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Fix ocl_kernel target
2019-08-12
M
.
Er
i
c Irrgang
Sep
a
rate out som
e
a
b
s
tract base classes
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Add gmxapi_pytest custom targ
e
t
t
o
CMake `
c
heck
`
t
a
rget
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Er
i
c Irrga
n
g
Allow gmxapi
Python package
tests to be
r
u
n from GROMA
C
S
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric I
r
rgang
Let base GROMACS docker image be a little more
use
f
ul
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Ir
r
g
ang
Reenable gtest_main tar
g
et
.
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric
Irrgang
Us
e
gmock an
d
gtest targets f
r
om
googletest
-
release
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irrgang
Separate o
u
t Opera
t
i
o
n
D
et
a
i
lsBase
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irrgang
Convert
test
infrastructure
t
argets to static librar
y
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
r
ic Irrga
n
g
Resolve a
c
ompiler warn
i
ng f
o
r the
gmxapi Pyth
o
n pac
k
age
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric
I
rrgang
Add li
b
gro
m
ac
s
dependency to gp
u
_ut
i
lstest_cuda target
.
commit
|
commitdiff
|
tree
2019-08-05
M
.
Eric Irr
g
ang
S
eparate o
u
t
O
perationDir
e
ctor
.
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eric Irrgang
Rear
c
hitect
g
mxa
p
i
.
o
p
er
a
tion
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eric Irrg
a
ng
Reduce
conflicts
with exter
n
a
l googletest files
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrg
a
ng
Remove one
o
f th
e
examples from sample_
r
estraint
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
i
c
Irrgan
g
Begin new sampl
e
_
re
s
traint develop
m
ent
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Fi
x
gmxa
p
i notebook imag
e
an
d
sampl
e
_restraint docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric
Irrgang
C
l
a
r
ify u
s
e of Python
venv
i
n
gmxapi
docker im
a
ge
s
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
i
c
Irrgang
Im
p
rov
e
gmxapi docker testi
n
g environment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrga
n
g
Improve doc
s
for gmxap
i
Py
t
hon e
n
v
ironmen
t
preparation
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
E
ric Irr
g
a
ng
Don't
i
nstall sam
p
l
e
restraint
p
a
ckage
b
y def
a
ult
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric
I
r
r
gang
Im
p
ro
v
e some docum
e
ntation formatting and
s
pelling
.
commit
|
commitdiff
|
tree
2019-07-18
M
.
Eric Ir
r
gang
Re
m
ov
e
e
xtrane
o
us fil
e
.
commit
|
commitdiff
|
tree
2019-07-10
M
.
Eric Ir
r
g
a
n
g
gmxapi Python pa
c
kage docume
n
tation layout
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Er
i
c Irr
g
a
n
g
Incor
p
o
r
ate sample_restraint r
e
pository
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irrga
n
g
Begin CMake fron
t
-end for Python packaging machi
n
ery
.
commit
|
commitdiff
|
tree
2019-07-05
M
.
E
r
ic Irrgang
Python bin
d
ing
s
f
o
r mdrun
.
commit
|
commitdiff
|
tree
2019-07-02
M
.
Eric Irrgang
P
ython detection consoli
d
a
t
ion
.
commit
|
commitdiff
|
tree
2019-07-02
M
.
Eri
c
Irrga
n
g
Rearra
n
ge some definitions
.
commit
|
commitdiff
|
tree
2019-07-02
M
.
E
r
ic
I
rrgang
Updat
e
gmxapi test fixt
u
re
s
.
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eric Irrgan
g
gmxapi P
y
thon
p
ac
k
age doc
u
m
e
n
t
atio
n
infrastructure
.
commit
|
commitdiff
|
tree
2019-06-27
M
.
Eric Irrg
a
ng
Ad
d
h
e
lpful note about g
m
xpai docker notebo
o
k
s
erve
r
.
commit
|
commitdiff
|
tree
2019-06-24
M
.
Er
i
c Ir
r
gang
Add a docker
l
ayer
with a jupyter notebook serve
r
.
commit
|
commitdiff
|
tree
2019-06-19
M
.
E
ric Irrgan
g
Updates to gmxapi dock
e
r
e
ntry po
i
n
ts
.
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irr
g
ang
R
edu
c
e doc
k
e
r
image size
f
o
r gmx
a
pi CI
.
commit
|
commitdiff
|
tree
2019-05-16
M
.
