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Improve use of object libraries in libgromacs
2019-08-01
Mark
A
b
r
aham
Improve use of obj
e
ct libraries in
l
ibgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
braham
Merge "Merge release
-
201
9
into master"
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add gromp
p
war
n
i
n
g
w
ith use of
GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Int
r
o
duce function that checks if the
computations
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Pál
l
F
ixe
s
for F buff
e
r ops change
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
R
emov
e
n
eed for GROMOS FF in
test
commit
|
commitdiff
|
tree
2019-07-31
Pascal Merz
Rename Simulator to
L
egac
y
S
i
mulat
o
r
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Pál
l
Move
c
ycle
cou
n
ting i
n
to
the GPU bonded modul
e
commit
|
commitdiff
|
tree
2019-07-31
Szilá
r
d Páll
R
eport when devel
o
pment feature
f
lags are use
d
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
Páll
Move end of st
e
p
G
PU tas
k
lau
n
ch
e
s to a function
commit
|
commitdiff
|
tree
2019-07-30
Paul B
a
u
e
r
Add wrapper fo
r
o
utpu
t
adap
t
e
r
methods
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
Con
v
er
t
Ewald correction tables t
o
C++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
A
d
d d
e
fa
u
lt initia
l
ization to interaction_const_t
commit
|
commitdiff
|
tree
2019-07-26
C
h
ristian Blau
Fix failing check-s
o
ur
c
e
t
arget
on p
y
thon3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk Hes
s
Split canDetectGpus()
commit
|
commitdiff
|
tree
2019-07-25
S
z
ilárd Páll
Only st
o
p the
C
UDA p
r
ofiler if there
ar
e
devices
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
Fix
d
ox
y
gen i
n
coordianteio files
commit
|
commitdiff
|
tree
2019-07-24
Paul
B
a
u
er
Add ou
t
putadapter
s
(3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Fi
x
gmxapi notebook
i
mage and sample_re
s
t
ra
i
nt docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Impro
v
e g
m
x
api
do
c
ker te
s
t
ing envir
o
nment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrg
a
ng
Don't inst
a
l
l sampl
e
restraint
package
by d
e
fault
.
commit
|
commitdiff
|
tree
2019-07-23
Kevin Boyd
Moderni
z
e syntax of enab
l
e_if and tra
i
ts to
u
se _t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
David v
a
n der Spoel
Fixed small bug in gmx an
a
e
i
g
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Ir
r
ga
n
g
Incorporate sample_restrain
t
rep
o
s
i
tory
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irr
g
a
n
g
Begi
n
CMake front-end for Py
t
hon packaging ma
c
h
inery
.
commit
|
commitdiff
|
tree
2019-07-08
Szi
l
árd Páll
Elim
i
nat
e
a us
e
of
d
ouble
p
recision in the
G
P
U bo
n
ded
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Berk He
s
s
Store
nb
n
xm gr
i
dSet data
i
n GridSetDat
a
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
Moder
n
ize FindHw
l
oc
.
c
m
ake
commit
|
commitdiff
|
tree
2019-07-05
M
.
Eric Irr
g
a
n
g
P
y
t
hon bindings for mdrun
.
commit
|
commitdiff
|
tree
2019-07-04
Mark
Abraham
Further clang-ti
d
y-7 fix
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zhmurov
Combine CUDA Le
a
p-Frog, LINCS a
n
d
SETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
Updates to math/vec
.
h
commit
|
commitdiff
|
tree
2019-07-02
M
a
rk Abraham
Clarify wording of rele
a
se
n
otes
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-enable affin
i
ty diagonostics with
MPI
commit
|
commitdiff
|
tree
2019-07-02
Kevi
n
Boyd
Add
fun
c
t
i
on
for calculating 3x3 matrix
d
e
term
i
nant
commit
|
commitdiff
|
tree
2019-07-02
K
e
vin Boyd
Remove
referen
c
es to ecut
s
GROUP
commit
|
commitdiff
|
tree
2019-07-01
Pascal M
e
r
z
F
i
x
m
odule det
e
ction
for phy
s
ical v
a
lid
a
tion
commit
|
commitdiff
|
tree
2019-07-01
Szilárd Páll
Refactor track
i
n
g
of
GPU
s
hort-ran
g
e
work/skippi
n
g
commit
|
commitdiff
|
tree
2019-07-01
Ber
k
Hess
Fix MPI deadlock in
a
ffinity settin
g
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eri
c
Ir
r
gang
gmxap
i
Py
t
hon pa
c
kage doc
u
menta
t
i
o
n
infrastru
c
tu
r
e
.
