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Support for portable hardware locality (hwloc)
2016-01-20
Dav
i
d
v
an der Spoel
Couple of
new q
u
o
t
es
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoel
Mad
e
n
o
r
m
al modes wo
r
k with
shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fixes newl
y
in
t
roduced bug
i
n ma
k
e_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Sp
o
e
l
Moved domde
c
stru
c
tures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David v
a
n der Spoe
l
Cleanups in
legacyheader/typ
e
s/c
o
mmr
e
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der S
p
oel
M
e
rged
l
ega
c
yheader
s
/types/qmmmrec
.
h
i
nto mdlib/
q
m
mm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David va
n
der Spoel
Merged genb
o
rn
.
h from legac
y
header
s
/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n de
r
S
p
oel
Move
d
legac
y
h
e
aders/types/group
.
h to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Me
r
ged
l
egacyh
e
a
ders/typ
e
s/n
s
.
h and nblist
.
h t
o
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
v
a
n der Spoe
l
Combine enu
m
s
.
h
a
n
d
n
a
m
e
s*
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der S
p
oel
Merged legacy
h
eaders/nrnb
.
h
a
nd t
y
pes/n
r
nb
.
h to g
m
x
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der Spoel
Moved md
a
tom
.
h from legacy
h
ea
d
e
r
/
type
s
to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der
S
poel
Moved legacyhea
d
er
s
/types/energy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
avi
d
van der Spoel
M
er
g
ed l
e
gacyheade
r
s/type
s
/inputrec
.
h
i
n
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Merged legacyhe
a
ders/types/state
.
h i
n
t
o mdtypes/
s
tate
.
h
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d
v
an
d
e
r
Spoel
Replaced
a
tom_id by
i
nt
.
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Moved genb
o
rn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van
d
er S
p
oel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Move
d
co
p
yrite
.
*
to filei
o
from gmx
l
ib
and legacyheade
r
s
.
commit
|
commitdiff
|
tree
2015-11-11
David
v
an der Sp
o
el
Move
d
i
nputrec
.
* from gmxli
b
and
l
egacyheaders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der
Spoel
Removed legacyheaders/typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Davi
d
van
der Spoel
Move
d
df_hist
o
r
y util
i
ty routines from typedefs t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
a
vid v
a
n
d
e
r
Spo
e
l
Rep
l
ace
d
NOTSE
T
from typede
f
s
.
h by loc
a
l so
l
u
t
ions
.
commit
|
commitdiff
|
tree
2015-10-23
David van
de
r
S
p
oel
R
e
moved
e
nergyhistory
c
o
d
e
f
r
om
t
ypedefs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
D
a
vid van
der Spoel
Mov
e
d
p
bc/cut-off rel
a
t
e
d utilities from
typed
e
fs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed memo
r
y
in legacy statistics routine
s
.
commit
|
commitdiff
|
tree
2015-10-03
David v
a
n der Spoel
Removed
s
im
p
le
.
h
commit
|
commitdiff
|
tree
2015-10-02
D
avid
v
an der
S
p
o
e
l
Removed
s
i
mple
.
h fro
m
nb_kerne
l
_s
s
e4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avi
d
v
a
n
der Spoel
Removed simpl
e
.
h fro
m
nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed si
m
p
l
e
.
h
f
rom nb_kernel
_
c
a
nd nb_kernel_sparc64_hp
c
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van de
r
Spoel
Removed include simp
l
e
.
h fr
o
m nb_kernel_a
v
x_128_
f
m
a
_
XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid v
a
n
d
e
r Spoel
Re
m
ove
d
sim
p
le
.
h from nb_kernel_a
v
x_25
6
_
X
X
commit
|
commitdiff
|
tree
2015-10-02
D
a
v
i
d
v
an der
Spoel
Removed output_env_t,
n
ow using gmx_outp
u
t_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Da
v
id van de
r
Spoel
Removed types/nrnb
.
h fr
o
m t
y
pede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spo
e
l
R
e
moved types/
n
blist
.
h
a
nd types/nsg
r
id
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der Sp
o
el
Remov
e
d types/mdatom
.
h
from typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van d
e
r Spoel
Rem
o
v
e
d
types/inputrec
.
h from typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
D
a
vid van der S
p
oel
Fixes bug in the compu
t
a
t
ion o
f
Coefficient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
Da
v
i
d
va
n
der S
p
oel
Remove
d
ty
p
es/
f
orcer
e
c
.
