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Update rules for release-2021.
2020-11-11
Berk Hess
Update gmx msd do
c
ume
n
t
ation
commit
|
commitdiff
|
tree
2020-11-10
Berk He
s
s
Fix dHdl and
f
oreign e
n
ergy clearing
a
t checkpo
i
nting
commit
|
commitdiff
|
tree
2020-11-09
Ber
k
Hess
Move
implementation to
cpp file
commit
|
commitdiff
|
tree
2020-11-05
Berk H
e
ss
D
isable MTS wit
h
SD inte
g
rator
commit
|
commitdiff
|
tree
2020-11-05
Berk Hess
Copy
posit
i
on restraint param
e
ters with MTS
commit
|
commitdiff
|
tree
2020-10-28
Berk Hes
s
Correct AWH initi
a
l
his
t
ogram size
commit
|
commitdiff
|
tree
2020-10-27
Berk Hes
s
Refactor MTS preprocessing and checkin
g
commit
|
commitdiff
|
tree
2020-10-21
Ber
k
H
e
s
s
Fix
pull code bug
w
ith DD
a
n
d
a
t
om
s
ets
commit
|
commitdiff
|
tree
2020-10-09
Berk He
s
s
Add MTS support
f
or pull
a
nd
AWH
commit
|
commitdiff
|
tree
2020-10-05
Berk He
s
s
Rem
o
ve incorr
e
ct cycle suppression
commit
|
commitdiff
|
tree
2020-10-01
Berk
H
e
s
s
Move computeSlowForces int
o
stepWork
commit
|
commitdiff
|
tree
2020-09-30
Berk H
e
s
s
Move computeSlo
w
F
orces into stepWork
commit
|
commitdiff
|
tree
2020-09-28
Berk Hess
Fi
x
d
ispe
r
sion correc
t
ion table g
e
neration
commit
|
commitdiff
|
tree
2020-09-25
Be
r
k Hess
F
ix
g
r
o
mpp group han
d
ling with frozen syste
m
commit
|
commitdiff
|
tree
2020-09-18
Berk Hess
Remove cutoff_scheme from t_forcere
c
and i
n
teract
i
on_const_t
commit
|
commitdiff
|
tree
2020-09-17
Berk
H
ess
Move bNo
n
bonded fla
g
from t_forc
e
rec
to
SimulationWorkload
commit
|
commitdiff
|
tree
2020-09-16
Berk Hess
Remove un
n
ecessary condition in DD force buffer resizin
g
commit
|
commitdiff
|
tree
2020-09-15
B
e
r
k
He
s
s
Only extend Ewald table w
h
en necessary
commit
|
commitdiff
|
tree
2020-09-15
B
e
rk Hess
Fix tas
k
a
s
s
i
gnment wit
h
m
u
l
t
i
r
uns
commit
|
commitdiff
|
tree
2020-09-13
B
e
r
k Hess
D
ecoupl
e
n
s
ttcouple a
n
d nstpcouple from nstlist
commit
|
commitdiff
|
tree
2020-09-10
Berk Hess
Add angles to ListedForces sele
c
tions
commit
|
commitdiff
|
tree
2020-09-10
Ber
k
Hess
Fix memor
y
corruption with string
s
i
n
grompp
commit
|
commitdiff
|
tree
2020-09-02
Berk Hess
M
o
ve listed and wall fo
r
ces ou
t
of do_force_lowlevel()
commit
|
commitdiff
|
tree
2020-09-02
B
e
rk H
e
s
s
Enabl
e
s
p
l
i
ttin
g
of listed interaction calcu
l
ation
commit
|
commitdiff
|
tree
2020-08-28
Berk
H
e
ss
Add SIMD
v
ersio
n
of har
m
onic b
o
nds
commit
|
commitdiff
|
tree
2020-08-27
B
e
r
k Hess
Add F
o
r
ceBuffers class
commit
|
commitdiff
|
tree
2020-08-14
Berk
He
s
s
Add S
I
M
D bonded te
s
ts and im
p
rove
SIMD angle
s
(
)
commit
|
commitdiff
|
tree
2020-08-13
Berk Hess
Add new FEP pertur
b
ation check functions
commit
|
commitdiff
|
tree
2020-08-12
Ber
k
Hess
Fix virtual si
t
e vsiten indexing bug
commit
|
commitdiff
|
tree
2020-08-07
Berk He
s
s
Add
accumula
t
ion checks to ForeignLambdaT
e
rms
commit
|
commitdiff
|
tree
2020-07-31
B
e
rk Hess
Move foreign pot
e
ntial energy accumul
a
tion
commit
|
commitdiff
|
tree
2020-07-06
Berk H
e
ss
M
o
ve foreign
p
otentia
l
ene
r
gy accumu
l
ation
commit
|
commitdiff
|
