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Add tests for gmx mindist
2019-01-16
B
e
rk
Hess
Renam
e
Host
V
ector to PaddedHostVector
commit
|
commitdiff
|
tree
2019-01-10
B
er
k
Hess
Split
nbn
x
n_atomdata_init()
commit
|
commitdiff
|
tree
2019-01-10
B
e
rk Hess
C
h
ange g
r
id poi
n
ters in nbn
x
n
search to
referen
c
es
commit
|
commitdiff
|
tree
2019-01-10
Berk
H
ess
Spli
t
nbnxn_
l
i
st_wo
r
k_t and change to C++
commit
|
commitdiff
|
tree
2019-01-10
B
e
r
k
H
e
s
s
Use
s
t
d
:
:v
e
ctor i
n
Nbn
x
nPairlistCpu
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
Added DefaultIni
t
ializ
a
t
i
o
n
Allocator
commit
|
commitdiff
|
tree
2019-01-04
Berk H
e
ss
Spl
i
t
n
bnxn pairli
s
t types for CPU and GPU
commit
|
commitdiff
|
tree
2019-01-04
Berk Hess
Replace N
B
N
X
N_CPU
_
C
L
USTER_I_S
I
ZE b
y
c_nbn
x
nCpuIClus
t
e
rSize
commit
|
commitdiff
|
tree
2018-12-27
Berk Hess
Use
A
tomPair
f
or LI
N
CS indexi
n
g
commit
|
commitdiff
|
tree
2018-12-27
Be
r
k Hess
Use arrayref in
L
INCS
commit
|
commitdiff
|
tree
2018-12-21
B
erk Hess
Improv
e
nbnx
n
cjFromCi() functio
n
commit
|
commitdiff
|
tree
2018-12-18
Be
r
k Hess
Use std::vec
t
or in LIN
C
S
commit
|
commitdiff
|
tree
2018-12-14
B
e
r
k
H
ess
Fix LINCS triangle constra
i
nin
g
with
O
penMP
commit
|
commitdiff
|
tree
2018-12-14
Berk
H
ess
Fixed nu
l
lptr
d
e
refence in LINCS error
commit
|
commitdiff
|
tree
2018-12-14
Ber
k
Hes
s
Fi
x
LINCS triangle constrai
n
in
g
with Op
e
nM
P
commit
|
commitdiff
|
tree
2018-12-12
Be
r
k He
s
s
Tem
p
o
r
ary fix for OpenCL PME gat
h
er
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Fix
update gr
o
up
s
with 2D/3D D
L
B
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Make large PME grids work on
GPU
commit
|
commitdiff
|
tree
2018-12-11
B
erk Hess
Document
mdrun mdp option
m
odification
commit
|
commitdiff
|
tree
2018-12-05
Berk Hess
Ad
d
upda
t
e groups to par
a
llel
i
zat
i
on do
c
s
commit
|
commitdiff
|
tree
2018-12-05
B
erk
Hess
Mak
e
l
arge PME grids wor
k
on GP
U
commit
|
commitdiff
|
tree
2018-11-26
Berk Hess
Fix
F
P exception in pu
l
l code
commit
|
commitdiff
|
tree
2018-11-16
Ber
k
H
e
ss
gr
o
m
pp now check
s
tau-p>=2*tau-t with NH+PR
commit
|
commitdiff
|
tree
2018-11-08
Be
r
k Hess
Fix bug with DD for dim
s
without PBC
commit
|
commitdiff
|
tree
2018-11-01
B
e
rk Hess
Fix broken update groups
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Limit aut
o
as
s
ign
m
en
t
of
bondeds to GP
U
s
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Pi
n
i
mport
a
nt buffers i
n
CUDA bondeds
commit
|
commitdiff
|
tree
2018-10-31
Berk He
s
s
Work a
r
ound expanded ense
m
ble issues
commit
|
commitdiff
|
tree
2018-10-31
Be
r
k Hess
F
i
x
FP excep
t
ion i
n
energy redu
c
ti
o
n
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Corre
c
t
VV integrator nstcalcen
e
rgy u
s
e
commit
|
commitdiff
|
tree
2018-10-31
Berk He
s
s
Corr
e
ct
grompp nstexpanded/nstcal
c
energy c
h
e
ck
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Add
missing mass
te
r
m to deltaH
commit
|
commitdiff
|
tree
2018-10-23
Berk
H
ess
Add missing co
n
straint term to deltaH
commit
|
commitdiff
|
tree
2018-10-21
Ber
k
Hes
s
Fix mdru
n
s
tart
/
end time print
commit
|
commitdiff
|
tree
2018-10-18
Berk
H
ess
Ad
d
e
nv
.
