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Use std::vector in nbnxn_grid_t
2018-05-22
Berk Hess
U
se std:
:
v
e
ctor in nbnxn_gri
d
_t
commit
|
commitdiff
|
tree
2018-05-22
K
e
v
in Boyd
Cosmeti
c
do
c
umenta
t
ion
c
hanges
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boyd
Minor fixes t
o
mdr
u
n
p
erformance documen
t
ation
commit
|
commitdiff
|
tree
2018-05-18
Al
e
ksei I
u
pin
o
v
prepareGpuKern
e
l
A
r
gument
s
()
and launchGpuK
e
rnel()
a
re
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
B
er
k
Hess
Spl
i
t off domdec
distributi
o
n and
cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split ato
m
redistribu
t
ion o
f
f fro
m
domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
B
e
r
k
H
ess
Remove
c
ommr
e
c f
r
om set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
R
o
la
n
d
S
chulz
Use same
Open
C
L ke
r
nel for diff
e
rent
V
end
o
r
s
commit
|
commitdiff
|
tree
2018-05-10
Carsten Kutz
n
er
I
n
troduce helper cla
s
ses for
force provider input
and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bauer
Fi
x
md -c
p
i -
n
oappend
commit
|
commitdiff
|
tree
2018-05-04
Mark
A
brah
a
m
Me
r
ge "
M
erge
b
ranc
h
release-2018"
commit
|
commitdiff
|
tree
2018-05-04
M
a
rk Abr
a
ham
Mor
e
const correc
t
ness
commit
|
commitdiff
|
tree
2018-05-03
Mar
k
Abr
a
ham
Merge branch release-2018
commit
|
commitdiff
|
tree
2018-05-02
Roland Schulz
E
n
able uncrus
t
ify for
O
penCL
commit
|
commitdiff
|
tree
2018-05-02
Rol
a
nd
Schulz
S
u
pport
4
sized
c
luste
r
for GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
B
e
rk Hess
Rem
o
ve p
u
ll
MPI cod
e
duplication
commit
|
commitdiff
|
tree
2018-04-26
Pau
l
B
auer
Reorg
a
n
iz
e
f
i
les f
o
r re
f
er
e
nc
e
m
a
nual
commit
|
commitdiff
|
tree
2018-04-26
P
a
ul Bauer
Spli
t
up
analys
i
s cha
p
ter in
r
e
f
erenc
e
man
u
al
commit
|
commitdiff
|
tree
2018-04-26
Paul Baue
r
Split up special topics sect
i
on
i
n manu
a
l
commit
|
commitdiff
|
tree
2018-04-25
P
a
ul Bau
e
r
Add pag
e
breaks
i
n
refere
n
ce manual
commit
|
commitdiff
|
tree
2018-04-25
P
a
ul B
a
ue
r
Split up I
n
te
r
action
functions manual page
commit
|
commitdiff
|
tree
2018-04-25
M
a
rk Abraha
m
R
efactor SD upd
a
te
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Change i
m
a
ge co
n
v
e
r
sion to
o
nly be build once
commit
|
commitdiff
|
tree
2018-04-23
Alekse
i
Iupinov
DeviceB
u
f
f
er headers are added
commit
|
commitdiff
|
tree
2018-04-23
Szilárd
P
áll
Fix
i
c
c
warni
n
g in pos
t
-submit
commit
|
commitdiff
|
tree
2018-04-21
Szilár
d
P
á
ll
Add post-su
b
mi
t
w
it
h
ARM HPC To
o
lchain
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Tweak
P
ME run mode check
s
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
C
o
nver
t
m
a
nua
l
from LaTeX to M
a
r
kup
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Second
c
hange tracking commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bau
e
r
Intermedia
t
e commit to
track ch
a
nges to manual
commit
|
commitdiff
|
tree
2018-04-17
Viveca Lindahl
Di
s
all
o
w
-skip values
<
=
0 fo
r
gmx trjc
o
nv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
B
a
uer
Fix leg
a
cy t
o
po
l
o
gy
m
e
m
or
y
erro
r
commit
|
commitdiff
|
tree
2018-04-17
M
a
r
k Abraha
m
Shift per-step control l
o
g
i
c t
o
do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Ab
r
aham
Break apar
t
u
p
date_constraints
commit
|
commitdiff
|
tree
2018-04-16
Sz
i
lárd Páll
Add
p
o
s
t
-submit te
s
t w
i
t
h
hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk Hes
s
Move natoms_mol
o
u
t of gmx
_
molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Ma
r
k A
b
raham
Updat
e
d mdrun
c
omp
a
r
iso
n
infrastru
c
ture
commit
|
commitdiff
|
tree
2018-04-13
Mark Abraham
Clean
u
p constraints code
commit
|
commitdiff
|
tree
2018-04-12
Mark
A
bra
h
am
Remove use of where(), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abrah
a
m
Reorganize
e
nergy e
v
aluat
i
on f
o
r EM
commit
|
commitdiff
|
tree
2018-04-10
Ale
k
s
ei Iupinov
Preve
n
t Ope
n
CL timing memor
y
le
a
k
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
C
o
nvert g
m
x
_molb
l
ock_t
t
o C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Abr
a
ham
Simplifi
e
d handling of simulation runn
e
rs
commit
|
commitdiff
|
tree
2018-04-05
Ma
r
k Abraham
Create grom
a
cs/mdrun
module a
n
d mo
v
e code there
commit
|
commitdiff
|
tree
2018-04-05
Szilárd P
á
l
l
Refactor cj
pr
e
load in the nonbond
e
d
OpenCL ke
r
nels
commit
|
commitdiff
|
tree
2018-04-04
Mark
A
br
a
h
am
Quiet checkpoint readin
g
commit
|
commitdiff
|
tree
2018-04-04
Pascal Merz
Move chec
k
N
umberOf
B
ondedI
n
teractions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
C
on
v
ert gmx_
m
top_t
to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abr
a
ham
R
emove lef
t
over m
e
n
tion of
t
win
-
rang
e
sch
e
me
commit
|
commitdiff
|
tree
2018-04-03
Mark Abrah
a
m
Merge
"
Merge branch release-2018"
commit
|
commitdiff
|
tree
2018-03-29
B
e
rk Hess
Mov
e
f
i
le o
p
ening out of init
_
pull()
commit
|
commitdiff
|
tree
2018-03-29
S
z
ilárd Pá
l
l
Twea
k
/e
n
able icc 1
8
post-
s
ubmit tests
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus Lu
n
d
borg
Improved c
h
eck of
i
f only
forces are computed in do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
Pau
l
Baue
r
Fix cma
k
e Sph
i
nx detection for
v
ersions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd
P
áll
Switc
h
CUDA 9
.