commit
|
commitdiff
|
tree
2019-06-30
S
z
ilárd P
á
ll
Create ded
i
cated subcoun
t
e
r
f
or
non
b
on
d
ed FEP
commit
|
commitdiff
|
tree
2019-06-30
K
evin
B
oyd
Remov
e
group s
c
he
m
e checks
from r
u
nn
e
r
commit
|
commitdiff
|
tree
2019-06-30
Magnus L
u
ndborg
C
leaning up the GPU bonded kernel
commit
|
commitdiff
|
tree
2019-06-20
P
aul Bau
e
r
U
s
e ISerializer
f
or TPR file I
O
commit
|
commitdiff
|
tree
2019-06-20
B
e
rk
H
ess
T
e
mplate
f
re
e
-energy kernel on
s
oft-core
commit
|
commitdiff
|
tree
2019-06-20
Christia
n
Blau
A
d
d
B
asicVector scali
n
g
,
m
ax, min
an
d
toIvec
commit
|
commitdiff
|
tree
2019-06-19
Szilárd Pál
l
Disable PME
G
PU on Apple Op
e
nCL
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Refactor PME atom
hand
l
ing
commit
|
commitdiff
|
tree
2019-06-19
P
aul
B
a
u
er
Split
tpr
h
ead
e
r reading read
i
ng from tpr
body
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
R
emov
e
d un
u
sed cod
e
pa
t
hs in the NB FE
k
e
rnel
commit
|
commitdiff
|
tree
2019-06-18
Paul Bauer
F
ix gmx
d
ump
commit
|
commitdiff
|
tree
2019-06-18
Mar
k
A
b
raham
Move c
o
de handl
i
ng mdrun -gpu_i
d
to ta
s
kassignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Mak
e
f
orcerec
const i
n
dispatchN
o
nb
o
nde
d
Kernel
(
)
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Mrc for
m
at heade
r
to lattice c
o
o
rdinat
e
tra
n
sform
commit
|
commitdiff
|
tree
2019-06-18
C
hristian
Bl
a
u
Densit
y
simil
a
rity measure and gradient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irrgang
Redu
c
e docker i
m
age
size
f
or gmxapi
C
I
.
commit
|
commitdiff
|
tree
2019-06-18
A
r
tem Zhmurov
Bug fix: Constraints tests
a
re not instantiated with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
M
a
rk Abraham
Fix
p
ygments detection fo
r
sphinx for docs
build
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Use RAII app
r
o
a
ches
fo
r
har
d
ware informa
t
ion de
t
ec
t
ion
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Clea
n
up multisi
m
, commu
n
ica
t
i
on, and REMD
cod
e
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
In
i
tia
l
ize all of gmx_
d
omdec_comm_t
commit
|
commitdiff
|
tree
2019-06-11
Paul B
a
ue
r
Fix res
i
due and molecule in
d
exing
i
n
select
i
ons
commit
|
commitdiff
|
tree
2019-06-11
B
e
rk H
e
ss
Allow AWH geometr
y
'directi
o
n' to be period
i
c
commit
|
commitdiff
|
tree
2019-06-11
Paul Bauer
Ad
d
check for too m
a
n
y grid poin
t
s in hbond
commit
|
commitdiff
|
tree
2019-06-05
Berk Hes
s
Fix reference
SIMD memory
alignme
n
t
commit
|
commitdiff
|
tree
2019-05-29
Be
r
k Hes
s
Fix missing int
e
rmolecular inter
a
ctions with DD
commit
|
commitdiff
|
tree
2019-05-29
Szilá
r
d Páll
T
e
m
p
late x buffer ops ca
l
l on whether GPU is used
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
C
l
ean up renam
e
d
simulator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal M
e
rz
Remove
d
epende
n
ce of mdoutf_wr
i
te_to_traje
c
tory
_
f
i
les
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pa
