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Add note for COM removal with position restraints
2019-12-17
Berk Hess
Ad
d
note for COM
remova
l
with
p
osition restr
a
int
s
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Ad
d
c
h
e
ck f
o
r coupl
e
d constraint
s
for CUDA
u
p
d
ate
commit
|
commitdiff
|
tree
2019-12-02
Berk He
s
s
Extract
LINCS
CUDA helper functi
o
ns
commit
|
commitdiff
|
tree
2019-11-29
Be
r
k Hess
Mer
g
e "M
e
rge bran
c
h release-2019 into
re
l
ease-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
Up
d
a
t
e documenati
o
n for NPT
GPU
u
pdate
commit
|
commitdiff
|
tree
2019-11-28
Berk
Hess
Rem
o
ve asse
r
tion failure in
AWH without initial sta
g
e
commit
|
commitdiff
|
tree
2019-11-28
Ber
k
H
e
ss
Fix bug with G
P
U
pressure scaling at no
n
T-scaling
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
B
e
rk Hess
F
i
x issu
e
s with AWH
with pe
r
iodic pull
i
ng
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Quiet
p
db2gmx and use gmx_fatal
commit
|
commitdiff
|
tree
2019-11-19
Berk Hess
Fix bo
n
ded atom communication performance
commit
|
commitdiff
|
tree
2019-11-18
B
e
rk Hess
Fix intermo
l
e
cular interact
i
ons with DD
commit
|
commitdiff
|
tree
2019-11-07
Berk Hes
s
Fix
.
gro la
r
ge box w
r
iting
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
D
epr
e
cated sc-r-pow
e
r=48
commit
|
commitdiff
|
tree
2019-11-01
Berk
H
e
ss
Add haveEwal
d
S
urfaceCont
r
ibuti
o
n to
S
imulati
o
nWorkl
o
ad
commit
|
commitdiff
|
tree
2019-10-31
Berk
H
e
ss
Update GPU up
d
ate restric
t
ions
commit
|
commitdiff
|
tree
2019-10-30
Berk Hes
s
Fix walls wit
h
GPU update
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Add md
r
u
n GPU u
p
d
ate documen
t
ation
commit
|
commitdiff
|
tree
2019-10-29
B
e
rk
Hess
F
i
x Ewald di
p
o
le
c
o
rrection with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
Disable pres
s
ure coupling with GPU update
commit
|
commitdiff
|
tree
2019-10-24
Ber
k
Hess
Add bool useDomainDecompo
s
i
tion
in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add
g
mx_mtop_intera
c
tion_count(
)
commit
|
commitdiff
|
tree
2019-10-24
Berk
Hess
Fix initial
i
zer
s
i
n locality
.
h
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Move
l
oca
l
i
ty
.
h from nbnxm t
o
mdtypes
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Use gmx::Ran
g
e
i
n Nbnxm
g
r
i
dd
i
ng functions
commit
|
commitdiff
|
tree
2019-10-23
Be
r
k
Hess
Fix illegal me
m
ory
a
ccess in FE calculations
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Expa
n
d
d
ocumentat
i
on f
o
r
nbnxn_put_on_grid()
commit
|
commitdiff
|
tree
2019-10-22
B
erk Hess
R
e
quire
-
ei for
essential
d
ynamics
commit
|
commitdiff
|
tree
2019-10-18
Berk H
e
ss
Update
g
rompp cutoff-scheme warnings
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
C
o
nst corr
e
ctness for genhy
d
ro
commit
|
commitdiff
|
tree
2019-10-12
B
e
rk Hess
Add
cl
a
ss F
i
xedCapa
c
ityVe
c
tor
commit
|
commitdiff
|
tree
2019-10-09
Be
r
k Hess
Incre
a
s
e s
p
c min
i
mizati
o
n test tol
e
rance
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
H
e
ss
Fix harmless OpenMP
write race
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix
G
PU atom
d
ata ini
t
timer i
s
sue
commit
|
commitdiff
|
tree
2019-10-09
B
erk
H
e
ss
F
ix random energ
y
and virial with PME
o
n
G
PU
on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
B
er
k
Hess
Make
n
bnxm
a
proper module
commit
|
commitdiff
|
tree
2019-10-08
Berk H
e
ss
Simplify
e
wald
_
LRcor
r
ection() c
a
ll sign
a
ture
commit
|
commitdiff
|
tree
2019-10-04
Be
r
k Hess
Fix
r
andom
e
nerg
y
a
n
d v
i
rial with PME o
n
GPU o
n
a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
B
erk Hess
Fi
x
GPU
a
t
om d
a
ta init timer issue
commit
|
commitdiff
|
tree
2019-10-03
B
erk Hess
Use gmx::Range for iZones in pair
sear
c
h
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix setting
m
axNumCo
l
umn
s
in Nbnxm::GridSet
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
Fix harm
l
ess OpenM
P
write
r
ace
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Us
e
gmx::Ran
g
e in do
m
de
c
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Completely remove c
h
arge
g
roups
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hess
Simplify DD
e
x
c
l
usion count
i
ng
commit
|
commitdiff
|
tree
2019-10-01
Berk He
s
s
Always outp
u
t cor
r
ect
kinetic at last s
t
ep
commit
|
commitdiff
|
tree
2019-09-30
Berk
Hess
Remove charg
e
g
roup
c
ode from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Actually fix gmx wham
w
it
h
angle
ge
o
m
e
t
ries
commit
|
commitdiff
|
tree
2019-09-29
B
e
r
k
Hess
I
ncrease ti
3
p5 minimization test
t
olerance
commit
|
commitdiff
|
tree
2019-09-28
Berk Hess
Fix C
G
minimization with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extra
