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Fix bug in v-rescale thermostat & replica exchange
2016-05-23
Berk Hess
F
ix bug in v-
r
e
s
ca
l
e
t
hermost
a
t &
replica exch
a
n
g
e
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
H
ess
Optimized the vsite threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Fi
x
C
U
DA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
Hess
S
u
pport
cmap with QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdr
u
n term
i
nation info
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
OpenMP
paralleliza
t
i
o
n f
o
r p
u
ll
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pull legend with
e
x
ternal potenti
a
l
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
ss
Al
l
ow rco
u
lomb>rvdw with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
B
r
oadcast
pull
e
xterna
l
potential p
r
ovi
d
er str
i
ng
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix
g
mx
h
bo
n
d group over
l
a
p
check
commit
|
commitdiff
|
tree
2016-04-14
Berk Hes
s
Add QMMM
c
hecks
commit
|
commitdiff
|
tree
2016-04-03
B
e
rk Hess
Correc
t
nrdf for
1D/2D sys
t
ems
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix i
n
cludes in readpull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
B
e
r
k
Hess
Add option for external pull po
t
ential
commit
|
commitdiff
|
tree
2016-03-30
Berk Hes
s
Correct mdr
u
n tMPI (non-)parallel
err
o
r
m
essa
g
e
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add real/SIMD t
e
m
p
l
a
te
f
o
r
LJ-1
4
pairs
commit
|
commitdiff
|
tree
2016-03-22
Ber
k
Hess
Avoid assertion failur
e
in pme_loadbal_
d
o
commit
|
commitdiff
|
tree
2016-03-22
Berk
Hess
Make gmx
va
n
h
ove
work without PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combination ru
l
e kernels for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Ber
k
Hess
Moved pul
l
initializ
a
tion
b
a
c
k to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Berk
H
ess
Fix non-normalization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
B
e
rk Hess
Remove restriction
o
n
dihdraltypes order
commit
|
commitdiff
|
tree
2016-03-12
B
e
r
k
H
e
ss
Split off Fermi kernel from CUDA kerne
l
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix Ewald 3DC dipole
with Verl
e
t scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
Converted
c
settle() to u
s
e real/SimdReal t
e
mplate
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use SIMD
transpose sc
a
tter
i
n bonded
s
commit
|
commitdiff
|
tree
2016-03-03
Berk
Hes
s
Use rvec
4
fo
r
listed force buffer
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remove epsfac from GPU kernel in
n
er-
l
oops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Minor code re
o
rdering in GPU k
e
r
n
e
l
s
commit
|
commitdiff
|
tree
2016-02-26
Ber
k
Hess
Fix
compil
a
tion with Simd4
F
loat
,
without Sim
d
4Double
commit
|
commitdiff
|
tree
2016-02-19
Berk
H
ess
Fi
x
e
x
c
e
ssive
li
s
t split
t
i
n
g
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Renamed nbnxn s
t
at
i
c const ints
commit
|
commitdiff
|
tree
2016-02-11
Berk Hess
Add SI
M
D version o
f
pbc_dx_ai
u
c
commit
|
commitdiff
|
tree
2016-02-09
Berk Hess
Rep
l
aced nbnxn
s
e
a
r
c
h+grid simd m
a
cros
commit
|
commitdiff
|
tree
2016-02-07
Berk He
s
s
Fix incorrect
cmap
p
arsing
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
F
ix inc
o
rr
e
ct cmap parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
R
e
p
laced literals in nbnxn lists b
y
ints
commit
|
commitdiff
|
tree
2016-02-03
Be
r
k Hess
Fix mdrun remov
i
ng Verl
e
t buffer
with
E
M
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix SETTLE error handling
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
A
dded docu
m
entation for pme grid indexing
commit
|
commitdiff
|
tree
2016-01-29
Berk He
s
s
F
ix TPI ignoring PME mes
h
contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -ntomp
_
pme
-n
p
me check
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add ch
e
c
k for double
p
erturba
t
ion
commit
|
commitdiff
|
tree
2016-01-29
Berk
H
ess
Fix LINCS triangle constraint
t
h
read iss
u
e
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Update pair-
l
i
st b
u
ffe
r
manual
commit
|
commitdiff
|
tree
2016-01-24
Berk Hes
s
Fix exa
c
t c
o
ntinu
a
tion
f
rom
non-energy
s
teps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix energy file co
n
ti
n
uat
i
on w
i
th md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix ene
r
g
y
a
v
erage with co
n
tinuat
i
o
n
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
F
ix
PME l
o
a
d
b
alancing skipping a setu
p
commit
|
commitdiff
|
tree
2015-12-29
B
erk
H
e
ss
Correct vect
o
r ch
e
ck of gmx che
c
k
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
