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Updates to math/vec.h
2019-07-03
Kevin Boy
d
Updates to math/vec
.
h
commit
|
commitdiff
|
tree
2019-07-02
Berk
Hes
s
Re-enable
a
ffi
n
ity diagonostic
s
w
i
t
h
M
P
I
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
Add function fo
r
calculating
3
x
3
matrix determinant
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
R
e
move references to ecutsGROUP
commit
|
commitdiff
|
tree
2019-07-01
P
a
sca
l
M
erz
Fix
mo
d
ule
detection
f
o
r
physi
c
al validation
commit
|
commitdiff
|
tree
2019-07-01
S
zilárd Pál
l
R
efa
c
tor tracking of G
P
U
short-
r
an
g
e work/skipp
i
ng
commit
|
commitdiff
|
tree
2019-07-01
Berk H
e
ss
F
i
x MPI deadlock in
a
ffinity setting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eri
c
Irrgan
g
gmxapi
Python pa
c
kage
d
o
cum
e
ntation infrastructure
.
commit
|
commitdiff
|
tree
2019-06-30
S
z
ilár
d
P
áll
Create
d
edic
a
ted subcounter for nonbond
e
d
FEP
commit
|
commitdiff
|
tree
2019-06-30
K
evin Boyd
Re
m
ove group scheme c
h
ecks from runner
commit
|
commitdiff
|
tree
2019-06-30
M
a
g
nus Lundborg
C
l
eaning
u
p
t
he GPU bonde
d
kernel
commit
|
commitdiff
|
tree
2019-06-20
Paul B
a
uer
Use ISerializer
f
o
r TP
R
file IO
commit
|
commitdiff
|
tree
2019-06-20
B
erk Hess
Template free-energy ke
r
ne
l
on soft-core
commit
|
commitdiff
|
tree
2019-06-20
Christian B
l
au
A
d
d BasicVector sc
a
ling, max
,
min and toIv
e
c
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Refactor
PME atom handling
commit
|
commitdiff
|
tree
2019-06-19
Paul Bauer
Split t
p
r
h
ea
d
er re
a
ding r
e
ading from tpr bod
y
commit
|
commitdiff
|
tree
2019-06-19
Berk He
s
s
Removed unu
s
ed code
p
at
h
s i
n
t
h
e NB FE kerne
l
commit
|
commitdiff
|
tree
2019-06-18
Paul Bauer
Fix gmx
dump
commit
|
commitdiff
|
tree
2019-06-18
Mark Abraham
Move code han
d
ling mdrun -gpu_id to task
a
s
signment
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Ber
k
Hess
Make force
r
ec const in dispatc
h
NonbondedKern
e
l()
commit
|
commitdiff
|
tree
2019-06-18
Chr
i
stian Bl
a
u
Mrc
for
m
at header to l
a
ttice coordinate
tr
a
nsform
commit
|
commitdiff
|
tree
2019-06-18
C
h
risti
a
n
Blau
Density simi
l
arity measur
e
and g
r
adient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irrgang
Reduce
d
ock
e
r image si
z
e for
g
mxapi
C
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmuro
v
Bug fix: Const
r
a
i
nt
s
tests
a
r
e no
t
instantiated with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Ab
r
ah
a
m
F
ix
p
ygments detection for sphinx
f
or
d
o
c
s build
commit
|
commitdiff
|
tree
2019-06-11
Mark A
b
rah
a
m
Us
e
RAII approa
c
he
s
for
hardware info
r
mation d
e
t
e
ction
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraha
m
Cl
e
a
n up mu
l
tisim, communication, and REM
D
code
commit
|
commitdiff
|
tree
2019-05-29
Szilárd Páll
Template
x
buffer ops call o
n
whether
G
PU is used
commit
|
commitdiff
|
tree
2019-05-27
Pascal
M
erz
Clean up renamed
s
imula
t
or
.
