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Updates to math/vec.h
2019-07-03
Kevin Boyd
Upd
a
tes to
m
ath/ve
c
.
h
commit
|
commitdiff
|
tree
2019-07-02
Berk
H
es
s
Re-ena
b
le affinity diagonost
i
cs with MPI
commit
|
commitdiff
|
tree
2019-07-02
Kevi
n
Boyd
Add
funct
i
on f
o
r cal
c
u
lating 3x3 ma
t
rix determi
n
ant
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
Remove references
to ecutsGROUP
commit
|
commitdiff
|
tree
2019-07-01
P
a
s
c
al Merz
Fi
x
module detection f
o
r
physical val
i
datio
n
commit
|
commitdiff
|
tree
2019-07-01
Szilár
d
Páll
Refactor trac
k
ing o
f
G
PU short-range work/s
k
ip
p
ing
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fix
MPI dead
l
ock in affinity s
e
tting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eric
I
rrgang
gmxapi Python package documentati
o
n
infrastr
u
cture
.
commit
|
commitdiff
|
tree
2019-06-30
Szilá
r
d Páll
Cre
a
te
dedicated subcounter for nonbonde
d
FEP
commit
|
commitdiff
|
tree
2019-06-30
K
evin Bo
y
d
Remove group scheme checks
from
r
u
nner
commit
|
commitdiff
|
tree
2019-06-30
Magnu
s
Lundb
o
rg
Cle
a
n
ing up th
e
GPU bonded kernel
commit
|
commitdiff
|
tree
2019-06-20
Paul Bauer
Us
e
ISe
r
i
alizer for
T
PR
file IO
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template fre
e
-energy kernel on soft-core
commit
|
commitdiff
|
tree
2019-06-20
C
hristian Blau
Add BasicV
e
ctor scaling,
max, m
i
n and toIv
e
c
commit
|
commitdiff
|
tree
2019-06-19
Berk
Hess
Refactor PM
E
at
o
m
h
andl
i
ng
commit
|
commitdiff
|
tree
2019-06-19
P
aul Bauer
S
plit t
p
r h
e
ader
reading
reading from tp
r
body
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk He
s
s
Re
m
oved unused code paths in the NB FE k
e
rnel
commit
|
commitdiff
|
tree
2019-06-18
Paul Bau
e
r
Fix gmx dump
commit
|
commitdiff
|
tree
2019-06-18
Mark Abraham
Mov
e
code handling mdrun
-gpu_id to taska
s
signm
e
nt
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Ber
k
Hess
Make forcerec c
o
nst in dispatch
N
onbondedKernel()
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Mrc format header to lattic
e
coordina
t
e
transform
commit
|
commitdiff
|
tree
2019-06-18
C
hristian Bl
a
u
D
e
nsit
y
similar
i
t
y
m
easure and gr
a
dient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irrg
a
ng
Reduce docke
r
image
size for gmxapi CI
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmuro
v
Bug f
i
x: Constraints tests are not instanti
a
t
e
d
with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark
A
braham
Fix
p
ygments detection for sphinx for docs build
commit
|
commitdiff
|
tree
2019-06-11
M
a
rk Abraham
Use RAII
approache
s
for
hard
w
ar
e
inf
o
rmation detect
i
on
commit
|
commitdiff
|
tree
2019-06-11
Mark A
b
r
a
ham
C
l
ean up multi
s
im, communicati
o
n, and REMD
code
commit
|
commitdiff
|
tree
2019-05-29
Szilárd Páll
Templ
a
te x buffer ops cal
l
on whether
GPU is us
e
d
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
Clean
up renamed simulator
.
