n
measure
.
.
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Bla
u
Stochasti
c
dy
n
a
m
ic
s
- document that nsttc
o
uple
is ignored
commit
|
commitdiff
|
tree
2019-10-22
Chr
i
stian Blau
F
ix nst in d
e
nsity-fit
t
ing modu
l
e
commit
|
commitdiff
|
tree
2019-10-18
C
h
ristian Blau
Basi
c
refactoring
genio
n
a
nd adding test
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an Blau
Adapti
v
e force sc
a
lin
g
f
or den
s
i
t
yf
i
t
ting
commit
|
commitdiff
|
tree
2019-09-22
Christian Bla
u
Ad
d
cross
-
correlation
as density simlarity measure
commit
|
commitdiff
|
tree
2019-09-13
Paul Baue
r
Fix
n
ightly
failu
r
e
s
commit
|
commitdiff
|
tree
2019-09-13
Chris
t
oph J
u
nghans
c
m
a
ke: add op
t
ion to
install legac
y
h
e
ade
r
s
commit
|
commitdiff
|
tree
2019-09-11
Ch
r
istian Blau
Add
comments to gro
m
pp
g
e
n
e
rated
.
mdp
output for densityfitting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
E
n
d to end test f
o
r
density fitti
n
g
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Densityfi
t
ting write i
n
t64_t indic
e
s
i
nstead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Use the current ma
s
s i
n
stead of massA in d
e
nsi
t
y fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Account for re
f
eren
c
e
d
e
n
sity origin shift in pbc correction
commit
|
commitdiff
|
tree
2019-09-09
C
hristian Bl
a
u
Add op
t
ion to
normalize den
s
iti
e
s prio
r
to densi
t
y
.
.
.
commit
|
commitdiff
|
tree
2019-09-06
Chri
s
t
i
an Blau
Periodic boundary correction for density fitti
n
g
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Fi
x
double o
v
e
rload in LocalAto
m
Set code when gm
x
:
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
C
hr
i
stian Bl
a
u
Index groups f
o
r MdModu
l
es
f
rom grompp
commit
|
commitdiff
|
tree
2019-08-15
C
hr
i
stian Blau
Move densityfitting opti
o
ns
a
nd output
i
nto
s
e
perate
.
.
.
commit
|
commitdiff
|
tree
2019-08-15
Ber
k
H
ess
Template bonded
i
nteractions
on ke
r
nel flavor
commit
|
commitdiff
|
tree
2019-08-13
Ar
t
em
Zhmur
o
v
M
ake use of r
e
ference data
i
n int
e
gra
t
or t
e
sts
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmurov
Make
use of reference data in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Pau
l
Baue
r
A
d
d
conv
e
rsion from le
g
acy to modern matrix
t
y
p
e
commit
|
commitdiff
|
tree
2019-08-08
Christian Bl
a
u
P
rovide callbacks/n
o
t
ifications for
M
DMo
d
u
les
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmur
o
v
Rem
o
v
e P
I
mpl s
c
a
f
folding from CUDA ve
r
s
i
o
n
of Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
Berk Hes
s
Add
F
orceWithShiftForces class
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fix
l
atex
f
ormula in reference manual
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
r
i
c Irrgang
Resolve a c
o
mpiler warning
f
o
r the gmxapi Python
pack
a
ge
.
commit
|
commitdiff
|
tree
2019-08-05
M
a
rk Abraham
Add qu
o
te
commit
|
commitdiff
|
tree
2019-08-05
Berk H
e
s
s
Make box co
n
st in
d
o_fo
r
ce()
commit
|
commitdiff
|
tree
2019-08-05
Paul Bau
e
r
Add repla
c
ements for
pbc enume
r
ations
commit
|
commitdiff
|
tree
2019-08-05
P
aul Bauer
A
dd free function to convert matrix type
commit
|
commitdiff
|
tree
2019-07-25
K
evin Boyd
Add
transpose operatio
n
to M
a
trix3x3
commit
|
commitdiff
|
tree
2019-07-24
C
h
ri
s
tian Blau
F
ix HTML source doc
u
menation error caused by
G
aussTransform3D
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Begin
n
ew
sa
m
ple_r
e
straint devel
o
pment
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric Irrgang
I
mprov
e
s
o
me documentation form
a
tt
i
ng
a
nd spe
l
ling
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric
I
rrgang
R
e
move ex
t
raneous f
i
le
.