h
f
ile
commit
|
commitdiff
|
tree
2019-05-25
Pascal M
e
rz
Remove d
e
pendence
o
f mdoutf_write_to_trajectory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
P
ascal M
e
rz
R
enam
e
Int
e
g
r
ator class
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhm
u
r
o
v
Clarify the EnergyOutpu
t
I
I
I
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmu
r
ov
Clarify th
e
EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-24
Mark Abraham
Reorder c
o
de before
thread-MPI spa
w
n
s thr
e
ads
commit
|
commitdiff
|
tree
2019-05-23
Szilár
d
Páll
Fix
m
ulitple
lin
k
r
e
fs in dev-
m
anua
l
commit
|
commitdiff
|
tree
2019-05-23
Mark
Abraha
m
T
e
ach A
r
r
a
yRefWithPadding
to make a co
n
st flavour
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
R
e
wr
i
te startin
g
b
eha
v
ior
commit
|
commitdiff
|
tree
2019-05-22
Ma
r
k Abraham
I
n
tro
d
uce tr
i
-sta
t
e e
n
ums for
r
es
t
arts
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Pin
X b
u
ffer
w
ith D
D
an
d
u
se pro
p
er abstrac
t
i
o
n in
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
J
i
nke Fan
Add suppor
t
for Hygo
n
D
h
y
a
n
a
proce
s
sor
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Move functi
o
nali
t
y to mdrunutility
commit
|
commitdiff
|
tree
2019-05-16
Erik Lindahl
Added mo
r
e q
u
otes
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
U
p
da
t
e
infrastruc
t
ur
e
needed for restart rewrit
e
commit
|
commitdiff
|
tree
2019-05-10
Paul Bau
e
r
Remo
v
e
more manual
m
emory management
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ric Irr
g
ang
More P
y
t
h
on testing infras
t
ructure
f
or gm
x
api
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ric Irrgang
Add gmxa
p
i
.
_
l
o
ggi
n
g submodule
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
ic
Irrga
n
g
U
p
date I/O ha
n
dl
i
ng in g
m
xapi
.
comm
a
ndline
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrga
n
g
Expan
d
g
m
xapi
.
operatio
n
tools to support the
d
ata
flow
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Fix formattin
g
and
t
yp
o
s
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric I
r
rgang
Support basic command line wrapper in
g
mxapi
commit
|
commitdiff
|
tree
2019-05-03
Mark
A
braham
More tests for how mdrun -cpi
r
esta
r
ts ha
n
dle files
commit
|
commitdiff
|
tree
2019-05-03
Pa
u
l Bauer
Add outputad
a
p
te
r
s (2/3
)
commit
|
commitdiff
|
tree
2019-05-02
Paul Bauer
Add outputadapters (
1
/3)
commit
|
commitdiff
|
tree
2019-05-02
M
.
Eric Irrgang
Infrastruct
u
re u
p
dates for d
e
pe
n
de
n
t changes
.
commit
|
commitdiff
|
tree
2019-05-02
Paul Bauer
Ad
d
bui
l
der for Traj
e
ctoryF
i
leWriter
commit
|
commitdiff
|
tree
2019-05-02
Berk Hess
Change nbnx
m
FEP pointer to unique_ptr
commit
|
commitdiff
|
tree
2019-05-02
Ma
r
k Abraham
Enhance path searc
h
func
t
ions
commit
|
commitdiff
|
tree
2019-04-30
Mark Abraha
m
Test the out
p
ut of
"
gmx mdrun h
e
l
p"
commit
|
commitdiff
|
tree
2019-04-27
Ch
r
istian
B
lau
mrc density map readin
g
/wri
t
ing
commit
|
commitdiff
|
tree
2019-04-27
Christian Bla
u
Th
r
ee dimen
s
ional co
o
rdian
t
e transformation
.
commit
|
commitdiff
|
tree
2019-04-26
Paul Bauer
Add
C
+
+ coordinate file writing met
h
od
.
commit
|
commitdiff
|
tree
2019-04-25
Ch
r
is
t
i
an
Blau
den
s
ity
f
i
tting
forces
commit
|
commitdiff
|
tree
2019-04-25
Paul
B
auer
A
d
d
I
nt
e
rface to ch
a
nge coordinate fi
l
e info
commit
|
commitdiff
|
tree
2019-04-25
Mark Abra
h
am
Up
d
ate style guide about
c
l
a
ss enu
m
s
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Clarify push
i
ng
of interacti
o
n
t
ype
s
commit
|
commitdiff
|
tree
2019-04-18
Berk
Hess
Remov
e
nbnx
m
kernel
t
ype from p
a
ir
l
ist gene
r
ation
commit
|
commitdiff
|
tree
2019-04-18
Be
r
k Hess
Remove charge groups fr
o
m domdec a
n
d lo
c
altop
commit
|
commitdiff
|
tree
2019-04-18
Mark Abr
a
ham
Crea
t
e gm
x
::compat::optional
commit
|
commitdiff
|
tree
2019-04-17
Paul Bauer
En
a
b
l
e p
r
inti
n
g of k
n
ow
n
issues in comm
a
ndline
commit
|
commitdiff
|
tree
2019-04-17
Mark A
b
raham
Fix post-subm
i
t
commit
|
commitdiff
|
tree
2019-04-17
Berk Hes
s
Re
d
uce nbnxm
CP
U
k
erne
l
argument
s
commit
|
commitdiff
|
tree
2019-04-17
Berk He
s
s
Simplify
nbnxm shift
f
orce handling
commit
|
commitdiff
|
tree
2019-04-16
Szilárd Páll
Mov
e
f
u
nctions op
e
ra
t
i
ng on enerdata out of f
o
rce
.