h
fil
e
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Re
m
o
v
e
d
ependen
c
e of mdoutf_writ
e
_to_traj
e
ctory_fi
l
es
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal
M
erz
R
en
a
me Integr
a
tor
class
commit
|
commitdiff
|
tree
2019-05-24
Artem
Zhmurov
C
larify the EnergyOutpu
t
I
II
commit
|
commitdiff
|
tree
2019-05-24
A
rt
e
m Zhmur
o
v
Clarify the EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-24
Mark
A
braham
Reorder code before thread-MPI spawns thre
a
ds
commit
|
commitdiff
|
tree
2019-05-23
Szilárd Páll
Fix mulitple link r
e
f
s
i
n
dev-
m
anual
commit
|
commitdiff
|
tree
2019-05-23
Mark Abraha
m
Tea
c
h ArrayR
e
fW
i
thPaddin
g
to make a const flav
o
ur
commit
|
commitdiff
|
tree
2019-05-22
Mar
k
Abraha
m
Rewrite starting behavior
commit
|
commitdiff
|
tree
2019-05-22
M
a
rk Abraham
I
n
trodu
c
e tri-state enu
m
s for
restarts
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Pin X buffer
w
ith DD and use pro
p
e
r
abstraction in
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
J
i
nk
e
Fan
Add support for Hygon Dhya
n
a pr
o
c
essor
commit
|
commitdiff
|
tree
2019-05-22
Mark
A
braham
M
o
ve functiona
l
ity
t
o mdrun
u
tility
commit
|
commitdiff
|
tree
2019-05-16
Erik Lind
a
h
l
A
d
d
ed more quote
s
commit
|
commitdiff
|
tree
2019-05-14
Ma
r
k A
b
raha
m
Update
i
nf
r
astructure needed for restart rewrite
commit
|
commitdiff
|
tree
2019-05-10
Paul Bau
e
r
Remove more manual me
m
ory man
a
g
e
ment
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ri
c
Irrgang
More Pyth
o
n
testin
g
infrastructure fo
r
g
m
xapi
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Ad
d
gmxapi
.
_logging
s
ubmodule
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Update
I
/O han
d
l
i
ng
i
n gmxapi
.
commandline
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
E
xpand gmxapi
.
operat
i
on tools to suppor
t
t
h
e data fl
o
w
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ric I
r
rgang
Fix formatting
a
n
d
typos
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Er
i
c Irrgan
g
Support basic
c
o
mmand l
i
ne wra
p
per in gmxapi
commit
|
commitdiff
|
tree
2019-05-03
Mark Abra
h
am
M
o
re tests for how mdrun -cpi restart
s
hand
l
e f
i
les
commit
|
commitdiff
|
tree
2019-05-03
Paul
B
aue
r
Ad
d
output
a
dapters (2/3)
commit
|
commitdiff
|
tree
2019-05-02
Pau
l
Bauer
Add
outpu
t
a
d
apters (
1
/3)
commit
|
commitdiff
|
tree
2019-05-02
M
.
Eric Irr
g
an
g
Infr
a
st
r
uc
t
ure upd
a
tes f
o
r
d
e
p
endent
changes
.
commit
|
commitdiff
|
tree
2019-05-02
Paul B
a
uer
Add
b
u
ilder for Trajectory
F
ileWri
t
er
commit
|
commitdiff
|
tree
2019-05-02
Berk Hess
Ch
a
nge nbnxm FE
P
po
i
n
te
r
to u
n
iqu
e
_pt
r
commit
|
commitdiff
|
tree
2019-05-02
M
a
rk Abraham
Enhanc
e
p
a
t
h
search funct
i
ons
commit
|
commitdiff
|
tree
2019-04-30
M
ar
k
Abraha
m
Test the
o
utput of "gmx mdrun help"
commit
|
commitdiff
|
tree
2019-04-27
Christia
n
Blau
mrc density
m
ap
read
i
ng/wri
t
ing
commit
|
commitdiff
|
tree
2019-04-27
Christ
i
an
B
lau
Three di
m
ensional coordiante transformation
.
commit
|
commitdiff
|
tree
2019-04-26
Pa
u
l Ba
u
e
r
A
d
d
C
++ coordi
n
ate file wri
t
ing method
.
