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Remove obsolete mdp option ns-type
2019-09-16
Ber
k
Hess
Remov
e
o
bsolete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Add some cool quo
t
es
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
Formatt
i
ng fixes for refe
r
ence ma
n
ual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eri
c
Irrgang
Add gmxapi release no
t
es
.
commit
|
commitdiff
|
tree
2019-09-16
Al
a
n Gray
GPU
halo ex
c
hange
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virtual
site ty
p
e
2F
D
commit
|
commitdiff
|
tree
2019-09-16
M
a
r
k Abraham
Avoid short-range GPU ope
r
ations
with no wo
r
k
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Remove cut-off schemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Szil
á
rd Páll
Eliminate unneces
s
ary G
P
U stream
de
p
en
d
ency call
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hess
Add optio
n
request 1D DD with 1 p
u
lse
commit
|
commitdiff
|
tree
2019-09-16
K
evin
Boyd
R
emove group scheme from depreca
t
ed r
e
leas
e
notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Introduce the modular simu
l
a
t
o
r
commit
|
commitdiff
|
tree
2019-09-15
Peter Kasson
Patch gmxapi for Py
t
hon
3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Er
i
c Ir
r
g
a
ng
N
ormalize usage of GMX
T
OOLCHAINDIR
i
n g
m
x
a
pi
s
e
t
up
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
I
r
rgan
g
Do
n
o
t use gromacs-t
o
ol
c
ha
i
n in d
a
rwin
gmxapi
builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgan
g
Update gmxa
p
i setup
.
py
commit
|
commitdiff
|
tree
2019-09-12
Mark Abraha
m
Disable r
e
port-me
t
hods end
-
to-
e
n
d
t
est
commit
|
commitdiff
|
tree
2019-09-12
Szi
l
árd
P
á
ll
Reo
r
ga
n
ize
on-GPU PME
f
o
rce reduction flag handling
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmu
r
o
v
C
hange Pa
d
ded
V
ec
t
or to PaddedH
o
stVector for force C
P
U
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Christia
n
Bla
u
Add release
n
ote for den
s
ity fittin
g
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
Up
d
a
t
e mo
d
ular simul
a
to
r
tests
commit
|
commitdiff
|
tree
2019-09-12
E
r
ik Lindah
l
Added SIM
D
log2 a
n
d po
w
m
ath functions
commit
|
commitdiff
|
tree
2019-09-12
E
r
ik Lind
a
hl
U
p
d
ate SIMD ma
t
h te
s
ts and improve accurac
y
commit
|
commitdiff
|
tree
2019-09-11
Paul Bau
e
r
Remove
-
sub opti
o
n from
trjconv
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Zhmuro
v
F
ix for t
h
e
post
-
su
b
mit
f
a
il
u
re
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
D
ecouple
GPU force buffer ma
n
a
gement from buf
f
er ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric
I
rrgang
Use
G
R
OMACS CMake toolchain fi
l
e for gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul
Bauer
Basic toolc
h
a
i
n to facil
i
tat
e
G
M
X
API build
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrgang
Add gmxapi
.
modify_in
p
ut op
e
ration
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric
I
rrgang
Provide
a
gmxapi
.
r
e
ad_tpr operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
i
c Ir
r
ga
n
g
Update
g
mxapi
.
simul
a
tion
.
c
o
ntext de
t
ails
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ric Irrgan
g
Update gmxapi Pyt
h
on p
a
ckage infrastructure for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
No
r
m
alize some tes
t
ing resources fo
r
the Python packag
e
s
.
commit
|
commitdiff
|
tree
2019-09-11
M
a
gnus Lundborg
Tidy up the FE
kern
e
l
commit
|
commitdiff
|
tree
2019-09-10
Paul Ba
u
er
Fix
n
i
g
htly build
commit
|
commitdiff
|
tree
2019-09-10
Szi
l
ár
d
Páll
Use thread-MPI
in the gpucomm
m
atrix
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Mer
z
Coordinate Propagators
commit
|
commitdiff
|
tree
2019-09-10
P
ascal Merz
StatePro
p
agat
o
rData: Introduc
e
d const box accessor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal M
e
rz
Add
t
r
ivial c
o
n
st qualifiers to s
h
ellfc
and EnergyOut
p
ut
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Merz
Cons
t
raint element for t
h
e m
o
dular
simul
a
t
or
commit
|
commitdiff
|
tree
2019-09-09
S
z
ilárd
P
á
ll
P
a
s
s gmx::Forc
e
Flags to
C
PU nb
n
xm d
i
s
p
at
c
h
code
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
Pass the n
e
w gm
x
:
:
ForceFla
g
s to the nbnxm module
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Re
m
ov
e
incorrect check
w
ith rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Pasc
a
l Merz
Domain
d
e
c
o
m
position and PME lo
a
d balancing for m
o
du
l
ar
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Christian Bla
u
Re
l
a
ti
v
e
e
ntropy
as
density similar
i
ty measure
commit
|
commitdiff
|
tree
2019-09-09
P
a
ul Bauer
Add g
m
x c
o
nvert-trj
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk H
e
ss
Ren
a
me DDSetu
p
to DD
G
r
i
dSe
t
up
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Cle
a
n up PME rank variables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
R
efactor init_domain_dec
o
mposition()
commit
|
commitdiff
|
tree
2019-09-07
Pascal Me
r
z
Make pme_loadbal_do()
i
ndependent of t_st
a
te
commit
|
commitdiff
|
tree
2019-09-07
Pasca
l
M
e
r
z
For
c
eElement and ShellFCElement for the modular simulator
commit
|
commitdiff
|
tree
2019-09-06
Szil
á
rd Pál
l
Add
g
pu
u
pdate and gpucomm OnDe
m
and t
o
ke
n
s
commit
|
commitdiff
|
tree
2019-09-06
Berk Hes
s
Extract g
e
tting of DDRank
S
et
u
p
commit
|
commitdiff
|
tree
2019-09-06
B
erk
H
ess
Add PP
g
rid
info to DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Mar
k
Abraham
Upda
t
e
mdrun test co
m
parison infrastructure
commit
|
commitdiff
|
tree
2019-09-05
Pascal
M
erz
Rename MicroState to S
t
atePropagator
D
ata for mo
d
ular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Christia
n
Blau
Add
r
eference
d
e
n
sity file option t
o
densityfitting
commit
|
commitdiff
|
tree
2019-09-05
Berk
H
ess
Split off getti
n
g
o
f the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Szilár
d
Páll
B
u
mp A
R
M HPC t
o
ol
c
h
ain in pos
t
-submi
t
to v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
Szilárd
P
áll
A
dd ba
c
k a clang-tid
y
exceptio
n
commit
|
commitdiff
|
tree
2019-09-04
Chri
s
t
i
an Blau
Read mrc file usin
g
file name
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update gro
u
p
i
ng to DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Magnus Lundborg
I
n
line functions of c
a
lculations
of F
E
interac
t
ion
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Cha
n
g
e
D
D pme fo
r
ce buffer to
std::ve
c
to
r
commit
|
commitdiff
|
tree
2019-09-04
B
erk Hess
Initial
i
ze
all
m
e
mbers of gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eric Ir
r
gang
Python
w
rapping co
d
e for gmxap
i
m
d
r
un bindings
.
