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Avoid -Wmissing-prototypes warnings in clang CUDA builds
2017-10-04
Ber
k
H
ess
Remove a for
c
e buffer argument
f
r
o
m
IF
o
rceProvid
e
r
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Move callin
g
of
special for
c
e fu
n
ctions
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Re
m
o
ve hybrid
g
p
u
+cpu nonbonded
m
ode
commit
|
commitdiff
|
tree
2017-09-25
Ber
k
Hess
Put
r
e
ru
n
state
p
re
p
aration in
a f
u
nc
t
ion
commit
|
commitdiff
|
tree
2017-09-25
Berk
Hess
Set gl
o
bal state on master ra
n
k
o
nl
y
commit
|
commitdiff
|
tree
2017-09-20
Berk Hess
C
h
ange
n
b
nxn indexing to te
m
plates
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remov
e
n
b
-para
m
eters from t_forc
e
rec
commit
|
commitdiff
|
tree
2017-09-14
Be
r
k Hess
Fix n
b
nxn SIMD 2xNN
PME tabulated
kernel
commit
|
commitdiff
|
tree
2017-09-12
B
erk Hess
Fix
except
i
o
n
in
SIMD
L
J PME
s
olve
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do
not pass s
t
a
t
e to init_replica_
e
x
c
hange
commit
|
commitdiff
|
tree
2017-09-11
B
erk Hess
Fix PBC bug
s
in
t
he
s
wap
code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avoid i
n
f
i
n SI
M
D double sqr
t
()
commit
|
commitdiff
|
tree
2017-09-07
B
er
k
Hess
Fix FEP state
w
i
t
h rerun
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Fix two
n
bnxn search indexing
bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk
H
e
s
s
Consolidate archi
t
ecture b
o
oleans
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put mdrun options in stru
c
t
s
commit
|
commitdiff
|
tree
2017-09-02
B
e
r
k Hess
P
u
t all domdec op
t
ions
i
n a struct
commit
|
commitdiff
|
tree
2017-09-02
B
e
rk H
e
s
s
Fix mdrun -
n
b option
p
oin
t
er
commit
|
commitdiff
|
tree
2017-09-01
B
erk Hess
F
i
x
m
d
run -nb opt
i
o
n p
o
int
e
r
commit
|
commitdiff
|
tree
2017-08-29
B
erk Hes
s
Ma
k
e pull potential registration thre
a
d-safe
commit
|
commitdiff
|
tree
2017-08-29
Berk
Hess
Set defau
l
t GMX_OP
E
N
MP_MAX_TH
R
EADS to 64
commit
|
commitdiff
|
tree
2017-08-28
B
e
rk Hes
s
Avoi
d
bonded
forces loops/timers on inputs with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk Hess
Enable dynamic pair list
p
r
u
ning
commit
|
commitdiff
|
tree
2017-08-18
Berk
Hess
Add
CPU re
f
eren
c
e and SIM
D
prun
i
ng k
e
rnels
commit
|
commitdiff
|
tree
2017-08-16
Berk H
e
ss
Add dynam
i
c
pair-li
s
t pr
u
ning framewo
r
k
commit
|
commitdiff
|
tree
2017-08-16
Berk
Hess
Clean up nbnxn cluster pair
a
dd
i
tion
c
ode
commit
|
commitdiff
|
tree
2017-08-15
Berk H
e
ss
Add OpenMP
f
or orient
a
ti
o
n res
t
raints
commit
|
commitdiff
|
tree
2017-08-15
Berk Hess
Use g
r
aph with
o
r
i
e
n
tatio
n
restraint
s
commit
|
commitdiff
|
tree
2017-08-12
B
e
rk Hess
R
e
m
ove loop o
v
er
all atoms
in init_mdatoms
commit
|
commitdiff
|
tree
2017-08-03
Berk Hes
s
Fix orientat
i
on restrain
t
reference
commit
|
commitdiff
|
tree
2017-08-03
Ber
k
He
s
s
Add ch
e
ck for nr of
o
r
ientation re
s
t
r
aints
commit
|
commitdiff
|
tree
2017-08-03
Be
r
k Hess
Fix bugs with orientation restraints
commit
|
commitdiff
|
tree
2017-08-02
B
e
rk Hess
Clean u
p
matrix in
v
ersion
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Fix orientat
i
on
r
estr
a
int ref
e
r
e
nc
e
commit
|
commitdiff
|
tree
2017-08-02
Berk Hes
s
Make
loop variabl
e
s in
o
rires
.
