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Modernize FindHwloc.cmake
2019-07-05
Mark
Abr
a
ham
Mo
d
ernize FindHwloc
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
Er
i
c Ir
r
g
a
n
g
Py
t
hon bin
d
ing
s
f
o
r mdrun
.
commit
|
commitdiff
|
tree
2019-07-04
M
a
rk Abraham
F
u
rther clang-tidy-7 fix
commit
|
commitdiff
|
tree
2019-07-03
A
rtem Zhmurov
Combine CUDA Leap-Frog, LINCS
a
nd SET
T
L
E
.
I
I
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
U
p
dates to math/v
e
c
.
h
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-
e
nable affinit
y
diagonosti
c
s
w
ith MPI
commit
|
commitdiff
|
tree
2019-07-02
Kevin
Boyd
Add function for calculati
n
g 3x3 matrix det
e
r
m
i
nant
commit
|
commitdiff
|
tree
2019-07-02
Kevin
Boyd
Remove references to ecutsGROUP
commit
|
commitdiff
|
tree
2019-07-01
Pascal Merz
F
i
x
module d
e
tecti
o
n
f
or physica
l
val
i
dation
commit
|
commitdiff
|
tree
2019-07-01
Szilárd Páll
Refacto
r
t
r
a
c
king of G
P
U shor
t
-
r
an
g
e work/
s
k
i
p
p
ing
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fix
M
PI deadl
o
c
k in affinity setting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eric Irrga
n
g
gmxapi
Python package
documentation infrastr
u
ct
u
re
.
commit
|
commitdiff
|
tree
2019-06-30
Szilárd Páll
C
reate
d
edicated su
b
c
o
unter f
o
r non
b
onded FEP
commit
|
commitdiff
|
tree
2019-06-30
Kevin Boyd
Re
m
o
ve
g
roup
sc
h
eme
c
h
e
cks fr
o
m runner
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lundborg
Cle
a
n
ing up t
h
e GPU
b
o
n
ded
k
ernel
commit
|
commitdiff
|
tree
2019-06-20
Paul
B
aue
r
Use ISerializ
e
r for TPR fil
e
IO
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template free-energy kerne
l
o
n
soft-core
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
stian Blau
Add Ba
s
icVe
c
to
r
s
c
a
li
n
g, max, m
i
n and t
o
Ivec
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Ref
a
ctor
P
ME atom handlin
g
commit
|
commitdiff
|
tree
2019-06-19
Paul Bauer
Split tpr header
reading
reading from tpr
b
o
dy
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Removed unused code pa
t
h
s in th
e
NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Paul
B
auer
Fix gmx dum
p
commit
|
commitdiff
|
tree
2019-06-18
Mark Abra
h
am
Move cod
e
handling mdrun -g
p
u_
i
d to
taskassignment
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Be
r
k Hess
Make forcere
c
const in dispat
c
hNonb
o
ndedK
e
rn
e
l(
)
commit
|
commitdiff
|
tree
2019-06-18
Christ
i
a
n
Bl
a
u
Mrc for
m
at header to latt
i
ce c
o
or
d
in
a
te
t
ransform
commit
|
commitdiff
|
tree
2019-06-18
Chr
i
sti
a
n Blau
D
e
ns
i
ty similarity measure
and
g
r
a
dient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irrgang
Red
u
ce doc
k
er image size for
g
m
x
a
pi CI
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmurov
Bu
g
fix: Constraints tests
are not
i
nstantiated wit
h
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark
A
b
r
a
ham
Fix pygment
s
detection for sph
i
nx
f
o
r
docs build
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
U
s
e RAII approaches for hardware
i
nformati
o
n
detect
i
on
commit
|
commitdiff
|
tree
2019-06-11
M
ark Abraham
Clean up multisi
m
, commu
n
ication
,
and
R
EMD code
commit
