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Set buffers appropriately so .xpm files can be read.
2020-03-17
Berk Hess
Disable Ewa
l
d dipole
correction without DD
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk He
s
s
Fix center of
m
as
s
motion
removal with frozen
a
t
oms
commit
|
commitdiff
|
tree
2020-03-02
Berk
H
ess
Fix gr
o
mpp
u
nbound atom ch
e
ck
commit
|
commitdiff
|
tree
2020-03-02
Berk Hes
s
Fix nrdf
w
i
t
h
p
a
rtial COMM removal
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk
Hess
F
ix
too s
m
all pairl
i
st bu
f
fer on Intel
G
PUs
commit
|
commitdiff
|
tree
2020-02-21
Berk H
e
ss
Ad
d
fatal error when multisim runs sharing
s
tate
hav
e
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Berk Hess
Actually
fix PME forces with FE
w
ith
o
ut p
e
rturbed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Berk Hess
A
ctual
l
y fix PME
forces with FE with
o
ut pe
r
t
urbe
d
q/LJ
commit
|
commitdiff
|
tree
2020-01-23
Be
r
k Hess
Fix DD rank count
p
rime
c
heck
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Fix illegal me
m
ory access in P
M
E communication
commit
|
commitdiff
|
tree
2020-01-22
B
erk Hess
Clarify COMM/pos
r
e
s
grom
p
p note
commit
|
commitdiff
|
tree
2020-01-17
Berk Hess
Add ch
e
ck
f
or shells and GPU u
p
dat
e
commit
|
commitdiff
|
tree
2020-01-16
Berk
Hess
Correct f
i
xed re
d
min
e
issue id from
3297 to 3
2
96
commit
|
commitdiff
|
tree
2020-01-15
Berk H
e
ss
Fix m
u
ltisim with paral
l
el simulatio
n
commit
|
commitdiff
|
tree
2019-12-19
Berk He
s
s
Fix mdr
u
n appendi
n
g invali
d
ating energy files
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
Change grompp
decoupling SD w
a
rning to note
commit
|
commitdiff
|
tree
2019-12-17
B
erk
H
e
ss
A
d
d
note for C
O
M
removal
w
ith p
o
sition restr
a
in
t
s
commit
|
commitdiff
|
tree
2019-12-02
Ber
k
H
e
ss
Add ch
e
ck for coupled co
n
straint
s
f
or CUDA update
commit
|
commitdiff
|
tree
2019-12-02
B
erk Hess
E
x
tract
LINCS
C
U
D
A
helper
functions
commit
|
commitdiff
|
tree
2019-11-29
Berk
Hess
Merge
"Merge branch release-2019 into
release-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
U
pdate
documenati
o
n for NPT GPU up
d
ate
commit
|
commitdiff
|
tree
2019-11-28
Berk H
e
ss
Rem
o
v
e assertion f
a
ilure in AWH witho
u
t ini
t
ial stage
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
F
ix bug with G
P
U pre
s
s
u
re scaling at non T-scalin
g
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
B
e
rk H
e
ss
F
ix
i
ssues with AW
H
with pe
r
iodic pulling
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Quiet pdb2gmx
a
nd use
g
mx_fatal
commit
|
commitdiff
|
tree
2019-11-19
Berk H
e
ss
Fix bonded atom commun
i
cation pe
r
for
m
ance
commit
|
commitdiff
|
tree
2019-11-18
Berk Hess
Fix intermolecular interactions with D
D
commit
|
commitdiff
|
tree
2019-11-07
Berk Hess
Fix
.
