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Clean up make_at2con
2017-11-23
Berk Hess
Update note in manua
l
o
n
SD
commit
|
commitdiff
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tree
2017-11-23
B
e
rk Hess
Correct PME GPU timin
g
namin
g
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
P
revent P
M
E
tuning
e
xc
e
ssive grid scali
n
g
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
A
ls
o
print 1x1 pair-list
s
etup to lo
g
commit
|
commitdiff
|
tree
2017-11-10
Berk He
s
s
Fix genion
charge summation accuracy
commit
|
commitdiff
|
tree
2017-11-02
B
e
rk Hess
Fix Ekin at s
t
ep 0
wi
t
h COM r
e
moval
commit
|
commitdiff
|
tree
2017-11-02
Berk
He
s
s
A
d
d mi
s
sing E
w
ald correct
i
on for pme
-
u
ser
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove unused s
i
g
n
paramete
r
from dih_a
n
g
le()
commit
|
commitdiff
|
tree
2017-10-29
Ber
k
Hess
Re
m
ove incorrect c
o
m
me
n
t
for CHA
R
MM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk
H
e
ss
Fix gmx chec
k
for
tprs wi
t
h
different
#atoms
commit
|
commitdiff
|
tree
2017-10-23
B
e
rk
H
ess
Fix
incorrect dV/dlambda for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merge
"
Merge branch rel
e
ase-2016"
commit
|
commitdiff
|
tree
2017-10-20
B
e
rk Hess
F
ix w
a
r
n
ing for c
o
n
f
out wit
h
periodic molecules
commit
|
commitdiff
|
tree
2017-10-18
Berk
H
ess
Made CUDA PME texture r
e
ference conditional
commit
|
commitdiff
|
tree
2017-10-15
Berk Hes
s
Impro
v
e vsite pa
r
allel ch
e
ck
i
n
g
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
S
i
m
plify
v
irial
handling
commit
|
commitdiff
|
tree
2017-10-11
B
e
rk Hess
Di
s
ab
l
e AR
M
N
e
on nati
v
e
rsqrt iteration
commit
|
commitdiff
|
tree
2017-10-06
Berk H
e
ss
A
d
d
a
c
celeration correc
t
ion VCM mode
commit
|
commitdiff
|
tree
2017-10-06
Berk
Hess
Fix max_size() in allocato
r
.
h
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k
Hess
Add SIMD
intrin
s
i
cs version of simple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hes
s
Impro
v
e
Padded
R
VecVector resi
z
i
ng
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make SIMD ambiguous test work wi
t
h float/d
o
uble onl
y
commit
|
commitdiff
|
tree
2017-10-04
Be
r
k Hess
Remove a fo
r
c
e
buffe
r
a
rgument from IForceProvider
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Move c
a
lling of special f
o
r
c
e
f
u
nctions
commit
|
commitdiff
|
tree
2017-10-02
Be
r
k Hess
R
e
move hybrid gp
u
+cpu non
b
onde
d
mode
commit
|
commitdiff
|
tree
2017-09-25
Berk H
e
ss
Put rerun state pre
p
aration in a function
commit
|
commitdiff
|
tree
2017-09-25
B
e
rk Hess
Se
t
g
l
obal st
a
te
on mas
t
e
r r
a
nk
o
nly
commit
|
commitdiff
|
tree
2017-09-23
Berk H
e
ss
F
ix grompp
with Anders
e
n m
a
ssive
and no C
O
M
removal
commit
|
commitdiff
|
tree
2017-09-20
Be
r
k Hess
C
ha
n
ge
n
bn
x
n index
i
ng
t
o tem
p
lates
commit
|
commitdiff
|
tree
2017-09-15
B
e
rk H
e
ss
Remove n
b
-param
e
t
ers from t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix nbnxn SIMD 2xNN PME tabulated kernel
commit
|
commitdiff
|
tree
2017-09-12
B
e
r
k
H
ess
Fix except
i
on in
S
IMD LJ PME solve
commit
|
commitdiff
|
tree
2017-09-12
Berk He
s
s
Do n
o
t pa
s
s st
a
te to init_replic
a
_exchange
commit
|
commitdiff
|
tree
2017-09-11
Be
r
k Hess
Fix PBC b
u
gs in the s
w
ap
code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
A
void in
f
in SIMD double sqrt()
commit
|
commitdiff
|
tree
2017-09-07
Be
r
k H
e
ss
Fix FEP
s
t
ate w
i
th rer
u
n
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Fix two nbnxn searc
h
indexing b
u
g
s
commit
|
