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Some overview content for Doxygen documentation.
2013-10-28
Teemu Murtola
Some
o
verview content f
o
r
D
o
x
ygen docum
e
ntation
.
commit
|
commitdiff
|
tree
2013-10-28
Te
e
mu
Mu
r
to
l
a
Mis
c
.
D
oxygen updates
for src/gromacs/utility/
.
commit
|
commitdiff
|
tree
2013-10-28
Mark Abraham
Cr
e
a
t
e filei
o
module
commit
|
commitdiff
|
tree
2013-10-28
Teemu
Murt
o
la
Sim
p
lify co
d
e str
u
cture f
o
r C++
a
nalysis tools
commit
|
commitdiff
|
tree
2013-10-26
Mar
k
Abrah
a
m
Cleaned up run time measu
r
ement
commit
|
commitdiff
|
tree
2013-10-26
Mar
k
Abraham
Added documentation for
g
mx_runtime_t
s
t
ruct
commit
|
commitdiff
|
tree
2013-10-20
Teemu
M
urtola
Remove useless warnings from
D
oxy
g
e
n logs
.
commit
|
commitdiff
|
tree
2013-10-18
Mark Abrah
a
m
BlueGene/Q Verlet cut-off scheme kernels
commit
|
commitdiff
|
tree
2013-10-18
Mark Abraha
m
C
all atomics fr
o
m
T
estAtomic
.
c
commit
|
commitdiff
|
tree
2013-10-18
Roland Schulz
Fix tMPI_Atomic_memory
_
b
arrier
for M
I
C
commit
|
commitdiff
|
tree
2013-10-17
M
ark
A
braham
M
ov
e
mdrun trajectory writing into wrapper function
commit
|
commitdiff
|
tree
2013-10-17
Mark Abraham
Fi
x
typo in g_m
e
mbe
d
d
o
cumentation
commit
|
commitdiff
|
tree
2013-10-17
Roland Schulz
Fix
S
I
M
D C r
e
f
e
rence nbnxn ker
n
els
commit
|
commitdiff
|
tree
2013-10-17
M
i
chael Shirts
Restarting f
r
om checkpoint
n
o
long
e
r reini
t
ializes
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
T
eemu Murtola
Remove
l
a
tex
hel
p
e
xport
.
commit
|
commitdiff
|
tree
2013-10-16
Mark
A
braham
Mov
e
manual repo
i
nto
c
o
d
e
repo,
and make i
t
build
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
a
void div
i
sion by zero in
S
I
M
D angles
and dihedrals
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirt
s
turning
o
ff expand
e
d ensemble for
a
ll integrators but
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Berk
H
ess
f
i
xed a hal
f
bin misalignment in gmx_vanhove -or
commit
|
commitdiff
|
tree
2013-10-16
Mic
h
ael
Shirts
Fixes a problem
with pair
t
ype
2 interacti
o
ns with
.
.
.
commit
|
commitdiff
|
tree
2013-10-15
Szila
r
d Pall
make use of CUDA stream priorit
i
es
commit
|
commitdiff
|
tree
2013-10-15
T
eemu Mu
r
tola
Fix/impro
v
e
installation direc
t
ory logic
.
commit
|
commitdiff
|
tree
2013-10-11
Berk
H
ess
intro
d
u
ced g
e
n
e
ra
l
4-
w
id
e
SIMD
support
commit
|
commitdiff
|
tree
2013-10-10
Mark
A
braham
Introduced M
P
I
ini
t
iali
z
ation counter
commit
|
commitdiff
|
tree
2013-10-07
T
e
e
m
u
Murtola
HTML export from
the w
r
apper binary
.
commit
|
commitdiff
|
tree
2013-10-04
Mar
k
Ab
r
aham
Further co
n
solidation of co
m
m
r
e
c initi
a
l
i
zation
commit
|
commitdiff
|
tree
2013-10-04
Mark Abraham
More conso
l
idatio
n
of MP
I
initializa
t
ion
commit
|
commitdiff
|
tree
2013-10-04
Teemu Murtola
Re
o
rganize sta
t
ic/sh
a
red libr
a
ry management
.
