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Rename atomGroups in gmx_domdec_t to atomGrouping
2018-06-28
Berk Hess
Ren
a
m
e a
t
omGroups in gmx_domd
e
c_t to atomGr
o
uping
commit
|
commitdiff
|
tree
2018-06-27
Be
r
k
H
ess
B
ase vacuum D
D
o
n atom coordinates
commit
|
commitdiff
|
tree
2018-06-27
Ber
k
H
e
ss
Correct DD
z
one size loop bound
commit
|
commitdiff
|
tree
2018-06-25
Mark Abraham
T
e
st
bo
t
h
i
nternal and external c
l
FFT buil
d
i
n Jen
k
ins
commit
|
commitdiff
|
tree
2018-06-25
Mark Abraham
Fix unused
v
aria
b
l
e
warnings
commit
|
commitdiff
|
tree
2018-06-14
K
evin Boyd
C
hanged
d
ocumen
t
ation on co
m
m
o
n errors during minimization
commit
|
commitdiff
|
tree
2018-06-14
B
e
rk
Hess
Minimizatio
n
now det
e
c
ts
infi
n
ite forc
e
s
commit
|
commitdiff
|
tree
2018-06-05
M
a
r
k Abraham
Separa
t
e flexibl
e
constr
a
int c
o
u
n
t
ing
commit
|
commitdiff
|
tree
2018-06-04
Mark Abraham
Remove redundant shell-code
fatal errors
commit
|
commitdiff
|
tree
2018-05-24
Mark A
b
raham
Move responsibi
l
ity for bonded threading decomposition
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Change nbs
i
n
nbv to std
:
:unique
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Convert gmx_domdec_master
_
t
to C++
commit
|
commitdiff
|
tree
2018-05-18
B
e
rk Hess
Clean up in nbnxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean
u
p
P
ME domain
c
o
u
nt passin
g
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
Enab
l
e SIMD versio
n
of updat
e
commit
|
commitdiff
|
tree
2018-04-24
Berk
Hess
Fix indexing i
s
sue in the
pull code
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
ess
Change w
a
rninp f
i
lenm to st
d
::string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
Do not calculate C
O
M for pull
group 0
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix gmx dump AWH formatting issue
commit
|
commitdiff
|
tree
2018-03-20
A
l
eksei
I
u
p
i
no
v
Cla
r
if
y
the mdrun G
P
U
option
s
docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
Iupino
v
R
e
s
tore the lost mc_te
m
p c
h
eck in grompp
commit
|
commitdiff
|
tree
2018-03-15
Berk
H
e
ss
Fi
x
vi
r
ial wit
h
external pull potential and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
ix C
O
M
p
ulling with ex
t
ernal p
o
tential w
i
th
#
ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
He
s
s
Fix pull b
u
g
with geometry
=
d
ire
c
tion
-
period
i
c
commit
|
commitdiff
|
tree
2018-03-07
B
er
k
Hess
Fix memo
r
y leak
i
n PME
commit
|
commitdiff
|
tree
2018-03-05
Berk H
e
ss
Work aroun
d
gcc bug with g
r
oup kernel
t
ab
l
es
commit
|
commitdiff
|
tree
2018-03-05
Berk Hes
s
Lea
v
e nu
l
lptr opt
in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk
Hess
F
ix cppcheck warn
i
ng
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
F
ix AWH bias-sharing wi
t
h parallel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun
m
ul
t
isim with separate PME ra
n
k
s
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simplify md
r
un tMP
I
thread
spawning
commit
|
commitdiff
|
tree
2018-02-19
Mark Abraham
Re
m
ove cycle suppression
commit
|
commitdiff
|
tree
2018-02-19
M
ark Ab
r
ah
a
m
Disallowed change of ensemb
l
e for
checkp
o
int res
t
art
commit
|
commitdiff
|
tree
2018-02-14
Mar
k
Abraha
m
Fix b
u
g in checkpoint er
r
or check
i
ng
commit
|
commitdiff
|
tree
2018-02-12
Szilárd Páll
Remov
e
sing
l
e/multi c
o
mp
i
lation unit
s
witching logi
c
commit
|
commitdiff
|
tree
2018-02-12
Szilárd P
á
ll
Re
m
ove te
x
ture refer
e
nce
s
upport in
t
he
C
UD
A
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Allo
w
b
o
nds with dis
t
anc
e
=0
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Only setup Ewal
d
in t
h
e gen
e
ric group kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set c
u
toff modifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix asser
t
i
o
n failure in
T
P
I
commit
|
commitdiff
|
tree
2018-01-30
Mark Abr
a
ham
Re
p
lace macros
f
or mult
i
-
sim
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Go
t
rid
of ma
n
u
al memory
m
ana
g
ement in
t
h
e
P
ME
o
verlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re-enabl
e
multi-rank PME tests (with the
f
ile
rac
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
B
e
rk Hess
A
dd check in grompp to avo
i
d assertion failure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
R
eplace
s
tderr pr
i
nts i
n
filenm
.