commit
|
commitdiff
|
tree
2019-04-25
Christian Blau
d
e
nsity fitting f
o
rces
commit
|
commitdiff
|
tree
2019-04-25
Paul Bauer
A
dd Interface
t
o
change coordinate
f
ile
i
nfo
commit
|
commitdiff
|
tree
2019-04-25
Mar
k
Abraham
U
p
date style gui
d
e a
b
out class enu
m
s
commit
|
commitdiff
|
tree
2019-04-23
Mark Ab
r
aham
Clarify pushing of interactio
n
types
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Re
m
ove nbnxm kernel type
fro
m
pair
l
is
t
genera
t
ion
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Remove charge g
r
o
u
ps from
domd
e
c a
n
d localtop
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Create
gmx::compat::optional
commit
|
commitdiff
|
tree
2019-04-17
Paul
B
auer
Enable pri
n
tin
g
of known issues in com
m
andline
commit
|
commitdiff
|
tree
2019-04-17
Mark
Abraham
Fix
p
ost
-
submit
commit
|
commitdiff
|
tree
2019-04-17
B
er
k
Hess
Reduce nbnx
m
CPU
kernel argu
m
ents
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
S
im
p
l
i
fy nbn
x
m
shift force handling
commit
|
commitdiff
|
tree
2019-04-16
Sz
i
lár
d
Páll
Move function
s
operating on enerdata o
u
t
of f
o
r
c
e
.
cpp
commit
|
commitdiff
|
tree
2019-04-16
B
erk
H
es
s
S
i
m
plify nbn
x
m
b
uffer cl
e
ari
n
g
commit
|
commitdiff
|
tree
2019-04-16
Be
r
k Hess
Remove
R
F_excl_corre
c
tion()
commit
|
commitdiff
|
tree
2019-04-16
Szilárd P
á
ll
Remove "coarse load bal
a
ncing vars"
f
rom forcerec
commit
|
commitdiff
|
tree
2019-04-16
Paul Bauer
R
efactor t_
p
in
d
ex
commit
|
commitdiff
|
tree
2019-04-16
M
ark Abra
h
am
Removed mdr
u
n -g
c
om
commit
|
commitdiff
|
tree
2019-04-16
Artem Zhmurov
Fix for the
m
emory acces
s
e
rror in constraints test
.
commit
|
commitdiff
|
tree
2019-04-10
Mark
A
braham
Start making
I
M
D
a
nd swap model IMDMod
u
le
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraham
Reuse
r
vecs_
d
iffer in InteractiveMD module
commit
|
commitdiff
|
tree
2019-04-10
M
ark A
b
raham
Make ImdSession into a Pimp
l
-ed class w
i
t
h
f
act
o
ry
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abrah
a
m
Reform IMD mod
u
le
commit
|
commitdiff
|
tree
2019-04-09
M
.
Eric Irrga
n
g
gmxa
p
i 2019
Q
1/Q2
p
roject ro
a
d
m
ap
.
commit
|
commitdiff
|
tree
2019-04-07
Pa
u
l Bauer
R
emove t_topol
o
g
y from two preprocess tools
commit
|
commitdiff
|
tree
2019-04-05
Ch
r
i
s
tian
Blau
densityfitting - MDModule declaratio
n
commit
|
commitdiff
|
tree
2019-04-05
Szi
l
árd Páll
R
ev
e
rt "Temporaril
y
disable ARM
HPC compiler in post
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Paul Bauer
Update devel
o
per guide for changes to
G
e
r
rit
commit
|
commitdiff
|
tree
2019-04-03
Mark Abrah
a
m
Initial d
e
activation
o
f group sch
e
me
.
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Refact
o
r gpp_b
o
nd_atomtype
commit
|
commitdiff
|
tree
2019-04-02
Pau
l
Ba
u
er
Add std::st
r
ing c
a
se insensitive comp
a
re
commit
|
commitdiff
|
tree
2019-04-02
Paul B
a
uer
Refactor gmx_gr
o
up_t to SimulationAtomGr
o
ups
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Fix simulated annealing and a
d
d t
e
st
commit
|
commitdiff
|
tree
2019-04-02
S
z
i
l
árd Páll
Tempo
r
arily disable ARM
H
PC compiler in post
-
submit
commit
|
commitdiff
|
tree
2019-04-01
Ma
r
k Abraham
Move MDModules initialization earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark
A
bra
h
am
Move enerdata owners
h
ip to mdrunner
commit
|
commitdiff
|
tree
2019-03-29
M
.
E
r
ic Irrgang
Plumbi
n
g f
o
r gmxapi 20
1
9
Q
1/Q2 projec
t
roadmap
.
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Simp
l
ify
n
bnx
m
final
force reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk
Hess
Move early
r
e
tur
n
fo
r
nbnxm fo
r
ce redu
c
tion
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
M
o
ve Pairl
i
stSet decl
a
ratio
n
commit
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commitdiff
|
tree
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