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Merge branch release-2016
2017-08-15
David van der Spoel
W
o
r
k
ed aro
u
nd missing OpenMP implementation in ori
r
es
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Sp
o
e
l
Fixe
d
bug in gmx dis
r
es index
i
ng
a
rr
a
ys
.
commit
|
commitdiff
|
tree
2017-08-02
David van der Spo
e
l
Worke
d
around missing OpenMP implementation in
o
rires
.
commit
|
commitdiff
|
tree
2017-07-28
Davi
d
va
n
der
S
poel
Add
e
d unit
-
test
for orientati
o
n restrain
t
s o
u
tput
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid v
a
n der Spoel
Re
m
oved
u
nne
c
e
ssary s
t
atic dec
l
a
rations for com
m
and
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van der Spoel
Fixed test-orde
r
dependenc
y
in gmxprep
r
o
c
ess t
e
st
s
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
an
d
er Spoel
Fix non-re
p
roduc
a
b
i
lity of clusts
i
ze tests
.
commit
|
commitdiff
|
tree
2017-05-01
Davi
d
v
an der Spoel
Xpm test for gmx
c
lustsi
z
e
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoel
Added t
e
sts for gmx
c
lu
s
tsiz
e
.
commit
|
commitdiff
|
tree
2017-03-04
Dav
i
d va
n
der Spoel
Removes rogue p
r
in
t
in
g
to
x
vg
fi
l
e in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
Davi
d
van der Spoel
Fixes
bug
i
n gmx so
l
v
a
te
w
ith
-
shell
t
hat yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
Da
v
id
van der
Spoel
Fi
x
es SEGV in
g
mx
o
rde
r
.
commit
|
commitdiff
|
tree
2017-02-02
David va
n
der Spoel
O
nly print all danglin
g
ato
m
s wit
h
gr
o
mp
p
-v
commit
|
commitdiff
|
tree
2017-01-23
David
v
an d
e
r S
p
oel
A
dded reference fo
r
dihedral
function in
O
PLS
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d v
a
n der Spoel
Coup
l
e of ne
w
quotes
commit
|
commitdiff
|
tree
2016-11-18
D
avid van
d
er S
p
oel
A
d
ded first te
s
ts o
f
bo
n
ded force f
u
nctions
.
commit
|
commitdiff
|
tree
2016-10-14
David
v
a
n
de
r
S
p
oel
Fix
e
s som
e
memory
l
e
a
k
s
associated
w
ith testing ap
p
lied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David va
n
d
er Spoel
Modularize elect
r
ic
field ha
n
d
l
in
g
commit
|
commitdiff
|
tree
2016-09-27
David van
der Sp
o
el
Fix
e
d script xplor2
g
m
x
.
pl
to work
w
ith GM
X
DATA
commit
|
commitdiff
|
tree
2016-09-26
D
a
vid v
a
n der Spo
e
l
Fixes is
s
ue with Rele
a
se
b
uild in correlatio
n
f
un
c
tions
.
commit
|
commitdiff
|
tree
2016-09-20
David
v
an
d
er Spoel
M
a
d
e correlat
i
on fun
c
tio
n
routin
e
use
st
d
:
:v
e
ctor
commit
|
commitdiff
|
tree
2016-09-05
D
a
vid van de
r
S
poel
M
e
r
ge "
M
erge b
r
anch release
-
20
1
6
"
commit
|
commitdiff
|
tree
2016-08-24
D
a
vid van
d
er Spoe
l
Add
e
d
d
ocumentation for shell potent
i
als
.
commit
|
commitdiff
|
tree
2016-08-03
D
avid va
n
der Spoel
Three
n
ew quotes
.
commit
|
commitdiff
|
tree
2016-07-31
Davi
d
van der
Sp
o
el
Merg
e
"Merge branch release
-
5-1 into release-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
Da
v
id van
d
er Spoe
l
Fi
x
es
incorrect charges in OPLS/AA-L for HISD
a
n
d H
I
SE
commit
|
commitdiff
|
tree
2016-07-08
David van d
e
r
S
poel
Me
r
ge "M
e
rg
e
b
ranch release-5-1 in
t
o
r
e
lease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van de
r
Spoel
Intr
o
duce fata
l
e
r
ro
r
fo
r
too few frames
i
n gmx
d
os
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made g
m
x
d
os
w
ork again
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
v
i
d van der Spo
e
l
Rem
o
ved s
p
urious r
_
i
j in force for Mors
e
po
t
entia
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David
van der S
p
oel
Modify lmf
i
t libr
a
ry t
o
a
v
oid clashes
with ot
h
er vers
i
o
n
s
.
