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Moved ngmx to C++, renamed it to view.
2013-09-21
David van der Spoel
Moved ngmx
t
o C
+
+, re
n
am
e
d it to vi
e
w
.
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraham
Remo
v
e
repeat sfree(state->
n
osehoover_xi)
commit
|
commitdiff
|
tree
2013-09-20
T
e
em
u
Murtola
CMak
e
cle
a
nup
.
commit
|
commitdiff
|
tree
2013-09-19
Tee
m
u Murtola
M
a
k
e
uncrust
i
fy
.
sh more ve
r
bose
on
er
r
o
r
s
.
commit
|
commitdiff
|
tree
2013-09-19
Teemu Murto
l
a
Uniform code p
a
th
f
or writing out console help
.
commit
|
commitdiff
|
tree
2013-09-19
Teemu Mu
r
t
ola
Fr
a
mework for help export from wrapper
b
i
nary
.
commit
|
commitdiff
|
tree
2013-09-18
Ma
r
k Abraha
m
Remove force
f
ield-scan featur
e
commit
|
commitdiff
|
tree
2013-09-13
Teemu Murtola
Add
optio
n
to build a standalone mdrun binary only
.
commit
|
commitdiff
|
tree
2013-09-13
Teem
u
Mu
r
t
o
l
a
Move mdrun into the wr
a
pper
b
ina
r
y
.
commit
|
commitdiff
|
tree
2013-09-13
Teemu Mu
r
t
ola
Make parse_comm
o
n_ar
g
s(
)
not exit
.
commit
|
commitdiff
|
tree
2013-09-13
Teemu Murtola
Remove u
n
us
e
d
-man output forma
t
s
.
commit
|
commitdiff
|
tree
2013-09-09
Teemu Mur
t
ola
Ma
k
e gmx_ana_pos_t a C++ class
.
commit
|
commitdiff
|
tree
2013-09-09
T
e
emu
Murto
l
a
Add som
e
l
e
gends
to
C++ tool output
.
commit
|
commitdiff
|
tree
2013-09-08
T
e
emu M
u
rtola
Remove duplicat
e
.
nr
m
embers from selectio
n
structs
.
commit
|
commitdiff
|
tree
2013-09-08
Teemu Murtola
Remove
gmx
_
an
a
_
indexmap_t
:
:
bMapStatic
.
commit
|
commitdiff
|
tree
2013-09-08
Te
e
m
u
Murtola
Move gm
x
_
a
na_pos_t:
:
g
i
nto gm
x
_ana_inde
x
m
a
p_
t
.
commit
|
commitdiff
|
tree
2013-09-05
Teem
u
Murtola
Abstrac
t
A
n
alysisData module
h
a
ndlin
g
i
n
to a separate
.
.
.
commit
|
commitdiff
|
tree
2013-09-01
T
e
e
mu Murt
o
l
a
Mer
g
e "Merge branch rele
a
se-4-6 into master"
commit
|
commitdiff
|
tree
2013-08-30
David van de
r
Spoel
Updated g_cluster
commit
|
commitdiff
|
tree
2013-08-30
Teemu Murt
o
la
Clean-up and im
p
rovements in C++ tools
.
commit
|
commitdiff
|
tree
2013-08-25
Ma
r
k A
b
raham
Fix de
t
ection and sug
g
estion in gmx
_
cpuid for IBM QPX
commit
|
commitdiff
|
tree
2013-08-25
Be
r
k Hess
intro
d
uced nbnxn
d
ata structure for boun
d
ing bo
x
e
s
commit
|
commitdiff
|
tree
2013-08-25
M
ark Abraham
Fixes fo
r
Bluegene/Q
commit
|
commitdiff
|
tree
2013-08-25
M
a
rk Abra
h
a
m
Consoli
d
ated NBNxN
S
IM
D
k
ernel util
i
ty rout
i
ne
s
commit
|
commitdiff
|
tree
2013-08-25
Ma
r
k
Abra
h
am
F
ix minor w
a
llcycle output is
s
ues
commit
|
commitdiff
|
tree
2013-08-25
Ma
r
k
A
braham
Fixed G
M
X_DD_DUMP_GR
I
D
commit
|
commitdiff
|
tree
2013-08-24
T
e
emu Murtola
Fi
n
e
-
tune copyrig
h
t printing
.