commit
|
commitdiff
|
tree
2013-10-03
T
eemu Murtola
C
Make helper for tracking cache variable changes
.
commit
|
commitdiff
|
tree
2013-10-03
Teemu M
u
rt
o
l
a
Remove unus
e
d
s
hift_util
.
c
.
commit
|
commitdiff
|
tree
2013-10-03
Teem
u
Murtola
Improve di
a
gnostics wi
t
h empty
s
e
le
c
ti
o
ns
.
commit
|
commitdiff
|
tree
2013-10-03
Te
e
m
u
Murtol
a
Ma
n
page exp
o
r
t fr
o
m the wrapper
b
i
nary
.
commit
|
commitdiff
|
tree
2013-10-03
Teemu Mur
t
ola
Use filenm
.
c data for FileNa
m
eOption
.
commit
|
commitdiff
|
tree
2013-10-03
Teemu Mu
r
to
l
a
Fix warnings with
D
oxygen 1
.
8
.
5
.
commit
|
commitdiff
|
tree
2013-10-02
Berk Hes
s
Fi
x
es reaction f
i
eld free ene
r
gy b
u
g
commit
|
commitdiff
|
tree
2013-10-01
Mark A
b
raham
Broke so
m
e
useless d
e
pendencies
commit
|
commitdiff
|
tree
2013-10-01
Mark
Abraham
Split
M
PI i
n
itializatio
n
from t_
c
omm
r
ec constr
u
ction
commit
|
commitdiff
|
tree
2013-10-01
M
a
rk Abraham
S
i
lence cl
a
ng warnings
commit
|
commitdiff
|
tree
2013-09-30
D
av
i
d van der Spoe
l
Change name of gmxdum
p
to
dump and gmxcheck to check
commit
|
commitdiff
|
tree
2013-09-29
Szilard Pal
l
allo
w
compilati
o
n to o
p
t
i
mize f
o
r
CUDA c
o
m
p
ute cap
.
.
.
commit
|
commitdiff
|
tree
2013-09-29
Teem
u
Murtola
Remove obsolete efHAT
a
n
d
s
rc/ng
m
x
/
d
l
g
te
s
t
.
commit
|
commitdiff
|
tree
2013-09-29
David van d
e
r Sp
o
e
l
Fixes bug in proce
s
si
n
g
virtual_sitesn in grompp
.
commit
|
commitdiff
|
tree
2013-09-29
J
a
rvist M
o
ore Frost
Corrected in
f
o text
.
-center --> -
b
oxcenter
commit
|
commitdiff
|
tree
2013-09-27
M
a
nuel
L
u
i
tz
Fixed lim
i
tation
s
i
n g_cluster
commit
|
commitdiff
|
tree
2013-09-26
Michael S
h
irts
logic fix for free energies with mdrun -r
e
run
commit
|
commitdiff
|
tree
2013-09-26
C
h
ristoph Ju
n
ghans
Dr
o
p md5
s
um check for GMX_BUILD_OWN_FFTW
commit
|
commitdiff
|
tree
2013-09-26
M
a
rk Abraham
Un-
d
uplic
a
te gmx_gettim
e
code
commit
|
commitdiff
|
tree
2013-09-26
Teemu
Murtola
M
e
rge "Merg
e
branch release-4-
6
"
commit
|
commitdiff
|
tree
2013-09-26
Alexey Sh
v
etsov
g_
t
une_p
m
e: Clean up -Wunused-param
e
t
er warnings
commit
|
commitdiff
|
tree
2013-09-26
D
avid van der Spoel
Made
MW of the Vsite p
a
rticle typ
e
.