commitdiff
|
tree
2017-09-04
Berk H
e
s
s
Consol
i
date architec
t
ure booleans
commit
|
commitdiff
|
tree
2017-09-03
Be
r
k
He
s
s
Put
m
drun options in structs
commit
|
commitdiff
|
tree
2017-09-02
B
erk Hess
Put all do
m
dec
opt
i
ons in
a
s
t
ruct
commit
|
commitdiff
|
tree
2017-09-02
B
e
rk Hess
F
ix mdru
n
-nb opt
i
on poin
t
er
commit
|
commitdiff
|
tree
2017-09-01
Berk Hess
F
i
x mdrun -n
b
option pointer
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Make
p
ull potential regis
t
rat
i
on thread-safe
commit
|
commitdiff
|
tree
2017-08-29
Berk H
e
ss
Set defa
u
lt GM
X
_OPENMP_M
A
X_T
H
READS t
o
64
commit
|
commitdiff
|
tree
2017-08-28
Berk Hes
s
Avoid bonded forces
loop
s
/timers on in
p
u
ts w
i
th
no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk He
s
s
Enable
d
yna
m
ic
pair list pruning
commit
|
commitdiff
|
tree
2017-08-18
Berk Hes
s
Add CPU refer
e
nce
a
n
d SIMD pruning
k
e
rnels
commit
|
commitdiff
|
tree
2017-08-16
B
erk Hess
Add dynamic pair-list pruning f
r
amework
commit
|
commitdiff
|
tree
2017-08-16
Berk
H
ess
Clea
n
up nbnx
n
c
l
uster
pair add
i
tion
c
o
d
e
commit
|
commitdiff
|
tree
2017-08-15
Berk
Hess
Add
O
penMP for orientat
i
o
n
rest
r
aints
commit
|
commitdiff
|
tree
2017-08-15
Be
r
k
H
ess
Use gr
a
ph
w
ith or
i
entatio
n
restr
a
ints
commit
|
commitdiff
|
tree
2017-08-12
Berk Hess
Re
m
ove loop over all ato
m
s in init_
m
datoms
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
F
ix orientation rest
r
aint
refere
n
ce
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
A
d
d
c
h
e
ck for
nr of orientation
r
e
str
a
i
nts
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix bugs with o
r
ient
a
tion restraints
commit
|
commitdiff
|
tree
2017-08-02
B
er
k
Hess
Clean up m
a
tri
x
i
n
v
e
r
sion
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
F
i
x orie
n
tation restraint refere
n
ce
commit
|
commitdiff
|
tree
2017-08-02
Berk He
s
s
Make
loop var
i
ables in orir
e
s
.
cpp local
commit
|
commitdiff
|
tree
2017-08-02
Be
r
k Hess
Add check for
n
r
o
f orientation restraints
commit
|
commitdiff
|
tree
2017-07-25
Berk Hess
F
ix
bu
g
s wi
t
h orientat
i
on r
e
straints
commit
|
commitdiff
|
tree
2017-07-09
Berk Hess
Restructure
t
he
lo
a
d balancing timing
commit
|
commitdiff
|
tree
2017-07-04
B
e
rk He
s
s
U
n
if
y
nb
n
x
n
kernel disp
a
tch
e
rs
commit
|
commitdiff
|
tree
2017-07-03
Berk Hess
Remove gm
x
_constexp
r
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Add
tolera
n
ce to calc_verletbuf test
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Disab
l
e PME tuning with the group
s
ch
e
m
e
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
F
i
x nu
l
l pointer print in DD
commit
|
commitdiff
|
tree
2017-06-10
B
e
rk Hess
Put r
e
plica exchange param
e
ters in a struct
commit
|
commitdiff
|
tree
2017-06-09
Be
r
k Hess
Rep
l
ace iso
b
y instea
d
o
f
commit
|
commitdiff
|
tree
2017-06-08
Berk
Hess
Fix COM pull
f
orce wi
t
h SD
commit
|
commitdiff
|
tree
2017-06-07
Berk Hess
Av
o
id grompp charge warni
n
g
with rounding
commit
|
commitdiff
|
tree
2017-06-04
B
e
rk Hess
Fix checkpoin
t
rea
d
i
ng w
i
tho
u
t energy histor
y
commit
|
commitdiff
|
tree
2017-06-02
Berk Hess
Fix init
i
al temperature reporting
commit
|
commitdiff
|
tree
2017-05-27
Berk Hes
s
M
a
d
e duplicate
a
toms in bondeds
a
n
error
commit
|
commitdiff
|
tree
2017-05-26
Berk Hess
Impro
v
e Verlet bu
f
fer constraint
estimate
commit
|
commitdiff
|
tree
2017-05-23
B
e
rk Hess
Add
c
onserved quanti
t
y
f
or Beren
d
sen P-couple
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Add c
o
nserved q
.