commit
|
commitdiff
|
tree
2019-07-18
P
a
ul
B
auer
Ext
e
nd MDLogger levels
commit
|
commitdiff
|
tree
2019-07-17
Paul Ba
u
e
r
Move methods
o
ut from trj
c
onv
commit
|
commitdiff
|
tree
2019-07-03
Mar
k
A
b
r
aham
Reorder opt
i
ons
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add cla
s
s to look up densit
y
f
i
t
tin
g
amplitud
e
s
commit
|
commitdiff
|
tree
2019-06-20
Christi
a
n Blau
A
d
d coordinat
e
scaling class and ex
t
end TranslateAnd
S
c
a
le
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
sti
a
n Bl
a
u
Allow non-un
i
f
orm Gaussians
commit
|
commitdiff
|
tree
2019-06-18
Pau
l
Bauer
Extend ISerializer funct
i
o
n
ality
commit
|
commitdiff
|
tree
2019-05-08
Mark Abraham
Provide hook for forks of G
R
OMACS to describe the
m
selves
commit
|
commitdiff
|
tree
2019-04-22
Christian Blau
Three d
i
mensiona
l
gauss transform
commit
|
commitdiff
|
tree
2019-04-22
Chr
i
stian Blau
One dimensiona
l
Gaussian functio
n
on lattice
.
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraham
Suppo
r
t A
r
rayRe
f
of Enumera
t
io
n
Array
commit
|
commitdiff
|
tree
2019-03-25
M
.
Eric Irrgan
g
Remove use
s
of
s
t
d
::iterator mix
-
i
n
.
commit
|
commitdiff
|
tree
2019-03-22
Pa
u
l B
a
uer
Add simple
tests for sy
m
bol ta
b
le
commit
|
commitdiff
|
tree
2019-03-20
Paul Bauer
A
dd simple tes
t
to preproc
e
ss b
o
nd
a
tom t
y
pe
commit
|
commitdiff
|
tree
2019-03-20
Paul Baue
r
A
d
d
t
e
s
t
f
or string
c
omparison
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
aham
Add support for
s
eri
a
lizing
3
2-bit integers
commit
|
commitdiff
|
tree
2019-03-19
Ch
r
istian Blau
densityfitting - density file f
o
rmat
(
mrc) h
e
ad
e
r
.
commit
|
commitdiff
|
tree
2019-03-19
P
a
u
l
Bauer
Fix case i
n
sensiti
v
e
string compari
s
o
n
commit
|
commitdiff
|
tree
2019-03-19
Ma
r
k Abra
h
am
F
ix c
l
ang w
a
rning
commit
|
commitdiff
|
tree
2019-03-19
Mar
k
Abr
a
ham
Upd
a
t
e
Electr
i
cField module
commit
|
commitdiff
|
tree
2019-03-13
Pau
l
Bauer
Add tests
f
o
r pr
e
proc
e
s
s atom
t
ypes
commit
|
commitdiff
|
tree
2019-03-13
Paul Bauer
R
e
factor t_
p
aram to Inter
a
ctionType
commit
|
commitdiff
|
tree
2019-03-08
P
aul Bauer
Re
f
a
c
tor prepro
c
e
ssing atom
types
.
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
New tests for pdb2gmx
and editconf
commit
|
commitdiff
|
tree
2019-03-06
P
a
ul
Bauer
Add error when manual cannot
b
e
built
commit
|
commitdiff
|
tree
next