commit
|
commitdiff
|
tree
2013-09-26
Alexey Shvetsov
progr
a
ms: clean
u
p -Wunused-par
a
meter wa
r
n
ings
commit
|
commitdiff
|
tree
2013-09-26
M
a
rk Abraham
Remove
m
d
run -ionize f
e
ature
commit
|
commitdiff
|
tree
2013-09-26
Teemu Murtola
t
h
read_m
p
i
: Clean up -Wun
u
sed-parameter war
n
ings
.
commit
|
commitdiff
|
tree
2013-09-26
Tee
m
u Murt
o
la
CMake helper for depe
n
dent cach
e
v
a
ria
b
l
e
s
.
commit
|
commitdiff
|
tree
2013-09-25
Erik L
i
ndahl
Fix bug in (long) neighborlist SIMD p
a
dding wh
e
n ad
d
ing
.
.
.
commit
|
commitdiff
|
tree
2013-09-24
Berk
H
es
s
op
t
imized generic
S
IMD in
v
sqrt
commit
|
commitdiff
|
tree
2013-09-23
Teemu Murtola
Merge "
M
e
rge br
a
nch 'release-4-6'"
commit
|
commitdiff
|
tree
2013-09-21
Be
r
k He
s
s
fixed multipl
e
distance r
e
st
r
aints with OpenMP
commit
|
commitdiff
|
tree
2013-09-21
T
e
emu M
u
r
t
ola
CMake helper for mu
l
t
ichoice op
t
ions
.
commit
|
commitdiff
|
tree
2013-09-21
David
v
an der
Spoel
M
o
ved
ng
m
x
to C++, renamed it to
v
iew
.
commit
|
commitdiff
|
tree
2013-09-20
Mark Abra
h
am
Remove repe
a
t
sfree(state-
>
nos
e
h
oo
v
er_xi)
commit
|
commitdiff
|
tree
2013-09-20
M
a
r
k Ab
r
aham
Described anoth
e
r w
a
y g_t
u
ne_pm
e
mi
g
ht re
a
son
a
bly fa
i
l
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraham
F
ix total
t
im
e
measurem
e
n
t
with separate PME nodes
commit
|
commitdiff
|
tree
2013-09-20
Teemu
Murtola
CM
a
ke cleanu
p
.
commit
|
commitdiff
|
tree
2013-09-19
Tee
m
u
Mur
t
o
l
a
Make unc
r
ustify
.
sh
mor
e
verb
o
se on errors
.
commit
|
commitdiff
|
tree
2013-09-19
M
a
rk A
b
raham
Fixed re
a
ding history_t from checkpo
i
nt
commit
|
commitdiff
|
tree
2013-09-19
M
a
rk Abrah
a
m
Fixed g_tune_pme as
s
ump
t
ion that MPI is available
commit
|
commitdiff
|
tree
2013-09-19
Teemu Mu
r
tola
Unif
o
rm code pa
t
h for writin
g
out
c
onsole help
.
commit
|
commitdiff
|
tree
2013-09-19
Tee
m
u Mu
r
to
l
a
Framew
o
rk for help
expor
t
from wrap
p
er
b
inar
y
.
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
ma
d
e free energy PME kernel
4
0
% faster
commit
|
commitdiff
|
tree
2013-09-18
Mark
Abraham
Remove force
f
ield
-
scan featu
r
e
commit
|
commitdiff
|
tree
2013-09-16
Michae
l
Shirt
s
F
i
xin
g
m
a
nua
l
for
sc-coul description
.
commit
|
commitdiff
|
tree
2013-09-16
Berk
Hess
mdrun withou
t
Op
e
nMP with thread-MP
I
now
u
s
es all cores
commit
|
commitdiff
|
tree
2013-09-13
Berk Hess
c
o
rrected grompp
c
ons
t
raint/DO
F
warni
n
g with vsit
e
s
commit
|
commitdiff
|
tree
2013-09-13
Teemu Murtola
Add o
p
tion to build a
standalone mdrun binary o
n
ly
.
commit
|
commitdiff
|
tree
2013-09-13
Te
e
mu
Mu
r
tol
a
Mo
v
e m
d
run
into the
w
rapper bin
a
ry
.