commit
|
commitdiff
|
tree
2013-08-21
Teemu Murtola
Statis
t
i
c
s for
g
mx-distance
.
commit
|
commitdiff
|
tree
2013-08-21
Teemu Mu
r
tola
Lifetim
e
sta
t
ist
i
cs into gmx-select
.
commit
|
commitdiff
|
tree
2013-08-20
M
ark Ab
r
aham
Remove OpenMM
commit
|
commitdiff
|
tree
2013-08-20
Berk Hess
fixed pa
r
a
llel normal modes with PME
commit
|
commitdiff
|
tree
2013-08-16
T
e
e
m
u Murtola
R
e
placement for g_bond and g_dist
.
commit
|
commitdiff
|
tree
2013-08-11
Teemu M
u
r
tola
Support for m
u
ltiple analysis
d
ata sets in modules
.
commit
|
commitdiff
|
tree
2013-08-11
Teemu Murtola
Base sup
p
ort for multiple
a
n
alysisdata data sets
.
commit
|
commitdiff
|
tree
2013-08-10
Teem
u
Mur
t
ol
a
Remove
s
uper
f
luous selectio
n
names
f
rom refda
t
a
.
commit
|
commitdiff
|
tree
2013-08-10
T
eemu Mu
r
tola
A
dd ch
e
ck for unsorted index gro
u
p
s in
s
elections
.
commit
|
commitdiff
|
tree
2013-08-09
Teemu Mur
t
ola
Treat exc
e
ptions bet
t
er i
n
int
e
r
active
selections
.
commit
|
commitdiff
|
tree
2013-08-05
M
a
rk Abraham
Fixed
r
e
f
erence SIMD code to work with MSVC
commit
|
commitdiff
|
tree
2013-08-05
Teemu Murtol
a
Add unit tests f
o
r index gr
o
ups
in selecti
o
ns
.
commit
|
commitdiff
|
tree
2013-08-04
Teemu Murto
l
a
Add unit
te
s
t cove
r
age for simple se
l
ection keywor
d
s
.
commit
|
commitdiff
|
tree
2013-08-03
Teemu Murt
o
la
File utils to C++
.
commit
|
commitdiff
|
tree
2013-08-02
Teemu
M
urtola
Add an o
p
tion
t
o
di
s
able
all asserts for coverage
.
commit
|
commitdiff
|
tree
2013-08-01
Mar
k
Abra
h
a
m
Refactored
p
reparati
o
n
of
b
u
f
fer for NBNxN table loads
commit
|
commitdiff
|
tree
2013-08-01
Ca
r
sten
Kutzner
Properly finalize MPI on mdrun -version
.
F
i
xes
#
1
313
commit
|
commitdiff
|
tree
2013-08-01
Mark Abraham
Fi
x
ed example
c
ode
f
unctio
n
name
commit
|
commitdiff
|
tree
2013-07-30
Mark
Abraham
Re
m
oved unused varia
b
les
commit
|
commitdiff
|
tree
2013-07-30
Teemu Mu
r
t
ola
Handle wrap
p
er binary opti
o
ns also for symlinks
.
commit
|
commitdiff
|
tree
2013-07-30
Teemu Murtol
a
Better c
o
mma
n
d-lin
e
opt
i
o
n
handling for tests
.
commit
|
commitdiff
|
tree
2013-07-25
Justin Lemkul
Update
d
d
l
ist
.