c
t gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix
location of ang
l
e
i
n
v
s
ite figure
commit
|
commitdiff
|
tree
2019-09-26
Berk Hes
s
Ma
d
e mdrun appending work again
commit
|
commitdiff
|
tree
2019-09-24
Berk Hess
R
e
m
ove obso
l
ete d
d
_ge
t
_ns_ranges()
commit
|
commitdiff
|
tree
2019-09-23
Be
r
k Hess
Li
m
it Zen nbnx
m
kerne
l
c
h
oice to Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Berk Hess
Remove cgs_gl from gm
x
_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
Be
r
k Hess
Fix incorrect shift for
c
e
s for C
M
AP
commit
|
commitdiff
|
tree
2019-09-20
Berk Hess
F
ix DD 1 pulse
c
hecks
w
ithou
t
DLB
commit
|
commitdiff
|
tree
2019-09-19
B
erk
Hess
Remove
bL
o
ca
l
CG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hes
s
R
emove obsol
e
t
e
ma
k
e
_
exclusi
o
ns_zo
n
e
_cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove charge g
r
ou
p
data from t_forc
e
rec
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add have
F
ree
E
nergyWork to Do
m
ainLifet
i
meWorkload fl
a
gs
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added
f
r
e
e
-
energy
k
e
rnel
p
e
r
f
o
rmance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix incorrect DD ndi
m
assertio
n
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Remov
e
s
p
urious newline fro
m
log file
commit
|
commitdiff
|
tree
2019-09-17
Berk
Hess
Fix tod
o
s for update groups
commit
|
commitdiff
|
tree
2019-09-16
Berk
Hess
Remove obsolet
e
mdp option ns-
t
ype
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virtual
site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remo
v
e cut-off schem
e
s from manual
commit
|
commitdiff
|
tree
2019-09-16
Berk
Hess
Add option re
q
u
e
st 1D DD with 1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Fix
n
onbonded-be
n
ch co
m
pila
t
ion issue
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Add nbnxm k
e
r
n
el benchm
a
rk
tool
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Updated mdp documentation for group
s
cheme removal
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Fix
master not compiling
commit
|
commitdiff
|
tree
2019-09-12
Berk He
s
s
Enable TPI with
t
he Verlet cut
-
off scheme
commit
|
commitdiff
|
tree
2019-09-09
B
e
r
k He
s
s
Re
m
ove
i
ncorrect
c
h
e
ck
with
r
f-zero
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
E
x
t
ract Cartesian d
a
ta
f
r
om DD
R
ankSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
s
s
Rename DDSetup
to
DD
G
ridSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hes
s
C
l
e
a
n up PME ra
n
k variables
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
Re
f
act
o
r
i
ni
t
_doma
i
n_decomp
o
sit
i
on()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
E
x
t
r
act getting of DD
R
ankSetup
commit
|
commitdiff
|
tree
2019-09-06
Ber
k
H
e
ss
Add PP grid info to DDRankSetu
p
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Extrac
t
DDRankSetup fro
m
g
mx_domdec_comm_
t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hes
s
Split off getting of the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hes
s
Collect se
t
t
ings for DD in DDSett
i
ngs
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk Hess
Ex
t
ract gett
i
ng of DDS
y
stemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
e
ss
Simp
l
ify handl
i
ng of DD b
o
n
d
ed di
s
tances
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
M
o
v
e
co
n
s
t
rai
n
t
a
n
d
bonded
f
ilte
r
ing i
n
fo
i
nt
o
DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update grouping to DD
S
y
stemInfo
commit
|
commitdiff
|
tree
2019-09-04
B
er
k
H
e
ss
Change DD pme f
o
rce buffer
to
s
td::ve
c
tor
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k He
s
s
I
n
itia
l
iz
e
all memb
e
rs of gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extract DDSyst
e
mInfo from gmx_
d
omdec_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-03
Berk
H
es
s
Unify manual and auto DD gr
i
d
c
hoices
commit
|
commitdiff
|
tree
2019-09-03
B
er
k
Hess
Remo
v
e gmx_d
o
mdec_t from d
d
_choose_grid()
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk Hess
E
x
tact UnitCellInfo from gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Fix
inc
o
rrect
r
vdw
o
n GPU
with
rvdw<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
B
e
rk Hess
Only use fsh
i
f
t
w
h
e
n needed
commit
|
commitdiff
|
tree
2019-08-26
Berk Hess
Fix
g
r
om
p
p
c
onstr
a
i
n
t
s
=a
l
l-an
g
le
s
with constrain
t
s
commit
|
commitdiff
|
tree
2019-08-22
B
e
rk Hess
Fix pe
r
turbe
d
bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
M
erge two dihedral fu
n
c
t
i
on
s
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
Hess
Use shi
f
tForces in ForceOu
p
uts
commit
|
commitdiff
|
tree
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