|
commitdiff
|
tree
2019-05-29
Szilárd
P
áll
Template x
b
uffer
o
p
s c
a
l
l
on wheth
e
r 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
Merz
Remov
e
d
ependen
c
e of mdoutf_write_to_traj
e
ctory_fil
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Rename I
n
tegrator class
commit
|
commitdiff
|
tree
2019-05-24
Artem
Zhm
u
r
o
v
Cl
a
rify th
e
Energ
y
Output II
I
commit
|
commitdiff
|
tree
2019-05-24
Arte
m
Zhmurov
Clarify the EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-24
Ma
r
k Abr
a
ham
Reorde
r
code before thread
-
MPI spa
w
ns th
r
eads
commit
|
commitdiff
|
tree
2019-05-23
S
zilárd P
á
ll
Fix mulitple
link refs i
n
dev
-
manu
a
l
commit
|
commitdiff
|
tree
2019-05-23
Mark
A
braham
Teach ArrayRefWith
P
adding
t
o m
a
ke a
c
onst flavour
commit
|
commitdiff
|
tree
2019-05-22
Mark
Abraham
Rew
r
ite st
a
rting behavior
commit
|
commitdiff
|
tree
2019-05-22
Mark
A
braham
Introd
u
c
e
tr
i
-state enums for restarts
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Pin
X
buffer wit
h
DD
and use prope
r
abstraction i
n
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
Jinke
F
an
Ad
d
support
f
o
r Hygon
D
hyana pro
c
es
s
or
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Move fu
n
ctiona
l
it
y
to
m
drunutili
t
y
commit
|
commitdiff
|
tree
2019-05-16
E
r
ik Li
n
dah
l
Added more q
u
otes
commit
|
commitdiff
|
tree
2019-05-14
M
a
r
k Abrah
a
m
Update infr
a
structure needed for
r
es
t
art r
e
wri
t
e
commit
|
commitdiff
|
tree
2019-05-10
Paul Bauer
R
e
move more manual memory mana
g
emen
t
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric
I
rrg
a
ng
More Python t
e
sting in
f
rastructure for gmxapi
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Add gmxapi
.
_logging sub
m
odule
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Ir
r
gang
Update I/O handling in gmxapi
.
co
m
mand
l
ine
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Ir
r
gang
Ex
p
and gmxap
i
.
op
e
ratio
n
tools to support
t
he d
a
ta flow
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
F
i
x
f
o
rmat
t
ing
a
nd typos
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irr
g
ang
S
uppor
t
basic
comm
a
n
d lin
e
wra
p
per in gmxa
p
i
commit
|
commitdiff
|
tree
2019-05-03
M
ark
A
braham
More tests
fo
r
h
ow
md
r
u
n -cpi
r
estarts handl
e
files
commit
|
commitdiff
|
tree
2019-05-03
P
a
ul B
a
uer
Add o
u
tput
a
dapte
r
s (2/3)
commit
|
commitdiff
|
tree
2019-05-02
Paul
Bauer
Add o
u
tput
a
dapters (1/3)
commit
|
commitdiff
|
tree
2019-05-02
M
.
E
ric Irrgang
Infras
t
ructu
r
e
up
d
ates for dependent ch
a
nges
.
commit
|
commitdiff
|
tree
2019-05-02
Pa
u
l Bauer
Add builde
r
for TrajectoryFileWriter
commit
|
commitdiff
|
tree
2019-05-02
B
e
rk Hess
Change nbnx
m
FEP point
e
r to unique_ptr
commit
|
commitdiff
|
tree
2019-05-02
Mark
Abraham
Enhan
c
e
p
a
t
h search function
s
commit
|
commitdiff
|
tree
2019-04-30
Mark Abraham
T
est the out
p
ut of "gmx mdrun help"
commit
|
commitdiff
|
tree
2019-04-27
Chr
i
s
t
i
a
n B
l
au
mr
c
density map re
a
ding/writing
commit
|
commitdiff
|
tree
2019-04-27
Christian Blau
Three dimensional co
o
rdiante transformatio
n
.
commit
|
commitdiff
|
tree
2019-04-26
Paul Bauer
Add
C
++ coordinate file
w
riti
n
g me
t
hod
.
