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Python wrapping code for gmxapi mdrun bindings.
2019-09-03
M
.
Eric Ir
r
g
ang
Pyth
o
n wrapping code for gmxapi md
r
un
b
i
ndings
.
commit
|
commitdiff
|
tree
2019-09-03
P
ascal Merz
Introduce energy el
e
ment
f
or m
o
dular sim
u
lator
commit
|
commitdiff
|
tree
2019-09-03
M
ark
Ab
r
aha
m
S
i
m
plify energy-file c
o
mparisons in test
s
commit
|
commitdiff
|
tree
2019-09-03
Arte
m
Zhmurov
Add Parrinello-Rah
m
an pres
s
ure
c
ou
p
li
n
g
t
o
CUDA L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
B
e
r
k
Hess
Only use fshi
f
t when needed
commit
|
commitdiff
|
tree
2019-09-01
Christian Bla
u
A
d
d checkpointing
f
or MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Local
A
tomSet con
s
t
ruction with vectors of
g
mx::index
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irrgang
Impo
r
t base code
for Pyt
h
on-driven si
m
ulat
i
on fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Mag
n
us L
u
n
d
b
or
g
Changed
s
ome variables from SCReal
t
o real in FE kernel
.
commit
|
commitdiff
|
tree
2019-08-30
Christia
n
Bl
a
u
Implemen
t
ing the
d
e
nsity fitting f
o
r
c
e provider
commit
|
commitdiff
|
tree
2019-08-29
Mark Ab
r
aham
More
q
u
otes
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introdu
c
e signallers for
modular integrat
o
r
commit
|
commitdiff
|
tree
2019-08-28
Pau
l
Bauer
F
i
x ret
u
r
n
v
a
lue
commit
|
commitdiff
|
tree
2019-08-28
Mark
Abr
a
ham
Fix integrati
o
n issues
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce the m
a
in modular simulator interfaces an
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul Bauer
Change toler
a
nce for norm
a
l mo
d
e
t
ests
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
A
dd clang-
t
idy nightly test with SIMD + OpenCL
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
Move nonbonded
G
P
U
wait timing into the
G
PU
m
odule
commit
|
commitdiff
|
tree
2019-08-27
Mark Abraham
Add integration tests for
e
xact rest
a
rts
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
A
dd d
e
nsi
t
y
f
i
tting parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Acc
e
ss
t
o
Gau
s
sTran
s
form3D data
commit
|
commitdiff
|
tree
2019-08-27
Christi
a
n
Bla
u
Add
i
n
d
ex gr
o
up o
p
tion to
density
f
itting
commit
|
commitdiff
|
tree
2019-08-26
Pau
l
Baue
r
Rem
o
ve section c
h
ecking api level
commit
|
commitdiff
|
tree
2019-08-26
Pau
l
Bauer
Remove installed
h
eaders from CMake
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
Add te
m
perature coupling to CUDA Leap-Frog
i
nte
g
rato
r
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
Move g
m
xapico
m
pat
TPR t
o
ols
t
o
libgm
x
ap
i
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
r
ic Irrgang
Reduce artific
i
al hea
d
er dependen
c
ies in rest
r
aint
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activation
o
f density fitting an
d
move of module notifications
commit
|
commitdiff
|
tree
2019-08-25
S
z
il
á
r
d
Páll
clang-tidy 8 fixes for the GP
U
h
o
st code-path
commit
|
commitdiff
|
tree
2019-08-25
Szilárd Páll
Further fixes for clang-tidy clan
g
version 8
commit
|
commitdiff
|
tree
2019-08-23
Pau
l
Ba
u
er
Removes
c
heck
e
r
for
i
nstalled files
commit
|
commitdiff
|
tree
2019-08-23
S
z
i
lá
r
d P
á
ll
Fix clang-tidy warnings
i
n the OpenCL build
commit
|
commitdiff
|
tree
2019-08-23
Mark Ab
r
aham
Update
clan
g
-
tidy to clan
g
version 8
commit
|
commitdiff
|
tree
2019-08-22
Mark Abr
a
ham
Merge branch rele
a
se-
2
019
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Impro
v
e clang-anal
y
zer build time
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
r
ic Irrgang
C++ code and Python
bin
d
ings for TPR parameter
read
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Ber
k
Hess
Fix
perturbed bonded bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
E
ri
c
Irrgang
E
nable
G
M
X
API b
y
d
e
fault
.
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge two dihe
d
ral function
s
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Use shiftForces in Forc
e
Ouput
s
commit
|
commitdiff
|
tree
2019-08-20
Erik L
i
ndahl
Avoid using
G
M
X_S
I
MD macros
t
o detect _mm_p
a
use()
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
F
ix issues fo
r
clang-an
a
l
yz
e
r-8
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded viria
l
computation conditional
commit
|
commitdiff
|
tree
2019-08-19
Szilárd
Páll
S
wit
c
h to AR
M
HPC toolchain v19
.
