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Improve mdrun performance user guide
2019-12-19
Berk Hess
Fix mdrun appending invali
d
ating en
e
rgy files
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
Change
grompp d
e
coupling SD warning to note
commit
|
commitdiff
|
tree
2019-12-17
B
e
rk Hess
Add note
f
or COM removal with positio
n
restraints
commit
|
commitdiff
|
tree
2019-12-02
B
e
r
k Hess
Add check f
o
r
c
oupled cons
t
r
a
i
nts
for CUDA update
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Extract LINCS CUDA help
e
r f
u
nctions
commit
|
commitdiff
|
tree
2019-11-29
Berk H
e
ss
Merge "M
e
rge
b
ran
c
h release-2019 i
n
to release-
2
020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Be
r
k
H
ess
Update documenatio
n
f
or NPT
GPU update
commit
|
commitdiff
|
tree
2019-11-28
Berk H
e
ss
R
emove as
s
ertion failure in AWH without initial sta
g
e
commit
|
commitdiff
|
tree
2019-11-28
Berk He
s
s
F
ix bug with GPU pressu
r
e scalin
g
at non T-scaling
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
Fix issues with A
W
H
with periodic p
u
l
ling
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Quiet pdb2gmx and
use
gmx_fa
t
al
commit
|
commitdiff
|
tree
2019-11-19
Berk Hess
Fix bon
d
ed
a
tom
c
ommuni
c
ati
o
n performance
commit
|
commitdiff
|
tree
2019-11-18
Berk Hess
Fix intermolecular interaction
s
wi
t
h DD
commit
|
commitdiff
|
tree
2019-11-07
Berk Hess
Fix
.
gro large box writ
i
ng
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Deprecated
s
c
-
r-
p
ower=48
commit
|
commitdiff
|
tree
2019-11-01
Berk Hess
Add haveEwald
S
urfaceContribu
t
ion to
S
imulationWorkl
o
ad
commit
|
commitdiff
|
tree
2019-10-31
B
erk Hess
U
p
date GPU update restrictions
commit
|
commitdiff
|
tree
2019-10-30
Berk Hess
Fix
walls wit
h
G
P
U update
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Add mdrun GP
U
upd
a
te documentati
o
n
commit
|
commitdiff
|
tree
2019-10-29
Berk H
e
s
s
Fix
Ewald dipole correction wit
h
G
P
U
upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
Disable pressur
e
coupling with GPU update
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bool useDoma
i
n
Decomposi
t
ion in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
B
e
rk He
s
s
Ad
d
gmx_mtop
_
i
ntera
c
t
i
o
n_co
u
nt()
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Fix i
n
it
i
alizers in locality
.
h
commit
|
commitdiff
|
tree
2019-10-23
B
e
r
k H
e
ss
Move loca
l
ity
.
h from nbnxm to m
d
t
y
pe
s
commit
|
commitdiff
|
tree
2019-10-23
Berk
H
ess
Use gmx::Range in Nbnxm grid
d
ing f
u
nctions
commit
|
commitdiff
|
tree
2019-10-23
Berk
H
ess
Fix
i
l
l
egal memory
a
ccess in
F
E cal
c
ulati
o
ns
commit
|
commitdiff
|
tree
2019-10-23
Be
r
k
Hess
Expand documenta
t
i
o
n for nbnxn_put_
o
n_gr
i
d
(
)
commit
|
commitdiff
|
tree
2019-10-22
Berk
H
e
s
s
Require -
e
i for essential dynamics
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Up
d
a
t
e
grompp
cutoff-scheme warnings
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
Cons
t
co
r
r
e
ctness for genhydro
commit
|
commitdiff
|
tree
2019-10-12
Be
r
k
H
ess
Add class
F
i
x
ed
C
apa
c
i
t
y
Vect
o
r
commit
|
commitdiff
|
tree
2019-10-09
Be
r
k Hess
Increase
s
pc min
i
mization test
tolera
n
ce
commit
|
commitdiff
|
tree
2019-10-09
Berk H
e
s
s
Fix harm
l
e
s
s OpenMP write race
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
F
i
x
GPU at
o
m data
i
n
it timer
issue
commit
|
commitdiff
|
tree
2019-10-09
Berk Hes
s
Fix random en
e
r
g
y and virial with PME on
G
PU on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Berk H
e
ss
Make nbn
x
m a
proper module
commit
|
commitdiff
|
tree
2019-10-08
Berk
H
ess
Simplify ewald_LRcorr
e
c
t
ion() c
a
ll s
i
g
n
ature
commit
|
commitdiff
|
tree
2019-10-04
Berk Hess
Fix random
e
nergy and viria
l
wit
h
P
M
E
o
n
GPU
on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
B
erk H
e
ss
Fix GPU atom dat
a
i
nit ti
m
er i
s
sue
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use
g
m
x::Rang
e
for
iZ
o
n
e
s in pair
s
earch
commit
|
commitdiff
|
tree
2019-10-03
Berk Hes
s
Fix se
t
ting m
a
xNumColumns in Nbnxm
:
:Grid
S
et
commit
|
commitdiff
|
tree
2019-10-02
B
erk Hess
Fix
h
ar
m
less
O
penMP
wri
t
e race
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
U
s
e
gmx
:
:Range in
domde
c
commit
|
commitdiff
|
tree
2019-10-01
Berk H
e
ss
Completely remove c
h
a
r
ge groups
commit
|
commitdiff
|
tree
2019-10-01
B
erk
He
s
s
Simpli
f
y
D
D excl
u
sion coun
t
ing
commit
|
commitdiff
|
tree
2019-10-01
Berk He
s
s
Always
o
utp
u
t c
o
rrec
t
k
in
e
tic at last s
t
e
p
commit
|
commitdiff
|
tree
2019-09-30
B
erk Hes
s
Remove charg
e
group code fr
o
m force
r
e
c
commit
|
commitdiff
|
tree
2019-09-30
Berk
Hess
Actual
l
y fix gmx w
h
am with ang
l
e g
e
ometries
commit
|
commitdiff
|
tree