commit
|
commitdiff
|
tree
2019-04-25
Ch
r
istia
n
Blau
den
s
ity fitt
i
ng forces
commit
|
commitdiff
|
tree
2019-04-25
Paul Bauer
Add Interface to change coordinate file inf
o
commit
|
commitdiff
|
tree
2019-04-25
M
a
rk Abraham
Update
st
y
le g
u
ide about class enums
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Clarify p
u
shin
g
of
interactio
n
t
y
p
es
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Re
m
ove n
b
nxm
k
e
r
n
e
l type from
pairl
i
st gene
r
ation
commit
|
commitdiff
|
tree
2019-04-18
Berk He
s
s
Remove charge groups fro
m
domde
c
and localtop
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
C
reate gm
x
::compa
t
::optional
commit
|
commitdiff
|
tree
2019-04-17
Paul Bauer
E
n
a
ble
p
rinti
n
g of know
n
i
s
sues in comm
a
ndline
commit
|
commitdiff
|
tree
2019-04-17
Mark
A
braham
F
i
x post-submit
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Red
u
ce nbnxm CPU kernel argum
e
nts
commit
|
commitdiff
|
tree
2019-04-17
Be
r
k Hess
Simplify nbnxm s
h
ift f
o
r
ce handling
commit
|
commitdiff
|
tree
2019-04-16
Szi
l
árd P
á
ll
Mo
v
e functions
o
peratin
g
on ene
r
dat
a
out of
force
.
cpp
commit
|
commitdiff
|
tree
2019-04-16
Berk H
e
ss
S
implify nbnxm buffer clearing
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Re
m
ove RF
_
e
x
cl_corre
c
ti
o
n()
commit
|
commitdiff
|
tree
2019-04-16
Szilárd Páll
Remov
e
"coar
s
e
loa
d
balancing vars" from forcerec
commit
|
commitdiff
|
tree
2019-04-16
Paul B
a
u
e
r
Refactor t_
p
i
n
dex
commit
|
commitdiff
|
tree
2019-04-16
Mark Ab
r
aham
Removed
m
d
r
u
n
-gcom
commit
|
commitdiff
|
tree
2019-04-16
Art
e
m
Z
hmurov
Fix for
t
he memory acce
s
s error i
n
constrain
t
s t
e
st
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abra
h
a
m
S
t
art ma
k
ing
I
M
D
and swap m
o
del IMDModule
commit
|
commitdiff
|
tree
2019-04-10
Mar
k
A
braham
Reuse rve
c
s
_dif
f
e
r
in InteractiveMD
m
odul
e
commit
|
commitdiff
|
tree
2019-04-10
M
a
r
k Abr
a
ham
Make ImdSessi
o
n into a
P
impl-
e
d class with
f
acto
r
y
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
M
a
rk Ab
r
a
h
a
m
Reform IM
D
module
commit
|
commitdiff
|
tree
2019-04-09
M
.
Er
i
c Irrgang
gmxapi 2019 Q1/Q2 pro
j
e
c
t roadmap
.
commit
|
commitdiff
|
tree
2019-04-07
Paul
Bauer
Remove t_
t
opo
l
o
g
y from t
w
o prepr
o
ce
s
s tools
commit
|
commitdiff
|
tree
2019-04-05
Chr
i
stian Blau
de
n
s
i
tyfitting - MD
M
o
d
u
l
e declaration
commit
|
commitdiff
|
tree
2019-04-05
Szil
á
rd Páll
Revert "Tempora
r
i
l
y disable ARM
HPC compiler in post
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
P
a
ul Bauer
Update dev
e
loper guide for changes t
o
Gerrit
commit
|
commitdiff
|
tree
2019-04-03
Mark Abraha
m
Initial de
a
ctivation of group
s
che
m
e
.
commit
|
commitdiff
|
tree
2019-04-02
Paul
B
auer
R
e
f
a
c
t
or gpp_bo
n
d
_
a
tomtype
commit
|
commitdiff
|
tree
2019-04-02
P
aul Bauer
A
dd
std::string ca
s
e inse
n
si
t
iv
e
compare
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Re
f
a
c
tor gmx_group_t to S
i
mulationA
t
omGro
u
ps
commit
|
commitdiff
|
tree
2019-04-02
Paul Bau
e
r
Fix sim
u
l
ated anneali
n
g
a
n
d
add test
commit
|
commitdiff
|
tree
2019-04-02
Szilárd
Pá
l
l
Temp
o
rarily d
i
sabl
e
ARM
H
PC co
m
pile
r
in post-s
u
bmit
commit
|
commitdiff
|
tree
2019-04-01
Mark Abra
h
am
Mo
v
e MDModules
initia
l
ization earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
Move enerd
a
ta ownership
to
mdr
u
nner
commit
|
commitdiff
|
tree
next