0/gcc 5 test to CUDA 9
.
1
/
gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize
p
ull_coord_work
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abra
h
am
Free more memory in gr
o
mpp and mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove mols
from
g
mx_mt
o
p_t
commit
|
commitdiff
|
tree
2018-03-28
Ma
r
k Abraham
Me
r
ge branch rele
a
s
e-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Clarifie
d
mdp options
r
e
lating to
b
o
nds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Mo
r
e gc
c
-8 fixes fo
r
PO
W
ER
commit
|
commitdiff
|
tree
2018-03-21
Davi
d
v
an der Spoel
R
e
name
d
entrop
y
.
* t
o
thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk A
b
r
aham
Version 201
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
M
ark Abraham
Merge
"Merge
bra
n
ch release-201
6
i
nto releas
e
-
2
018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abra
h
am
Update release
notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Merge branch re
l
e
a
s
e-2016 into
r
elease-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use of
g
pu_id in
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
Berk He
s
s
Disallo
w
si
n
gle simulatio
n
wi
t
h mult
i
s
im
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braham
Update use of gpu_
i
d in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abra
h
a
m
U
p
d
ate
u
se of gpu_i
d
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
A
b
r
a
ha
m
A
dd
hel
p
er function to make a vector from a
n
A
r
rayR
e
f
commit
|
commitdiff
|
tree
2018-03-19
Mar
k
Ab
r
aham
Fix
V
SX S
I
MD with
g
cc 8
commit
|
commitdiff
|
tree
2018-03-16
Pau
l
Ba
u
er
Only fre
e
topology whe
n
a
l
located
commit
|
commitdiff
|
tree
2018-03-16
Ber
k
Hess
Correct PMF sign error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Imp
r
o
v
e inter-simu
l
ation sig
n
aling
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Mak
e
a persistent
phy
s
ical
n
o
d
e
c
o
m
municator
commit
|
commitdiff
|
tree
2018-03-14
Berk H
e
ss
Fi
x
mdrun sign
a
lling with AWH bias sh
a
r
ing
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k Hess
Add AWH fixes to rele
a
se
n
otes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd
P
áll
Require OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH en
s
emble checkpoi
n
ting
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
i
x AWH decon
v
olution when
sha
r
i
n
g
a
bias
commit
|
commitdiff
|
tree
2018-03-13
Mar
k
Abraham
Introduce co
n
strain_shake
commit
|
commitdiff
|
tree
2018-03-13
Szilárd
P
áll
Fix clang 6
.
0
wi
t
h
C
UDA
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Me
r
ge "Merge branch release-2018"
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
C
orrect
p
d
b2gmx -missing op
t
ion
commit
|
commitdiff
|
tree
2018-03-06
Ber
k
H
ess
Co
n
vert
t_filenm to
C
++
commit
|
commitdiff
|
tree
2018-03-06
M
ark Abraham
Merge
b
ranch r
e
lease-
2
018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Fixed dvdla
m
bda fo
r
SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
S
zilárd
P
áll
Ad
d
to the contribu
t
or sect
i
on
commit
|
commitdiff
|
tree
2018-03-01
Ber
k
Hess
Detect AM
D
S
M
T t
o
polo
g
y
commit
|
commitdiff
|
tree
2018-02-28
Mark
Abraham
Mo
v
ed and remov
e
d
c
onstra
i
n
t
c
od
e
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
Reor
g
anize
d
con
s
traint code
commit
|
commitdiff
|
tree
2018-02-27
Mar
k
Ab
r
a
h
am
Fi
x
GPU utils test
commit
|
commitdiff
|
tree
2018-02-26
Paul Bauer
Change TNG
f
ile opening
commit
|
commitdiff
|
tree
2018-02-26
Mark
A
braham
Permit define
.
mdp field to assign
values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei I
u
pi
n
ov
A
d
vice users on infinite o
u
tput
o
f
TPI
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abra
h
am
Organize
f
or
recording 2
0
16-era release
notes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
F
ix md integrator with Nose-H
o
ove
r
coupling
commit
|
commitdiff
|
tree
2018-02-21
Mark Abra
h
a
m
Enhanced docs of
pimpl pointer helper
commit
|
commitdiff
|
tree
2018-02-16
Mark Abra
h
am
M
e
rg
e
branch
re
l
eas
e
-
2
0
16 i
n
to release-2018
commit
|
commitdiff
|
tree
next