c to re
c
o
g
n
i
ze more
atom na
m
es
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey Shvetsov
nb_kern
e
l_sp
a
rc64_hpc_ace_d
o
uble: clean up
-
Wunused
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Ale
x
ey Shvets
o
v
nb_kerne
l
_sse4_1
_
do
u
b
l
e:
c
lean up -Wu
n
u
s
e
d
-
parame
t
er
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey
S
hv
e
tsov
nb_kernel_sse2_double: clean up -Wunused-parameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexe
y
Shvets
o
v
nb_kernel_a
v
x_256_double:
cl
e
an up -W
u
n
u
sed-pa
r
ameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Ale
x
ey Shve
t
sov
n
b_kernel_a
v
x_128_
f
m
a
_d
o
uble
:
clean up -Wunus
e
d-parameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey Shve
t
sov
n
b_kernel_
s
se2
_
single: cl
e
an up -W
u
nused-pa
r
ameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey Shvetsov
nb_kern
e
l_sse4_1
_
single: clean up -Wunused-parameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey S
h
vetso
v
nb_kernel
_
avx_128_fma_single: clean up -
W
un
u
sed-paramet
e
r
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey Shvet
s
ov
nb_kernel_avx_256_single: clean
u
p
-Wunu
s
ed-param
e
ter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Mark Abraham
Cl
a
r
ified logic i
n
g
_wham
commit
|
commitdiff
|
tree
2013-07-25
M
a
r
k
Abraham
Find mkl
.
h
o
n more icc version
s
commit
|
commitdiff
|
tree
2013-07-25
A
l
e
xey Shvet
s
ov
nonbond
e
d a
n
d nb_kernel_c: clean up -W
u
n
used
-
parameter
.
.
.
commit
|
commitdiff
|
tree
2013-07-25
Alexey
Shvetsov
mdlib:
c
lean
u
p -Wunused-parame
t
er warnings
commit
|
commitdiff
|
tree
2013-07-25
Mark Abraham
Update
m
anagement
o
f l
i
n
ear a
l
gebra libra
r
ies
commit
|
commitdiff
|
tree
2013-07-25
T
e
emu
M
urtola
Add
u
nit tests for selec
t
ion position
c
alculation
.
commit
|
commitdiff
|
tree
2013-07-24
Mark Abraham
Add fiv
e
new quo
t
es
commit
|
commitdiff
|
tree
2013-07-24
Teemu M
u
rtola
Fix pthread det
e
c
tion for GMock
commit
|
commitdiff
|
tree
2013-07-24
B
erk Hess
implement
e
d pl
a
in-C
S
I
MD macro
s
f
o
r refere
n
ce
commit
|
commitdiff
|
tree
2013-07-24
Mark Abraham
Rem
o
ved buggy -seppot outpu
t
commit
|
commitdiff
|
tree
2013-07-24
Roland Schulz
Merge "
M
erge bra
n
c
h release-4-6 into
master"
commit
|
commitdiff
|
tree
2013-07-22
Te
e
mu
M
urtola
Conveni
e
nce methods fo
r
i
mplementing main(
)
.
commit
|
commitdiff
|
tree
2013-07-22
Tee
m
u Murtola
Improve prog
r
am name
reporting
.
commit
|
commitdiff
|
tree
2013-07-21
Te
e
mu Murto
l
a
U
n
iform
"generate
d
by" information in o
u
tput files
.
commit
|
commitdiff
|
tree
2013-07-20
Tee
m
u
M
u
rto
l
a
Options
f
o
r
con
t
rolli
n
g
s
tar
t
up
out
p
ut
.
commit
|
commitdiff
|
tree
2013-07-20
Teemu Murt
o
la
Be less
verbose with pro
g
ram
o
ptions
.
commit
|
commitdiff
|
tree
2013-07-19
T
e
emu
Murtola
Pre-emptiv
e
ly fix some C++ warnings
.
commit
|
commitdiff
|
tree
2013-07-19
T
e
em
u
Murtol
a
Unif
o
rm and
l
ess ver
b
o
s
e
s
ta
r
tup for all
bin
a
ries
.
