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Python wrapping code for gmxapi mdrun bindings.
2019-09-03
M
.
Er
i
c Irrgang
Py
t
h
o
n wrapp
i
n
g code for
gmx
a
pi mdrun bindings
.
commit
|
commitdiff
|
tree
2019-09-03
Pascal Merz
Introduce
energy element for mo
d
u
lar simu
l
a
t
or
commit
|
commitdiff
|
tree
2019-09-03
Mark Abraham
Simplify en
e
rg
y
-
file compa
r
ison
s
in tests
commit
|
commitdiff
|
tree
2019-09-03
A
rtem Zhm
u
rov
Add Parrinel
l
o
-Rah
m
an pr
e
ssure c
o
upl
i
ng to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
Ber
k
Hess
Onl
y
us
e
fshift when ne
e
ded
commit
|
commitdiff
|
tree
2019-09-01
Christian Bla
u
Add
c
h
eck
p
ointing
f
o
r MdModu
l
es
commit
|
commitdiff
|
tree
2019-08-30
Christi
a
n Blau
LocalAtomSet c
o
nstruction with vectors o
f
gmx
:
:i
n
dex
commit
|
commitdiff
|
tree
2019-08-30
M
.
E
r
i
c
Irrgan
g
Im
p
ort base code for Pytho
n
-
d
r
i
ven simulat
i
on from
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Ma
g
n
u
s Lundborg
Changed some
v
ariables fr
o
m SCReal
to
real
i
n FE ke
r
nel
.
commit
|
commitdiff
|
tree
2019-08-30
C
hr
i
s
t
ian Blau
Im
p
l
emen
t
ing the density fitting force provider
commit
|
commitdiff
|
tree
2019-08-29
Mark
A
b
raham
More quotes
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce signal
l
ers
f
or mod
u
lar integ
r
a
tor
commit
|
commitdiff
|
tree
2019-08-28
Paul
B
a
uer
Fix return v
a
l
u
e
commit
|
commitdiff
|
tree
2019-08-28
M
a
r
k
Ab
r
a
ham
Fix integr
a
t
i
on issues
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Intro
d
uce
the main modular simula
t
or inter
f
ac
e
s
and
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul Bauer
Chan
g
e tolerance for
normal
mode tests
commit
|
commitdiff
|
tree
2019-08-28
S
zilá
r
d Páll
Add clang
-
ti
d
y night
l
y test with SI
M
D + Ope
n
CL
commit
|
commitdiff
|
tree
2019-08-28
Szilár
d
Páll
Move
n
o
nbonded GP
U
w
ait
t
i
ming into the GPU module
commit
|
commitdiff
|
tree
2019-08-27
Mark
Abraham
Add inte
g
rat
i
o
n
t
e
s
t
s
for exact restarts
commit
|
commitdiff
|
tree
2019-08-27
Ch
r
istian
B
lau
Add density fitting parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian
B
lau
Ac
c
ess to
Gau
s
sT
r
ansform3D da
t
a
commit
|
commitdiff
|
tree
2019-08-27
Christ
i
an Bl
a
u
Add
i
ndex g
r
oup option to density fi
t
ting
commit
|
commitdiff
|
tree
2019-08-26
Paul Ba
u
er
Remove
s
e
ction check
i
ng ap
i
lev
e
l
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
Remove insta
l
led he
a
d
e
rs from CM
a
ke
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
Add temperat
u
re coupling
t
o CUDA
L
eap-Frog
int
e
grator
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric
Irrgang
Move gmxapicompat
T
PR tools to
l
ibgmxapi
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric
I
rrgang
R
educe artificial header dependen
c
ie
s
in restraint
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activation
of
d
ens
i
ty fitting and
m
ove
of
modu
l
e notifications
commit
|
commitdiff
|
tree
2019-08-25
Szilárd
Páll
clang-tidy
8
fixes for the G
P
U host code-pat
h
commit
|
commitdiff
|
tree
2019-08-25
Sz
i
lárd P
á
ll
F
u
rther
fixes for clang-tidy clang version 8
commit
|
commitdiff
|
tree
2019-08-23
Paul Bauer
R
emoves chec
k
e
r
for i
n
stal
l
ed files
commit
|
commitdiff
|
tree
2019-08-23
S
zilárd P
á
ll
F
ix clang-tid
y
warnings in the Open
C
L build
commit
|
commitdiff
|
tree
2019-08-23
M
a
rk Abrah
a
m
Update c
l
an
g
-tidy to clang version
8
commit
|
commitdiff
|
tree
2019-08-22
M
ark A
b
raham
Merge branch release-2019
commit
|
commitdiff
|
tree
2019-08-22
Mark
A
braham
Imp
r
ove clang
-
an
a
lyzer build ti
m
e
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
ric Irr
g
an
g
C++ code and
P
y
thon bind
i
ngs for TPR parameter read
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
Fi
x
per
t
urbed bo
n
ded bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eric Irrgang
Ena
b
l
e
GMXAPI by
d
efault
.
