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Disable pressure coupling with GPU update
2019-10-29
Be
r
k
Hes
s
Disable
pressure coupling with GPU
update
commit
|
commitdiff
|
tree
2019-10-24
Berk H
e
ss
Add boo
l
useDom
a
inDecomposition in
mdrunne
r
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add gmx_mtop
_
i
nter
a
ction_count()
commit
|
commitdiff
|
tree
2019-10-24
Berk H
e
ss
Fix initializers
i
n l
o
c
a
lity
.
h
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Move loc
a
li
t
y
.
h
from nbnxm to mdtypes
commit
|
commitdiff
|
tree
2019-10-23
B
erk Hess
Use gmx::R
a
nge in Nbnxm gridding f
u
n
c
tions
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Fix illegal memory
a
ccess in FE calc
u
l
ations
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Expand docum
e
ntati
o
n for nb
n
xn_put_on_
g
rid()
commit
|
commitdiff
|
tree
2019-10-22
Berk He
s
s
Re
q
uire -ei
f
or essential
d
y
nami
c
s
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Update
g
rompp cutoff-s
c
heme warnings
commit
|
commitdiff
|
tree
2019-10-15
B
e
rk Hess
Const co
r
rec
t
ness for gen
h
ydro
commit
|
commitdiff
|
tree
2019-10-12
Berk
Hess
Add
c
lass Fix
e
dCa
p
acityV
e
ctor
commit
|
commitdiff
|
tree
2019-10-09
Be
r
k Hes
s
I
ncrea
s
e spc mini
m
iz
a
tion
t
est
t
olerance
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix harm
l
ess OpenMP
w
r
ite race
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
Hess
Fix
G
P
U
atom data ini
t
tim
e
r
i
ssue
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
F
ix
random e
n
ergy an
d
virial with PME on
G
PU o
n
a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Berk Hess
Make
n
b
nxm a p
r
ope
r
module
commit
|
commitdiff
|
tree
2019-10-08
Berk Hess
Simplify ew
a
ld
_
LRc
o
r
rection() c
a
ll
s
ignature
commit
|
commitdiff
|
tree
2019-10-04
B
e
rk He
s
s
Fix rand
o
m energy and viria
l
with PME on GPU on
a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Ber
k
Hess
Fi
x
GPU ato
m
data init time
r
issue
commit
|
commitdiff
|
tree
2019-10-03
Be
r
k
H
e
ss
Use gmx::
R
a
nge for iZones in pair
s
ear
c
h
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix setting maxNumColu
m
ns
i
n Nbnx
m
:
:GridSet
commit
|
commitdiff
|
tree
2019-10-02
B
e
rk Hess
Fix harmless OpenM
P
write
r
ace
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
Use gmx::R
a
nge i
n
domdec
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hes
s
C
o
mpletely rem
o
ve c
h
arge gro
u
ps
commit
|
commitdiff
|
tree
2019-10-01
B
erk Hess
Simp
l
ify
D
D exclu
s
ion
c
o
u
nt
i
n
g
commit
|
commitdiff
|
tree
2019-10-01
B
erk He
s
s
A
lways output corr
e
c
t
kinetic at last step
commit
|
commitdiff
|
tree
2019-09-30
B
e
rk Hess
Remove charge group
code from fo
r
c
ere
c
commit
|
commitdiff
|
tree
2019-09-30
Ber
k
H
ess
Act
u
ally
fix g
m
x wh
a
m wi
t
h angle ge
o
met
r
ies
commit
|
commitdiff
|
tree
2019-09-29
Berk Hess
In
c
r
ea
s
e ti3p5 mi
n
imization te
s
t toleranc
e
commit
|
commitdiff
|
tree
2019-09-28
Berk
H
ess
Fi
x
C
G min
i
mization
w
ith
DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extract gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk
H
ess
Fix lo
c
ation of
ang
l
e
i
n
vsite
f
igure
commit
|
commitdiff
|
tree
2019-09-26
Berk
H
e
s
s
Made m
d
run
a
pp
e
n
d
ing work again
commit
|
commitdiff
|
tree
2019-09-24
Berk Hes
s
Remove obsolete d
d
_get_ns_range
s
(
)
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
L
i
mit Zen nbn
x
m kernel ch
o
ice to Z
e
n 1
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
Hess
R
e
m
o
ve c
g
s
_
g
l from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
B
erk H
e
s
s
Fix incorrect
s
hift forces for CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk H
e
ss
Fix DD 1
p
ul
s
e chec
k
s without DLB
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
ess
Remove bL
o
calC
G
from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
Remov
e
obso
l
ete m
a
k
e_exclusions_
z
one_cg()
commit
|
commitdiff
|
tree
2019-09-19
Be
r
k Hess
Remove char
g
e g
r
ou
p
dat
a
from t_fo
r
cerec
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
ess
Add haveFreeEn
e
rgyW
o
rk to Doma
i
nLifetimeWo
r
kl
o
ad
f
lags
commit
|
commitdiff
|
tree
2019-09-18
B
erk Hess
Added f
r
e
e
-en
e
r
g
y ker
n
el performance no
t
e
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix incor
r
e
c
t DD ndim
assertion
commit
|
commitdiff
|
tree
2019-09-17
Berk H
e
ss
Remove sp
u
r
i
ous newli
n
e from l
o
g file
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
F
i
x todos for up
d
ate
g
roups
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove
o
bsolete mdp optio
n
ns-type
commit
|
commitdiff
|
tree
2019-09-16
B
erk
Hess
Add virt
u
al site
t
yp
e
2F
D
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Re
m
o
v
e cut-off
sche
m
e