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d
van der Spo
e
l
Removed sre
n
ew that
w
as m
a
king array sma
l
ler incor
r
ec
t
ly
.
commit
|
commitdiff
|
tree
2016-03-18
Dav
i
d van der Spoe
l
F
ixed divisio
n
b
y
z
ero
in polariz
e
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Spoel
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
D
a
v
id van
d
e
r
Spoel
Ma
d
e
norm
a
l
mo
d
es work
w
i
t
h shell
s
and v
s
ites
commit
|
commitdiff
|
tree
2015-11-24
David v
a
n
der Spoel
F
i
xes newly introduced bug i
n
make_
n
d
x
.
commit
|
commitdiff
|
tree
2015-11-23
Dav
i
d v
a
n der Spoel
Moved domdec structures
out
o
f c
o
m
mrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David
va
n
der Spoel
Cle
a
nups in le
g
acyhe
a
der/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
id van der Spoel
Merged legacyheaders/typ
e
s
/
qmm
m
rec
.
h in
t
o
m
dlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
S
poel
Merged genbo
r
n
.
h from leg
a
cyheaders/types int
o
md
l
ib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der S
p
oel
Moved legacyheaders/types/g
r
oup
.
h to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der
Spoel
Merged legacyhea
d
ers/
t
ypes/ns
.
h
and nblist
.
h to mdty
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der
Spoel
Combine enums
.
h and n
a
mes*
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der
S
p
oel
Merged
l
e
gacyheaders/nrnb
.
h and ty
p
es/nrnb
.
h to
g
mxlib
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van de
r
Spo
e
l
Move
d
mdatom
.
h from legacyheader/t
y
pes
to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der Spoel
Moved legacyhea
d
ers/types/energy
.
h to m
d
typ
e
s
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Me
r
ged legacyheaders/types/inputrec
.
h i
n
to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
van der Sp
o
el
Merged
legacyhea
d
ers/types/stat
e
.
h
into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
D
avid van
d
er
S
poel
Replaced
atom_id
b
y i
n
t
.
commit
|
commitdiff
|
tree
2015-11-13
David
van der
S
p
oel
M
o
ved g
e
nborn
.
h to
m
d
lib
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
van der Spoe
l
M
oved
t
x
t
du
m
p
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
a
vi
d
v
a
n d
e
r Spoel
Moved co
p
yrite
.
* to fi
l
eio from gmxlib a
n
d
leg
a
c
yheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der Sp
o
el
Moved inputrec
.
* from gmxlib an
d
legacyheaders
to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-10
D
a
vid v
a
n der Spoel
Removed
l
egacyheaders
/
typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der S
p
oel
Moved df_history uti
l
ity rout
i
nes
f
rom typedefs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Davi
d
v
an der Spoel
Replaced NOTSET fr
o
m
type
d
efs
.
h by loca
l
solu
t
ions
.
commit
|
commitdiff
|
tree
2015-10-23
David van d
e
r Spoel
Remo
v
ed
ene
r
g
yhis
t
ory code from typ
e
defs to
a
separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van d
e
r
S
p
oel
M
o
ved pbc/cut-off related utilities fr
o
m
typede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
a
vid van
d
e
r
S
p
oel
Freed memory in
l
e
gacy statistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David
v
an der
S
poel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
van de
r
S
p
oel
Removed simple
.
h from nb_kerne
l
_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van der Spo
e
l
R
e
mov
e
d simp
l
e
.
h fro
m
nb_
k
ernel_sse
2
_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
v
a
n
der
Spoel
Removed
s
imple
.
h fr
o
m nb
_
ker
n
el_c
a
nd nb_kernel
_
s
p
ar
c
64_h
p
c
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoe
l
Removed
i
ncl
u
d
e
simple
.
h from nb_kernel_avx_128_fma_X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Re
m
oved s
i
mp
l
e
.
h from n
b
_ker
n
el_a
v
x_256_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid va
n
der S
p
oe
l
Remov
e
d ou
t
put_
e
nv_t, now
u
sing
g
mx_output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Dav
i
d van der Spoel
Re
m
oved ty
p
es/nrnb
.