var
.
to disable up
d
ate
g
roups
commit
|
commitdiff
|
tree
2018-10-12
Berk Hess
Implement assi
g
ning
b
ondeds to the GPU
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Move pull output functions to output
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk H
e
ss
Minor
refact
o
ring
in bonded thr
e
ading
commit
|
commitdiff
|
tree
2018-10-09
Berk Hess
Fi
x
compiler warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update
g
r
o
u
ps
commit
|
commitdiff
|
tree
2018-10-05
Berk Hess
Add upda
t
e
groups to DD atom dis
p
l
ace
m
ent
commit
|
commitdiff
|
tree
2018-10-04
Berk
H
ess
Ma
k
e AVX2 pass T
S
AN
commit
|
commitdiff
|
tree
2018-10-04
Berk H
e
s
s
Add n
o
te to avoi
d
c
o
n
st
r
a
i
nts=all-bonds
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
Remove unnecessar
y
clearing i
n
gm
x
cpp
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
C
o
nvert gmx_cpp to
C
+
+
commit
|
commitdiff
|
tree
2018-10-02
Berk Hess
Update DD
cutoffs for u
p
dat
e
g
r
o
ups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hess
Correct
u
p
date
g
roup angle
p
a
ram type
commit
|
commitdiff
|
tree
2018-09-29
B
er
k
Hess
Refactori
n
g in calc_verletbu
f
.
c
pp
commit
|
commitdiff
|
tree
2018-09-29
Berk
H
ess
Add UpdateGroupsCog to DD
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
M
o
ve maxReferenc
e
Temperatu
r
e()
to inp
u
trec
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
I
m
prove update group rad
i
i
commit
|
commitdiff
|
tree
2018-09-27
Be
r
k Hes
s
Reorgani
z
e R
V
ec
s
caling f
u
n
c
tions
commit
|
commitdiff
|
tree
2018-09-26
Berk
Hess
Extract settle test
w
ater coordinat
e
s
commit
|
commitdiff
|
tree
2018-09-26
B
e
rk Hess
Supp
o
r
t
a
tom grou
p
s
i
n nbnxn_sear
c
h
commit
|
commitdiff
|
tree
2018-09-25
Berk Hess
Add UpdateGroup
s
Cog class
commit
|
commitdiff
|
tree
2018-09-24
Be
r
k
H
ess
Fix
performance report when init_s
t
ep!=0
commit
|
commitdiff
|
tree
2018-09-22
Berk H
e
ss
Add upd
a
te gro
u
ps
boolean to DD
commit
|
commitdiff
|
tree
2018-09-22
B
er
k
H
e
s
s
Rename
DD con
s
traint boole
a
ns
commit
|
commitdiff
|
tree
2018-09-22
B
erk H
e
s
s
Add update groups
commit
|
commitdiff
|
tree
2018-09-20
Berk
H
ess
Change
pu
l
l buffers to std::v
e
c
t
or
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Fix
t
yp
e
b
u
g in trilinic DD code
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert gmx_cmap_
t
t
o C++
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert gmx_
f
fparam
s
_t
to
C
+
+
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
Introduce extractILists helper func
t
ion
commit
|
commitdiff
|
tree
2018-09-18
Berk H
e
ss
R
e
fa
c
tor ddbox handling
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Move
i
func
stuff f
r
om idef
.
h to ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Chang
e
point
e
r
s
t
o Int
e
r
actionList to refere
n
ces
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
Refactoring in DD redistrib
u
te
commit
|
commitdiff
|
tree
2018-09-14
B
e
rk Hess
Re
f
actor ge
t
AtomG
r
oupD
i
stribut
i
on()
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
Chang
e
gm
x
_
m
o
l
t
ype_t
.