c
p
p local
commit
|
commitdiff
|
tree
2017-08-02
B
er
k
H
e
s
s
Add
c
heck fo
r
nr
of
orient
a
tion restraints
commit
|
commitdiff
|
tree
2017-07-25
Berk Hess
Fix bugs with orientation
r
estrai
n
t
s
commit
|
commitdiff
|
tree
2017-07-09
Berk Hess
Restructure the load ba
l
a
ncing timi
n
g
commit
|
commitdiff
|
tree
2017-07-04
B
e
rk Hes
s
U
n
if
y
nbnxn kern
e
l di
s
p
atchers
commit
|
commitdiff
|
tree
2017-07-03
B
erk Hess
Remove gmx_con
s
te
x
pr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Add toleranc
e
to calc
_
ve
r
let
b
uf test
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Disable
PME tuning with
t
he group sche
m
e
commit
|
commitdiff
|
tree
2017-06-12
Berk He
s
s
F
i
x
nu
l
l pointer print in DD
commit
|
commitdiff
|
tree
2017-06-10
Berk
H
ess
Put replica exchange para
m
eters in a s
t
ruc
t
commit
|
commitdiff
|
tree
2017-06-09
Ber
k
Hess
Replace iso by instead
o
f
commit
|
commitdiff
|
tree
2017-06-08
Berk Hess
Fix COM pul
l
force
w
ith SD
commit
|
commitdiff
|
tree
2017-06-07
B
e
rk He
s
s
A
v
o
id gromp
p
charg
e
warning with rounding
commit
|
commitdiff
|
tree
2017-06-04
B
e
rk Hess
F
ix checkpo
i
nt reading w
i
t
h
out e
n
ergy h
i
story
commit
|
commitdiff
|
tree
2017-06-02
Berk Hess
Fix i
n
itial temperature reporti
n
g
commit
|
commitdiff
|
tree
2017-05-27
Be
r
k Hess
Made dupl
i
c
a
te atoms i
n
bond
e
ds
a
n e
r
ror
commit
|
commitdiff
|
tree
2017-05-26
Berk Hess
I
m
prove Ver
l
et buffer constraint
e
s
ti
m
ate
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Add conserve
d
qua
n
tity for
Be
r
endsen P-couple
commit
|
commitdiff
|
tree
2017-05-23
Ber
k
Hess
Add conserved q
.
for PR an
d
Berendsen T-couple
commit
|
commitdiff
|
tree
2017-05-23
B
erk Hess
Mak
e
DD setup obey
PME restri
c
t
ions
commit
|
commitdiff
|
tree
2017-05-22
Ber
k
H
ess
I
n
troduce ObservablesHistory container
commit
|
commitdiff
|
tree
2017-05-16
B
erk Hess
Fix confout
.
gro with energy mi
n
im
i
zation
commit
|
commitdiff
|
tree
2017-05-15
Berk Hess
Fix LJPME + swi
t
c
h
grompp
erro
r
commit
|
commitdiff
|
tree
2017-05-14
Be
r
k Hess
F
i
x bugs in doub
l
e Simd
4
impl
e
men
t
ations
commit
|
commitdiff
|
tree
2017-04-21
Ber
k
Hess
Fi
x
bugs in d
o
uble AVX(
2
)_25
6
Simd4
commit
|
commitdiff
|
tree
2017-04-19
B
e
rk Hess
F
i
x un
u
sed SI
M
D
PME table kerne
l
commit
|
commitdiff
|
tree
2017-04-18
Berk Hess
Suppress two comp
i
l
e
r
w
arnings
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
Replace
i
nstan
c
e
o
f
g
r
o
u
p by coor
d
in pull mdp do
c
s
commit
|
commitdiff
|
tree
2017-03-14
Be
r
k Hess
Make gro
m
pp -r obliga
t
ory
with p
o
sres
commit
|
commitdiff
|
tree
2017-02-28
Berk H
e
ss
Add
l
oad ba
l
ance frac
t
ion to DLB
p
rint
commit
|
commitdiff
|
tree
2017-02-07
B
erk Hess
A
d
d mdp op
t
i
on check with
decouple
d
modes
commit
|
commitdiff
|
tree
2017-02-02
Ber
k
Hess
Really fi
x
arr
a
y of complex
in cross
_
c
o
r
r
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Fix array of complex in cr
o
ss
_
corr
commit
|
commitdiff
|
tree
2017-01-20
Berk
Hess
Disallow ove