s
from
m
a
nual
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
ss
Add
o
p
tion request 1D DD with 1
p
ulse
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Fix nonbo
n
ded
-
benc
h
compilation i
s
sue
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Add nbn
x
m ker
n
el benchmark tool
commit
|
commitdiff
|
tree
2019-09-12
B
er
k
Hess
Updated mdp do
c
umentation f
o
r group sc
h
eme rem
o
val
commit
|
commitdiff
|
tree
2019-09-12
Ber
k
Hess
Fix mas
t
er not compilin
g
commit
|
commitdiff
|
tree
2019-09-12
Berk H
e
ss
Enable TPI with the Verlet cut-o
f
f scheme
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Remove in
c
orr
e
ct check wi
t
h rf-
z
er
o
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
E
xtract Cart
e
s
i
a
n data fro
m
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk
Hess
R
ename DDSetup to DD
G
r
idSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
H
e
s
s
Clean up
PME rank variables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
Ref
a
cto
r
init_domain_decomposi
t
i
o
n()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
E
x
tract getting of DD
R
ankS
e
tup
commit
|
commitdiff
|
tree
2019-09-06
Be
r
k Hess
Add PP grid i
n
fo to DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Berk He
s
s
E
xtra
c
t
DDRankSetup from gmx_domdec_comm
_
t
commit
|
commitdiff
|
tree
2019-09-05
Berk H
e
ss
Spli
t
off getting of the DD setu
p
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
C
o
llec
t
settings for
D
D in DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
ss
Ext
r
a
ct
g
etting of DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
S
i
mplify handling of DD bonded dista
n
ces
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hes
s
M
o
ve const
r
ain
t
and bonded
f
il
t
ering info into
D
DSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update gro
u
ping to DDSystemI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Change
DD pme
f
orce buffe
r
t
o
s
td::
v
e
ctor
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Initia
l
ize all members of gmx_d
o
mdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extract
DDSystemInf
o
f
rom gmx_do
m
dec_comm_
t
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk Hess
Unify
m
anual and auto
DD grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Remove
gmx_
d
omde
c
_
t from dd_choose_grid()
commit
|
commitdiff
|
tree
2019-09-03
Berk Hes
s
E
xtact UnitCellInfo
from
g
mx_d
o
mdec_t
commit
|
commitdiff
|
tree
2019-09-02
Ber
k
Hess
Fix inco
r
r
ec
t
r
vd
w
on G
P
U
with rvd
w
<rco
u
l
omb
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Only
use fshift
w
h
en
n
eeded
commit
|
commitdiff
|
tree
2019-08-26
Berk
H
ess
Fix gr
o
mpp constraints=all-angl
e
s with constraint
s
commit
|
commitdiff
|
tree
2019-08-22
Be
r
k
H
ess
Fix per
t
urbed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge two dihed
r
a
l
func
t
ions
commit
|
commitdiff
|
tree
2019-08-20
Berk Hes
s
Use shiftForces in ForceOup
u
ts
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded v
i
rial computat
i
o
n
conditional
commit
|
commitdiff
|
tree
2019-08-20
Berk Hes
s
Fix
m
issin
g
bond
e
d
forces with CU
D
A GPUs
a
nd DD
commit
|
commitdiff
|
tree
2019-08-15
B
e
rk
Hes
s
Te
m
plate
bond
e
d inte
r
actions on k
e
rnel
flav
o
r
commit
|
commitdiff
|
tree
2019-08-09
Be
r
k
H
ess
Move bonded function table
i
n
t
o bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
B
e
rk
Hess
SIM
D
acceleration for
F_F
O
URDI
H
S and F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Add F
o
rceWithShiftForces cl
a
ss
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fi
x
latex f
o
rmula in
reference manual
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Make box const in do_force()
commit
|
commitdiff
|
tree
2019-08-05
Be
r
k
Hess
C
h
ange F
o
rc
e
Outpu
t
s to a class
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Re
m
o
v
e sem
i
colon from GPU TE
R
M macros
commit
|
commitdiff
|
tree
2019-08-02
B
e
rk Hess
Made gmx
d
i
s
re work wit
h
non-c
o
nsecutive
l
y labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remove a pointer in t
_
forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
F
ix
n
b
n
xm GPU
m
emory
r
ese
r
v
ation issue
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk He
s
s
Remove unused CGL
O
_IN
I
T
I
ALIZATION
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remov
e
vcm rem
o
val from com
p
ute
_
g
lobals()
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk Hess
A
d
d g
r
ompp warning with
use
of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
B
e
r
k
Hes
s
R
e
move need
f
or GRO
M
OS FF in test
commit
|
commitdiff
|
tree
2019-07-30
Berk
H
e
s
s
Us
e
i
nvsqrt and cbrt in free energy
k
e
rnel
commit
|
commitdiff
|
tree
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