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Use stack buffer for LINCS&bonded gather/scatter
2015-06-03
Roland Schulz
Use stack buffer for
LIN
C
S&b
o
nded g
a
th
e
r
/scatter
commit
|
commitdiff
|
tree
2015-06-02
R
o
s
s
e
n
A
p
ostol
o
v
C
o
nverted r
a
ndom m
o
dule to C++
.
commit
|
commitdiff
|
tree
2015-05-28
Teemu Murtola
Additional selecti
o
n examples
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Refa
c
toring
of
PM
E
load balancing
commit
|
commitdiff
|
tree
2015-05-27
Rossen Apostolov
Converted pu
l
ling
c
ode to C++
.
commit
|
commitdiff
|
tree
2015-05-26
M
ark A
b
raham
Avoid
p
ossible floating-po
i
nt
e
xce
p
tion
commit
|
commitdiff
|
tree
2015-05-24
Teemu Murtola
Include selection keyword details i
n
u
se
r
guide
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Base to get al
l
'gmx he
l
p
'
c
on
t
ents to user guide
commit
|
commitdiff
|
tree
2015-05-22
T
eemu Mur
t
ola
Av
o
id crash w
i
th empty reference for 'same
a
s'
selection
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murt
o
l
a
A
dd subsection depth to Hel
p
Wr
i
te
r
Con
t
ext
commit
|
commitdiff
|
tree
2015-05-22
Tee
m
u Murtola
Add n
o
te
about atom order i
n
sel
e
ct
i
on
s
commit
|
commitdiff
|
tree
2015-05-21
Teemu M
u
r
tola
Restr
u
cture
CommandLineModu
l
eMan
a
ger tests
commit
|
commitdiff
|
tree
2015-05-21
Mark Ab
r
a
ham
Add integration t
e
st for empty d
o
main
commit
|
commitdiff
|
tree
2015-05-20
T
e
emu Murtola
Fix
d
e
pendencies for reg
r
e
s
sion
t
est
custom
t
arget
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtola
Some test
s
for 'gmx help -ex
p
ort rst'
commit
|
commitdiff
|
tree
2015-05-19
M
a
r
k
A
braha
m
Refa
c
t
o
r F
F
TW setup
commit
|
commitdiff
|
tree
2015-05-18
Teemu M
u
rtola
Me
r
ge "
M
erge bran
c
h
o
rigin/re
l
ease-5-0"
commit
|
commitdiff
|
tree
2015-05-17
Erik Lin
d
ahl
Added h
a
ck
s
for SIMD rvec/load stor
e
in lin
c
s &
b
ondeds
commit
|
commitdiff
|
tree
2015-05-17
Te
e
mu M
u
rtola
Move
a
few defin
e
s
t
o
build
i
nfo
.
h
commit
|
commitdiff
|
tree
2015-05-16
B
e
rk Hess
L
INCS thr
e
ad task
s
can no
w
b
e independ
e
nt
commit
|
commitdiff
|
tree
2015-05-16
Mark Abr
a
h
a
m
Sup
p
ress
G
CC5 warnings
w
ith interna
l
B
oost
commit
|
commitdiff
|
tree
2015-05-16
Ma
g
nus Lundborg
TNG version 1
.
7
.
5
commit
|
commitdiff
|
tree
2015-05-16
Ale
x
e
y
Shvetsov
Make bond-atomt
y
p
e
s
c
a
se sensitive
commit
|
commitdiff
|
tree
2015-05-14
M
ark Abr
a
ham
Fix o
w
n-FFTW build
commit
|
commitdiff
|
tree
2015-05-13
T
e
emu Murtola
Remov
e
remaining old-ht
m
l co
n
tent
commit
|
commitdiff
|
tree
2015-05-13
Berk Hes
s
Fi
x
segv
i
n
g_covar
commit
|
commitdiff
|
tree
2015-05-13
Szilard Pall
Fix auto
-
d
o
w
nl
o
aded reg
r
ession test e
x
ec
u
ti
o
n
commit
|
commitdiff
|
tree
2015-05-13
Ro
l
and Sc
h
ulz
Facilit
a
te li
n
ki
n
g of stat
i
c binaries
commit
|
commitdiff
|
tree
2015-05-12
Mark
A
braham
Fix
u
ninitialized fields
in gro
m
pp
t
_state
commit
|
commitdiff
|
tree
2015-05-11
Mark Abraham
Work arou
n
d g
c
c
5 warni
n
gs with Google Test
commit
|
commitdiff
|
tree
2015-05-10
Mark Abraham
Me
r
ge "Merge bra
n
ch
r
elease-5-0"
commit
|
commitdiff
|
tree
2015-05-10
Teem
u
M
u
r
t
ola
Print correc
t
order for i
n
c
lude or
d
er/style i
s
su
e
s
commit
|
commitdiff
|
tree
2015-05-10
Te
e
mu
M
u
rtola
Im
p
rove build system for Sphinx
commit
|
commitdiff
|
tree
2015-05-10
T
eemu
Murtola
Conv
e
rt developer
ma
n
ua
l
t
o
rst
commit
|
commitdiff
|
tree
2015-05-06
Mark Abrah
a
m
Fixed re
c
ently-introduced coup
l
e-lambda warning mes
s
age
commit
|
commitdiff
|
tree
2015-05-06
Sz
i
l
á
rd Páll
Mer
g
e "Merge relea
s
e-4-6 into
release-5-0"
i
nto release-5-0
commit
|
commitdiff
|
tree
2015-05-06
Mark Abraham
Fi
x
SI
M
D
u
nit t
e
sts on
BG/Q
commit
|
commitdiff
|
tree
2015-05-05
Teemu Murtola
Avoid rounding
erro
r
s affecting
r
e
sults in one test
commit
|
commitdiff
|
tree
2015-04-30
Olivi
e
r Fisette
F
ix error handlin
g
in g
m
x
_
tm
p
nam
commit
|
commitdiff
|
tree
2015-04-30
Michael Shirts
F
i
x for rarely
occuring repli
c
a exch
a
nge e
r
ror
.