h
f
rom typed
e
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
Removed types/nblist
.
h and types/n
s
grid
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
R
emoved t
y
pes/m
d
atom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van
d
er S
p
o
e
l
R
e
moved typ
e
s/inp
u
tre
c
.
h
from typed
e
fs
.
h and rele
t
ed
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
F
ixes bug in the
comp
u
tation o
f
Coef
f
icient
of The
r
m
a
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoel
Removed
t
ypes/forcere
c
.
h
f
rom typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Removed in
c
lude
o
f
t
y
pes/ifunc
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
id va
n
der Spoel
Removed four includes from l
e
gacyheaders/t
y
pede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David
v
an der
Spoel
Removed legacyheaders/types/commrec_fwd
.
h from
t
ype
d
ef
.
h
commit
|
commitdiff
|
tree
2015-09-10
Da
v
i
d
van der Spoel
Moved co
n
tent fr
o
m mdrun
.
h to separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der S
p
oel
Removed <sy
s
/types
.
h>
a
nd "types/
c
o
n
s
t
r
.
h
" from typedefs
commit
|
commitdiff
|
tree
2015-09-09
Dav
i
d
v
an der Spoel
Rem
o
ved fileio/t
r
x
.
h from t
y
pede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
v
an
der
Sp
o
el
Moved functions operating on
forcer
e
c
t
o s
e
parate header
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
v
i
d va
n
der Spoel
Added energy (e
d
r) f
i
le
t
ype to
O
ptions headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
vid
v
a
n der
Spoel
Adde
d
addi
t
ional constructor to StringStream c
l
ass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David v
a
n der S
p
oel
Made output from dumping
n
eightborlists easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
David van der Spoe
l
Chan
g
e
i
nitial
p
ar
a
me
t
ers for testing expf
i
t
.
commit
|
commitdiff
|
tree
2015-07-29
D
avid van
d
e
r
Spoel
Cod
e
for chec
k
i
ng xvg files
in
testutils
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoel
Updated exponent
i
a
l fitting to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
Da
v
id van d
e
r S
p
oel
Clarifi
e
d comments for time-depend
e
n
t
electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van der Spoel
Fixed inc
o
rrect output
of gb_algorith a
s
s
a_a
l
g
o
rit
h
m
.
commit
|
commitdiff
|
tree
2015-03-02
David van d
e
r Spoel
Up
d
a
ted
documen
t
ation
fo
r
e
l
ectric
f
i
e
lds
.
commit
|
commitdiff
|
tree
2014-12-13
D
a
vid van
der Spoel
Four new qu
o
t
es from arou
n
d the
world
.
commit
|
commitdiff
|
tree
2014-11-28
D
a
vi
d
van d
e
r Sp
o
el
Fi
x
es recentl
y
i
ntroduced
bug
i
n
g
mx ana
l
yze
.
commit
|
commitdiff
|
tree
2014-11-24
David van der Sp
o
el
Added warnings for ewald-geometry
a
n
d surface-epsilon
commit
|
commitdiff
|
tree
2014-10-28
David v
a
n der Spoel
Even
more refreshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David van d
e
r Spo
e
l
Re
o
r
gan
i
z
i
ng analysis o
f
correlati
o
n functions
.
commit
|
commitdiff
|
tree
2014-09-23
David van der
Spoel
Fi
x
es potent
i
al bug in neighbo
r
sea
r
ching
.
commit
|
commitdiff
|
tree
2014-09-17
David van der
S
p
o
el
Merg
e
relea
s
e-5-0
i
n
to m
a
st
e
r
commit
|
commitdiff
|
tree
2014-09-10
David
van
d
er
S
poel
R
e
move
.
tpa,
.
tpb,
.
tpx,
.
trj files
.
Part of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
David van der
S
p
oel
Fixes issue
with vsiten and ve
r
l
e
t buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van
d
er
Spoel
Fixed
i
nconsistency
i
n bloc
k
a handlin
g
.
commit
|
commitdiff
|
tree
2014-06-29
David
van de
r
Spoel
F
i
xe
s
#1
5
3
2
,
SEGV
in g_current
.
commit
|
commitdiff
|
tree
2014-06-25
D
avid van
der
Spoel
Add
e
d ch
e
ck
f
or domain decompositio
n
and shells
.
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