tree
2020-06-26
Berk Hess
Move dis
p
e
rsion cor
r
ection call to do_force(
)
commit
|
commitdiff
|
tree
2020-06-24
Berk Hess
Add
c
l
a
ss
L
istedForces
commit
|
commitdiff
|
tree
2020-06-24
Berk Hess
Change
g
rompp disr
e
s cost to
line
a
r
commit
|
commitdiff
|
tree
2020-06-23
Berk
Hess
A
dd virtu
a
l site
with one con
s
t
r
uc
t
ing
at
o
m
commit
|
commitdiff
|
tree
2020-06-22
Berk
Hess
Fix t
p
xio function type
update table
commit
|
commitdiff
|
tree
2020-06-22
B
erk Hes
s
Move soft-core p
a
rameter
s
to in
t
eraction_const_t
commit
|
commitdiff
|
tree
2020-06-18
B
e
rk He
s
s
Conver
t
t_
f
orcetable to C++
commit
|
commitdiff
|
tree
2020-06-05
Berk Hess
Remo
v
e
COM
f
rom SET
T
LE
commit
|
commitdiff
|
tree
2020-06-03
B
erk He
s
s
Fix missing
P
B
C in SHA
K
E
commit
|
commitdiff
|
tree
2020-06-03
B
e
rk
H
es
s
Turn SettleData into a class
commit
|
commitdiff
|
tree
2020-05-20
B
e
r
k H
e
ss
Remove t_
m
datoms from Nbnxm setAtomPrope
r
ties()
commit
|
commitdiff
|
tree
2020-05-19
Berk Hes
s
Refact
o
r
print_miss
i
n
g
_
i
nteractions(
)
commit
|
commitdiff
|
tree
2020-05-14
Be
r
k
Hess
Ext
r
act postProcessForceW
i
thShiftForces()
commit
|
commitdiff
|
tree
2020-05-12
Berk Hess
Ex
t
ract helper
f
orc
e
buffers t
o
a separate cl
a
ss
commit
|
commitdiff
|
tree
2020-05-12
B
e
rk He
s
s
R
ef
a
ctor
virtual site
inter
f
ace
commit
|
commitdiff
|
tree
2020-05-07
B
erk Hess
Avoi
d
warning during
PME tuning
commit
|
commitdiff
|
tree
2020-04-06
Berk Hess
Move force
b
u
ffer resiz
i
ng
t
o mdset
u
p
commit
|
commitdiff
|
tree
2020-03-20
B
e
r
k
H
ess
Rename
c
lass Gr
i
d
to BiasGrid in AWH module
commit
|
commitdiff
|
tree
2020-03-19
Ber
k
He
s
s
Simpl
i
f
y
f
inish
_
update()
commit
|
commitdiff
|
tree
2020-03-19
B
erk Hess
Remov
e
at_
s
tart
f
rom t_graph
commit
|
commitdiff
|
tree
2020-03-18
Berk He
s
s
Remove
u
s
e
of graph
in do_fo
r
ce()
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
U
se Wh
o
leMoleculeTrans
f
o
rm for o
r
ires and e
p
silon-su
r
face
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
Add WholeMoleculeTr
a
nsfor
m
clas
s
commit
|
commitdiff
|
tree
2020-03-17
Berk Hess
Co
n
vert t_graph to C++
commit
|
commitdiff
|
tree
2020-03-17
B
e
r
k He
s
s
Di
s
abl
e
Ewald dipole
c
orrection
w
ithout DD
commit
|
commitdiff
|
tree
2020-03-13
Berk Hess
Add
t
e
sts for Ewald surface ter
m
s
commit
|
commitdiff
|
tree
2020-03-11
Ber
k
Hess
Add
tests for graph
commit
|
commitdiff
|
tree
2020-03-10
Be
r
k Hess
F
ix type in ra
n
ge and ad
d
tests
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make shak
e
wo
r
k w
i
thout graph
commit
|
commitdiff
|
tree
2020-03-05
B
er
k
Hess
Add I
n
teractio
n
Definit
i
ons
commit
|
commitdiff
|
tree
2020-03-02
Ber
k
Hess
Fix center of mass
m
otion removal with
frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix grompp
unb
o
u
n
d atom c
h
ec
k
commit
|
commitdiff
|
tree
2020-03-02
Berk H
e
s
s
Fix nrdf with partial COMM removal
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
F
ix too sm
a
ll pairl
i
st buffer on In
t
e
l GPUs
commit
|
commitdiff
|
tree
2020-02-21
Berk Hess
Add fatal
error when
multisi
m
r
u
ns
sharing state
h
ave
.