s
c
al Me
r
z
R
e
name Integrator class
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhm
u
rov
C
larify the
E
nergyOutput II
I
commit
|
commitdiff
|
tree
2019-05-24
Art
e
m Zhmurov
Cla
r
ify the EnergyOutput I
I
commit
|
commitdiff
|
tree
2019-05-24
Mark Abraham
Reorder c
o
de be
f
ore thread-MPI spawns threads
commit
|
commitdiff
|
tree
2019-05-23
Szilárd P
á
ll
Fi
x
muli
t
ple
link refs in dev-manual
commit
|
commitdiff
|
tree
2019-05-23
Mark
A
b
raham
Teach ArrayR
e
fWithPadding to
m
ake a const flav
o
ur
commit
|
commitdiff
|
tree
2019-05-23
B
e
rk
H
ess
Fix
SHAKE dH/d
l
amb
d
a
contribut
i
ons
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraha
m
Rewr
i
te sta
r
ting beh
a
vior
commit
|
commitdiff
|
tree
2019-05-22
Ma
r
k Abraham
I
n
troduce tri-state enums for restarts
commit
|
commitdiff
|
tree
2019-05-22
A
lan Gray
Pin X bu
f
fer with DD and use proper abstraction i
n
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
Jinke Fan
A
dd support f
o
r Hygon Dhyana processor
commit
|
commitdiff
|
tree
2019-05-22
M
ar
k
Abraham
Move
functionali
t
y
to mdrun
u
tility
commit
|
commitdiff
|
tree
2019-05-20
Mar
k
A
b
raham
Fix equation typo
commit
|
commitdiff
|
tree
2019-05-16
Erik Lind
a
hl
Added
more
q
uotes
commit
|
commitdiff
|
tree
2019-05-14
Mark A
b
raham
Update inf
r
astructure n
e
eded
f
or
r
e
s
t
a
rt rewrit
e
commit
|
commitdiff
|
tree
2019-05-10
Pa
u
l B
a
uer
R
e
move more manual memory managemen
t
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
i
c
Irrgan
g
More
P
ython
testing inf
r
ast
r
uct
u
r
e
for
gmxapi
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Add gmxa
p
i
.
_logging s
u
bmodul
e
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Er
i
c Irrgang
Update
I
/O ha
n
dli
n
g in gmxapi
.
c
omman
d
line
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrga
n
g
Expand gmxapi
.
operation tools to support the data flow
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
ic Irrgang
Fix formatting
a
nd
t
ypos
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eri
c
Irrg
a
ng
Support b
a
s
i
c command
line wrapper in gm
x
api
commit
|
commitdiff
|
tree
2019-05-07
Mark Abraham
Add an e
x
ampl
e
of using an MPI
wrapper compiler
commit
|
commitdiff
|
tree
2019-05-03
Mar
k
Abraham
More tes
t
s for how mdrun -cpi resta
r
ts handle files
commit
|
commitdiff
|
tree
2019-05-03
Paul Bauer
Add outputadapters (2/3)
commit
|
commitdiff
|
tree
2019-05-02
Paul Bau
e
r
Add outputad
a
pte
r
s (1/3)
commit
|
commitdiff
|
tree
2019-05-02
M
.
Eric Irrga
n
g
I
n
fras
t
ruc
t
ur
e
updat
e
s for dependent c
h
anges
.
commit
|
commitdiff
|
tree
2019-05-02
Paul Bauer
Add builder for Tr
a
jectoryFileWriter
commit
|
commitdiff
|
tree
2019-05-02
Berk Hess
Change nbnxm
F
EP pointer to unique_p
t
r
commit
|
commitdiff
|
tree
2019-05-02
Mark A
b
raham
Enhance
p
a
t
h s
e
a
rch
f
unctions
commit
|
commitdiff
|
tree
2019-04-30
Mark Abrah
a
m
Test the
output
o
f "gmx mdrun he
l
p"
commit
|
commitdiff
|
tree
next