commit
|
commitdiff
|
tree
2013-09-13
Teemu Mu
r
tola
Make parse_common_args() no
t
exit
.
commit
|
commitdiff
|
tree
2013-09-13
Teemu Murtola
Remove unu
s
ed -man output formats
.
commit
|
commitdiff
|
tree
2013-09-09
Teemu Murt
o
la
Make gm
x
_ana_p
o
s_t a C+
+
class
.
commit
|
commitdiff
|
tree
2013-09-09
Teemu Mur
t
o
l
a
Add some legends to C
+
+
t
ool ou
t
put
.
commit
|
commitdiff
|
tree
2013-09-08
T
e
emu Murtola
Remove dup
l
icate
.
nr me
m
bers fr
o
m
s
elec
t
io
n
s
t
ructs
.
commit
|
commitdiff
|
tree
2013-09-08
Te
e
mu
Murtola
R
e
move gmx_ana_ind
e
x
m
a
p
_t::bMapStatic
.
commit
|
commitdiff
|
tree
2013-09-08
Teemu Murtola
M
ove g
m
x_ana_pos_
t
::g int
o
gmx_ana_indexmap_t
.
commit
|
commitdiff
|
tree
2013-09-05
Teemu Murtola
AbstractAnalysisDa
t
a module
h
andling in
t
o
a
separate
.
.
.
commit
|
commitdiff
|
tree
2013-09-01
Teemu M
u
r
t
ol
a
Merge "Merg
e
branch rele
a
s
e
-4-6 into master"
commit
|
commitdiff
|
tree
2013-08-30
David v
a
n der Spoel
Updated g_c
l
uster
commit
|
commitdiff
|
tree
2013-08-30
Teemu Mu
r
t
ola
Clean
-
up
an
d
improvements in C++ tools
.
commit
|
commitdiff
|
tree
2013-08-25
Ma
r
k Ab
r
a
h
am
Split up Verlet SI
M
D kerne
l
s for fa
s
ter compila
t
ion
commit
|
commitdiff
|
tree
2013-08-25
M
a
r
k Abraham
Fix
detection a
n
d
sugg
e
stion in gmx_cpuid
f
or IBM QPX
commit
|
commitdiff
|
tree
2013-08-25
Berk Hess
introdu
c
e
d nb
n
xn data
s
tru
c
t
ur
e
for boundi
n
g
b
oxes
commit
|
commitdiff
|
tree
2013-08-25
M
a
r
k Abraham
F
i
xe
s
for Blue
g
ene
/
Q
commit
|
commitdiff
|
tree
2013-08-25
M
ark Abraham
Consoli
d
a
t
ed NBNxN SIMD kernel utility rou
t
ines
commit
|
commitdiff
|
tree
2013-08-25
Mark
Abra
h
am
Fix minor wal
l
cycl
e
output
issues
commit
|
commitdiff
|
tree
2013-08-25
Mark A
b
rah
a
m
F
ixed
G
M
X
_DD_
D
U
MP_GRID
commit
|
commitdiff
|
tree
2013-08-24
Teemu Murtola
F
in
e
-
tune copyright prin
t
ing
.
commit
|
commitdiff
|
tree
2013-08-21
Teemu Murto
l
a
Stati
s
tics fo
r
gmx
-
distance
.
commit
|
commitdiff
|
tree
2013-08-21
Teemu Murto
l
a
Lifetime statistics i
n
to gmx
-
select
.
commit
|
commitdiff
|
tree
2013-08-20
M
a
r
k Abraha
m
Remove OpenMM
commit
|
commitdiff
|
tree
2013-08-20
Berk Hes
s
fixed para
l
lel norm
a
l mode
s
wit
h
PME
commit
|
commitdiff
|
tree
2013-08-16
Tee
m
u Murtola
R
epla
c
e
m
e
n
t for g_
b
o
n
d and g_
d
i
s
t
.
commit
|
commitdiff
|
tree
next