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Remove LINCS prints to log file
2018-06-13
Berk Hess
Remove
LINC
S
prints t
o
l
og file
commit
|
commitdiff
|
tree
2018-06-13
Berk Hes
s
Par
t
ial co
n
version
of gmx_domdec_t to C
+
+
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Clean
up
make_at2co
n
commit
|
commitdiff
|
tree
2018-06-05
Berk Hes
s
Make
nbnxn_grid_t coun
t
s and sizes array
s
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fix grompp bug with blocks of same m
o
lecules
commit
|
commitdiff
|
tree
2018-05-24
Ber
k
Hess
Simpli
f
y i
d
ef_fe in calc_lis
t
ed_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
C
hange
n
bs in nbv to std::u
n
ique
commit
|
commitdiff
|
tree
2018-05-24
B
e
rk Hess
Convert
g
m
x_domdec_ma
s
ter_t to C++
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Spl
i
t
o
ff collect
.
cpp from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk H
e
ss
Con
v
e
rt nbnxn_search to C
+
+
commit
|
commitdiff
|
tree
2018-05-22
B
erk
H
e
s
s
Change nbn
x
n grid reallocation
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk Hess
Use std::ve
c
tor i
n
nbnxn_search
_
t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
U
se std
:
:
vector in
n
bn
x
n_grid_
t
commit
|
commitdiff
|
tree
2018-05-18
Ber
k
H
ess
Clean
u
p
in
n
bnxn_gr
i
d
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split o
f
f domdec
distri
b
ution
and c
e
llsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split a
t
o
m
r
edis
t
ribution off
from
d
omdec
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
R
e
move commrec from se
t
_ddb
o
x()
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Cl
e
an
u
p
PME dom
a
in
coun
t
pa
s
sing
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
En
a
ble SIM
D
versi
o
n of
u
p
d
ate
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove p
u
ll MPI c
o
de duplic
a
tion
commit
|
commitdiff
|
tree
2018-04-24
B
er
k
Hess
F
i
x index
i
ng issue
in the pull code
commit
|
commitdiff
|
tree
2018-04-16
B
e
rk
H
ess
Move nat
o
ms_mol out
o
f gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
B
erk Hess
Con
v
ert gmx_molbl
o
ck_t to
C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
o
nvert gmx_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
e
s
s
Change
war
n
inp filenm to std::s
t
ring
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk Hess
Do not calc
u
late COM
for p
u
l
l
group 0
commit
|
commitdiff
|
tree
2018-03-29
Be
r
k H
e
ss
Move file o
p
ening ou
t
o
f ini
t
_p
u
ll()
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
H
ess
M
o
dul
a
r
ize pu
l
l_coor
d
_work_t
commit
|
commitdiff
|
tree
2018-03-28
B
erk Hess
R
e
mov
e
mols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk
He
s
s
Fix gmx dump AWH format
t
i
ng is
s
ue
commit
|
commitdiff
|
tree
2018-03-20
Berk He
s
s
D
is
a
llow singl
e
simulation with multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF sign error in AWH bi
a
s
s
har
i
ng
commit
|
commitdiff
|
tree
2018-03-16
B
erk Hess
Fix recent mdrun signaling b
u
g
commit
|
commitdiff
|
tree
2018-03-15
Berk
Hess
Fix virial with external pull pot
e
ntial and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve i
n
ter-simulation signal
i
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
i
x
mdr
u
n signa
l
ling with AWH bias shar
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
ix COM pulling with external pot
e
ntial with
#ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix pull bug with geo
m
etry=direc
t
ion-periodic
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k Hess
Add AWH
fi
x
es
t
o
release n
o
tes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble
chec
k
pointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH de
c
onvolution when shari
n
g
a bias
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correc
t
pdb2g
m
x
-missin
g
op
t
i
on
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix memor
y
leak in PME
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk
H
e
ss
Convert t_f
i
lenm to C+
+
commit
|
commitdiff
|
tree
2018-03-06
Berk
Hes
s
M
a
ke multi-atom TP
I
reproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work aro
u
n
d
gcc b
u
g
wit
h
group kernel table
s
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave null
p
t
r o
p
t in
t
_
f
ilenm
commit
|
commitdiff
|
tree
2018-03-02
B
e
r
k Hess
Fix cppche
c
k warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH bias-sharing with parallel simul
a
tio
n
commit
|
commitdiff
|
tree
2018-03-01
Be
r
k He
s
s
Dete
c
t AMD SM
T
topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun
multis
i
m with
s
ep
a
ra
t
e PM
E
ranks
commit
|
commitdiff
|
tree
2018-02-23
B
e
rk Hess
Fix md integrator
w
i
th
N
ose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk
Hess
Simpl
i
fy
mdru
n
tMPI thread spawning
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Cor
r
ect multisim MPI ba
r
rie
r
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remo
v
e support f
o
r tpx ve
r
sion befor
e
5
8
/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
ess
Fix ra
n
ge bug in
add_selec
t
io
n
_groups in tngio
.
