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Clean up make_at2con
2018-06-06
Berk Hess
Clean up make_
a
t2con
commit
|
commitdiff
|
tree
2018-06-05
Berk H
e
ss
Make nbnxn_g
r
id_t counts and
s
izes arra
y
s
commit
|
commitdiff
|
tree
2018-05-24
Ber
k
Hess
Fix grompp bu
g
with
bl
o
cks
of same molecul
e
s
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
Simplify i
d
ef_f
e
i
n
calc_l
i
sted_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Change nbs in nbv to std:
:
uni
q
ue
commit
|
commitdiff
|
tree
2018-05-24
Berk
H
e
s
s
Convert
g
m
x
_domdec_ma
s
te
r
_
t
to C++
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Split off collect
.
cpp f
r
om domdec
.
c
pp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Co
n
vert nbnxn_s
e
a
r
c
h
to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
C
hange nbnxn grid r
e
allocation
commit
|
commitdiff
|
tree
2018-05-22
Berk
H
ess
Use
s
td::v
e
cto
r
in nbnxn_s
e
arch_t
commit
|
commitdiff
|
tree
2018-05-22
B
erk Hess
U
se std
:
:vector
in nbn
x
n_grid_t
commit
|
commitdiff
|
tree
2018-05-18
Berk Hess
Cl
e
an up in
n
bnxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
B
e
r
k
Hess
Sp
l
it
o
f
f
d
o
m
de
c
distribution and
cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split atom redistribut
i
on o
f
f from dom
d
ec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk He
s
s
Remove commrec from se
t
_
d
dbo
x
(
)
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Cle
a
n up P
M
E domain c
o
unt
p
assing
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
Enable SI
M
D version of update
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove pull MPI code duplic
a
tion
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
Fix indexing issue in the pull c
o
de
commit
|
commitdiff
|
tree
2018-04-16
Berk Hes
s
M
o
ve
n
a
toms_m
o
l ou
t
of gmx_m
o
lblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk He
s
s
C
on
v
ert
g
m
x_
m
olblo
c
k_t to C++
commit
|
commitdiff
|
tree
2018-04-03
B
erk H
e
ss
Convert
g
mx_mtop
_
t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
ess
Change warn
i
np filenm t
o
std::
s
tring
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calculate COM f
o
r pull group
0
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hes
s
M
o
ve fi
l
e open
i
ng
o
u
t of in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk He
s
s
Modu
l
arize
pul
l
_coord_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove mols from gmx_
m
top_t
commit
|
commitdiff
|
tree
2018-03-20
Berk
Hess
Fix gmx d
u
mp AWH form
a
tting issue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow single simulation with multisim
commit
|
commitdiff
|
tree
2018-03-16
Be
r
k Hes
s
Correct
PMF sign
e
rror in
AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fix rec
e
n
t mdrun s
i
gnal
i
ng bug
commit
|
commitdiff
|
tree
2018-03-15
Berk
Hess
F
i
x virial with e
x
t
e
rnal pull poten
t
ial
and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hess
Im
p
r
ove int
e
r-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
Hes
s
Fix md
r
u
n sign
a
lling with AWH
b
ia
s
sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
Fix COM pul
l
ing wit
h
ex
t
e
r
nal potent
i
a
l
with #ranks
>
32
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Fix pull bug w
i
th geometry=direction-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hess
Add AWH fixe
s
to relea
s
e notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix A
W
H e
n
sembl
e
c
heckpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix A
W
H dec
o
nvolution
when shar
i
ng a bia
s
commit
|
commitdiff
|
tree
2018-03-09
Be
r
k Hess
C
o
rrect pdb2gmx -m
i
ssing o
p
tion
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fi
x
memory leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Convert t
_
filenm
to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Make multi
-
a
t
om
T
PI r
e
pr
o
d
u
cible
commit
|
commitdiff
|
tree
2018-03-05
B
e
rk Hess
Work aroun
d
gcc b
u
g
wit
h
group k
e
r
nel
tables
commit
|
commitdiff
|
tree
2018-03-05
Ber
k
Hess
L
eave
n
u
l
l
ptr op
t
in
t_fi
l
enm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix cppcheck warning
commit
|
commitdiff
|
tree
2018-03-02
Ber
k
Hes
s
Fix AWH bias-
s
haring wit
h
parallel
simul
a
tion
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD SM
T
t
opology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun multisim with s
e
p
arate PME
ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix
m
d inte
g
rator with Nose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simpl
i
fy mdr
u
n tMP
I
t
hr
e
ad spawning
commit
|
commitdiff
|
tree
2018-02-16
B
e
rk He
s
s
Correct mult
i
si
m
MP
I
barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remove
s
upport for tpx versio
n
before 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range
b
ug in add
_
selection
_
g
r
oups
in tngio
.