Eric
Irrgang
Fix ty
p
o
s re
g
ar
d
ing GMX
_
P
H
YS
I
CAL_VALIDA
T
ION
C
Make
v
a
riable
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
M
ore Python
t
e
s
ting infras
t
r
ucture for gmxapi
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
ic Irrg
a
ng
Add
g
mxapi
.
_log
g
ing submo
d
ul
e
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
ic Irr
g
ang
Update I/O hand
l
i
n
g
in gmxa
p
i
.
comm
a
ndli
n
e
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Expand gmxap
i
.
operat
i
on t
o
ol
s
to s
u
ppo
r
t t
h
e data
flow
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
F
ix
f
ormatting and typos
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eri
c
Irrgang
Suppo
r
t basi
c
command line
wrapper
i
n
gmxapi
commit
|
commitdiff
|
tree
2019-05-02
M
.
Eric Irr
g
ang
I
nfra
s
tructure
updates for dependen
t
changes
.
commit
|
commitdiff
|
tree
2019-04-10
M
.
Eric Irrgang
Add GROMA
C
S library depen
d
ency to gmxapi package
.
commit
|
commitdiff
|
tree
2019-04-10
M
.
E
r
ic Irrgan
g
Use pybind11 to make a minimal C+
+
Python extension
.
commit
|
commitdiff
|
tree
2019-04-09
M
.
E
r
ic Irrgang
Introduce gmxapi operations and basic data mod
e
l
.
commit
|
commitdiff
|
tree
2019-04-09
M
.
Eric Irrgang
g
mxapi 2019 Q
1
/Q2 pr
o
ject roadmap
.
commit
|
commitdiff
|
tree
2019-04-08
M
.
Eric I
r
rgang
Rem
o
ve stale "TOD
O
"
.
commit
|
commitdiff
|
tree
2019-03-29
M
.
Er
i
c Irrgang
Plumbing
for gmx
a
pi 2019 Q1/Q2 projec
t
roa
d
map
.
commit
|
commitdiff
|
tree
2019-03-25
M
.
Eric Ir
r
gang
R
emove uses of std::iterator mix-in
.
commit
|
commitdiff
|
tree
2019-01-18
M
.
Eri
c
I
r
r
gang
Remove
.
travis
.
y
m
l Tr
a
vis-CI config file
.
commit
|
commitdiff
|
tree
2018-12-19
M
.
E
ric Irrgang
Restrict number
o
f OpenMP t
h
read
s
during
t
es
t
i
n
g
.
commit
|
commitdiff
|
tree
2018-11-20
M
.
Eric
I
rrgang
Bump gmxapi version number f
o
r 2020 d
e
velopment cycl
e
.
commit
|
commitdiff
|
tree
2018-11-16
M
.
Eric Ir
r
g
a
ng
E
x
pand gmxapi testi
n
g to in
c
lude
threa
d
-MP
I
.
commit
|
commitdiff
|
tree
2018-11-16
M
.
Eric Ir
r
gang
Conve
r
t unhelp
f
ul as
s
e
rtion to better documentation
.
commit
|
commitdiff
|
tree
2018-11-16
M
.
Eric Irrg
a
ng
Remove extra
n
eous C
M
ak
e
config
.
commit
|
commitdiff
|
tree
2018-11-15
M
.
Eri
c
Irrgan
g
No
t
e
G
MX_ENABLE_CCAC
H
E in build system doc
s
.
commit
|
commitdiff
|
tree
2018-11-14
M
.
Eric Irrgang
N
ote GMXAPI CMake va
r
iables and
build targets
.
commit
|
commitdiff
|
tree
2018-11-01
M
.
E
ric I
r
rgang
Fully
d
efine symbols in restraintpotential
.
h
commit
|
commitdiff
|
tree
2018-11-01
M
.
Eric Irrgang
A
d
d missing blame for re
s
traint mod
u
l
e
f
ile
s
.
commit
|
commitdiff
|
tree
2018-10-19
M
.
E
r
ic Irrgang
Documen
t
ation
b
ug in
gmxapi/c
o
ntext
.
h
commit
|
commitdiff
|
tree
2018-10-15
M
.
Eric Irrgang
Release notes for restraint m
o
dule and gmxapi
.
commit
|
commitdiff
|
tree
2018-10-15
M
.
Eric
Irrgang
Igno
r
e
pyenv config fi
l
e
.
commit
|
commitdiff
|
tree
2018-10-15
M
.