commit
|
commitdiff
|
tree
2013-07-19
Teemu Murtol
a
E
xtract Doxygen
c
ommen
t
s within
#ifd
e
f _
_
cplusplu
s
.
commit
|
commitdiff
|
tree
2013-07-18
Mark A
b
raham
Fi
x
ed pdb
2
gmx -vsite hydrogen -o conf
.
pdb
commit
|
commitdiff
|
tree
2013-07-17
T
eem
u
Murto
l
a
Su
p
port
f
o
r s
t
oring mul
t
ipoi
n
t anal
y
sis dat
a
.
commit
|
commitdiff
|
tree
2013-07-17
David va
n
d
e
r Spoel
Add
e
d citation to free volume paper
.
commit
|
commitdiff
|
tree
2013-07-14
Mark Abraha
m
F
ixed possib
l
e dere
f
er
e
nce of n
u
ll po
i
nter
commit
|
commitdiff
|
tree
2013-07-11
Mark
Abra
h
am
Fi
x
ed typos in #includ
e
gua
r
d #defines
commit
|
commitdiff
|
tree
2013-07-09
Mark Abraham
Remove orphan
CMak
e
fil
e
commit
|
commitdiff
|
tree
2013-07-07
Mark Abraham
Fixed mi
n
or
a
dmin issues
commit
|
commitdiff
|
tree
2013-07-05
Mark
A
br
a
h
a
m
Bump ve
r
s
i
on after 4
.
6
.
3 relea
s
e
commit
|
commitdiff
|
tree
2013-07-03
Teemu Murtola
S
p
l
i
t AnalysisDataStor
a
geFr
a
me into two
.
commit
|
commitdiff
|
tree
2013-07-03
Tee
m
u Murtola
Switch remaining
main() functions and
c
o
p
yri
t
e
.
c
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-07-03
T
eemu Murtola
Remove
g_hi
g
hway a
n
d
v
box
.
c
.
commit
|
commitdiff
|
tree
2013-07-03
Teemu Murto
l
a
Furth
e
r copyrite
.
h
c
leanup
.
commit
|
commitdiff
|
tree
2013-07-01
M
a
r
k
Abraham
Corrected de
f
initi
o
n of EEL_USER
commit
|
commitdiff
|
tree
2013-07-01
Sander
P
ron
k
Compreh
e
nsi
v
e hwinfo str
u
cture concurrency fix
.
commit
|
commitdiff
|
tree
2013-06-30
Teemu Murt
o
l
a
Script for running
uncrustify for m
o
di
f
ied files
.
commit
|
commitdiff
|
tree
2013-06-28
Jus
t
in Lemkul
M
inor tweaks to qm_orca
.
c
commit
|
commitdiff
|
tree
2013-06-28
Justi
n
L
e
m
ku
l
Fixe
s
to conf
i
g
.
h
.
cma
k
e
in t
o
set
G
MX_QMMM_ORCA
.
commit
|
commitdiff
|
tree
2013-06-27
Teemu Murtola
More flexible positio
n
input for nbsear
c
h
routi
n
es
.
commit
|
commitdiff
|
tree
2013-06-27
Teemu Murtola
C
+
+-ify
an
a
lysis
n
bsearch more
.
commit
|
commitdiff
|
tree
2013-06-27
Tee
m
u
Mu
r
tola
Remove C API
f
or analysis neighborhoo
r
search
.
commit
|
commitdiff
|
tree
2013-06-27
Teemu Murtola
Better
concu
r
rency support
f
or analy
s
is
n
bsearch
.
commit
|
commitdiff
|
tree
2013-06-27
T
e
e
mu
M
urtola
Fix analysis nei
g
hborhood sear
c
h for 2D
/
screw
P
B
C
.
commit
|
commitdiff
|
tree
2013-06-27
Szilar
d
Pall
Adapted clang-AMD-FMA workar
o
und for both
C
a
n
d
C++
commit
|
commitdiff
|
tree
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