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Fix LINCS bug from recent commit 211039fc
2019-01-25
B
e
rk Hess
Fix LINC
S
bug from
r
ecent comm
i
t
211039fc
commit
|
commitdiff
|
tree
2019-01-23
Ber
k
He
s
s
Fix error with 2D/3D DLB
commit
|
commitdiff
|
tree
2019-01-22
Berk Hess
A
d
d utility metho
d
to NbnxnP
a
irlistGpu
commit
|
commitdiff
|
tree
2019-01-22
Berk Hes
s
Remo
v
e no
w
usused
G
PU alloc/free func
t
ions
commit
|
commitdiff
|
tree
2019-01-22
Berk
H
ess
Conv
e
rt NbnxnPairlistGpu t
o
C++
commit
|
commitdiff
|
tree
2019-01-21
Berk Hess
C
onve
r
t nbn
x
n_ato
m
dat
a
_t
to
C
++
commit
|
commitdiff
|
tree
2019-01-16
Berk
H
ess
Rename HostVect
o
r to
PaddedHostVector
commit
|
commitdiff
|
tree
2019-01-10
Berk
H
e
ss
Split nbnxn_a
t
omd
a
ta_in
i
t()
commit
|
commitdiff
|
tree
2019-01-10
Berk
H
ess
Change
gri
d
p
ointers in nb
n
xn s
e
a
r
c
h to references
commit
|
commitdiff
|
tree
2019-01-10
B
e
rk Hes
s
Split nbnxn_li
s
t_work_t and change
t
o C
+
+
commit
|
commitdiff
|
tree
2019-01-10
Berk Hess
Use std::vector in NbnxnP
a
irl
i
stCpu
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
F
i
x gcc-
8
release
warnings in
tng_io
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
Adde
d
Defaul
t
Initia
l
iz
a
tionAllocator
commit
|
commitdiff
|
tree
2019-01-04
Berk Hess
Split nbnx
n
pairlist types f
o
r CPU and GP
U
commit
|
commitdiff
|
tree
2019-01-04
B
e
rk
Hess
Repl
a
ce N
B
NXN_CP
U
_
CLUSTER_
I
_SIZE by
c_nbnxnC
p
uIClust
e
r
S
i
z
e
commit
|
commitdiff
|
tree
2019-01-03
Berk Hess
F
ix
s
e
gm
e
nta
t
i
o
n fault
i
n DD code
commit
|
commitdiff
|
tree
2018-12-27
Berk Hess
U
s
e
AtomPa
i
r
for LINCS
i
n
de
x
ing
commit
|
commitdiff
|
tree
2018-12-27
B
e
r
k
Hess
U
s
e arrayref in LINCS
commit
|
commitdiff
|
tree
2018-12-21
Ber
k
He
s
s
I
mpr
o
ve
n
b
nxn cjFro
m
Ci(
)
function
commit
|
commitdiff
|
tree
2018-12-18
Berk Hess
Use std::
v
ector
i
n L
I
N
CS
commit
|
commitdiff
|
tree
2018-12-14
Berk
H
e
ss
Fi
x
LINCS tria
n
gle c
o
nstrain
i
ng
w
ith OpenMP
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
Fixed
nul
l
ptr dere
f
e
n
ce in
LINCS error
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
F
i
x LINCS trian
g
le constra
i
ning w
i
t
h
OpenMP
commit
|
commitdiff
|
tree
2018-12-12
B
e
rk Hess
T
emp
o
rary fix fo
r
OpenCL PME gather
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Fix update grou
p
s
with
2D/3D
D
LB
commit
|
commitdiff
|
tree
2018-12-11
B
erk H
e
ss
Make la
r
g
e P
M
E grids work
o
n GPU
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Docume
n
t mdrun
m
dp
opti
o
n modification
commit
|
commitdiff
|
tree
2018-12-05
B