commit
|
commitdiff
|
tree
2019-08-20
Be
r
k
Hess
M
e
rge two dihedral functions
commit
|
commitdiff
|
tree
2019-08-20
Berk
Hess
Use s
h
iftForces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Erik Linda
h
l
Avoid using
G
M
X_SIM
D
mac
r
os
t
o
d
ete
c
t _mm_pause()
commit
|
commitdiff
|
tree
2019-08-20
Ma
r
k Abraham
Fix issu
e
s for clang-analyzer
-
8
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded viri
a
l computati
o
n condi
t
ional
commit
|
commitdiff
|
tree
2019-08-19
Szilár
d
Pál
l
Switc
h
to ARM HPC toolchain v
1
9
.
2
in
p
ost-su
b
mit
commit
|
commitdiff
|
tree
2019-08-19
M
ar
k
Abrah
a
m
Modernize t_matrix, t_m
a
pping,
t
_
rgb
commit
|
commitdiff
|
tree
2019-08-19
M
a
r
k Abrah
a
m
M
o
dernize t_psdata
commit
|
commitdiff
|
tree
2019-08-19
Sz
i
lár
d
Páll
Work around clang CUDA de
v
i
c
e code codegen bug
commit
|
commitdiff
|
tree
2019-08-16
Szilárd P
á
ll
F
i
x
s
i
m
_util
.
cpp copyright he
a
der
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraha
m
U
pdate testing matrices
a
nd fix warnin
g
s
commit
|
commitdiff
|
tree
2019-08-16
M
a
r
k Abr
a
h
am
Stop nbnxm
/
gri
d
.
h depending on S
I
MD modu
l
e
commit
|
commitdiff
|
tree
2019-08-15
Szilárd Páll
Fix OpenCL gather reduction
commit
|
commitdiff
|
tree
2019-08-14
Chri
s
tian
B
la
u
Info
c
l
ass
to name and generate the dens
i
tyfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mark Abra
h
am
Fi
x
vv integrato
r
s
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
Add initial
.
c
l
a
ng-format file
.
commit
|
commitdiff
|
tree
2019-08-13
Mark
Abraham
Fix icc 19 codeg
e
n is
s
ue
commit
|
commitdiff
|
tree
2019-08-12
M
.
E
ri
c
Irrgang
Introduce Con
t
ext
r
e
qui
r
eme
n
t
.
commit
|
commitdiff
|
tree
2019-08-12
M
ark Ab
r
ah
a
m
Quiet warni
n
g
commit
|
commitdiff
|
tree
2019-08-12
Mark
Abraham
F
i
x ocl_kern
e
l target
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
Use new sete
n
v function for energyout
p
ut test
commit
|
commitdiff
|
tree
2019-08-12
M
.
E
r
ic Irrgang
Sepa
r
ate out some ab
s
tract
b
as
e
c
l
asses
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zh
m
urov
P
repare
Up
d
ate and Constra
i
nts
f
or Domain Decom
p
osition
commit
|
commitdiff
|
tree
2019-08-09
A
rtem
Zhmurov
Refactoring of the SETTL
E
tests
commit
|
commitdiff
|
tree
2019-08-09
Berk H
e
ss
S
I
MD a
c
celerat
i
o
n fo
r
F_FOURDIHS and F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
M
a
rk Abraham
Fix est
i
mate
o
f the size
o
f a j list
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Add gmxapi_p
y
test custom target to CMa
k
e `chec
k
` target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Er
i
c Irrgang
Allow gmxapi Pyt
h
on package tests to be run from GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
s
tian Bla
u
Harmo
n
ize mrc density fo
r
mat extents with
r
e
s
t o
f
code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic Irrgang
Reenable gtest_main
target
.