h
fro
m
t
yp
e
d
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
D
a
vid van der Sp
o
el
Removed inc
l
ude of typ
e
s/ifunc
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
v
id v
a
n der Spoe
l
Rem
o
ved four includes f
r
om legacyh
e
a
d
e
r
s
/
typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van
der Spoel
Remo
v
ed
l
e
g
a
c
yh
e
aders/types/commrec_
f
wd
.
h
f
r
om typed
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
David v
a
n
d
er Spoel
Moved
content from mdrun
.
h to separate
h
eaders
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoe
l
Removed
<
sys/types
.
h>
and "ty
p
es/constr
.
h" f
r
o
m
typedefs
commit
|
commitdiff
|
tree
2015-09-09
Davi
d
van der Spoel
R
e
moved fileio/trx
.
h
f
rom ty
p
e
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
v
an
d
er Sp
o
el
Moved functions op
e
rating on fo
r
c
erec to
sepa
r
ate head
e
r
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
vid va
n
der Spoel
Added energy (edr) file type to Options
h
eaders
.
commit
|
commitdiff
|
tree
2015-08-28
Dav
i
d
van der Spoel
Ad
d
ed
a
d
d
itional constructor to StringStream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van
der
S
po
e
l
Made output from
d
umping neightborlists easi
e
r to read
.
commit
|
commitdiff
|
tree
2015-07-31
David
van
der
S
p
oe
l
Change initial pa
r
ameters
f
or te
s
ti
n
g
expfit
.
commit
|
commitdiff
|
tree
2015-07-29
Da
v
id van
d
er Spoel
Code
f
or che
c
king xvg files
i
n
testutils
.
commit
|
commitdiff
|
tree
2015-04-17
D
a
vid v
a
n der Spoel
U
p
dated
e
xpone
n
tial fi
t
ting to make i
t
r
o
bust
.
commit
|
commitdiff
|
tree
2015-04-09
David
va
n
der S
p
oel
Cl
a
rified comments for time-
d
e
p
endent electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van
der
Spoel
Fixed i
n
correc
t
output o
f
gb_
a
lgorit
h
as sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Spoel
U
p
d
ated do
c
umentation for
e
lectric f
i
elds
.
commit
|
commitdiff
|
tree
2014-12-13
D
a
vid van
d
er Spoel
Four new quotes f
r
o
m
a
round the world
.
commit
|
commitdiff
|
tree
2014-11-28
David
v
an der
S
p
o
el
Fixes
rec
e
ntly introduced bug in gmx ana
l
yz
e
.
commit
|
commitdiff
|
tree
2014-11-24
David van de
r
Spoe
l
A
dded wa
r
ni
n
gs for ewald-geom
e
try and
s
ur
f
ace-epsilon
commit
|
commitdiff
|
tree
2014-10-28
D
a
vi
d
v
an der Spoel
Ev
e
n more refr
e
shing quot
e
s
.
commit
|
commitdiff
|
tree
2014-10-14
Da
v
id van der Sp
o
el
R
e
organizing
analysis of cor
r
el
a
t
io
n
functions
.
commit
|
commitdiff
|
tree
2014-09-23
David van der Spoel
Fixes pot
e
ntial bug in neigh
b
o
r
se
a
rching
.
commit
|
commitdiff
|
tree
2014-09-17
David van der
S
poel
Merge r
e
lease-5-0 i
n
t
o master
commit
|
commitdiff
|
tree
2014-09-10
David va
n
der Sp
o
el
Remov
e
.
tpa,
.
tpb,
.
tpx,
.
trj fi
l
es
.
P
a
r
t
of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
D
avid
van der Spoel
Fixes
issue wit
h
vsiten and verlet bu
f
f
e
rs
.
commit
|
commitdiff
|
tree
2014-07-05
David van
der Spoel
Fixed inco
n
sisten
c
y in blocka hand
l
ing
.
commit
|
commitdiff
|
tree
2014-06-29
Davi
d
van der Spoel
Fixes #1532
,
SEGV in g_current
.
commit
|
commitdiff
|
tree
2014-06-25
Dav
i
d
v
an der Spoel
A
d
ded check for domain decomposition and sh
e
l
ls
.
commit
|
commitdiff
|
tree
2014-06-24
David van
der Spoel
A
d
de
d
check in
gr
o
m
p
p for shells and inputrec issue
s
.
commit
|
commitdiff
|
tree
2014-06-22
David va
n
der Spoel
I
m
ple
m
ented
f
at
a
l erro
r
for n
s
tcalcenergy
!