r
w
ri
t
ing of
dihedral type 9
commit
|
commitdiff
|
tree
2017-01-20
B
e
r
k
Hess
O
n
ly pr
e
dict shel
l
s
w
it
h
v
elocitie
s
commit
|
commitdiff
|
tree
2017-01-19
Berk Hess
Fix
P
ME order and grid size
che
c
ks
commit
|
commitdiff
|
tree
2017-01-17
Be
r
k Hess
Correct
assert on pme-order
commit
|
commitdiff
|
tree
2017-01-05
Berk
Hess
Fix
flat-bottom positio
n
restra
i
nts
+
DD + OpenMP
commit
|
commitdiff
|
tree
2016-12-14
Berk Hess
Add bonded #threa
d
runtim
e
check
commit
|
commitdiff
|
tree
2016-12-08
Berk
H
ess
Made mdrun -pf
o
rce termin
a
te with no
n
-f
i
nit
e
forces
commit
|
commitdiff
|
tree
2016-11-24
Ber
k
H
ess
Change spline moduli
c
a
l
c
ulation to doub
l
e
commit
|
commitdiff
|
tree
2016-11-23
B
e
rk Hess
Convert en
e
rgy
h
i
s
t
o
ry_t to
u
s
e
std:
:
v
e
c
t
or
commit
|
commitdiff
|
tree
2016-11-23
B
erk Hes
s
Use templating
in che
c
k
p
oint
.
cpp
commit
|
commitdiff
|
tree
2016-11-01
Berk Hess
Fix
t
i
me label print i
n
gmx va
n
hove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
Add gmx
du
m
p
o
p
tio
n
for printing par
a
meter
s
commit
|
commitdiff
|
tree
2016-10-28
Berk He
s
s
D
LB can
no
w
t
u
r
n of
f
,
w
hen slower
commit
|
commitdiff
|
tree
2016-10-28
Be
r
k Hess
F
ix DLB tim
i
n
g
w
ith C
U
DA
a
nd O
p
enCL
commit
|
commitdiff
|
tree
2016-10-15
Be
r
k Hess
M
o
ve en
e
rgyhistory_t
out o
f
t_state
commit
|
commitdiff
|
tree
2016-10-14
Berk Hess
Ap
p
ly
B
ere
n
dsen
P-couple at ns
t
p
coup
l
e steps
commit
|
commitdiff
|
tree
2016-10-13
Berk
Hess
Extend mtop_lookup
.
h
commit
|
commitdiff
|
tree
2016-10-12
Ber
k
Hess
Fixed
e
xc
e
p
t
i
on in u
s
use
d
result
commit
|
commitdiff
|
tree
2016-10-12
B
er
k
He
s
s
Fixe
d
print bug in gmx w
h
am
commit
|
commitdiff
|
tree
2016-10-12
Be
r
k He
s
s
Refactor NPT energy ca
l
culation
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
R
e
structure leap-frog int
e
grators
commit
|
commitdiff
|
tree
2016-10-11
Berk He
s
s
S
peed up
mtop_util ato
m
lookup
commit
|
commitdiff
|
tree
2016-10-08
Berk Hess
Add rea
d
Conf
A
ndTopology
commit
|
commitdiff
|
tree
2016-10-07
Berk H
e
ss
Ch
a
nged
f
r->f
_
novirsum to Padd
e
dRVecVector
commit
|
commitdiff
|
tree
2016-10-01
Berk
H
ess
Fix inpu
t
rec
in
i
tialization in
4 too
l
s
commit
|
commitdiff
|
tree
2016-09-29
Berk Hess
Use std::vector
in t
_
state
commit
|
commitdiff
|
tree
2016-09-29
Berk
H
e
s
s
Add
f
lags for optional t_atom
s
entries
commit
|
commitdiff
|
tree
2016-09-22
Berk
H
e
ss
F
i
x g
c
c war
n
ing in
A
l
ignedAllocator
commit
|
commitdiff
|
tree
2016-09-20
Ber
k
Hes
s
Remove state dupl
i
cation in serial runs
commit
|
commitdiff
|
tree
2016-09-16
Berk Hes
s
Fixed unused v
a
riables in domdec
.
cpp
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Merge branch release-20
1
6
commit
|
commitdiff
|
tree
2016-09-16
Berk
H
ess
Made distance re
s
traints work with threads and DD
commit
|
commitdiff
|
tree
2016-09-13
Be
r
k Hes
s
M
ove
d
expa
n
ded e
n
semble hist
o
ry to pointer in t_sta
t
e
commit
|
commitdiff
|
tree
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