commit
|
commitdiff
|
tree
2019-09-03
Pa
s
cal Merz
Introduce en
e
r
gy
element for modular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-03
Mark Abrah
a
m
S
i
mplify energy-file comparisons in tests
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add Pa
r
rin
e
llo-Rahman
p
ressure couplin
g
to
C
UDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
Berk
H
ess
Only u
s
e fshift w
h
en
n
eeded
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
Add checkpointing fo
r
MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christian Bla
u
LocalAtomS
e
t
co
n
stru
c
tion with vect
o
rs o
f
gmx::inde
x
commit
|
commitdiff
|
tree
2019-08-30
M
.
E
ri
c
Irrg
a
ng
Import base code for Python-driven simulation from
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
M
a
gnus
Lundb
o
rg
Changed some variables fro
m
S
C
R
e
al
t
o real in F
E
kernel
.
commit
|
commitdiff
|
tree
2019-08-30
Chri
s
tian
B
lau
Impleme
n
ting the density fitting
f
orce provider
commit
|
commitdiff
|
tree
2019-08-29
Mark
Abraham
Mo
r
e quote
s
commit
|
commitdiff
|
tree
2019-08-28
Pascal M
e
r
z
In
t
ro
d
uce signallers for
m
o
dul
a
r
integrator
commit
|
commitdiff
|
tree
2019-08-28
Paul
B
a
uer
Fix r
e
t
u
rn value
commit
|
commitdiff
|
tree
2019-08-28
Mark Abraham
Fix integ
r
ation iss
u
es
commit
|
commitdiff
|
tree
2019-08-28
Pasca
l
Merz
I
n
troduce the main modular simulator interfaces and
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul
B
a
u
e
r
Change tolerance for normal mode tests
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
Add
clang-tidy nightly test wi
t
h SIMD + Ope
n
CL
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
Mov
e
n
o
nbonded GPU w
a
it timing
i
nto
t
he GPU module
commit
|
commitdiff
|
tree
2019-08-27
M
a
rk Ab
r
aham
Add integration tests
for exact restar
t
s
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add
d
e
nsity fi
t
ting
p
arameters
commit
|
commitdiff
|
tree
2019-08-27
Chr
i
stian Blau
Acc
e
ss to
G
aussTransfo
r
m3
D
data
commit
|
commitdiff
|
tree
2019-08-27
Ch
r
istian Blau
Add index gro
u
p
option to den
s
ity
f
itting
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
Remove section che
c
king api level
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
Rem
o
ve
i
nst
a
lled head
e
rs from C
M
ake
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
Add
t
emperature coupling to CUDA Leap-Frog
i
ntegrator
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric
I
rrgang
Mo
v
e gmxapicompa
t
TPR tools to l
i
bgmxapi
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric
I
rrgang
Reduce artificial header dep
e
ndencies in re
s
t
r
aint
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christi
a
n
B
l
a
u
Act
i
vation of densit
y
fi
t
ti
n
g
and move of mo
d
ule notifications
commit
|
commitdiff
|
tree
2019-08-25
Szilárd Páll
clang-ti
d
y 8 fixes
for th
e
GPU ho
s
t code-path
commit
|
commitdiff
|
tree
2019-08-25
Sz
i
lárd P
á
ll
Furthe
r
fixes for cla
n
g-tidy cl
a
ng version 8
commit
|
commitdiff
|
tree
2019-08-23
Paul Bauer
Rem
o
ves checker for installed files
commit
|
commitdiff
|
tree
2019-08-23
Szilárd Pá
l
l
F
i
x
cl
a
n
g
-tidy war
n
ings
in the
O
penCL buil
d
commit
|
commitdiff
|
tree
2019-08-23
Mark
A
b
raham
Upd
a
te cl
a
ng-tid
y
to c
l
ang versi
o
n 8
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Merge bran
c
h release-2
0
19
commit
|
commitdiff
|
tree
2019-08-22
Ma
r
k
A
b
rah
a
m
Improve cla
n
g-analyzer b
u
ild time
commit
|
commitdiff
|
tree
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