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Fix Ewald 3DC dipole with Verlet scheme
2016-03-09
B
e
rk Hess
Fix
Ewald 3
D
C
dip
o
l
e
with Verle
t
scheme
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix incor
r
ect cmap pars
i
n
g
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
F
ix inco
r
re
c
t cmap p
a
rsing
commit
|
commitdiff
|
tree
2015-11-19
Berk
H
ess
R
emoved m
d
run fatal
_
error with P3M-AD
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Correct LINCS
d
Hdl contribution
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix b
u
g
in
GPU list balancing
commit
|
commitdiff
|
tree
2015-06-26
Berk He
s
s
Fi
x
e
d
Verlet buffer iss
u
e with
2
-wide SIMD
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
F
ix g_energy average/RMSD bug
commit
|
commitdiff
|
tree
2015-06-05
Berk Hess
Don't us
e
PME ranks with GP
U
s an
d
-npme=-1
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fixed
C
UDA error with empty domains
commit
|
commitdiff
|
tree
2015-05-13
Berk He
s
s
Fix seg
v
in
g
_co
v
ar
commit
|
commitdiff
|
tree
2015-05-11
B
e
rk Hess
Chang
e
d FFTW wa
r
ning from
A
V
X
to no SSE
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed G
P
U non
-
local F copy local condi
t
ion
a
l
commit
|
commitdiff
|
tree
2015-04-28
Berk
H
ess
Re-enabled FMA f
o
r AVX-128
-
F
MA
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Correct -ntmp
i
auto f
o
r
inte
l
ne
h
a
l
em and
o
l
d
er
commit
|
commitdiff
|
tree
2015-04-01
Be
r
k Hess
Corr
e
cted force-swit
c
h manual
s
e
c
t
i
o
n
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
R
e
-f
i
x
e
d PM
E
bug wi
t
h
h
i
gh OpenM
P
threa
d
co
u
nt
commit
|
commitdiff
|
tree
2015-02-04
B
e
rk Hess
Correct CUDA kern
e
l
e
n
e
rgy fl
a
g
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Corrected
R
D
TSCP warning te
x
t
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
Fix all
o
c
ation issu
e
with VV integrator
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed pbc
=
xy +
2
walls + Verlet s
c
h
e
me
commit
|
commitdiff
|
tree
2014-12-22
Berk
Hess
Fix bug FE + GPU
+ 2/3D doma
i
n decomposit
i
on
commit
|
commitdiff
|
tree
2014-12-11
B
e
rk
He
s
s
Added grompp error
f
or p
u
lli
n
g to neg
a
tive
d
istance
commit
|
commitdiff
|
tree
2014-12-09
B
e
rk Hess
F
ix recent bug with trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed
p
ull coord init wit
h
rate!=0,
t
_start!=
0
commit
|
commitdiff
|
tree
2014-12-08
Berk H
e
ss
Added
PBC note to com
m
-m
o
de=angu
l
a
r warning
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Cla
r
ified grompp pull
erro
r
messages
commit
|
commitdiff
|
tree
2014-12-05
Be
r
k Hess
Avoi
d
race on dvdl
w
ith Verlet+OpenMP+LI
N
CS+
F
E+VV
commit
|
commitdiff
|
tree
2014-12-01
B
erk Hess
Added w
a
rn
i
ng for
u
n
necessar
y
soft-core
commit
|
commitdiff
|
tree
2014-11-26
B
e
rk H
e
ss
Fixed tric
l
inic 1xNx1 dom
a
in de
c
ompositi
o
n
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
Fixed twin-range
+ freeze
+ constraints
commit
|
commitdiff
|
tree
2014-11-24
B
erk H
e
ss
A
v
o
id Na
N
in rl
i
st buffer c
a
lc
u
lation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Correcte
d
p
a
rameter for sorting on search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk
H
e
ss
Fix DD
bon
d
ed int