=1 with s
h
ells
.
commit
|
commitdiff
|
tree
2014-06-13
Da
v
id
v
a
n
der Spoel
F
i
x
m
emory-usage
e
r
ror i
n
g_chi
commit
|
commitdiff
|
tree
2014-06-11
David
van der Spoel
F
ixes bug wher
e
-e and -dt flags did n
o
t work
anymo
r
e
.
commit
|
commitdiff
|
tree
2014-06-07
David v
a
n der
S
poel
Merge "Merge
r
e
l
ease-5-0 int
o
mast
e
r"
commit
|
commitdiff
|
tree
2014-06-07
David van
der
Spoel
M
erge release-5-0 into ma
s
ter
commit
|
commitdiff
|
tree
2014-06-02
David van der Spoel
Fixed wrong journal reference
in
m
a
n
ual
commit
|
commitdiff
|
tree
2014-05-31
D
avid van de
r
Spoel
Permit
t
rjconv to read an
d
wri
t
e velocities with
TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van der Spoe
l
Fixes a complica
t
ed bug in g_ana
e
ig
.
commit
|
commitdiff
|
tree
2014-05-15
Dav
i
d van der Spoel
Added cmake profil
i
n
g
support
commit
|
commitdiff
|
tree
2014-04-02
D
a
vi
d
van der Spoel
R
emoved
p
o
s
sibility of compilin
g
with GSL
.
commit
|
commitdiff
|
tree
2014-03-31
Dav
i
d van der Spoel
F
i
x
e
d compilati
o
n issue in fgrid
.
cpp due t
o
int/enum
commit
|
commitdiff
|
tree
2014-03-06
David van der
Spoel
Si
x
new quot
e
s from c
l
as
s
ic l
i
terat
u
re
.
commit
|
commitdiff
|
tree
2014-02-11
David van der Sp
o
el
Fixed a
n
other vmdio issu
e
.
commit
|
commitdiff
|
tree
2014-02-10
David van der Spo
e
l
Moved conditional cm
a
k
e
cod
e
for
vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
Da
v
id van
der Spoel
Moved random number generato
r
code
to separate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David va
n
de
r
Spoe
l
T
h
is patch m
o
ves the statistics library
to it
s
own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David v
a
n
der Spoel
T
h
is patch moves prepro
c
essi
n
g h
e
aders to gmx
p
r
eprocess
commit
|
commitdiff
|
tree
2014-01-15
Dav
i
d van der Spoel
This patc
h
mov
e
s t
h
e nrama
.
[ch] to the gmxan
a
d
ir
.
commit
|
commitdiff
|
tree
2014-01-13
David van der Spoel
Cle
a
n
ed u
p
list
of GROMAC
S
authors
commit
|
commitdiff
|
tree
2014-01-09
Dav
i
d van de
r
Spoe
l
Fixe
d
precision
in
thermal expans
i
o
n co
e
fficie
n
t ca
l
c
.
commit
|
commitdiff
|
tree
2013-12-23
David van der Sp
o
el
Fi
x
ed
c
ompilation
is
s
ue due to gcc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David van d
e
r Spoel
More Nob
e
l quo
t
e
s and others
commit
|
commitdiff
|
tree
2013-11-07
David van der Spoel
1
2 new
quotes
commit
|
commitdiff
|
tree
2013-09-30
David van der Spoel
Change name of gmxdump to dump and
gmxch
e
ck to check
commit
|
commitdiff
|
tree
2013-09-29
David van d
e
r
Spoel
Fixes bug
i
n pro
c
essi
n
g virtual_sitesn in
grompp
.
commit
|
commitdiff
|
tree
2013-09-26
D
a
vid van der Spoel
Made MW of th
e
Vsite
p
article type
.
commit
|
commitdiff
|
tree
2013-09-21
David
van der
Spoe
l
M
oved ngm
x
to C+
+
, renamed it to view
.
commit
|
commitdiff
|
tree
2013-08-30
David van der Spoel
Up
d
ated g_cl
u
ster
commit
|
commitdiff
|
tree
2013-07-24
David van d
e
r
S
p
oel
Fixe
s
#1312 uninit
i
alized
e
rror in g_enemat
.
commit
|
commitdiff
|
tree
2013-07-17
D
a
v
i
d van der Spo
e
l
Adde
d
c
i
tation t
o
fr
e
e
volume paper
.
commit
|
commitdiff
|
tree
2013-06-14
David van der Spo
e
l
New analysis tool to comp
u
te
t
he f
r
ee
volume
a
n
d
total
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
David van der S
p
oel
Fixes #1194 error reading
4
.
5
.
5
t
pr f
i
les with dihr
e
s
commit
|
commitdiff
|
tree
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