commit
|
commitdiff
|
tree
2019-08-08
Mark
Abr
a
ham
Stop te
s
ting ICC o
n
Wi
n
d
ows
commit
|
commitdiff
|
tree
2019-08-08
Art
e
m Zh
m
urov
R
e
factor
L
eap-Frog tests
a
nd connect
t
h
em to CP
U
version
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric Irrgang
U
se gmock
a
nd gtest tar
g
e
ts fr
o
m googletes
t
-release
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pasca
l
Merz
Move
ownership of kinetic
energy
o
bject
t
o ISimu
l
at
o
r
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Added Simulator comparison test
commit
|
commitdiff
|
tree
2019-08-05
Mark Abraham
Remove libgromac
s
_gene
r
ated contribution
s
from Find
C
UDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
y
o
n
gwangCPH
Solve issue
w
i
th demux
.
pl
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remove a po
i
nte
r
in t
_
forcerec
commit
|
commitdiff
|
tree
2019-08-01
B
e
rk Hess
Fix
nbnxm GP
U
me
m
o
r
y
reservation issue
commit
|
commitdiff
|
tree
2019-08-01
Mark Ab
r
a
h
am
Manage compiler flags an
d
some
i
nclude options per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Ma
r
k
Abraham
Improve
u
se of obj
e
ct
l
ib
r
a
rie
s
in
libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark
Abraham
Merge "Me
r
ge
r
elease-2019 int
o
master"
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add grompp warning with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
I
ntrodu
c
e fun
c
t
ion that checks if the
compu
t
ations
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
Páll
Fi
x
e
s for F
b
uffer ops
c
h
a
nge
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove need
f
or
G
ROMOS FF in
t
est
commit
|
commitdiff
|
tree
2019-07-31
P
a
scal Merz
Rename Simulator
t
o
L
egacy
S
im
u
lator
commit
|
commitdiff
|
tree
2019-07-31
Szilárd P
á
ll
M
o
ve c
y
cle c
o
unti
n
g into th
e
GP
U
bonded
m
o
dule
commit
|
commitdiff
|
tree
2019-07-31
S
zilárd Páll
Repo
r
t w
h
en developm
e
nt feature f
l
a
gs are used
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Move end of
step GPU t
a
sk
lau
n
ches to a f
u
nctio
n
commit
|
commitdiff
|
tree
2019-07-30
Paul Bauer
A
d
d wrapper for o
u
tp
u
t
ada
p
te
r
m
e
th
o
d
s
commit
|
commitdiff
|
tree
2019-07-28
Ber
k
He
s
s
Convert Ew
a
ld c
o
rrection tables t
o
C+
+
commit
|
commitdiff
|
tree
2019-07-26
Ber
k
H
e
ss
A
dd d
e
fa
u
lt i
n
i
tial
i
zation to interaction_con
s
t_t
commit
|
commitdiff
|
tree
2019-07-26
Chri
s
t
ian
B
lau
Fix failing ch
e
ck-source target on pyt
h
on3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk Hess
Spl
i
t
c
anD
e
tectG
p
us()
commit
|
commitdiff
|
tree
2019-07-25
Szilárd Páll
Only st
o
p
the
CUDA profiler if there are devices
commit
|
commitdiff
|
tree
2019-07-24
Paul B
a
uer
Fi
x
d
o
xygen in coordianteio fi
l
es
commit
|
commitdiff
|
tree
2019-07-24
Pa
u
l Bauer
A
dd outputadapt
e
rs
(3
/
3
)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgan
g
F
ix
g
mxapi note
b
ook image and sa
m
ple_restraint docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
ic Irrgang
Improve gmx
a
pi dock
e
r testin
g
environment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
E
r
ic I
r
rgang
Don't install s
a
m
p
l
e r
e
straint
p
acka
g
e
by defa
u
lt
.
commit
|
commitdiff
|
tree
2019-07-23
K
evin Boyd
Mode
r
ni
z
e
s
y
n
tax of
e
nable_if and trait
s
to use _t
.
.
.
commit
|
commitdiff
|
tree
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