gro large box wri
t
ing
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Deprecated sc-r-p
o
wer=
4
8
commit
|
commitdiff
|
tree
2019-11-01
Berk Hess
A
dd h
a
veEwald
S
urfaceContribution to S
i
mulationWorkload
commit
|
commitdiff
|
tree
2019-10-31
Berk He
s
s
Update G
P
U upd
a
te
r
estrictions
commit
|
commitdiff
|
tree
2019-10-30
B
erk Hess
Fix
walls
with GPU update
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
A
d
d mdrun G
P
U
update documentation
commit
|
commitdiff
|
tree
2019-10-29
Be
r
k Hess
F
i
x
Ewald
d
i
pole correction wit
h
GPU update
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Di
s
able pressur
e
coup
l
in
g
with GPU update
commit
|
commitdiff
|
tree
2019-10-24
Berk Hes
s
Add bool useDomain
D
ecomposition in mdrunn
e
r
commit
|
commitdiff
|
tree
2019-10-24
B
e
rk Hess
Add gmx_mtop_intera
c
tion_count()
commit
|
commitdiff
|
tree
2019-10-24
Be
r
k Hes
s
Fix
i
nitial
i
zers
i
n local
i
ty
.
h
commit
|
commitdiff
|
tree
2019-10-23
Ber
k
Hess
M
o
ve locality
.
h from nbnxm to md
t
ype
s
commit
|
commitdiff
|
tree
2019-10-23
Berk H
e
ss
Use
g
mx::Range in Nbnxm grid
d
ing
f
u
n
ctions
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
F
i
x illegal
memory access i
n
FE cal
c
ulati
o
ns
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Exp
a
n
d
d
ocume
n
tation for nbnx
n
_p
u
t
_
o
n_grid()
commit
|
commitdiff
|
tree
2019-10-22
Berk Hess
Require -ei fo
r
essent
i
al dynam
i
cs
commit
|
commitdiff
|
tree
2019-10-18
Be
r
k Hess
Update gr
o
mpp
c
utoff-scheme wa
r
ni
n
gs
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Const correc
t
n
e
ss for
g
enh
y
dro
commit
|
commitdiff
|
tree
2019-10-12
Berk Hess
Add class F
i
xedCapac
i
tyVector
commit
|
commitdiff
|
tree
2019-10-09
Berk H
e
s
s
Incr
e
ase spc
minimization
t
est toler
a
nc
e
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fi
x
h
a
rm
l
ess Op
e
nMP write r
a
c
e
commit
|
commitdiff
|
tree
2019-10-09
Be
r
k Hess
Fi
x
GPU ato
m
da
t
a init timer
issue
commit
|
commitdiff
|
tree
2019-10-09
B
er
k
Hess
Fix ran
d
om energy
and virial w
i
th PM
E
on GPU on a
PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Be
r
k Hess
M
a
k
e nbnxm a
p
ro
p
er module
commit
|
commitdiff
|
tree
2019-10-08
B
e
rk Hess
Simpli
f
y
ewald_LRcorre
c
t
ion()
c
all signat
u
r
e
commit
|
commitdiff
|
tree
2019-10-04
Berk Hess
Fix random energ
y
and virial with
P
M
E o
n
GPU
o
n a
P
ME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix GPU
a
to
m
data init timer issue
commit
|
commitdiff
|
tree
2019-10-03
Berk
Hess
Us
e
gmx:
:
Ra
n
ge for
i
Zon
e
s
i
n pair search
commit
|
commitdiff
|
tree
2019-10-03
Be
r
k
H
e
ss
Fix se
t
tin
g
max
N
umCo
l
u
m
n
s in Nbnxm::GridSet
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
Fix harm
l
ess O
p
enMP write ra
c
e
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Us
e
gm
x
:
:
Range i
n
domdec
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hess
C
o
mpletely remove
charge
g
roups
commit
|
commitdiff
|
tree
2019-10-01
B
e
r
k
Hess
Simplify DD exc
l
u
s
ion counting
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
Always outpu
t
co
r
rect
ki
n
etic at last
s
tep
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
R
emove charge group code f
r
o
m
f
o
rcer
e
c
commit
|
commitdiff
|
tree
2019-09-30
B
erk Hess
Actually fix gmx
w
ham wi
t
h
a
ngle geom
e
tries
commit
|
commitdiff
|
tree
2019-09-29
Berk H
e
ss
Inc
r
