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Update instructions in containers.rst
2019-11-14
B
e
rk
H
e
s
s
Simpl
i
f
y t_forcerec destruction
commit
|
commitdiff
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tree
2019-11-07
Berk Hess
F
i
x
.
gr
o
l
a
r
g
e bo
x
writin
g
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
D
ep
r
ecated sc-r-power
=
48
commit
|
commitdiff
|
tree
2019-11-01
Berk H
e
ss
Add hav
e
EwaldSurfaceContribution to Simulati
o
nWorkload
commit
|
commitdiff
|
tree
2019-10-31
B
erk
H
ess
Update GPU update restrictions
commit
|
commitdiff
|
tree
2019-10-30
Be
r
k Hes
s
Fix walls with GPU update
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
A
d
d
mdr
u
n
GPU upd
a
te
document
a
tion
commit
|
commitdiff
|
tree
2019-10-29
Be
r
k
H
e
ss
Fix Ewal
d
dipole correction with GP
U
update
commit
|
commitdiff
|
tree
2019-10-29
Berk
Hess
Disable pr
e
ssure coupling with GPU up
d
ate
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bool
u
seDo
m
ainDecomposition
i
n md
r
un
n
er
commit
|
commitdiff
|
tree
2019-10-24
B
e
rk Hess
Add
g
mx_mtop_interacti
o
n
_
coun
t
(
)
commit
|
commitdiff
|
tree
2019-10-24
Berk
H
ess
Fix i
n
itia
l
iz
e
rs
i
n l
o
cality
.
h
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Mov
e
l
ocalit
y
.
h from nbnxm to
m
d
t
ypes
commit
|
commitdiff
|
tree
2019-10-23
B
e
rk Hess
Use
gmx:
:
Range in Nbnxm gridding
functions
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Fix ill
e
gal
memo
r
y
acc
e
s
s in FE calc
u
la
t
i
o
ns
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Expa
n
d
doc
u
ment
a
tio
n
f
or
nbnx
n
_p
u
t_on_grid()
commit
|
commitdiff
|
tree
2019-10-22
Be
r
k He
s
s
Req
u
ire -ei for essen
t
ial dynamics
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Upda
t
e grompp cutoff-scheme
w
arnings
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Const correct
n
ess fo
r
genhydro
commit
|
commitdiff
|
tree
2019-10-12
Berk
Hess
Add clas
s
F
i
x
e
dCa
p
acityVect
o
r
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
Hess
I
n
crease
spc min
i
mization test tolerance
commit
|
commitdiff
|
tree
2019-10-09
Berk He
s
s
Fix harm
l
ess OpenMP wr
i
t
e race
commit
|
commitdiff
|
tree
2019-10-09
Berk
Hess
Fi
x
GPU atom
d
ata
in
i
t
timer
issue
commit
|
commitdiff
|
tree
2019-10-09
B
erk
Hess
Fi
x
r
a
ndom
e
n
ergy an
d
vi
r
i
al w
i
th PME on GPU on a
P
M
E
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
B
e
rk He
s
s
Make nbn
x
m
a
proper mo
d
ule
commit
|
commitdiff
|
tree
2019-10-08
Berk
H
e
ss
Simp
l
if
y
ewald
_
L
R
correction() call si
g
nature
commit
|
commitdiff
|
tree
2019-10-04
Ber
k
Hess
Fix random
e
nergy and virial
w
ith PME on GPU on a
PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk
Hess
Fix GPU atom data
init ti
m
er issu
e
commit
|
commitdiff
|
tree
2019-10-03
B
e
r
k He
s
s
Use gmx::Ran
g
e for i
Z
on
e
s in pair se
a
rch
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix setting
maxNum
C
o
lum
n
s in Nbnx
m
::GridS
e
t
commit
|
commitdiff
|
tree
2019-10-02
Berk
Hess
Fix
harmless O
p
enMP wr
i
te race
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
Use g
m
x::Range i
n
domdec
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Com
p
l
e
t
e
ly remov
e
charge
groups
commit
|
commitdiff
|
tree
2019-10-01
B
e
r
k Hess
Simplify DD
exclusion coun
t
ing
commit
|
commitdiff
|
tree
2019-10-01
Berk
Hess
Always out
p
ut corre
c
t kinetic at l
a
st step
commit
|
commitdiff
|
tree
2019-09-30
B
e
rk Hess
Rem
o
ve charge group code
from force
r
ec
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Actually fix gmx wham with an
g
le ge
o
m
e
tri
e
s
commit
|
commitdiff
|
tree
2019-09-29
Be
r
k Hess
In
c
rease t
i
3p5
minim
i
zation te
s
t tolerance
commit
|
commitdiff
|
tree
2019-09-28
Berk Hess
Fix CG minimizatio
n
with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
E
x
trac
t
gm
x
::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
F
ix loca
t
i
o
n of an
g
l
e
in vsite figu
r
e
commit
|
commitdiff
|
tree
2019-09-26
Berk Hess
Made mdrun
appendin
g
work aga
i
n
commit
|
commitdiff
|
tree
2019-09-24
Berk
Hess
Remove obsolete dd
_
get_ns_rang
e
s()
commit
|
commitdiff
|
tree
2019-09-23
Ber
k
Hess
L
i
mit Zen nbnxm kernel
c
h
oice to Z
e
n 1
commit
|
commitdiff
|
tree
2019-09-22
Be
r
k Hess
R
emove cgs_gl from
gmx_
d
omdec_c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-21
Berk Hess
Fi
x
incorrect shift
forces for CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk Hes
s
Fix DD 1 pulse checks wit
h
o
ut DLB
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
e
s
s
Remo
v
e
bLo
c
a
lCG from DD co
d
e
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
e
s
s
Re
m
ove o
b
solete make_e
x
clusions_zone
_
cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove
c
harge grou
p
da
t