commit
|
commitdiff
|
tree
2015-04-28
M
a
r
k Abraham
Add appl
i
catio
n
-clock
N
V
ML
-
based
s
upport for Quadro
.
.
.
commit
|
commitdiff
|
tree
2015-04-27
Mark Abraham
Clean
u
p
remnant
s
in mdrun
commit
|
commitdiff
|
tree
2015-04-21
S
z
ilárd Páll
Al
l
o
w manu
a
lly s
e
t
ti
n
g target
G
PU
a
r
c
hitectures
commit
|
commitdiff
|
tree
2015-04-21
Magnus Lun
d
borg
TNG version 1
.
7
.
3
commit
|
commitdiff
|
tree
2015-04-21
Mark Abra
h
a
m
Merge "Merge
branch release-5-0"
commit
|
commitdiff
|
tree
2015-04-17
Be
r
k Hess
A
dd val
u
e_ref an
d
value to p
u
l
l
_coor
d
_t
commit
|
commitdiff
|
tree
2015-04-17
Szilárd P
á
ll
d
efine CUD
A
version and texob
j
s
upport in config
.
h
commit
|
commitdiff
|
tree
2015-04-17
Mark Ab
r
ah
a
m
Add comment about
Andersen
t
h
emostat and c
o
nstraints
commit
|
commitdiff
|
tree
2015-04-17
D
avid
van der Spoel
Up
d
ated expon
e
ntial fitting to make
i
t robust
.
commit
|
commitdiff
|
tree
2015-04-08
Berk Hess
Added pull geometry direction-relative
commit
|
commitdiff
|
tree
2015-04-01
Mark Abra
h
am
In
i
tialize n_tricvec fi
e
ld of t_pbc alw
a
ys
commit
|
commitdiff
|
tree
2015-04-01
B
erk Hess
Co
r
rected
force-sw
i
tch manual
sec
t
ion
commit
|
commitdiff
|
tree
2015-03-30
Mark Abr
a
h
am
Improved man-pag
e
ma
c
h
i
n
ery
commit
|
commitdiff
|
tree
2015-03-25
Erik Lind
a
hl
Quote
f
rom
Jen-Hsun at
the
N
VIDIA
GTC conference 2015
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Removed reduction o
f
dH/dl without F
E
commit
|
commitdiff
|
tree
2015-03-13
Mark Abraham
Made
GPU war
n
i
ng
m
essa
g
es more user fri
e
ndly
commit
|
commitdiff
|
tree
2015-03-12
B
e
r
k
H
e
ss
Fixe
d
mdrun fp ex
c
e
p
tion with
-debu
g
commit
|
commitdiff
|
tree
2015-03-11
B
e
rk Hess
Add
e
d update x copy-back t
o
update timer
commit
|
commitdiff
|
tree
2015-03-06
Berk Hess
I
m
prov
e
threading
of bond
e
d
s
commit
|
commitdiff
|
tree
2015-03-06
M
a
rk Abraham
Restor
e
wallcycle su
b
c
ounte
r
name to "Bon
d
ed F"
commit
|
commitdiff
|
tree
2015-03-05
Ma
r
k
Abraham
Fi
x
Andersen thermostats
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
SIMD
a
c
celeration for LINCS
commit
|
commitdiff
|
tree
2015-03-04
B
e
r
k Hess
CO
M
pul
l
ing options per c
o
o
rd, improved cylinder
commit
|
commitdiff
|
tree
2015-03-04
R
oland
S
chul
z
Fix G
C
C5 warni
n
gs
commit
|
commitdiff
|
tree
2015-03-03
Mark Abra
h
am
Re-imple
m
ent gmx tune_pm
e
-cpi
commit
|
commitdiff
|
tree
2015-03-03
Erik
Lindahl
Ad
d
ed single-accuracy S
I
MD double mat
h
fu
n
c
tions
commit
|
commitdiff
|
tree
2015-03-03
Berk He
s
s
Fix
d
iv by ze
r
o in PP/PME ratio
commit
|
commitdiff
|
tree
2015-03-03
M
ark Abraha
m
Add test that
p
lain mult
i
-sim
u
lation w
o
rk
s
commit
|
commitdiff
|
tree
2015-03-02
David van der
S
po
e
l
Update
d
document
a
tion for el
e
ctric
f
i
e
lds
.