c
pp
commit
|
commitdiff
|
tree
2018-02-14
B
erk He
s
s
Fix grompp net charge che
c
k
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gr
o
mpp net c
h
arge check
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Use SIMD bondeds without perturbed
interactions
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Al
l
ow bon
d
s
w
i
t
h distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk
H
ess
Set cutoff modifiers
i
n
f
orcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk H
e
ss
Fix assertio
n
failure in TPI
commit
|
commitdiff
|
tree
2018-01-30
B
erk Hess
Removed unused
f
lag PCA_CAN_RE
A
D_N
O
D
E
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix CO
M
M
removal on part o
f
the
system
commit
|
commitdiff
|
tree
2018-01-18
Berk He
s
s
Ad
d
c
h
eck in grompp
to avoi
d
assertion failure
commit
|
commitdiff
|
tree
2018-01-17
B
e
r
k Hes
s
Replace stderr prints in
f
i
lenm
.
cpp by as
s
ert
s
commit
|
commitdiff
|
tree
2018-01-17
Ber
k
Hess
R
e
-enabl
e
G
PU with walls
a
nd 1 energy
group
commit
|
commitdiff
|
tree
2018-01-16
Berk
Hes
s
Re
m
ove tu
m
bling ice-cub
e
warning
with S
D
commit
|
commitdiff
|
tree
2018-01-16
Be
r
k Hess
Avoid
mdr
u
n
echoing "No opti
o
n -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
ess
Reword CPU/GPU imbalance notes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not
turn on DLB
at replica exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk
Hess
Fix triclinic do
m
ain decomposition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make acceleration correctio
n
VCM m
o
d
e
work
commit
|
commitdiff
|
tree
2017-12-19
Ber
k
Hess
Make over
s
ub
s
cription warning consistent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -
n
tm
p
i with setting -
n
tomp
w
ith GPUs
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k He
s
s
Check f
o
r
l
arg
e
e
nergy at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
A
void yel
l
ing abou
t
thread pinning tw
i
ce
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add g
r
om
p
p no
t
e for PR pcouple
+
posit
i
o
n
r
estraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hes
s
Rem
o
ve
SIMD
w
arn
i
ng
for A
M
D Z
e
n
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone down note about
not p
i
nni
n
g threads
commit
|
commitdiff
|
tree
2017-12-08
Berk He
s
s
C
orrect
Shake test tole
r
ances
commit
|
commitdiff
|
tree
2017-12-08
Berk
H
ess
Add V
i
veca Lindahl
as contributor
commit
|
commitdiff
|
tree
2017-12-07
Berk H
e
ss
C
h
oose f
a
ster nbnxn SIMD ker
n
els on
A
MD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hes
s
Fix DD
exact continua
t
ion bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hes
s
Fix pme gather in
d
ouble wi
t
h A
V
X(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
M
e
rge "Mer
g
e branch release
-
2016
i
nto release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixe
d
i
n
itial tem
p
erature repo
r
ting
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update mdru
n
sign
a
l help text
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
Only stop at nstlist st
e
ps with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Be
r
k Hess
Clear vsite velocities for s
i
mple in
t
egrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
T
i
gh
t
en B
-
spline
m
o
d
uli singl
e
precision test to
l
erance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk He
s
s
Avoi
d
assertion fa
i
lure in A
W
H
commit
|
commitdiff
|
tree
2017-11-29
B
erk Hess
Change t
h
e GPU SMT cut-of
f
to qua
d
ratic
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
Hess
Upda
t
e document
i
on of No
s
e-Hoover output
commit
|
commitdiff
|
tree
2017-11-28
B
e
r
k Hess
R
efac
t
or nbnxn exclusi
o
n s
e
tting
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
Hess
Extend gromp
p
m
i
ssin
g
energy term message
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Enable auto thread pinning with thread limiting
commit
|
commitdiff
|
tree
2017-11-27
Ber
k
Hess
Fix P
M
E
G
PU with walls
commit
|
commitdiff
|
tree
2017-11-25
Berk
H
ess
Fix compiler
w
arning witho
u
t MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disa
b
le
d
CUDA
ti
m
ings
commit
|
commitdiff
|
tree
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