c
p
p
b
y asserts
commit
|
commitdiff
|
tree
2018-01-16
B
erk Hess
R
e
move tumbling ic
e
-c
u
be
warning
w
i
th SD
commit
|
commitdiff
|
tree
2018-01-12
Szilárd P
á
l
l
Call GP
U
profiler reset
o
n separate PME r
a
n
k
s
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
e
s
s
Reword CPU/GPU imbalance not
e
s
commit
|
commitdiff
|
tree
2018-01-09
Mark Ab
r
a
h
am
Deactivate autoselect
o
f PME on GPU on
s
e
parate rank
commit
|
commitdiff
|
tree
2018-01-08
B
erk
H
e
s
s
Fix t
r
iclinic
d
omain decomposit
i
on bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Mak
e
acceleration c
o
rrect
i
on VCM mode work
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -
n
tmp
i
with setti
n
g -nto
m
p with GP
U
s
commit
|
commitdiff
|
tree
2017-12-11
Pau
l
B
a
uer
D
i
s
a
l
low comb
i
n
a
t
i
on
o
f PME-us
e
r an
d
verlet cutoff
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupi
n
ov
P
r
ov
i
d
e
dummy ini
t
i
a
l
ization
to s
i
l
ence a
w
arnin
g
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix pme gather in doubl
e
w
ith A
V
X(2)_12
8
commit
|
commitdiff
|
tree
2017-12-04
Ale
k
sei Iupi
n
ov
Refo
r
mulate P
M
E
s
olving tests toleranc
e
s
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Merge "
M
erge
branch release-2016 into rele
a
se-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
e
s
s
Fi
x
ed
i
nitial
t
e
m
p
erature reporti
n
g
commit
|
commitdiff
|
tree
2017-12-04
Mark Abraham
Fix unused variab
l
es
i
n CPU pruning ke
r
nels
commit
|
commitdiff
|
tree
2017-11-30
Viveca Lindah
l
Correct AW
H
inpu
t
file name in do
c
ume
n
ta
t
ion
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Up
d
ate doc
u
me
n
tion of
Nose-Ho
o
ver outp
u
t
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Ex
t
end grompp miss
i
ng energy term message
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix P
M
E GPU
w
i
th walls
commit
|
commitdiff
|
tree
2017-11-25
Be
r
k H
e
ss
Fix
compi
l
er warning without
MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Spe
e
d u
p
nbnxn
b
u
f
fer clearing
commit
|
commitdiff
|
tree
2017-11-23
B
e
r
k
Hess
Up
d
a
t
e note in m
a
n
ual on
S
D
commit
|
commitdiff
|
tree
2017-11-23
B
e
rk Hess
Cor
r
e
ct PME GPU t
i
ming na
m
ing
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Us
e
m
u
ch less Padd
e
d
R
VecVect
o
r and more ArrayR
e
f o
f
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
Ber
k
Hess
Fix geni
o
n
c
harge s
u
m
m
a
t
ion
accuracy
commit
|
commitdiff
|
tree
2017-11-10
R
ola
n
d S
c
hulz
Rename
l
o
a
d1Dua
l
Hsimd to loadU1DualHsimd
commit
|
commitdiff
|
tree
2017-11-10
Roland Schulz
AVX
:
Improve loa
d
1DualHs
i
m
d
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
F
i
x E
k
i
n
at st
e
p 0 wit
h
C
O
M
remov
a
l
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
A
dd
m
issing Ewald correction
f
o
r
pme-u
s
er
commit
|
commitdiff
|
tree
2017-10-30
M
ark Abraham
Fix a
n
d
u
pdate hw_in
f
o
commit
|
commitdiff
|
tree
2017-10-29
Be
r
k He
s
s
Remove
i
ncorr
e
ct com
m
ent for CHAR
M
M tips3p
commit
|
commitdiff
|
tree
2017-10-26
S
zil
á
rd Pá
l
l
R
e
or
g
a
nize
P
M
E G
P
U l
a
u
n
ch
commit
|
commitdiff
|
tree
2017-10-24
B
erk Hess
F
ix gmx che
c
k
fo
r
t
prs with different #
a
toms
commit
|
commitdiff
|
tree
2017-10-24
Alekse
i
Iu
p
inov
Move
c
ommrec duty checking into simple getters
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix incorre
c
t
dV
/
dlambda for walls
commit
|
commitdiff
|
tree
2017-10-23
Dav
i
d van der Spoel
S
plit of
f
the NMR r
e
la
t
ed analy
s
es from g
m
x energy
.