2 in post
-
su
b
mit
commit
|
commitdiff
|
tree
2019-08-19
Mark
A
b
ra
h
a
m
Mod
e
rnize t_matrix, t_mapping, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
Mark Abrah
a
m
Modernize t_psdata
commit
|
commitdiff
|
tree
2019-08-19
Szilá
r
d P
á
l
l
Work ar
o
und clang CUDA device
c
ode c
o
degen
b
ug
commit
|
commitdiff
|
tree
2019-08-16
Szilárd
P
áll
Fix sim_ut
i
l
.
cpp
c
opy
r
i
g
ht h
e
ader
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Update testing matri
c
es
a
nd fi
x
warnin
g
s
commit
|
commitdiff
|
tree
2019-08-16
Mark A
b
raham
Stop nbn
x
m
/
g
rid
.
h
depend
i
ng on SI
M
D module
commit
|
commitdiff
|
tree
2019-08-15
Sz
i
l
á
rd Páll
Fix OpenCL gather re
d
uction
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info c
l
ass to name a
n
d gen
e
rat
e
the densit
y
fitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mark Abr
a
ham
Fix
vv
integra
t
ors
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgan
g
Add
i
nitia
l
.
clang-form
a
t file
.
commit
|
commitdiff
|
tree
2019-08-13
Mark Abraham
F
i
x
i
c
c
1
9
co
d
eg
e
n i
s
sue
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irrgang
Introduce Context requirement
.
commit
|
commitdiff
|
tree
2019-08-12
Mark
Abrah
a
m
Quiet
w
arning
commit
|
commitdiff
|
tree
2019-08-12
Ma
r
k
A
braham
Fix o
c
l_kernel t
a
r
g
e
t
commit
|
commitdiff
|
tree
2019-08-12
P
a
s
c
al Merz
Use new setenv fun
c
t
ion for e
n
e
r
g
youtput
test
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irrgang
Se
p
ar
a
te out some abstract b
a
se classes
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Prepa
r
e Update and Constraints for Domain D
e
composition
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmur
o
v
R
efac
t
or
i
n
g
of
t
he SETTLE tes
t
s
commit
|
commitdiff
|
tree
2019-08-09
B
erk He
s
s
S
I
MD acceleration f
o
r F_FOURDIHS
a
n
d
F
_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
Fi
x
estimate of the size of a j
list
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic Irrgang
Add gmxapi_
p
ytest
c
ustom targe
t
t
o CMake `ch
e
ck`
target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Allow gm
x
api Python package tests to be r
u
n
f
rom GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Chri
s
tian Blau
Harmonize mrc densit
y
format extents with rest o
f
code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Re
e
nable gtest_main
t
arget
.
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
S
top testing
ICC on W
i
ndows
commit
|
commitdiff
|
tree
2019-08-08
Artem Zhmurov
R
efactor Leap-Frog tests
and con
n
ect them to CPU
ve
r
sion
commit
|
commitdiff
|
tree
2019-08-07
M
.
E
ric Irrgang
Use gmoc
k
and gtest tar
g
e
ts from
g
oogletest-re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
M
ove ownership of kinetic en
e
r
gy ob
j
ect to ISimulato
r
commit
|
commitdiff
|
tree
2019-08-05
Pascal Me
r
z
Ad
d
ed S
i
mulator comparison test
commit
|
commitdiff
|
tree
2019-08-05
Mark
Abraham
R
e
move li
b
g
r
o
m
acs_
g
enerated
c
ontributions f
r
om FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
yongwa
n
gCPH
Solve issue with demux
.
p
l
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
R
e
move a pointer in t_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
F
i
x
n
bnx
m
GPU me
m
o
r
y
reser
v
ation i
s
s
ue
commit
|
commitdiff
|
tree
2019-08-01
M
a
rk
Abraham
M
an
a
ge
compi
l
er flags
a
n
d some include options per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
brah
a
m
I
mprove use
o
f
object librarie
s
in libg
r
om
a
c
s
commit
|
commitdiff
|
tree
2019-08-01
Mar
k
Abraham
Mer
g
e "Merge release-2
0
19 into
m
aster"
commit
|
commitdiff
|
tree
2019-07-31
B
erk Hess
Add grompp
w
arn
i
ng wit
h
use of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem
Z
h
murov
Introduce function tha
t
ch
e
cks if
t
h
e
comput
a
tions
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
P
áll
F
i
x
es
f
or F buffer
ops change
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
Remove need fo
r
GROMOS FF in te
s
t
commit
|
commitdiff
|
tree
2019-07-31
P
ascal Merz
Re
n
ame Simulator to
L
egacySimulator
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
M
ove cycle counting
into the GPU
bonded module
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Rep
o
rt when
d
evelopm
e
nt f
e
atu
r
e
flags are used
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Move end of step GPU task launches to a f
u
n
c
tion
commit
|
commitdiff
|
tree
2019-07-30
Paul Bauer
A
dd wr
a
p
per for outputad
a
pte
r
m
ethods
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk H
e
ss
Conv
e
rt Ewald correctio
n
t
a
bl
e
s
to C+
+
commit
|
commitdiff
|
tree
2019-07-26
B
e
rk Hess
A
d
d default initialization
t
o int
e
r
act
i
on_const_
t
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing che
c
k
-
source target on
p
ython3
.
6
commit
|
commitdiff
|
tree
2019-07-25
B
e
r
k
Hess
Spl
i
t
canDetectGpus()
commit
|
commitdiff
|
tree
2019-07-25
S
z
i
lárd Pál
l
O
n
ly stop the CUDA profiler if there are de
v
ices
commit
|
commitdiff
|
tree
2019-07-24
Paul Baue
r
Fix doxygen in coordia
n
teio files
commit
|
commitdiff
|
tree
2019-07-24
Paul B
a
ue
r
Add outputad
a
pters (3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
F
ix gmxapi notebook image
and sample_re
s
trai
n
t doc
k
er
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irr
g
an
g
Im
p
rove g
m
xapi d
o
cker
testin
g
e
nvironment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
E
ric I
r
rgang
Don't
inst
a
ll s
a
m
p
l
e r
e
strain
t
p
a
c
k
a
ge by d
e
fault
.
commit
|
commitdiff
|
tree
2019-07-23
Kevin B
o
y
d
M
odernize sy
n
tax of enable_if
a
n
d
traits t
o
use _t
.
.
.
commit
|
commitdiff
|
tree
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