a from t_force
r
ec
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
e
s
s
Add haveFr
e
eEn
e
rg
y
Work to Dom
a
i
nLi
f
etimeWo
r
kload
f
l
ags
commit
|
commitdiff
|
tree
2019-09-18
B
erk Hess
Ad
d
ed free-e
n
er
g
y
k
e
rnel performance
no
t
e
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fi
x
incorrec
t
DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-17
B
e
rk
H
ess
Remov
e
spu
r
io
u
s newline
f
r
o
m
log f
i
l
e
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fi
x
todos for update groups
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k
H
ess
Remove obsolete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add vi
r
t
ual si
t
e type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove cu
t
-off
sc
h
emes fr
o
m manual
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add option requ
e
st 1D DD
w
ith 1
p
ulse
commit
|
commitdiff
|
tree
2019-09-13
B
e
rk Hess
F
ix nonbonded-bench compilati
o
n issue
commit
|
commitdiff
|
tree
2019-09-13
Berk
Hess
A
dd nbnxm kernel benchmark tool
commit
|
commitdiff
|
tree
2019-09-12
B
erk Hess
Updat
e
d mdp
documentation for g
r
oup
scheme
r
emoval
commit
|
commitdiff
|
tree
2019-09-12
Berk
H
ess
Fix master not compilin
g
commit
|
commitdiff
|
tree
2019-09-12
Berk
H
es
s
Enable TPI
w
ith t
h
e Verlet c
u
t-off s
c
h
e
me
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Remove incor
r
ect check
with rf
-
zero
commit
|
commitdiff
|
tree
2019-09-09
Berk He
s
s
E
xtra
c
t Cartesian data from D
D
RankSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Rename DDS
e
tup to DDGri
d
Se
t
up
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hes
s
Clean up PME rank va
r
iables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Refact
o
r init
_
dom
a
in_dec
o
mposit
i
on(
)
commit
|
commitdiff
|
tree
2019-09-06
Be
r
k Hess
Ex
t
rac
t
g
etting of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
B
e
rk Hess
Add
P
P gri
d
i
n
fo t
o
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Berk
Hess
Ex
t
ract DDR
a
nkSetup f
r
om gmx_domdec_c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-05
Berk
H
ess
S
plit off getting of the DD
s
e
tup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Col
l
ect
s
ettin
g
s
for
D
D in DDSetti
n
gs
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Extract getting
o
f DD
S
yste
m
Info
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
ess
Simplify handling of DD bond
e
d distances
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move
c
onstraint and bonded filtering
info into
D
DSystemI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move
u
pd
a
t
e
g
r
ouping to D
D
Syst
e
mInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Change
DD pme force b
u
ffer to std::
v
ect
o
r
commit
|
commitdiff
|
tree
2019-09-04
Berk
Hess
Initial
i
z
e
all m
e
mb
e
r
s
of g
m
x_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
B
e
r
k Hess
Extract DDSys
t
emInfo from gmx_dom
d
ec_comm_t
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk Hess
Uni
f
y
m
anual and auto
DD grid choices
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k Hess
Remove gmx_domde
c
_t from dd_
c
hoose_grid
(
)
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Ext
a
ct UnitCellInf
o
from
g
mx_domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Fix incorrec
t
rvdw on GPU
with rvdw<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
On
l
y
u
s
e
f
sh
i
f
t
whe
n
n
ee
d
ed
commit
|
commitdiff
|
tree
2019-08-26
Berk Hess
Fix grompp constraints=all-an
g
les w
i
th constr
a
int
s
commit
|
commitdiff
|
tree
2019-08-22
Berk H
e
s
s
Fix
p
ert
u
rbed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge
two d
i
hed
r
al functions
commit
|
commitdiff
|
tree
2019-08-20
B
erk Hess
Use shiftForces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
B
erk Hess
Make bonded vir
i
al computation condit
i
onal
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Fix
m
issin
g
bonde
d
force
s
with CUDA
G
PUs and DD
commit
|
commitdiff
|
tree
2019-08-15
Be
r
k Hes
s
Template b
o
n
ded intera
c
tions on kernel flavo
r
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
Move bonde
d
functi
o
n
table into
b
onded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
SIMD accelera
t
io
n
fo
r
F_F
O
URDIH
S
a
n
d F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Add Force
W
ithSh
i
ftForces class
commit
|
commitdiff
|
tree
2019-08-06
Berk He
s
s
Fix latex formul
a
in referen
c
e manual
commit
|
commitdiff
|
tree
2019-08-05
Berk
H
ess
Mak
e
box con
s
t
i
n
d
o
_for
c
e()
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Cha
n
ge ForceOutpu
t
s to a class
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Re
m
ove sem
i
colon from
G
PU TERM mac
r
os
commit
|
commitdiff
|
tree
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