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Fixed opening of wall table files
2016-08-17
Berk Hess
Fix
e
d opening of wall table files
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
Re
d
u
ce F
E
pa
i
r-li
s
t
me
m
o
ry
usage
commit
|
commitdiff
|
tree
2016-08-10
B
erk Hess
Fix deadl
o
c
k
w
i
t
h
t
hread-MPI
commit
|
commitdiff
|
tree
2016-07-07
Be
r
k Hess
Re
l
ax pull PBC check
commit
|
commitdiff
|
tree
2016-07-05
Berk H
e
ss
Add checks for
t
oo much memory
in g_n
m
eig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add
g
rompp chec
k
for pull group
commit
|
commitdiff
|
tree
2016-06-28
Ber
k
Hess
Pr
o
perl
y
re
s
et C
U
DA
application clocks
commit
|
commitdiff
|
tree
2016-06-27
B
erk Hess
U
se sysc
o
nf(_S
C
_NPR
O
CESSO
R
S
_
O
NL
N
)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix vsite bu
g
with MPI+Open
M
P
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix Ver
l
et buffer ca
l
c
u
lation w
i
t
h nstli
s
t
=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hess
More accurate G
P
U list splitting
commit
|
commitdiff
|
tree
2016-06-22
B
e
rk Hess
Up
d
a
t
ed OpenCLTODOLis
t
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Ber
k
Hess
Ad
d
nbnxn pair-list
rebal
a
ncing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Re
m
ove Op
e
n
MP overhead at hig
h
parallelizat
i
on
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Correct G
P
U
pair estimate for list splitting
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
Fix bug with fbposres+MPI+
O
pe
n
MP
commit
|
commitdiff
|
tree
2016-06-19
B
e
r
k Hess
Remo
v
e warnin
g
s on checkpoint mismatc
h
commit
|
commitdiff
|
tree
2016-06-17
Be
r
k Hess
Remove std::thread::hardware_concurr
e
n
cy()
commit
|
commitdiff
|
tree
2016-06-14
Berk Hess
Fix OpenCL er
r
or with
em
p
ty do
m
ain
s
commit
|
commitdiff
|
tree
2016-06-13
Berk Hess
Handle constraint
e
r
r
o
rs w
i
th E
M
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
F
i
x data race
i
n hwinfo wi
t
h thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
Ber
k
Hess
Handle pa
r
tially frozen and constrained atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
R
eposition
n
b
nxn filler particles
commit
|
commitdiff
|
tree
2016-05-31
Berk He
s
s
Avoi
d
nume
r
ical
overflo
w
wi
t
h
o
ve
r
l
a
ppin
g
a
t
oms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add
check fo
r
f
i
n
i
t
e
e
nergies
commit
|
commitdiff
|
tree
2016-05-30
Be
r
k Hess
A
d
d grompp check for u
n
b
o
und
a
t
oms
commit
|
commitdiff
|
tree
2016-05-23
B
e
rk
H
ess
Fix bug in v-
r
escale
t
hermosta
t
&
r
eplica exchange
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Optimize
d
th
e
vsit
e
thre
a
d
ing
commit
|
commitdiff
|
tree
2016-05-10
B
erk Hess
Fix CUD
A
s
h
m
em bug
commit
|
commitdiff
|
tree
2016-05-10
Ber
k
Hess
Suppor
t
cmap with
Q
M
MM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdrun te
r
mi
n
ation info
commit
|
commitdiff
|
tree
2016-05-06
Berk
H
ess
O
p
e
n
M
P
paralleli
z
a
tion
for pul
l
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pu
l
l legend w
i
t
h
ext
e
rnal potential
commit
|
commitdiff
|
tree
2016-04-19
Berk He
s
s
Al
l
ow rcou
l
omb>rv
d
w with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcast
pull ex
t
ernal potential provi
d
er string
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix gmx hbon
d
g
roup overlap check
commit
|
commitdiff
|
tree
2016-04-14
Berk Hess
Add QM
M
M ch
e
c
k
s
commit
|
commitdiff
|
tree
2016-04-03
Berk
H
e
s
s
C
o
rrect nrdf
fo
r
1D/2D syste
m
s
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fi
x
includes
in
r
e
adpull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hes
s
Add option for ext
e
r
n
al pull potential
commit
|
commitdiff
|
tree
2016-03-30
B
e
rk Hes
s
C
orrect
m
drun tMPI (
n
on-)parallel error message
commit
|
commitdiff
|
tree
2016-03-26
B
e
r
k Hess
Ad
d
real
/
SIMD templat
e
f
o
r LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
B
erk Hess
Avoid
ass
e
rtion
failure in
pme_
l
oadbal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk H
e
ss
Make gmx va
n
hove work without
P
BC
commit
|
commitdiff
|
tree
2016-03-22
Berk
Hes
s
LJ comb
i
nation
r
ule
k
ernels for
CU
D
A
commit
|
commitdiff
|
tree
2016-03-21
Be
r
k
Hess
Moved
pull ini
t
ializati
o
n back to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix no
n
-normalization
of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk
H
es
s
R
emove restric
t
ion on dihdr
a
l
types
order
commit
|
commitdiff
|
tree
2016-03-12
Ber
k
H
e
s
s
Split off Fermi kerne
l
fr
o
m CUDA kernel
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix
Ew
a
ld
3
DC dip
o
le
wi
t
h
V
erlet sche
m
e
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
C
o
nverted csettle() to use
re
a
l/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
s
e
S
IMD transpose
s
catt
e
r
in
bo
n
deds
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use rvec4 for
l
isted f
o
rce bu
f
fer
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
R
e
mo
v
e e
p
sfac f
r
om
GPU kernel inner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Minor co
d
e reordering
i
n
G
PU
kernels
commit
|
commitdiff
|
tree
2016-02-26
Berk H
e
ss
Fi
x
compilation with
Simd4Fl
o
a
t, without Simd4Double
commit
|
commitdiff
|
tree
2016-02-19
B
e
rk Hess
Fix excessive list
split
t
ing
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Renamed n
b
nxn static c
o
nst ints
commit
|
commitdiff
|
tree
2016-02-11
Berk Hes
s
Add
SIMD
v
ersion
of pbc_d
x
_aiuc
commit
|
commitdiff
|
tree
2016-02-09
B
er
k
Hess
Replaced nb
n
x
n
search+grid sim
d
macros
commit
|
commitdiff
|
tree
2016-02-07
Be
r
k
H
ess
Fix incorrec
t
c
m
a
p pars
i
ng
commit
|
commitdiff
|
tree
2016-02-05
B
erk Hess
Fix incorr
e
ct cmap parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Replac
e
d literals
i
n nbnxn lists by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix mdrun re
m
o
v
ing Verl
e
t buffer
w
ith EM
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix SETTLE error h
a
ndli
n
g
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
Added do
c
umentat
i
on for pme grid i
n
dexing
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
Fix TPI
ignoring PME
m
e
sh cont
r
ibutions
.
