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Add grompp check for unbound atoms
2016-05-30
Berk
Hess
Add g
r
ompp check for unbound atoms
commit
|
commitdiff
|
tree
2016-05-23
Berk Hes
s
Fix bug in v-rescale thermostat &
replica
ex
c
h
a
ng
e
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Optim
i
zed
the vsi
t
e t
h
reading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Fix CUDA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Support cmap w
i
t
h QM
M
M
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdrun te
r
mination info
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
Open
M
P p
a
r
alleliza
t
ion for
p
ull
commit
|
commitdiff
|
tree
2016-04-20
Ber
k
Hess
Fi
x
p
u
l
l
legen
d
with external potent
i
al
commit
|
commitdiff
|
tree
2016-04-19
B
erk Hess
Allow rc
o
ul
o
mb>rv
d
w w
i
th PME
commit
|
commitdiff
|
tree
2016-04-19
B
erk Hess
Broadcast pull external
potential pro
v
ider stri
n
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
F
ix gm
x
hbond group overlap check
commit
|
commitdiff
|
tree
2016-04-14
Berk
H
ess
Add QMMM c
h
ec
k
s
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Co
r
rect nr
d
f for 1D/2D s
y
s
t
ems
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix includes in rea
d
pull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk H
e
ss
Add option
f
o
r external pu
l
l potential
commit
|
commitdiff
|
tree
2016-03-30
Berk
Hess
Correct mdru
n
tMPI
(no
n
-)parallel e
r
ror message
commit
|
commitdiff
|
tree
2016-03-26
Berk H
e
ss
Add real/SIMD temp
l
at
e
for
LJ-14 p
a
i
rs
commit
|
commitdiff
|
tree
2016-03-22
Berk H
e
ss
Av
o
id as
s
ertion f
a
ilu
r
e in pme_loa
d
bal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Make gmx
v
anhove work without
P
BC
commit
|
commitdiff
|
tree
2016-03-22
Berk He
s
s
LJ combination
rule kernels
for
CUDA
commit
|
commitdiff
|
tree
2016-03-21
B
e
rk
Hess
Moved pull initial
i
zat
i
on
b
a
ck to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Berk
Hess
Fix n
o
n-n
o
rmalization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
B
e
rk Hess
Remove
r
estriction on
dihdral
t
y
pes orde
r
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split off Fermi kern
e
l fr
o
m CUDA kernel
commit
|
commitdiff
|
tree
2016-03-09
B
e
rk
Hess
F
i
x
E
w
ald 3DC dipol
e
with Ve
r
l
e
t sc
h
e
me
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
Co
n
verted cse
t
tle() to use rea
l
/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
se
SIMD tr
a
n
spos
e
s
c
a
t
ter in bondeds
commit
|
commitdiff
|
tree
2016-03-03
B
e
rk Hess
Use rvec4 f
o
r
l
isted force buffer
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remov
e
epsfac from GPU
k
e
rnel inner-lo
o
p
s
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
M
i
nor cod
e
r
eo
r
dering in GPU kernels
commit
|
commitdiff
|
tree
2016-02-26
B
e
rk He
s
s
F
ix compilation with Simd4Floa
t
,
w
i
thout Simd4Doub
l
e
commit
|
commitdiff
|
tree
2016-02-19
Be
r
k
Hess
F
ix excess
i
ve
l
ist
s
pli
t
ting
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Renamed nbnxn
s
t
a
t
i
c co
n
st
i
nts
commit
|
commitdiff
|
tree
2016-02-11
B
erk
Hess
Ad
d
S
I
MD version
o
f pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
B
e
rk Hess
Replaced nbnxn search+g
r
id simd macros
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix in
c
orr
e
ct cma
p
pars
i
ng
commit
|
commitdiff
|
tree
2016-02-05
B
erk Hess
Fix
i
ncorrect cmap parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Replaced literals in nbnxn lists by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk
Hes
s
Fix
mdrun removing
V
erlet buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
B
erk Hess
Fix SETTLE erro
r
h
a
ndling
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hess
Added documentati
o
n for
p
me grid
i
n
d
exing
commit
|
commitdiff
|
tree
2016-01-29
Berk
H
ess
F
i
x TPI ig
n
or
i
n
g PME m
e
sh co
n
t
r
ibu
t
ions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hes
s
Update -n
t
o
mp_pme -npme check
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add
c
heck for double pertu
r
bat
i
on
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hess
Fix
LI
N
CS
t
riangle constraint thread issue
commit
|
commitdiff
|
tree
2016-01-28
B
e
rk
H
e
ss
Up
d
a
t
e
pair
-
list buff
e
r man
u
al
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix
exact
cont
i
n
uation
f
rom non-energy
s
teps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix e
n
ergy file con
t
inuation with md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
Fix ener
g
y av
e
rage wit
h
c
o
ntinuation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
Fix PME load
b
a
lancing skipping a setu
p