ease ti3p5 mini
m
i
z
ation
t
es
t
tolera
n
ce
commit
|
commitdiff
|
tree
2019-09-28
Berk Hess
Fix CG mini
m
ization with D
D
commit
|
commitdiff
|
tree
2019-09-27
Berk
H
es
s
Extract gmx::Ra
n
ge
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Fix locat
i
on of angle in vsite
f
igure
commit
|
commitdiff
|
tree
2019-09-26
Be
r
k Hess
Made mdrun appending work again
commit
|
commitdiff
|
tree
2019-09-24
Berk Hess
Remove obsolete dd_get
_
ns_ranges()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
Limit Zen nbnx
m
kerne
l
choice
t
o Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Berk
H
ess
R
emov
e
cgs_
g
l
f
r
o
m gmx_domdec_co
m
m_t
commit
|
commitdiff
|
tree
2019-09-21
Berk Hess
Fi
x
incorrect shift
forces fo
r
CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk Hess
Fix DD 1 pulse c
h
e
c
ks
w
ithout D
L
B
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remov
e
bLo
c
alCG from
D
D
c
o
de
commit
|
commitdiff
|
tree
2019-09-19
Berk H
e
ss
Rem
o
ve ob
s
olete make_exclusions_zon
e
_cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
e
s
s
Remov
e
charge grou
p
data from t_f
o
rcerec
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add haveFreeEne
r
gy
W
ork
to
Do
m
ainLifetimeWorkl
o
ad fla
g
s
commit
|
commitdiff
|
tree
2019-09-18
B
er
k
H
ess
Added free-energy
k
er
n
el p
e
rfo
r
mance note
commit
|
commitdiff
|
tree
2019-09-18
Berk
H
e
s
s
Fix
i
ncor
r
e
c
t
DD ndim
assertio
n
commit
|
commitdiff
|
tree
2019-09-17
Berk
H
ess
Remove spurious newline
from log file
commit
|
commitdiff
|
tree
2019-09-17
Berk H
e
ss
F
i
x t
o
dos for update gr
o
ups
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove
obs
o
l
e
te mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virt
u
al si
t
e type 2
F
D
commit
|
commitdiff
|
tree
2019-09-16
B
erk Hess
Remove cut-off sc
h
e
mes f
r
om manua
l
commit
|
commitdiff
|
tree
2019-09-16
Berk Hes
s
Add
option r
e
quest 1D DD wi
t
h 1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk He
s
s
Fix no
n
bonded-benc
h
c
om
p
i
l
a
tion
iss
u
e
commit
|
commitdiff
|
tree
2019-09-13
B
erk Hes
s
Add nbnxm kern
e
l benchmark tool
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Updated mdp documentation for
group sche
m
e
r
em
o
val
commit
|
commitdiff
|
tree
2019-09-12
B
erk Hess
Fix master not compiling
commit
|
commitdiff
|
tree
2019-09-12
Berk
Hess
Enable TPI with the
Verl
e
t cut-off
s
cheme
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k
H
es
s
Remo
v
e incorrect
che
c
k with r
f
-
z
ero
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
Ext
r
act C
a
rte
s
ian data f
r
o
m
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Re
n
ame DDSetup
to D
D
Grid
S
e
tup
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk Hess
Clean
u
p PME rank
v
a
riables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
e
f
a
c
tor
ini
t
_
d
om
a
in_decompos
i
tion()
commit
|
commitdiff
|
tree
2019-09-06
Ber
k
Hess
Extra
c
t getting
o
f DDRa
n
kSetup
commit
|
commitdiff
|
tree
2019-09-06
B
erk Hess
Add PP gri
d
info
t
o
DDRankS
e
tup
commit
|
commitdiff
|
tree
2019-09-05
Ber
k
Hess
Extract
DDRank
S
etup fr
o
m
g
m
x_domdec_com
m
_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Spl
i
t off getting
o
f the DD setup
commit
|
commitdiff
|
tree
2019-09-04
B
erk Hess
Col
l
ect sett
i
ngs
for DD
i
n DDSetting
s
commit
|
commitdiff
|
tree
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