cp
p
commit
|
commitdiff
|
tree
2019-04-16
Berk He
s
s
Simplify
nbnxm buffe
r
clearing
commit
|
commitdiff
|
tree
2019-04-16
B
erk
H
ess
Remove
RF_exc
l
_correction()
commit
|
commitdiff
|
tree
2019-04-16
S
z
ilárd Pá
l
l
Remov
e
"
c
o
a
rse
load bala
n
cing va
r
s" f
r
om forcerec
commit
|
commitdiff
|
tree
2019-04-16
Paul Bauer
R
e
factor t_p
i
n
dex
commit
|
commitdiff
|
tree
2019-04-16
Mark Abra
h
am
Removed
mdrun -gcom
commit
|
commitdiff
|
tree
2019-04-16
Artem Zhmurov
Fix for
t
he memory a
c
c
ess
e
rror i
n
const
r
aints test
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abrah
a
m
St
a
r
t making IMD and swap m
o
del
IMDModu
l
e
commit
|
commitdiff
|
tree
2019-04-10
M
a
r
k
A
braha
m
Reuse rvec
s
_differ in
Int
e
ractiveMD module
commit
|
commitdiff
|
tree
2019-04-10
Mar
k
Abrah
a
m
Make ImdS
e
ssion int
o
a
P
impl-ed class wit
h
factor
y
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
M
a
r
k
Abraha
m
Reform IMD module
commit
|
commitdiff
|
tree
2019-04-09
M
.
Eric Irrgang
gmxapi 2019 Q1/Q2 proje
c
t
r
oa
d
map
.
commit
|
commitdiff
|
tree
2019-04-07
P
aul Bauer
Remove t_to
p
olo
g
y from two pr
e
proc
e
ss tools
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
densityfitt
i
ng - MDM
o
dule decl
a
rat
i
on
commit
|
commitdiff
|
tree
2019-04-05
Szilárd Páll
R
evert "Tempor
a
ri
l
y d
i
sable
A
RM H
P
C comp
i
ler in po
s
t
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Paul Bauer
Updat
e
deve
l
op
e
r
gui
d
e for chan
g
es to Gerrit
commit
|
commitdiff
|
tree
2019-04-03
Mark A
b
raham
Initial
deac
t
i
vat
i
on of gr
o
up
sc
h
em
e
.
commit
|
commitdiff
|
tree
2019-04-02
P
a
ul Baue
r
Refactor gpp_bon
d
_atom
t
ype
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Add std::string ca
s
e insensi
t
ive compare
commit
|
commitdiff
|
tree
2019-04-02
P
aul Ba
u
er
R
efactor g
m
x_gro
u
p_t to
Simul
a
tion
A
t
o
mGroups
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Fix simulated annealing and ad
d
test
commit
|
commitdiff
|
tree
2019-04-02
Szilár
d
Páll
Temporarily disable
A
RM HPC compiler i
n
p
ost-submit
commit
|
commitdiff
|
tree
2019-04-01
M
a
rk Abrah
a
m
Move MDModules initialization earlier
commit
|
commitdiff
|
tree
2019-04-01
Mar
k
Abraham
Move enerd
a
ta ow
n
er
s
hi
p
to
m
drunner
commit
|
commitdiff
|
tree
2019-03-29
M
.
Eric Irrgang
Plumbing for gm
x
api 2019 Q1/Q2 project roadmap
.
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Simp
l
ify nbnxm fin
a
l f
o
rce reductio
n
commit
|
commitdiff
|
tree
2019-03-28
Berk He
s
s
Move early ret
u
rn for nbnxm force reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk Hes
s
Move Pairl
i
s
tSet declaration
commit
|
commitdiff
|
tree
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