cp
p
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
Fix gromp
p
net charge chec
k
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net c
h
arge check
commit
|
commitdiff
|
tree
2018-02-08
Berk H
e
s
s
Use SIM
D
bond
e
ds with
o
ut pertur
b
ed interacti
o
ns
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
Allow b
o
nds with d
i
stance=
0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set
c
utoff mo
d
ifiers in
f
orce
r
ec
commit
|
commitdiff
|
tree
2018-02-05
B
e
rk Hess
Fix asse
r
t
io
n
failur
e
in
T
P
I
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Removed unused flag PC
A
_CAN_
R
EAD_N
O
D
E
commit
|
commitdiff
|
tree
2018-01-18
Berk He
s
s
Fix C
O
MM r
e
moval o
n
p
a
r
t
of the system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check
in grompp to avoid assertion failure
commit
|
commitdiff
|
tree
2018-01-17
Berk H
e
ss
R
e
place s
t
derr
prints in filenm
.
cpp by ass
e
rts
commit
|
commitdiff
|
tree
2018-01-17
Berk He
s
s
R
e-enable GPU with walls and 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
B
e
r
k
H
e
ss
Remo
v
e tumbl
i
ng
i
ce-cub
e
warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk
H
e
ss
Avoi
d
mdrun echoing "N
o
o
p
tio
n
-mul
t
i"
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
Hess
Reword C
P
U/GPU
i
mb
a
lance notes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not turn on DLB at re
p
lica
e
xchange
commit
|
commitdiff
|
tree
2018-01-08
Berk He
s
s
Fix triclinic dom
a
in d
e
composition
b
ug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make ac
c
eleration correction VCM mode wo
r
k
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make over
s
u
b
s
cri
p
tion w
a
rning
c
onsistent
commit
|
commitdiff
|
tree
2017-12-14
Berk H
e
ss
Require -ntmp
i
w
i
th setting -nto
m
p w
i
th
GPUs
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk Hess
C
heck
for large e
n
ergy at firs
t
step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid yelling a
b
out thread pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add gromp
p
note
for PR pcouple +
position restraints
commit
|
commitdiff
|
tree
2017-12-10
B
e
rk Hess
Remo
v
e SI
M
D warning
f
or AM
D
Ze
n
commit
|
commitdiff
|
tree
2017-12-10
B
erk Hess
Tone down
note about not pin
n
ing thre
a
ds
commit
|
commitdiff
|
tree
2017-12-08
Berk H
e
ss
Cor
r
ect Sh
a
ke test tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk H
e
s
s
Add Viveca Lindahl as contributor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose faster nb
n
xn SIMD
ker
n
els on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Be
r
k Hess
F
i
x DD exact co
n
tinuation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Fix pme gath
e
r in d
o
u
b
le with AVX(
2
)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Merge "Me
r
ge branch release-201
6
into release-2
0
18
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
F
i
xed initial temperature rep
o
rtin
g
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k
Hes
s
Upd
a
te mdrun
signal help
t
ext
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Only
s
t
op at nstlist steps with -rep
r
o
d
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Clear vsite velocitie
s
for simple
integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tigh
t
en B-spline modu
l
i s
i
ng
l
e precision test tol
e
rance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk
He
s
s
Avo
i
d assertion
f
ailur
e
in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Cha
n
ge the
G
PU SMT
cut-off to
q
uadra
t
ic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Up
d
ate documentio
n
of
Nose
-
Hoover output
commit
|
commitdiff
|
tree
2017-11-28
B
er
k
Hes
s
Refa
c
t
o
r
nbnxn e
x
clusion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Extend grompp miss
i
n
g
e
n
erg
y
term m
e
ssage
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Enable aut
o
thr
e
ad pinning with thr
e
ad limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
F
i
x PM
E
GPU with
walls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix compiler w
a
rning wi
t
hout
MPI
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k Hess
Disabled CUDA
t
imings
commit
|
commitdiff
|
tree
2017-11-24
B
erk
H
ess
Speed up
n
bnxn b
u
ffer cleari
n
g
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
L
i
m
it SMT
with PME
on GPU
commit
|
commitdiff
|
tree
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