2019-09-29
Berk Hess
Increase
t
i
3
p
5
minimization
t
es
t
tol
e
r
a
nce
commit
|
commitdiff
|
tree
2019-09-28
Be
r
k Hess
Fix
C
G min
i
m
ization with
DD
commit
|
commitdiff
|
tree
2019-09-27
Berk He
s
s
Ext
r
act gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
F
i
x
locati
o
n o
f
angle in vsite
f
igure
commit
|
commitdiff
|
tree
2019-09-26
Ber
k
Hess
Ma
d
e mdr
u
n appending
work again
commit
|
commitdiff
|
tree
2019-09-24
Berk Hess
Remove obsolete
d
d_get_ns_ranges
(
)
commit
|
commitdiff
|
tree
2019-09-23
Be
r
k Hess
Limit Zen nbnxm kernel
choice to Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
Hess
R
emove
cgs_gl fr
o
m gmx_do
m
dec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
Be
r
k H
e
ss
Fix incorrect shift forces for
C
MAP
commit
|
commitdiff
|
tree
2019-09-20
Berk Hes
s
Fix DD 1 pulse checks wi
t
hou
t
DLB
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Rem
o
ve
bLocalCG f
r
om DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
Re
m
ove obsolete m
a
ke_e
x
clusions_
z
one_cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove ch
a
rge grou
p
d
ata from t_forcerec
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
Hes
s
Add ha
v
eFree
E
nergyWork to DomainL
i
fetimeWorkload
f
lags
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Ad
d
ed free-
e
nergy
k
ernel performa
n
ce note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
F
i
x in
c
orr
e
ct DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-17
Berk H
e
ss
Re
m
ove
s
p
u
r
ious new
l
in
e
from log file
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix t
o
d
o
s for
updat
e
group
s
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Rem
o
v
e obsolete
m
d
p option ns-type
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add vi
r
tual site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remo
v
e c
u
t-
o
ff schemes fr
o
m
m
anual
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add
o
p
tion r
e
quest 1
D
DD wit
h
1
p
ulse
commit
|
commitdiff
|
tree
2019-09-13
Berk H
e
ss
F
i
x nonbonded-ben
c
h c
o
mpilation issue
commit
|
commitdiff
|
tree
2019-09-13
Be
r
k He
s
s
Add nbnxm ker
n
el
b
enc
h
mark tool
commit
|
commitdiff
|
tree
2019-09-12
B
e
r
k Hess
U
p
d
ated mdp
d
o
cumentation for
g
r
oup scheme remova
l
commit
|
commitdiff
|
tree
2019-09-12
B
e
r
k Hess
Fix
m
aster not c
o
mpiling
commit
|
commitdiff
|
tree
2019-09-12
B
e
r
k
Hess
Enable TPI with the V
e
rlet
cu
t
-of
f
s
cheme
commit
|
commitdiff
|
tree
2019-09-09
Berk He
s
s
Remove incorrec
t
check
w
ith rf-ze
r
o
commit
|
commitdiff
|
tree
2019-09-09
B
erk Hess
Extract C
a
rtesia
n
data from DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hess
Rename DDSetup to DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
B
erk Hess
C
lean up
P
ME rank variabl
e
s
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
efact
o
r
i
nit_
d
omain_dec
o
mpositio
n
()
commit
|
commitdiff
|
tree
2019-09-06
Berk
H
es
s
Extract
getti
n
g of DDRan
k
Set
u
p
commit
|
commitdiff
|
tree
2019-09-06
Ber
k
H
e
ss
Add PP grid info to D
D
R
a
nkSetup
commit
|
commitdiff
|
tree
2019-09-05
Berk
Hess
Ex
t
ract DDRankSetu
p
fro
m
gmx_domde
c
_
c
o
m
m_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Split off
getting
o
f the DD s
e
t
up
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Collect s
e
t
tings for DD in DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
ss
Ext
r
act getting of DDSys
t
em
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Berk
Hess
S
i
mplify handling of
D
D
b
onded di
s
tan
c
es
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move constrain
t
and
b
onded filte
r
in
g
info into DDSy
s
temInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
M
ov
e
update
g
r
oupin
g
to D
D
Syste
m
Info
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Cha
n
ge DD pme for
c
e buffer to std::vector
commit
|
commitdiff
|
tree
2019-09-04
Ber
k
Hess
Initi
a
lize al
l
members of gm
x
_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extr
a
ct DDSystemInfo fro
m
g
m
x_
d
o
m
dec_c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk Hess
Uni
f
y m
a
n
u
al
an
d
auto DD grid choic
e
s
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
R
e
move g
m
x
_dom
d
ec_t from dd_choose_grid()
commit
|
commitdiff
|
tree
2019-09-03
Berk He
s
s
E
x
tact UnitCell
I
n
f
o from gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Fix i
n
c
orrect rv
d
w
o
n GPU with
rvdw<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
B
erk
H
ess
Only us
e
f
s
hift
w
h
e
n need
e
d
commit
|
commitdiff
|
tree
2019-08-26
Berk Hes
s
F
i
x grompp const
r
aints
=
all-angles with con
s
traints
commit
|
commitdiff
|
tree
2019-08-22
B
erk Hess
Fix p
e
rturbed
bonded bug
commit
|
commitdiff
|
tree
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