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k Hess
Update -ntomp_pme -
n
pme
check
commit
|
commitdiff
|
tree
2016-01-29
Berk He
s
s
Add check for dou
b
le pertur
b
a
tion
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix
L
I
N
C
S triangle constraint thread
i
ssue
commit
|
commitdiff
|
tree
2016-01-28
Berk
H
ess
U
p
date pair-lis
t
buffer manual
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
Fix exact
c
o
n
t
inuation from non-energy st
e
ps
commit
|
commitdiff
|
tree
2016-01-24
Berk
Hess
Fix
e
n
e
r
gy file continuation w
i
t
h md-v
v
commit
|
commitdiff
|
tree
2016-01-24
B
erk H
e
s
s
Fix en
e
rgy average with continuatio
n
commit
|
commitdiff
|
tree
2016-01-08
Berk
Hess
Fix PME
l
oad ba
l
a
ncing skipping a setup
commit
|
commitdiff
|
tree
2015-12-29
Berk He
s
s
Correct
v
ector check of
g
m
x
check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorgani
z
ed d
o
mde
c
initi
a
lizatio
n
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
Merg
e
rele
a
se-5-1
i
n
t
o mas
t
er
commit
|
commitdiff
|
tree
2015-12-19
B
e
rk Hes
s
Bri
n
g per
f
ormance
e
st
i
mation up to d
a
te
commit
|
commitdiff
|
tree
2015-12-17
Berk H
e
ss
R
emoved topology po
i
nte
r
s from DD struct
commit
|
commitdiff
|
tree
2015-12-16
Berk Hes
s
Add
o
ne el
e
ment to state
rvec array
s
commit
|
commitdiff
|
tree
2015-12-12
B
e
rk Hess
R
e
moved unused mdrun op
t
ion -dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fix bug wit
h
pull group
w
eights
commit
|
commitdiff
|
tree
2015-12-07
B
erk Hes
s
M
o
ved pull pa
r
ams to mdtypes/pull-param
s
.
h
commit
|
commitdiff
|
tree
2015-12-02
B
e
rk
H
ess
Increa
s
e pdb chain ids to 62 i
n
output
commit
|
commitdiff
|
tree
2015-12-02
Berk
H
ess
R
efacto
r
e
d
se
t
_pbc_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk
Hess
Made
t
_inputrec const in PME
load balancin
g
commit
|
commitdiff
|
tree
2015-12-01
Ber
k
Hes
s
Pull g
r
o
up count fo
r
coords st
o
red in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk He
s
s
Removed mdrun
fata
l
_erro
r
wit
h
P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
erk
H
ess
Rem
o
ved Reaction-Field
-
nec
commit
|
commitdiff
|
tree
2015-11-14
Berk He
s
s
Optimized the
b
o
n
ded th
r
ead
f
orce
r
eduction
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fixed (harmless) fp exception in wallcycle_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk H
e
ss
Correct LINCS dHdl contribution
commit
|
commitdiff
|
tree
2015-11-03
Berk He
s
s
Fix no wallcycle supp
o
rt
commit
|
commitdiff
|
tree
2015-11-03
Berk
H
ess
Removed nbnxn
k
ernel blendv optim
i
zation
commit
|
commitdiff
|
tree
2015-11-02
Berk H
e
ss
Fix inte
r
mol
e
c
ular int
e
ractions with small mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fi
x
ed nbnxn_4xN
p
erformance regressio
n
commit
|
commitdiff
|
tree
2015-10-07
B
erk Hes
s
Fix bug
s
with intermol interactions and DD
commit
|
commitdiff
|
tree
2015-10-01
Ber
k
H
ess
Removed CUDA
poll
i
ng wai
t
commit
|
commitdiff
|
tree
2015-09-27
Berk Hes
s
Mo
v
e
gm
x
_dom
d
ec_comm_t definition
commit
|
commitdiff
|
tree
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