ilist to Interacti
o
nLists
commit
|
commitdiff
|
tree
2018-09-13
Berk
He
s
s
Add C+
+
version o
f
t_
i
list
commit
|
commitdiff
|
tree
2018-09-12
Berk
He
s
s
Conver
t
vsite structs to C++
commit
|
commitdiff
|
tree
2018-09-12
Berk He
s
s
Convert DD
g
m
x_reverse_
t
op_t to C+
+
commit
|
commitdiff
|
tree
2018-09-10
Berk H
e
ss
F
i
x PME
forces with FE
without perturbed q/LJ
commit
|
commitdiff
|
tree
2018-08-29
Berk He
s
s
Refact
o
r wall
p
oten
t
ial cal
c
ula
t
io
n
commit
|
commitdiff
|
tree
2018-08-24
Be
r
k He
s
s
Repla
c
e gmx_
h
ash_t by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Be
r
k Hess
M
e
rge "Merge branch rele
a
se-2018
"
commit
|
commitdiff
|
tree
2018-08-24
Berk
H
ess
Add
size optim
i
zatio
n
to Ha
s
h
e
dMap
commit
|
commitdiff
|
tree
2018-08-24
Be
r
k
H
ess
A
dd tests f
o
r HashedMap
commit
|
commitdiff
|
tree
2018-08-22
B
e
rk H
e
ss
Fix mi
s
sing interactions with GPU
a
nd DD
commit
|
commitdiff
|
tree
2018-08-21
B
erk Hess
Ensure
dom
a
ins
a
re
l
arge e
n
ough for ato
m
m
o
t
ion
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
F
i
xed mdrun
segv wi
t
h QM/MM ONIOM sche
m
e
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k
H
e
s
s
Refacto
r
calc
_
verlet_buffer_
s
iz
e
()
commit
|
commitdiff
|
tree
2018-08-20
Berk
H
ess
Remove compact
i
ng fr
o
m
DD red
i
stribute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Ve
r
l
et buff
e
r estimat
e
w
ith BD
commit
|
commitdiff
|
tree
2018-08-20
B
erk Hes
s
F
i
x clang names
p
a
ce c
o
mment warning
commit
|
commitdiff
|
tree
2018-08-20
Ber
k
Hes
s
Fix
ass
e
rtion f
a
ilure in CG
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk Hess
Re
a
lly fix CG w
i
th multip
l
e domains
commit
|
commitdiff
|
tree
2018-08-20
B
e
r
k Hess
Ma
k
e gmx_ga2la_t a
p
r
ope
r
c
l
a
s
s
commit
|
commitdiff
|
tree
2018-08-18
Berk
Hess
A
d
d check
f
or pull
g
r
ou
p
PBC t
o
g
romp
p
commit
|
commitdiff
|
tree
2018-08-17
B
e
rk Hess
M
ake pu
l
l pbc atom us
e
LocalAtomS
e
t
commit
|
commitdiff
|
tree
2018-07-18
Berk Hess
Apply loca
l
atom sets
i
n
pul
l
code
commit
|
commitdiff
|
tree
2018-07-03
Be
r
k He
s
s
C
o
n
vert gmx_ha
s
h_t to C++
commit
|
commitdiff
|
tree
2018-07-03
B
e
rk Hess
Localize variab
l
es
in dd_r
e
distribute_
c
g()
commit
|
commitdiff
|
tree
2018-07-02
Berk Hess
C
o
nvert DD DLB
c
ell
size handling to C
+
+
commit
|
commitdiff
|
tree
2018-07-02
Berk
H
ess
Fix recent bug wi
t
h 2D/3D DLB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
Removed
smallo
c
.
h
fr
o
m many DD
file
s
commit
|
commitdiff
|
tree
2018-06-29
B
e
rk He
s
s
Convert gmx_domdec_c
o
nstraints_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Conve
r
t
gmx_domdec_specat_comm_t to C++
commit
|
commitdiff
|
tree
2018-06-29
Berk Hess
Initialize DD DLB v
a
r
i
a
b
le
commit
|
commitdiff
|
tree
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