erk Hess
A
d
d
u
pdate gro
u
ps
t
o
p
aralleliza
t
ion doc
s
commit
|
commitdiff
|
tree
2018-12-05
Be
r
k
Hess
M
ake large PME grid
s
w
ork on
G
PU
commit
|
commitdiff
|
tree
2018-11-26
Ber
k
Hess
Fix FP ex
c
eption in pu
l
l cod
e
commit
|
commitdiff
|
tree
2018-11-16
Ber
k
Hess
gromp
p
now ch
e
cks tau-p>=2*tau-t with NH+PR
commit
|
commitdiff
|
tree
2018-11-08
B
erk Hess
F
ix
b
u
g with DD for
dims without PBC
commit
|
commitdiff
|
tree
2018-11-01
Berk Hess
Fix broken update gr
o
ups
commit
|
commitdiff
|
tree
2018-10-31
B
e
rk
He
s
s
Limit auto assi
g
nment of
bondeds to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
P
in imp
o
rtant buffers in CUDA
b
ondeds
commit
|
commitdiff
|
tree
2018-10-31
Berk Hes
s
Wor
k
a
r
oun
d
expanded ensemble issues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Fix
FP exception
in energy reduc
t
i
o
n
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
C
or
r
e
ct VV
i
n
t
egrator nstcalcenergy use
commit
|
commitdiff
|
tree
2018-10-31
Berk
H
ess
Correct gr
o
mp
p
nstexp
a
nded/n
s
tcalcene
r
gy c
h
eck
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
A
d
d missi
n
g mass
t
e
rm
to deltaH
commit
|
commitdiff
|
tree
2018-10-23
Berk Hess
Add missi
n
g co
n
strai
n
t t
e
rm t
o
delt
a
H
commit
|
commitdiff
|
tree
2018-10-21
Be
r
k H
e
ss
F
i
x
m
dru
n
st
a
r
t
/
end time print
commit
|
commitdiff
|
tree
2018-10-18
B
e
r
k
Hess
A
dd env
.
va
r
.
to
dis
a
bl
e
update g
r
oups
commit
|
commitdiff
|
tree
2018-10-12
B
erk Hess
Impleme
n
t
assigning bo
n
deds to the GP
U
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Move pull outp
u
t fu
n
c
tions to outp
u
t
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Ber
k
H
e
ss
M
i
nor refa
c
t
oring in b
o
nded thr
e
ading
commit
|
commitdiff
|
tree
2018-10-09
Berk He
s
s
Fi
x
c
ompile
r
w
arnin
g
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enab
l
e u
p
d
a
te groups
commit
|
commitdiff
|
tree
2018-10-05
Be
r
k
He
s
s
Add update groups to DD atom displacem
e
nt
commit
|
commitdiff
|
tree
2018-10-04
B
e
rk Hes
s
M
a
ke A
V
X2 pass T
S
AN
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Add note to av
o
id con
s
traints=all-bo
n
ds
commit
|
commitdiff
|
tree
2018-10-03
Ber
k
Hess
Remov
e
unn
e
cessar
y
clearing in gmxcpp
commit
|
commitdiff
|
tree
2018-10-03
Be
r
k Hes
s
Con
v
ert gmx_cpp to
C++
commit
|
commitdiff
|
tree
2018-10-02
Berk Hess
U
p
date DD cut
o
ffs for update groups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hes
s
Corr
e
ct upda
t
e grou
p
an
g
l
e
p
a
ram type
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Refactoring in ca
l
c
_
verletbuf
.