commit
|
commitdiff
|
tree
2017-10-21
Berk
H
ess
Merge "Merge bran
c
h
r
e
lease-2016
"
commit
|
commitdiff
|
tree
2017-10-18
Berk Hess
M
a
d
e
CUDA PME texture reference
conditi
o
nal
commit
|
commitdiff
|
tree
2017-10-13
Roland Schul
z
R
epla
c
e all ConstAr
r
ayRef with
ArrayRef<const T>
commit
|
commitdiff
|
tree
2017-10-13
Magnus L
u
ndborg
Do not include headers related to ObservablesHi
s
tory
commit
|
commitdiff
|
tree
2017-10-13
Mar
k
Abraham
Fix cpuinfo on clang
+ non-x86
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupinov
R
e
v
e
r
t "Dro
p
NB_ from GMX_CUDA_NB
_
S
I
N
G
L
E_C
O
MPI
L
ATION
_
UNIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
Simpl
i
fy virial
h
andlin
g
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
F
i
x m
a
x_size() in allocator
.
h
commit
|
commitdiff
|
tree
2017-10-05
S
z
ilárd Páll
Refac
t
or scaled box handl
i
ng for PME/Ewald
commit
|
commitdiff
|
tree
2017-10-05
Ma
r
k Abraham
Conti
n
ue removin
g
-nb gpu_cpu
commit
|
commitdiff
|
tree
2017-10-04
Ro
l
a
n
d
Schulz
Al
l
ow non
-
cons
t
acce
s
s fo
r
co
n
st Arr
a
yRef
commit
|
commitdiff
|
tree
2017-10-04
Berk Hess
Remove
a
force buff
e
r arg
u
ment from IF
o
rceProvide
r
commit
|
commitdiff
|
tree
2017-10-03
A
leksei Iup
i
nov
Template/move CUDA
t
extur
e
cleanup code from NB
C
U
D
A
.
.
.
commit
|
commitdiff
|
tree
2017-09-28
Sz
i
l
á
rd
Pál
l
Correct misp
l
aced CUDA timing e
v
en
t
r
e
cord
commit
|
commitdiff
|
tree
2017-09-28
tom
a
skubar
QM/MM
:
rem
o
ve optimi
z
ation and
t
rans
.
state search
commit
|
commitdiff
|
tree
2017-09-26
Szilárd Pá
l
l
Rename GPU laun
c
h/w
a
i
t
cyc
l
e
c
ou
n
ters
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp
with A
n
dersen massive and n
o
COM removal
commit
|
commitdiff
|
tree
2017-09-20
Berk Hes
s
C
h
a
nge
n
bnxn
inde
x
ing t
o
templ
a
tes
commit
|
commitdiff
|
tree
2017-09-18
A
l
eksei Iupino
v
Skip GPU reallocation of
an e
m
pty
non-
l
ocal pairl
i
st
commit
|
commitdiff
|
tree
2017-09-18
Szilár
d
Pál
l
Min
o
r refactoring
o
f C
U
DA n
o
n-bonded kerne
l
s
commit
|
commitdiff
|
tree
next