R
e
organized d
o
mdec in
i
ti
a
liza
t
ion
commit
|
commitdiff
|
tree
2015-12-20
B
e
r
k
H
ess
Merge rel
e
ase-5-1 into master
commit
|
commitdiff
|
tree
2015-12-19
Ber
k
H
e
ss
B
r
ing
p
e
rf
o
rmance estimation up
t
o date
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
R
e
moved to
p
ology pointers from
D
D stru
c
t
commit
|
commitdiff
|
tree
2015-12-16
Berk
H
ess
Add
o
ne element t
o
state rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Removed
u
nused
mdrun option -dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
F
i
x
bug
with pull grou
p
weight
s
commit
|
commitdiff
|
tree
2015-12-07
Be
r
k
H
e
ss
Moved pull params to mdtypes/pull
-
pa
r
ams
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Incr
e
ase
p
db
c
hain ids
t
o 62 in
output
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
R
e
f
actor
e
d se
t
_pbc_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk H
e
ss
M
ade t_i
n
putre
c
co
n
st in
P
ME lo
a
d ba
l
anc
i
ng
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pu
l
l gr
o
u
p
count for
c
oords st
o
red in tpr
commit
|
commitdiff
|
tree
2015-11-19
Ber
k
Hess
Remov
e
d mdrun f
a
t
al_error
wi
t
h
P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
e
rk
Hes
s
R
e
moved Reaction-Field-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Optimi
z
ed the
b
onded thread force reduc
t
ion
commit
|
commitdiff
|
tree
2015-11-11
Ber
k
Hess
F
ixed (harm
l
ess)
fp e
x
ception in wallc
y
cle_su
m
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Correc
t
LINCS
dHdl co
n
tribu
t
io
n
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Fix no wall
c
ycle support
commit
|
commitdiff
|
tree
2015-11-03
Berk He
s
s
Removed nbnx
n
kernel bl
e
ndv
optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk Hes
s
Fix intermolecular intera
c
tio
n
s with sm
a
ll
m
ols
commit
|
commitdiff
|
tree
2015-10-15
Berk H
e
ss
Fix
e
d nb
n
xn_4xN p
e
r
f
ormance
r
egression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs with intermol interact
i
ons
a
n
d DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
Removed C
U
DA polling w
a
it
commit
|
commitdiff
|
tree
2015-09-27
B
erk Hess
M
o
ve g
m
x_d
o
mdec
_
c
o
mm_t
d
efin
i
tion
commit
|
commitdiff
|
tree
2015-09-22
Berk Hess
Re
m
oved
useless multip
l
e
s
hifts in
p
bc
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hes
s
S
plit nbnxn_grid
.
c off from nbnxn_search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
Detect i
n
correct
c
y
cle counti
n
g
commit
|
commitdiff
|
tree
2015-08-25
B
e
rk Hess
S
implif
y
changi
n
g the tpx_version
commit
|
commitdiff
|
tree
2015-08-14
Berk Hess
M
ake mdrun -
n
t work again
commit
|
commitdiff
|
tree
2015-08-13
Berk Hess
A
dde
d
set
_
pull_coord_reference_
v
a
l
ue
commit
|
commitdiff
|
tree
2015-08-12
Berk
Hess
Added const
qua
l
ifier
s
to
c
ore
M
D
r
outines
commit
|
commitdiff
|
tree
2015-07-08
Berk Hess
Se
p
arated
bonded and Ew
a
ld correction threading
commit
|
commitdiff
|
tree
2015-07-06
Berk
H
ess
Fix t
o
o small
G
PU pair count estimates
commit
|
commitdiff
|
tree
2015-07-06
Berk
H
ess
Fix bug in GPU lis
t
b
alancing
commit
|
commitdiff
|
tree
2015-07-05
B
erk
Hess
F
ix DD DLB state issu
e
commit
|
commitdiff
|
tree
2015-07-05
Berk
H
ess
Fix bug in
G
P
U l
i
s
t balanci
n
g
commit
|
commitdiff
|
tree
2015-07-04
Ber
k
H
e
ss
Ob
e
y OpenMP thread c
o
un
t
l
imit wi
t
h tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
F
i
x
two PME DL
B
trigger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
Correct g
r
om
p
p pull warning message
commit
|
commitdiff
|
tree
2015-06-30
Berk Hes
s
F
i
x incon
s
is
t
ent OpenMP auto
m
ation
commit
|
commitdiff
|
tree
2015-06-30
Berk H
e
ss
enabl
e
d
1 PP +
1 PME no
d
e
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add c
h
ecks for ineffici
e
nt resour
c
e usage
commit
|
commitdiff
|
tree
2015-06-29
Berk
Hess
Improve
D
L
B+PME tuning with G
P
Us
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Improve
p
air search thread lo
a
d balance
commit
|
commitdiff
|
tree
2015-06-27
Berk
Hess
Improved the
i
n
tra-GPU
l
o
a
d
balancing
commit
|
commitdiff
|
tree
2015-06-27
Berk Hes
s
Reduce the u
s
e
of nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
B
erk Hess
C
orrected ns
t
cal
c
l
r
/
ns
t
fep
/
ns
t
_repl_e
x
che
c
ks
commit
|
commitdiff
|
tree
2015-06-26
B
e
rk Hess
Fixed Verlet
b
uffer i
s
sue with 2
-
wide
S
IM
D
commit
|
commitdiff
|
tree
2015-06-25
B
erk Hess
Intermolecu
l
a
r
b
o
nded intera
c
tion support ad
d
ed
commit
|
commitdiff
|
tree
2015-06-25
B
erk
H
e
s
s
R
e
en
a
bled SIMD kernels wit
h
out cut-off
s
commit
|
commitdiff
|
tree
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