for PR and Berendsen T-
c
ouple
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
M
ake DD setup obey
P
ME restrictions
commit
|
commitdiff
|
tree
2017-05-22
Be
r
k He
s
s
Introduce Obser
v
ablesHistory c
o
n
tainer
commit
|
commitdiff
|
tree
2017-05-16
Berk Hess
Fix co
n
fout
.
gro with energy
m
i
nim
i
zation
commit
|
commitdiff
|
tree
2017-05-15
B
e
r
k Hes
s
Fi
x
LJPME
+ swit
c
h
g
rompp
e
rror
commit
|
commitdiff
|
tree
2017-05-14
Berk He
s
s
Fix
bugs
i
n
double Simd4 implem
e
ntations
commit
|
commitdiff
|
tree
2017-04-21
Berk Hess
Fix
bugs in double
AV
X
(
2
)_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Berk He
s
s
Fix
u
nused SIMD PME tab
l
e
k
ernel
commit
|
commitdiff
|
tree
2017-04-18
Berk
Hess
S
uppress
t
wo compile
r
warnings
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
R
eplace inst
a
nce of gro
u
p by coord in pu
l
l md
p
docs
commit
|
commitdiff
|
tree
2017-03-14
Ber
k
Hess
Make grompp -r ob
l
ig
a
tory with posr
e
s
commit
|
commitdiff
|
tree
2017-02-28
B
erk He
s
s
Add load balance fraction
to DLB p
r
int
commit
|
commitdiff
|
tree
2017-02-07
Ber
k
Hess
Add
m
dp optio
n
check with decoupled mod
e
s
commit
|
commitdiff
|
tree
2017-02-02
B
e
rk
Hess
Really fix array of
c
o
m
pl
e
x in cross_corr
commit
|
commitdiff
|
tree
2017-02-02
Berk Hes
s
F
ix ar
r
ay
of
complex in cross
_
corr
commit
|
commitdiff
|
tree
2017-01-20
B
e
rk Hess
Disal
l
ow overw
r
iting
o
f dihedral type
9
commit
|
commitdiff
|
tree
2017-01-20
Berk Hess
Only
predict shells with velocities
commit
|
commitdiff
|
tree
2017-01-19
Ber
k
He
s
s
Fix PME o
r
der and grid size ch
e
cks
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Correct assert on pme-o
r
der
commit
|
commitdiff
|
tree
2017-01-05
Be
r
k Hess
Fix fla
t
-
bot
t
o
m
p
osition restraints + DD +
O
p
enMP
commit
|
commitdiff
|
tree
2016-12-14
Berk Hess
Add bonded
#
thread runtim
e
ch
e
c
k
commit
|
commitdiff
|
tree
2016-12-08
Berk Hess
M
ade md
r
un -pforce terminat
e
with non-finite f
o
r
c
e
s
commit
|
commitdiff
|
tree
2016-11-24
Berk
H
e
s
s
Change spline moduli
c
alcu
l
ation to doub
l
e
commit
|
commitdiff
|
tree
2016-11-23
Ber
k
H
ess
Convert energyhistory_t to use
s
td::vector
commit
|
commitdiff
|
tree
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