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Correct vector
c
h
eck
of gm
x
ch
e
ck
commit
|
commitdiff
|
tree
2015-12-27
B
e
rk
Hess
R
eorgani
z
ed d
o
mdec initialization
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
Merge release-
5
-1
i
nto master
commit
|
commitdiff
|
tree
2015-12-19
B
erk Hess
B
r
ing perf
o
rman
c
e est
i
mation up to date
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
Removed topo
l
o
gy pointers from DD st
r
u
ct
commit
|
commitdiff
|
tree
2015-12-16
Ber
k
H
e
ss
Add o
n
e ele
m
ent to state rvec arr
a
ys
commit
|
commitdiff
|
tree
2015-12-12
Berk
Hess
R
e
moved un
u
s
e
d mdrun opti
o
n
-dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fix bug w
i
th
pul
l
gr
o
up weights
commit
|
commitdiff
|
tree
2015-12-07
B
e
rk
Hess
M
o
ved pul
l
p
a
ram
s
to
m
dtypes/pull-pa
r
ams
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
In
c
rease pdb
c
hain ids to 62 in
outp
u
t
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Refactored se
t
_pbc_d
d
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Made t_inputre
c
cons
t
in PME
l
o
ad balancing
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pull g
r
oup c
o
unt for coord
s
stor
e
d in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk
Hess
R
e
moved mdr
u
n f
a
tal_erro
r
with P3M
-
AD
commit
|
commitdiff
|
tree
2015-11-18
B
erk Hess
R
e
mo
v
ed Re
a
ction-Field-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
O
ptim
i
zed t
h
e bonded thre
a
d force reduction
commit
|
commitdiff
|
tree
2015-11-11
Be
r
k
H
e
ss
Fixed (ha
r
ml
e
ss) fp exceptio
n
i
n
wall
c
ycle_sum
commit
|
commitdiff
|
tree
2015-11-09
Be
r
k He
s
s
Correct LINCS dHdl contribution
commit
|
commitdiff
|
tree
2015-11-03
B
erk Hess
Fix no w
a
llc
y
cle s
u
pport
commit
|
commitdiff
|
tree
2015-11-03
Berk
Hess
Removed nbnxn
k
ernel blen
d
v optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk Hess
Fix
i
ntermol
e
cular intera
c
tions with sma
l
l
mo
l
s
commit
|
commitdiff
|
tree
2015-10-15
B
e
rk Hess
Fixed nbnxn_4x
N
perf
o
rmance regre
s
sion
commit
|
commitdiff
|
tree
2015-10-07
Berk
H
ess
Fi
x
b
u
gs with int
e
rmol interactions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
Removed CUDA po
l
ling wait
commit
|
commitdiff
|
tree
2015-09-27
Berk Hess
Move gmx_domde
c
_
c
omm_t definition
commit
|
commitdiff
|
tree
2015-09-22
Berk H
e
ss
Re
m
oved useless multip
l
e
shifts in pbc
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Be
r
k Hess
Split nb
n
xn_grid
.
c off f
r
om
nbnxn_
s
e
arc
h
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk
Hess
Detect inco
r
rec
t
cycle counting
commit
|
commitdiff
|
tree
2015-08-25
Berk He
s
s
Simplify
cha
n
ging
t
he tpx_
v
ersion
commit
|
commitdiff
|
tree
2015-08-14
Berk Hess
Mak
e
m
d
run
-
nt wo
r
k ag
a
in
commit
|
commitdiff
|
tree
2015-08-13
Berk Hess
A
d
d
ed set_pull_coord_reference_value
commit
|
commitdiff
|
tree
2015-08-12
Berk
Hess
Added c
o
n
s
t qualifiers
t
o
c
ore MD routines
commit
|
commitdiff
|
tree
2015-07-06
Be
r
k Hess
F
i
x too s
m
all GPU pair coun
t
e
s
tim
a
tes
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fi
x
bug in GPU
l
i
st bal
a
ncing
commit
|
commitdiff
|
tree
2015-07-05
Ber
k
Hess
Fix DD DLB state issue
commit
|
commitdiff
|
tree
2015-07-05
B
e
rk Hess
Fix
b
u
g in
GPU list
b
alancing
commit
|
commitdiff
|
tree
2015-07-04
Berk
H
ess
Obey OpenMP
thread count limit
wit
h
tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk He
s
s
F
ix two
PME
D
LB tri
g
g
er issues
commit
|
commitdiff
|
tree
2015-07-03
B
e
rk
H
e
ss
Corre
c
t
g
rompp pull w
a
rning message
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Fi
x
inconsistent OpenMP
automa
t
ion
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
ena
b
led
1 PP + 1 PME node
commit
|
commitdiff
|
tree
2015-06-30
Ber
k
Hess
Add
checks for inefficient reso
u
rce us
a
g
e
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
Improve DLB+PM
E
tuning
wi
t
h G
P
Us
commit
|
commitdiff
|
tree
2015-06-27
Berk
H
ess
Impr
o
ve pair
s
earch t
h
re
a
d load balance
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
I
m
proved the i
n
tra-
G
PU l
o
ad balancing
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Reduce the use of nbn
x
n_con
s
ts
.
h
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Corrected nstcalclr/n
s
t
fep/nst_repl_ex checks
commit
|
commitdiff
|
tree
2015-06-26
Berk Hess
F
i
x
e
d Verl
e
t buffer issue
w
ith
2-w
i
de
SIMD
commit
|
commitdiff
|
tree
2015-06-25
B
e
rk
H
ess
Int
e
rmolecular
b
o
nded interaction
s
upport added
commit
|
commitdiff
|
tree
2015-06-25
Be
r
k
H
ess
Reena
b
led SIMD kern
e
ls wi
t
hout c
u
t-of
f
s
commit
|
commitdiff
|
tree
next