e
r
acti
o
n
range pr
i
nt
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Removed f_no
v
irsu
m
reduction in Verlet scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
Fixes issue with vsiten
a
nd Verlet buffe
r
s
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Avoi
d
DLB with overl
o
aded PME ra
n
ks
commit
|
commitdiff
|
tree
2014-09-30
B
e
rk Hes
s
Added GPU local wait to load bala
n
cing
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
D
o
m
ain de
c
ompositio
n
now checks the rl
i
st buf
f
er
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
SIMD acceleration fo
r
RB di
h
ed
r
als
commit
|
commitdiff
|
tree
2014-09-29
B
e
rk
Hess
Av
o
id PME tuning d
e
cr
e
asin
g
rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
Berk
Hess
Fix calc
_
grid avoiding
PME grid factor 84
commit
|
commitdiff
|
tree
2014-09-09
Berk He
s
s
Fix
e
d DD
s
t
a
te
c
olle
c
tion issue
commit
|
commitdiff
|
tree
2014-09-08
Berk Hess
Check for i
m
plicit solvent +
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fixe
d
two PME issues with
M
PI+OpenMP
commit
|
commitdiff
|
tree
2014-08-25
Ber
k
He
s
s
Fix
e
d bugs in
v
site
N
with Ope
n
MP
commit
|
commitdiff
|
tree
2014-08-24
B
erk He
s
s
Initiali
z
e unused velo
c
ity co
n
str
a
int com
p
onents
commit
|
commitdiff
|
tree
2014-08-17
B
erk Hess
Halved the cos
t
o
f
the p
u
ll com
m
u
nication
commit
|
commitdiff
|
tree
2014-08-14
Berk
He
s
s
Corrected SIMD
m
a
th overflo
w
d
o
c
u
mentation
commit
|
commitdiff
|
tree
2014-08-10
Berk
Hess
Add
e
d checks for T
P
I + Ver
l
et sc
h
em
e
commit
|
commitdiff
|
tree
2014-08-05
Berk Hess
Fix hang
with
LJ-PME and e
m
pty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
Fixed PME bug w
i
th hi
g
h O
p
enM
P
thr
e
a
d count
commit
|
commitdiff
|
tree
2014-07-31
B
erk
H
ess
Av
o
id division
b
y 0 in nbnxn_
s
earch
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
T
a
ke LJ-P
M
E into account for
t
able spacing
commit
|
commitdiff
|
tree
2014-06-29
Ber
k
Hess
Updated LJ-PME
docu
m
ent
a
tion
commit
|
commitdiff
|
tree
2014-06-24
Berk Hess
F
ixe
d
the sign
o
f mass perturb
e
d
contribution
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix g_mindist with
pbc=
X
Y
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fixed shells wit
h
p
a
rticl
e
decompositio
n
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
Fi
x
e
d
sign
e
rr
o
r in posres dvdl
commit
|
commitdiff
|
tree
2014-06-17
B
erk Hess
Update
d
mdrun -npm
e
d
o
cumen
t
ation
commit
|
commitdiff
|
tree
2014-06-17
Berk
H
e
ss
Removed r
o
unding issue i
n
nbnx
n
Ewald
table
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
Fixed
P
ME bug w
i
t
h #O
p
enMP-threads a large pri
m
e
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Changed appe
n
di
n
g file name error messag
e
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Made shells work with the Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk
Hess
Fixed perturbed wal
l
i
nt
e
racti
o
ns
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
Made gm
x
check -rmsd work a
g
ain with forc
e
s
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Decoupled repl
_
ex_nst from nstc
a
l
cenergy
commit
|
commitdiff
|
tree
2014-06-11
B
e
r
k He
s
s
Made repl_ex time s
t
ep more
r
e
adable