Eric I
r
rga
n
g
Preparatio
n
for de-duplicating mdrun
s
etup
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrga
n
g
Add
some
"to do"s
fo
r
MDModules
an
d
Impl
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Er
i
c Irrgang
Resol
v
e some lin
t
er war
n
i
n
g
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eri
c
Ir
r
g
a
ng
T
e
st signaling fa
c
ility thro
u
gh session res
o
urces
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irr
g
ang
Clean
u
p gmxapi
t
e
stsu
p
port ou
t
p
u
t
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
ri
c
Irrg
a
n
g
gmxapi::Usag
e
Error
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
A
l
low API access to simulat
i
on
s
ign
a
ls
.
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eri
c
Irrgang
Add gm
x
api
sessi
o
n resources
.
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric I
r
rgang
Enable
r
e
straints facili
t
ies
.
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
Add A
P
I f
o
r adding MDModules / Restraints
.
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
Initialize f
o
rce
v
ector in Pot
e
ntialPointData construct
o
r
.
commit
|
commitdiff
|
tree
2018-10-12
M
.
E
ric Irr
g
ang
A
dd res
t
raints fr
a
mework
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irr
g
an
g
Add gmx
a
pi::Wor
k
flo
w
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irrgang
A
d
d gm
x
api::Session
.
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eric Irrgang
gmxapi expect
s
pos
i
tion independent code
.
commit
|
commitdiff
|
tree
2018-10-05
M
.
E
r
ic Irrgang
A
d
d gmxapi::System
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eri
c
I
rrgang
A
dd gmxapi::Contex
t
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eri
c
Irrgang
Combin
e
private sections of Md
r
un
n
er defin
i
tion
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric I
r
rgang
Mov
e
mdr
u
n
mainFunctio
n
to client c
o
d
e
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
ric Ir
r
gang
A
d
d test data for
gmxapi
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
Add g
m
xapi
e
xcepti
o
ns
.
commit
|
commitdiff
|
tree
2018-10-02
M
.
E
r
i
c
Ir
r
g
an
g
Add gmxapi::Status
.
commit
|
commitdiff
|
tree
2018-09-25
M
.
Eric Irrgang
Allow explicit
r
eset
o
f
s
imulation stop
c
ondition
.
commit
|
commitdiff
|
tree
2018-09-24
M
.
Er
i
c Irrgang
Fix gmxapi::Version test regr
e
ssi
o
n
.
commit
|
commitdiff
|
tree
2018-09-23
M
.
Eric Irrgang
Add gmxapi
:
:
MDModule
.
commit
|
commitdiff
|
tree
2018-09-19
M
.
Eric Irrgang
Change n
a
mes of gmxapi::Version func
t
i
o
ns
.
commit
|
commitdiff
|
tree
2018-09-17
M
.
E
ric Ir
r
gang
F
r
amework
i
n which to build gm
x
api
.
commit
|
commitdiff
|
tree
2018-09-14
M
.
Eric Irrgang
Re
a
rrang
e
m
dr
u
n/runner
.
h
commit
|
commitdiff
|
tree
2018-09-12
M
.
E
r
ic Irrg
a
ng
S
impl
i
f
y add_su
f
fix_to_
o
utpu
t
_names()
commit
|
commitdiff
|
tree
2018-09-10
M
.
E
r
ic Irrgang
Remove c
o
nst fro
m
poin
t
ers in t_filenm
.
commit
|
commitdiff
|
tree
2018-09-05
M
.
Eric Irrgang
Adjust loader path resolution on Mac OS X
.
commit
|
commitdiff
|
tree
2018-08-29
M
.
Eric
I
rrgang
Allow extensible MDMod
u
les and forceProviders
.
commit
|
commitdiff
|
tree
2018-08-08
M
.
Eric
Irrgang
Enable
ccache compiler wrapp
e
r w
h
en
a
vailable
.
commit
|
commitdiff
|
tree
2018-08-07
M
.
Eric
I
r
rgang
Add some
deve
l
oper help to Deve
l
ope
r
G
uide
.
commit
|
commitdiff
|
tree
2018-08-01
M
.
Eri
c
Irrgang
Remove
e
xtr
a
neous gitig
n
o
r
e line
.
commit
|
commitdiff
|
tree
2017-09-02
M
.
E
ric
Irrgang
R
e
move mac
r
o th
a
t confuses some
debugge
r
s
commit
|
commitdiff
|
tree
2017-09-02
M
.
Eric Irrgang
m
ake a
box
parameter const
commit
|
commitdiff
|
tree
2017-08-31
M
.
Eric
I
rrgang
Add more git
i
gno
r
es
commit
|
commitdiff
|
tree
next