cpp
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add UpdateGro
u
psCog to
DD
commit
|
commitdiff
|
tree
2018-09-27
Berk
Hess
Move m
a
xRef
e
re
n
ceTemperatur
e
() to input
r
ec
commit
|
commitdiff
|
tree
2018-09-27
B
e
r
k He
s
s
Improve update group radii
commit
|
commitdiff
|
tree
2018-09-27
Berk
H
e
ss
Reorganize RV
e
c scaling
functions
commit
|
commitdiff
|
tree
2018-09-26
Ber
k
He
s
s
Extract set
t
l
e tes
t
wat
e
r co
o
rdinates
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Support atom
g
roups in nbnxn_search
commit
|
commitdiff
|
tree
2018-09-25
B
e
rk H
e
ss
Add
U
p
date
G
ro
u
psCog class
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix per
f
ormance repo
r
t whe
n
i
n
it_st
e
p!=
0
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Add update groups b
o
olean
t
o
D
D
commit
|
commitdiff
|
tree
2018-09-22
Berk
H
e
s
s
Rename DD constraint bo
o
leans
commit
|
commitdiff
|
tree
2018-09-22
B
e
rk Hess
Add update
g
ro
u
ps
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
C
hange pull
b
uffers to std
:
:vect
o
r
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Fix ty
p
e bug in trilinic D
D
c
ode
commit
|
commitdiff
|
tree
2018-09-19
B
e
rk Hess
C
onvert gmx_cmap_t to C++
commit
|
commitdiff
|
tree
2018-09-19
Berk
H
ess
Conve
r
t gm
x
_ffpar
a
ms_t t
o
C
+
+
commit
|
commitdiff
|
tree
2018-09-18
Berk H
e
ss
Introduce extractI
L
ists
helper function
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
Refactor ddbox
h
andling
commit
|
commitdiff
|
tree
2018-09-17
Berk He
s
s
Move ifunc
s
tuff fro
m
idef
.
h to ifun
c
.
h
commit
|
commitdiff
|
tree
2018-09-17
Ber
k
Hess
C
hange poi
n
t
e
rs
to InteractionList
to
references
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
Refac
t
o
r
ing in DD redistribute
commit
|
commitdiff
|
tree
2018-09-14
B
erk Hess
Refactor getAtomGroupDist
r
i
b
ution()
commit
|
commitdiff
|
tree
2018-09-14
Ber
k
Hess
Change gmx_moltype_t
.
ilist to I
n
ter
a
ctionLists
commit
|
commitdiff
|
tree
2018-09-13
Ber
k
Hess
A
d
d C++ ve
r
si
o
n of
t_il
i
st
commit
|
commitdiff
|
tree
2018-09-12
Berk He
s
s
Convert vsi
t
e structs to C++
commit
|
commitdiff
|
tree
2018-09-12
Berk H
e
ss
Convert DD gmx_rev
e
r
se
_
top_t to C++
commit
|
commitdiff
|
tree
2018-09-10
B
e
rk
H
ess
Fix
P
ME force
s
with FE
w
i
t
h
o
ut perturbed q/L
J
commit
|
commitdiff
|
tree
2018-08-29
Be
r
k Hes
s
Refac
t
or wall
p
otential
c
a
l
c
u
l
a
tion
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Replac
e
g
m
x_hash_t by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk H
e
ss
M
e
rge "Merge bran
c
h release-2018"
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add size opti
m
ization to HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add
tests for Hashe
d
Map
commit
|
commitdiff
|
tree
2018-08-22
Berk
H
ess
F
i
x missing interactions with GPU and DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
E
ns
u
re
do
m
ains
are large enough for atom motion
commit
|
commitdiff
|
tree
2018-08-21
Berk
H
es
s
Fixed mdru
n
s
egv with QM/MM
O
NIOM
s
cheme
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k Hess
Ref
a
ctor calc_verlet
_
bu
f
fer_s
i
z
e()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hes
s
R
emove compa
c
ting from DD redistribute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix V
e
rlet buffer est
i
mate wi
t
h BD
commit
|
commitdiff
|
tree
2018-08-20
Ber
k
H
e
s
s
Fix clang na
m
e
spa
c
e comme
n
t warning
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix
assertion fai
l
ure in C
G
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Really fix CG w
i
th multiple domains
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Make gmx_ga2la_t a
p
roper
c
lass
commit
|
commitdiff
|
tree
2018-08-18
Berk Hess
Add check for pull group PBC
to grompp
commit
|
commitdiff
|
tree
2018-08-17
B
e
rk Hess
Make pull pbc atom use LocalA
t
omS
e
t
commit
|
commitdiff
|
tree
2018-07-18
Berk Hess
Apply local atom sets in p
u
ll
c
ode
commit
|
commitdiff
|
tree
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