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Remove unused functions from gmxpreprocess
2019-10-22
e
jjor
d
a
n
Rem
o
ve unused fun
c
tion
s
from
g
mxpreprocess
commit
|
commitdiff
|
tree
2019-10-22
B
erk Hess
Requ
i
re -ei for essential
d
y
namics
commit
|
commitdiff
|
tree
2019-10-22
e
j
jordan
Rem
o
v
e unused function generate
_
e
x
cls and
make
c
lean_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
C
onst co
r
rec
t
n
e
s
s
for genhyd
r
o
commit
|
commitdiff
|
tree
2019-10-15
Paul Bauer
Fix
b
ug in
prepro
c
essin
g
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrgang
Fix logic e
r
ror in gmxapi
.
ver
s
ion
.
api
_
i
s_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
M
ar
k
Abraham
Ensure environment
v
ariable use does no
t
give warning
s
commit
|
commitdiff
|
tree
2019-10-12
Berk H
e
ss
Add class
FixedCa
p
acityVector
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Zhmurov
Central
i
ze management of
c
oordinat
e
s ready on GPU event
commit
|
commitdiff
|
tree
2019-10-08
Prashanth K
a
nduri
Fused two if branc
h
es with the same cond
i
tional
commit
|
commitdiff
|
tree
2019-10-02
Berk H
e
ss
F
i
x
harmless OpenMP
w
ri
t
e race
commit
|
commitdiff
|
tree
2019-10-02
Mark
A
braham
Improve P
M
E
test
i
ng
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Use gmx::Rang
e
in domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
A
r
tem Zhmurov
StateP
r
opag
a
torDataGpu object to
mana
g
e GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark Abra
h
am
Fix icc warnings
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Complete
l
y remove
cha
r
ge groups
commit
|
commitdiff
|
tree
2019-10-01
Chr
i
stoph Junghan
s
cmake: add missing he
a
der to legacy api
commit
|
commitdiff
|
tree
2019-10-01
M
a
rk A
b
raham
Rem
o
ved
d
ependency on
co
m
m
rec of mdr
u
n setup
commit
|
commitdiff
|
tree
2019-09-30
Cars
t
en Ku
t
zner
Move F
o
rcePr
o
vi
d
ers class into th
e
gmx nam
e
s
p
ace
commit
|
commitdiff
|
tree
2019-09-30
Mark
A
b
raham
Make a builder f
o
r
DD
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Rem
o
ve c
h
arge group code
from
f
o
r
cerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
M
a
ke th
e
wait on PME G
P
U results
conditional
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
Abraham
Improve MiMiC
test implem
e
ntation
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
A
b
raham
Fix
g
ro file outp
u
t
wit
h
index groups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abrah
a
m
R
e
move le
f
tover support
f
o
r
p
re-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Pa
u
l B
a
u
e
r
Ad
d
tes
t
f
o
r
noapp
e
n
d
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix no-MPI C
U
D
A build
commit
|
commitdiff
|
tree
2019-09-24
M
a
rk Abraha
m
Merge "Merge
b
r
a
nch
rel
e
a
s
e-2019 into master"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix clang u
n
used-func
t
ion warnings
commit
|
commitdiff
|
tree
2019-09-24
Paul
B
a
u
er
Add release notes
f
or modular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-23
Paul Bauer
Fix issu
e
s when
PME rank reque
s
t bec
o
mes nega
t
i
v
e
commit
|
commitdiff
|
tree
2019-09-23
Paul
B
a
uer
C
hang
e
MPI s
e
tup to communicate TPR as
bu
f
fe
r
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Zero p
r
essure a
n
d virial tenso
r
s at
b
eginning of
st
e
p
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
I
ntro
d
uce FEP into modular simulator
commit
|
commitdiff
|
tree
2019-09-22
Ch
r
istoph
Junghans
workaround for rhel bug #1749463, cma
k
e b
u
g #18349
commit
|
commitdiff
|
tree
2019-09-22
P
aul Ba
u
er
Re
m
ov
e
u
p
date f
l
ag ag
a
in
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
H
e
ss
Remove cg
s
_g
l
from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-20
Mark Abraham
Re
f
a
c
tor to create a GpuT
a
s
kAssign
m
e
nts object
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
R
e
m
ove bLoca
l
CG fro
m
DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove ob
s
o
l
ete make_
e
xclus
i
ons_zon
e
_c
g
(
)
commit
|
commitdiff
|
tree
2019-09-19
C
hristian Blau
Check inp
u
t
r
eco
r
d
also in tests
commit
|
commitdiff
|
tree
2019-09-19
Mar
k
Abraham
Use GPU
h
alo exchange
only wh
e
n com
p
atibl
e
DD is av
a
i
lable
commit
|
commitdiff
|
tree
2019-09-19
Mark Abraham
Fur
t
her improve getDDGridSetup
commit
|
commitdiff
|
tree
2019-09-19
Paul Bauer
Ad
d
basic interface to run updat
e
on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
Add
haveFre
e
EnergyWor
k
to DomainLifetimeWorkl
o
ad f
l
ags
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consistently change
d
ensityfi
t
ting spr
e
a
d
ing w
e
ig
h
t
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Be
r
k H
e
ss
A
d
ded free-energy
k
ernel performance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix in
c
orrect D
D
ndim a
s
sertion
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-re
s
c
ale t
h
e
rmostat
f
or modular si
m
ulator
commit
|
commitdiff
|
tree
2019-09-18
Paul
B
a
uer
Read TPR file body in
b
uf
f
er
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
G
P
U
Force Halo Exch
a
nge
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix p
o
sition pinning for
m
odula
r
sim
u
lat
o
r
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove obsolete
m
dp option
n
s-type
commit
|
commitdiff
|
tree
2019-09-16
ejjo
r
dan
Ad
d
some
c
ool
qu
o
tes
commit
|
commitdiff
|
tree
2019-09-16
Pau
l
Bauer
Formatting fixe
s
fo
r
reference manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric Irrgang
Add gmxap
i
re
l
ease n
o
tes
.