.
.
commit
|
commitdiff
|
tree
2020-02-15
Berk
H
ess
Remove 1 pul
s
e DD reque
s
t
commit
|
commitdiff
|
tree
2020-02-05
Berk
H
ess
Actually fix PME forces wit
h
FE without p
e
rt
u
rbe
d
q/
L
J
commit
|
commitdiff
|
tree
2020-02-04
Berk Hess
Actual
l
y
fix
P
ME forces with FE without
perturbed q/LJ
commit
|
commitdiff
|
tree
2020-01-23
B
e
rk Hess
F
i
x DD rank count prime check
commit
|
commitdiff
|
tree
2020-01-22
B
erk Hess
Mi
n
or cleanup in co
n
stra
i
nt and shellfc code
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Fi
x
illegal me
m
ory access in PME c
o
mm
u
nication
commit
|
commitdiff
|
tree
2020-01-22
Berk H
e
s
s
C
l
arify C
O
MM/po
s
res grompp note
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use
A
rrayRef(WithPadding) in
c
onstraint
code
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
U
s
e
std::vec
t
or i
n
shellfc
commit
|
commitdiff
|
tree
2020-01-17
B
e
rk Hess
Add
c
heck for
s
hells and GPU
u
pdate
commit
|
commitdiff
|
tree
2020-01-16
Be
r
k Hes
s
Correct fixed
r
edmine
i
ssue
i
d fro
m
3297 to 3
2
96
commit
|
commitdiff
|
tree
2020-01-15
Berk
Hess
Fi
x
multisim with parallel s
i
mulation
commit
|
commitdiff
|
tree
2020-01-13
Berk H
e
ss
Avoid unnece
s
sary exclusion generation in DD
commit
|
commitdiff
|
tree
2019-12-22
Berk Hess
Use
ListOfLists for atom to co
n
st
r
aint map
p
ing
commit
|
commitdiff
|
tree
2019-12-22
B
e
r
k
Hes
s
Move nr
_
n
o
n
perturbed out
of
t
_ilis
t
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Expand L
i
stOfLists push
B
ack() func
t
ionalit
y
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Rem
o
ve e
x
clusions from
t
_
topolo
g
y
commit
|
commitdiff
|
tree
2019-12-19
B
er
k
Hess
Fix mdrun a
p
pending invalidating en
e
rgy
f
iles
commit
|
commitdiff
|
tree
2019-12-18
B
erk Hess
Change gro
m
pp decoupling SD warning to note
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
A
d
d note for CO
M
removal with position r
e
st
r
aint
s
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Us
e
ListO
f
Lis
t
s in gmx_mtop_t and g
m
x_lo
c
alt
o
p_t
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Fix i
s
sues in ListOf
L
ists
commit
|
commitdiff
|
tree
2019-12-12
B
e
rk Hes
s
Add class Li
s
tOfL
i
st
s
commit
|
commitdiff
|
tree
2019-12-02
B
erk Hess
Add check for c
o
upled cons
t
raint
s
for CUDA update
commit
|
commitdiff
|
tree
2019-12-02
Berk He
s
s
Extract LINCS CUDA helper
fun
c
tio
n
s
commit
|
commitdiff
|
tree
2019-11-29
Berk Hess
Merge "M
e
r
ge
b
ranch r
e
lease-2019
i
nt
o
release-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
B
e
rk Hess
Update
documena
t
ion for NPT G
P
U update
commit
|
commitdiff
|
tree
2019-11-28
B
e
rk Hess
Remove ass
e
rtion
fail
u
re i
n
AWH
w
i
thou
t
initi
a
l stage
commit
|
commitdiff
|
tree
2019-11-28
B
erk Hess
F
i
x bug
w
ith
GPU pressur
e
scalin
g
at non T-scaling
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Berk Hes
s
Fix issues
w
i
t
h AWH with
p
e
r
iodi
c
pulling
commit
|
commitdiff
|
tree
2019-11-20
Ber
k
H
ess
Q
u
ie
t
pdb2gm
x
and use
g
mx_fata
l
commit
|
commitdiff
|
tree
2019-11-19
Berk Hess
Fix bonde
d
a
t
o
m co
m
munication perfor
m
an
c
e
commit
|
commitdiff
|
tree
2019-11-18
Berk Hess
Fix i
n
ter
m
olecular i
n
te
r
actions with DD
commit
|
commitdiff
|
tree
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