commit
|
commitdiff
|
tree
2014-06-10
Berk Hess
Replaced gmx_ho
s
tname_num b
y
gmx_p
h
y
s
i
calnode_id_hash
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
Set make_n
d
x max
n
ame le
n
gth
a
n
d
c
o
unt
to 102
4
commit
|
commitdiff
|
tree
2014-06-05
Be
r
k Hess
Fixed
shi
f
t
and switc
h
modif
i
er
s
,
p
a
r
ticular
l
y for
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
B
e
rk
H
es
s
Fix constraint virial wit
h
multiple time
steppin
g
commit
|
commitdiff
|
tree
2014-06-02
Berk He
s
s
Fixed
g
_ene
r
gy
E
instein viscosity
commit
|
commitdiff
|
tree
2014-05-22
Ber
k
Hess
Avoid energy drif
t
with verlet-buf
f
er-tolerance
commit
|
commitdiff
|
tree
2014-05-09
Berk Hess
Minor t
w
eaks to the DD setup
commit
|
commitdiff
|
tree
2014-04-29
Berk Hess
Remove
d
t
runcation of nrdf in v-rescale
ther
m
ostat
commit
|
commitdiff
|
tree
2014-04-23
Berk Hes
s
Fixed nbnxn FE list all
o
cation issue
commit
|
commitdiff
|
tree
2014-04-02
Berk Hess
Added
LJ-PME and
L
J Pot-
s
witc
h
t
o PME
l
oad estimate
commit
|
commitdiff
|
tree
2014-03-24
Berk H
e
ss
A
d
ds
cu
t
-off
c
hecks
f
or triclinic
d
omai
n
d
ecompositi
o
n
commit
|
commitdiff
|
tree
2014-03-23
B
erk Hess
Fixed bug in parallel v/f con
s
training
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
CU
D
A
cu
t
-of
f
kernels now shift
ex
c
lusion ene
r
gies
commit
|
commitdiff
|
tree
2014-03-11
Berk
Hess
PME
l
o
ad balancing
n
ow
w
orks with LJ-PME
commit
|
commitdiff
|
tree
2014-03-06
Berk Hess
Fix
e
d
e
x
it
w
ith FEP wi
t
h PME
n
odes wit
h
o
u
t LJ-PME
commit
|
commitdiff
|
tree
2014-03-05
Berk H
e
ss
Buffer es
t
imate now works with rvd-switch=
0
commit
|
commitdiff
|
tree
2014-02-26
B
er
k
H
ess
F
ree
-
energ
y
no
w
works with the Verlet scheme
commit
|
commitdiff
|
tree
2014-02-25
B
e
rk H
e
ss
Fixes seperate PME nodes w
i
thout LJ-PME
commit
|
commitdiff
|
tree
2014-02-24
B
e
r
k
H
es
s
Implemented LJ-PME
n
bnxn
k
ernels
commit
|
commitdiff
|
tree
2014-02-24
Berk
H
ess
Fi
x
e
d bu
g
with LJ
pot-switch i
n
4xN kernels
commit
|
commitdiff
|
tree
2014-02-19
Berk Hess
Impleme
n
ted
nbnx
n
L
J
switc
h
functio
n
s
commit
|
commitdiff
|
tree
2014-01-30
B
erk
H
ess
M
ade ref
e
rence SIMD work again
commit
|
commitdiff
|
tree
2014-01-29
Berk Hess
Automated Ve
r
let
r
list for NV
E
simulation
s
commit
|
commitdiff
|
tree
2013-12-03
Be
r
k He
s
s
Re
m
ov
e
d restr
i
c
tio
n
of on
e
reference pull g
r
oup
commit
|
commitdiff
|
tree
2013-12-02
B
e
rk He
s
s
Mad
e
cutoff-
s
cheme=Ver
l
et the defa
u
l
t
commit
|
commitdiff
|
tree
2013-12-02
B
erk
H
e
s
s
Re
n
amed v
e
rlet-buffer-drif
t
to ve
r
le
t
-bu
f
fer-tolerance
commit
|
commitdiff
|
tree
2013-12-01
Berk Hes
s
Fixe
d
zero h
a
rdware
t
h
rea
d
count
commit
|
commitdiff
|
tree
2013-11-29
Ber
k
Hess
Created SIMD modul
e
commit
|
commitdiff
|
tree
2013-11-26
Berk
H
ess
Fixed return value of gmx_
m
top_bonded
s
_fr
e
e_energy
commit
|
commitdiff
|
tree
2013-11-15
Berk
H
ess
correct
e
d pote
n
ti
a
l nb
n
xn SIMD m
e
mo
r
y issue
commit
|
commitdiff
|
tree
2013-11-08
Berk Hess
fix nbnxn
a
t
om
s
orting with dista
n
t bond
e
d
s
commit
|
commitdiff
|
tree
2013-11-07
Berk Hess
c
orrect
e
d dynam
i
c load balancing when sharin
g
GPU
s
commit
|
commitdiff
|
tree
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