commit
|
commitdiff
|
tree
2019-09-16
Alan Gr
a
y
G
P
U halo
exchange
commit
|
commitdiff
|
tree
2019-09-16
Berk He
s
s
A
dd
v
irtual site ty
p
e 2F
D
commit
|
commitdiff
|
tree
2019-09-16
Mar
k
Abraham
A
v
oid
s
h
o
r
t
-
range GPU opera
t
ions with no wor
k
commit
|
commitdiff
|
tree
2019-09-16
Berk He
s
s
Remove cut-off sc
h
emes from
m
a
nual
commit
|
commitdiff
|
tree
2019-09-16
Szilárd Páll
E
liminate unnec
e
ss
a
ry GPU stre
a
m
d
epen
d
ency call
commit
|
commitdiff
|
tree
2019-09-16
Berk He
s
s
A
dd op
t
io
n
request 1D DD
w
i
t
h 1 pul
s
e
commit
|
commitdiff
|
tree
2019-09-16
Kevin Boyd
Remove group scheme from depreca
t
ed release notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal
M
erz
I
ntro
d
uc
e
the mo
d
u
l
ar simulator
commit
|
commitdiff
|
tree
2019-09-15
Peter
Kasson
Patch gmxapi
for Py
t
h
on 3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric
I
rrga
n
g
No
r
malize usa
g
e
of GMXTOOLCHA
I
NDI
R
in gmxapi setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
ric Irrgang
Do not use gromacs-toolc
h
ain in darwin gmxapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
Upda
t
e gmxapi setup
.
p
y
commit
|
commitdiff
|
tree
2019-09-12
Mark Abraha
m
Disabl
e
rep
o
rt
-
me
t
hods e
n
d-to-end test
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Páll
Reorganiz
e
o
n
-GPU PME fo
r
ce
r
e
duction flag handling
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmur
o
v
Cha
n
ge P
a
ddedVec
t
or
to Padde
d
HostVector fo
r
force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Chr
i
stian Blau
Add
r
ele
a
se n
o
te
for density
f
i
t
t
i
ng
.
commit
|
commitdiff
|
tree
2019-09-12
Pa
s
cal Me
r
z
U
p
date modular simulator tests
commit
|
commitdiff
|
tree
2019-09-12
Er
i
k Linda
h
l
Added SIMD log2 and pow math functions
commit
|
commitdiff
|
tree
2019-09-12
Er
i
k Lin
d
ahl
Update SIMD math
t
e
sts and i
m
p
rove accuracy
commit
|
commitdiff
|
tree
2019-09-11
P
a
ul Bauer
Remo
v
e -sub option from trjconv
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Zhmurov
Fix for the post-submi
t
fai
l
u
re
commit
|
commitdiff
|
tree
2019-09-11
A
r
tem Zhmurov
D
e
couple GPU
f
orce buffer ma
n
agement
f
rom
b
u
f
fer op
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ric Irrgang
Use G
R
OMA
C
S
C
M
a
k
e toolchain fi
l
e
for gmx
a
pi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
P
aul Bauer
B
asic toolchain to fac
i
l
i
tate GMXAPI build
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c Irrgang
Add gmxapi
.
modify_inpu
t
opera
t
ion
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric I
r
rgang
P
rovid
e
a
gm
x
api
.
read_
t
pr o
p
eration
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
p
date
g
mxapi
.
simula
t
ion
.
co
n
text details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
pdate gmxapi Python pac
k
age infrastructure
for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c Irrgan
g
N
o
rmal
i
ze some
t
esting resourc
e
s
f
or the Pyt
h
on
p
ackage
s
.
commit
|
commitdiff
|
tree
2019-09-11
Magnus L
u
ndborg
Tidy up the FE
kern
e
l
commit
|
commitdiff
|
tree
2019-09-10
Paul Bau
e
r
Fix nightly build
commit
|
commitdiff
|
tree
2019-09-10
Szi
l
á
rd
Páll
Use thread-M
P
I
i
n
the gp
u
comm matrix
commit
|
commitdiff
|
tree
2019-09-10
Pascal Mer
z
Coord
i
nate Propagators
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
StatePropagatorData: Introduced cons
t
box acc
e
sso
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Add triv
i
al const qualifier
s
to shellfc and EnergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
C
onstraint element fo
r
the
m
odular simu
l
a
t
or
commit
|
commitdiff
|
tree
2019-09-09
S
z
i
l
árd Páll
Pass gmx::For
c
eFl
a
gs
to CPU nbnxm dispatch code
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
Pass the new gmx::F
o
rceFlags to the n
b
nxm module
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
Rem
o
ve incorrect check wi
t
h
r
f
-zero
commit
|
commitdiff
|
tree
2019-09-09
Pasca
l
Merz
Domain
d
ecomposit
i
on
and PME l
o
ad balancing for mo
d
ular
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
Ch
r
is
t
ian Blau
R
e
la
t
ive entropy
as
d
e
n
sity similarity measure
commit
|
commitdiff
|
tree
2019-09-09
P
a
ul Bauer
A
dd gmx con
v
ert-trj
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
R
e
n
am
e
DDSetup to DDG
r
idS
e
tu
p
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk Hes
s
C
l
ea
n
up PME
rank variables
commit
|
commitdiff
|
tree
next