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Added parenth
e
ses f
o
r c
a
sts in SIMD mac
r
os
commit
|
commitdiff
|
tree
2015-03-02
Ro
l
and Schulz
Don'
t
search in
s
tall
a
tion prefix if binary is not
fo
u
n
d
commit
|
commitdiff
|
tree
2015-03-02
Mark
A
braham
Add infrastructur
e
for
r
unnin
g
MPI integration t
e
sts
commit
|
commitdiff
|
tree
2015-02-25
Ro
l
and S
c
hu
l
z
C++ conversion for PME spread/gather
commit
|
commitdiff
|
tree
2015-02-25
Mark
Abraham
Add
c
onte
n
t to user guide
commit
|
commitdiff
|
tree
2015-02-25
M
ark Abra
h
am
Split pm
e
.
c
i
nto
multiple
f
iles
commit
|
commitdiff
|
tree
2015-02-25
M
ark
Abra
h
am
Add mdp-option
s
to user guide
commit
|
commitdiff
|
tree
2015-02-24
Berk H
e
ss
Fixed para
l
lel dis
t
ribu
t
ion a
n
d t
h
r
ead count reporti
n
g
commit
|
commitdiff
|
tree
2015-02-24
Erik
L
indahl
Add AVX-512F SIM
D
support
commit
|
commitdiff
|
tree
2015-02-18
M
a
rk Abraham
Ree
n
able
S
I
MD for
R
-
B
dihedrals
commit
|
commitdiff
|
tree
2015-02-14
E
ri
k
Ma
r
k
l
u
nd
gm
x
hbond n
o
longer
r
e
mo
v
es PBC when no
n
e
is p
r
esent
commit
|
commitdiff
|
tree
2015-02-13
M
a
rk Ab
r
a
h
am
Implement
e
d document
a
tion with sphin
x
commit
|
commitdiff
|
tree
2015-02-12
Vedran Miletić
Fix removal of
s
y
mli
n
ks crea
t
ed
dur
i
ng
install
a
ti
o
n
commit
|
commitdiff
|
tree
2015-02-10
Rola
n
d Schulz
Don't set CFL
A
GS for P
h
i in
toolchain
commit
|
commitdiff
|
tree
2015-02-07
Roland Sc
h
ulz
Make FindBo
o
st quite
commit
|
commitdiff
|
tree
2015-02-07
T
e
emu Murtola
Suppo
r
t more co
m
plex fixed position select
i
o
n
s
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-enabled SI
M
D
for
a
ngle
s
and d
i
h
edrals
commit
|
commitdiff
|
tree
2015-02-04
Berk
H
ess
Co
r
rect CUDA kern
e
l e
n
ergy
f
lag
commit
|
commitdiff
|
tree
2015-02-02
Roland Schu
l
z
Fix FP ex
c
eption in FE
commit
|
commitdiff
|
tree
2015-02-02
M
a
rk A
b
raham
Fix use
o
f si
m
d
.
h
commit
|
commitdiff
|
tree
2015-01-29
Teem
u
Mur
t
ola
Add
input fil
e
o
ptions that acce
p
t m
i
ss
i
n
g files
commit
|
commitdiff
|
tree
2015-01-29
John Baxter
Removes some unnec
e
ssary ternary conditi
o
nal
s
commit
|
commitdiff
|
tree
2015-01-24
Te
e
mu Murtola
Improve selection
error m
e
ss
a
ges (use
exception
s
)
commit
|
commitdiff
|
tree
2015-01-23
Mark Abraham
Chang
e
some
l
isted-forces
headers to
b
e library-onl
y
commit
|
commitdiff
|
tree
2015-01-23
Teemu Murtol
a
I
g
nore test-only dependency cycles
commit
|
commitdiff
|
tree
2015-01-20
Teemu Murtola
Make data file
path search more
r
eusable
commit
|
commitdiff
|
tree
2015-01-20
Teemu
M
urtola
Convert forcef
i
e
ld se
a
rch to C++
commit
|
commitdiff
|
tree
2015-01-19
Erik Lindahl
Added two
quotes from Julie
Bernauer
h
abilitation
commit
|
commitdiff
|
tree
2015-01-19
James
B
arnet
t
A
d
d tip4pe
w
parameters to
oplsaa
.
ff
commit
|
commitdiff
|
tree
2015-01-19
Te
e
m
u Murt
o
la
Remove
A
n
a
l
ysisNeighborhood
:
:setUseBoundi
n
gBo
x
()
commit
|
commitdiff
|
tree
2015-01-17
Teemu Murtola
Merge "Merge
b
r
a
nch release-
5
-0"
commit
|
commitdiff
|
tree
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